CA2230689A1 - Ubiquitin conjugating enzymes having transcriptional repressor activity - Google Patents

Abstract

A human ubiquitin conjugating enzyme, designated hUBC-9, its full amino acid sequence, and nucleic acid polymers which encode hUBC-9 are disclosed. In addition to having functional ubiquitin conjugating activity, this enzyme has transcriptional repressor activity which is independent of the conjugating activity. The conjugating activity of hUBC-9 enhances transcription through degradation of transcription suppressor proteins such as WT1, and possibly, of hUBC-9 itself. The repressor activity of hUBC-9 suppress gene transcription, probably by disrupting the transcriptional initiation complex through specific interactions with the DNA binding region of the TATA binding protein (TBP). In use, hUBC-9, yUBC-9 and other ubiquitin conjugating enzymes having repressor activity can be fused to proteins having a DNA binding domain, such as Ga14, or used in conjunction with repressors such as Wilm's tumor suppressor gene product, WT1. Such enzymes and the nucleic acid polymers encoding them can be used for regulating transcription of a target gene in both pharmaceutical and non-pharmaceutical applications.

Description

WO 97/08195 PCTnJS96~14~13 UBIQ~ lN CONJUGATING ENZYME'3 HAVING
TRANSCRIPTIONAL REPRESSOR A~:11V1-1Y

The present invention claims priority to copending United States provisional application Serial 5 No. 60/002,995 and to copending United States provisional application Serial No. 60/018040. This invention was developed, in part, through research supported by grants from the National Institute of Health (2POlCA49712). The U.S. government may have certain rights in this invention.

BACKGROUND OF THE INVENTION
The present invention relales to a novel m~mm~lian ubiquitin conjugating enzyme, and more particularly, to the identification, isolation, and purification of a human ubiquitin conjugating enzyme, the complete amino acid sequence of which has been elucidated, and to nucleotide sequences encoding the enzyme. The invention further relates to novel methods of using the enzyme and similar enzyrnes to regulate gene transcription and, particularly to suppress transcription of a target gene in a human and non-human host cells. In a preferred application, the invention relates to methods for enhancing the repressor activity of WT1, Wilm's tumor suppressor gene product.
Ubiquitin has been identified as playing a central role in tagging proteins for degradation, and thus in modulating their life-span in the cell. For example, nuclear proteins that are known to be regulated by ubiquitination include NFxb, cyclin B, c-jun, p53 and ~ 30 histones. Ubiquitin conjugating enzymes (UBCs) activate and attach ubiquitin to a protein targeted for degradation in the proteolytic proteosome pathway by transferring activated ubiquitin in t:hioester linkage.
At least twelve separate yeast ubiquitin conjugating W O 97/08195 PCT~US96/14013 enzymes have been identified and sequenced. Prior to the present invention, however, only two mammalian UBCs have been identified and sequenced, and the human counterparts of yUBC-9 and other yeast UBCs have not been identified.
While two yeast ubiquitin conjugating enzymes have been reported to mediate cell cycle progression, yUBC 3 (Goeble, M.G., et al. 1988) and yUBC 9 (Seufert, W. et al. 1995), ubiquitin conjugating enzymes have not heretofore been characterized as having other activities independent of their conjugating activities.
Tumor suppressor genes, such as the p53 gene, the retinoblastoma (Rb) gene and the Wilm's tumor suppressor gene, encode proteins which inhibit cell reproduction and/or transcription in various ways. For example, p53 gene protein is believed to bind to DNA and induce transcription of another regulatory gene, the product of which blocks the kinase activity of proteins important for normal cell cycle progression, thereby precluding cell replication. The Rb gene protein is thought to act by masking the activation domain of an activator protein. A Rb gene product protein and a method therapeutic use thereof are disclosed in U.S.
Patent No. 5,496,731 to Benedict et al. Gene suppressor proteins may also act in other ways, including, for example, by competing with activator proteins for specific DNA binding sites, and/or by direct or indirect interaction with the general transcription factors.
Other tumor suppressor genes and gene products are disclosed in U.S. Patent No. 5,491,064 to Howley et al.
(HTS-1 gene).
The Wilm's Tumor ~WT) suppressor gene product (WT1) is a bifunctional transcription factor of the Kruppel zinc-finger family. Loss of function of both alleles of the WT1 gene (llpl3) is associated with some Wilm's tumors and associated syndromes. WT1 is a 52~57 kd nuclear protein which contains a glutamine/proline-WO 97/08195 PCT~US96J141)~3 rich N-terminal region and four zinc-fingers of the C2-H2 subclass in the C-terminal region. WT1 is a potent ~ repressor of the promoter activity of several growth related genes, including the IGF-II, PDGF A-chain, CSF-1 and IGF-R promoters. WT1 has an independent repressor domain which is active when WT1 interacts with DNA
through the zinc-finger domains. While the activity of repressor gene products such as WT1 is known to affect transcription, control over the biochemical mechanism by which transcriptional repression is effected is not thoroughly understood and higher lev,els of repression are desirable for commercial application~.

SUMMARY OF THE INVENTION
It is therefore an object of the present invention to provide a means for regulating transcription in cells, and particularly, a means for suppressing transcription of a target gene in a host cell. It is also an object of the invention to enhance the repressor activity of known repressor proteins such as WT1, Wilm's tumor suppressor gene product.
The present invention, therefore, is directed to a novel, isolated and substantially purified m~mm~l ian ubiquitin conjugating enzyme, hUBC-9, having a molecular weight of about 16 kilodaltons to about 18 kilodaltons, preferably about 17 kilodaltons, a sequence length of from about 150 to 165 amino acid residues, preferably 158 amino acid residues, and having conjugating activity and/or transcriptional repressor activity. The present invention is also directed to a protein having an amino acid sequence which includes the amino acid sequence of hUBC-9. The invention is directed as well to a protein which has ubiquitin conjugating activity or transcriptional repressor activity and which includes a portion of the amino acid sequence of hUBC-9 at least about 12 amino acid residues in length. The included portion of the hUBC-9 sequence confers the conjugating activity or the repressor activity on the protein. The invention is directed to proteins which have transcriptional repressor activity and have at least about 60% sequence identity to h~3C-9, more preferably at least about 65% sequence identity, more preferably at least about 75% sequence identity, more preferably at least about 85% sequence identity and most preferably at least about 95% sequence identity to h~3C-9. A C93 mutant of hUBC-9, which does not have ubiquitin conjugating activity, but retains its transcriptional repressor activity, is a particularly preferred protein.
The invention is directed, moreover, to substantially isolated nucleic acid polymers encoding hUBC-9. The nucleic acid polymer preferably has a nucleic acid sequence selected from the group consisting of: (a) Nucleotide Seq. 1, Fig. lA; (b) Nucleotide Seq.

2, Fig. lA; (c) a nucleic acid sequence which includes the nucleic acid residues defined by the sequence from position 88 to position 564 of Nucleotide Seq. 2, Fig.
lA. The invention is also directed to a substantially isolated nucleic acid polymer which encodes a protein having ubiquitin conjugating activity or transcriptional repressor activity and having an amino acid sequence which includes a portion of the amino acid sequence of hUBC-9. The included portion is at least about a 12 amino acid residues in length and confers the conjugating activity or the repressor activity on the protein. The invention is directed to a nucleic acid polymer which is at least about 36 nucleic acid residues in length and which encodes a protein which has transcriptional repressor activity. Such a nucleic acid fragment can encode a protein which has at least about 60% sequence identity to hUBC-9, or alternatively, can hybridize to a nucleic acid polymer which is complementary to the aforementioned nucleic acid polymers which constitute a WO 97108195 PCTnUS96/14013 part of the invention. The inventiorL is also directed to nucleic acid polymers which are complementary to the r aforementioned nucleic acid polymers of the invention.
The invention is directed as well to methods 5 for producing hUBC-9 or a segment thereof using a host cell transfected with a vector having a DNA which encodes hUBC-9 or a segment thereof. The method preferably comprises producing a plasmid vector having DNA
(including genomic DNA and/or genomic DNA). The DNA
10 encodes the aforementioned hUBC-9 protein or a segment or homolog thereof. The plasmid vector is transfected into a host cell and hUBC-9 is expressed :i.n the host cell. If desired, the expressed hUBC-9 may be purified from the host cell. The invention is also directed to the vector 15 and to the host cell transfected therewith.
The invention is further di.rected to a host cell co-transfected with first and second plasmid vectors each comprising DNA. The DNA of the first vector comprises a nucleic acid polymer which encodes a 20 transcriptional repressor protein other than a UBC-9 protein, including for example, WT1. The DNA of the second vector comprises a nucleic acid polymer which encodes an adapter protein having transcriptional repressor activity which is preferab:Ly independent of the 25 transcriptional repressor activity of the transcriptional repressor protein. The adapter protein associates or interacts with the transcriptional repressor protein after both are co-expressed in the host cell. The adapter protein has an amino acid sequence which includes 30 a portion of the amino acid sequence of a ubiquitin conjugating enzyme that has transcriptional repressor activity. Exemplary ubiquitin conjugating enzymes include hUBC-9, yUBC-9, other members of the UBC-9 family and other ubic~itin conjugating enzyrnes. The included portion of the amino acid sec~uence is at least about 12 amino acid residues in length.

W O 97/08195 PCT~US96/14013 The lnvention is directed, moreover, to a fusion protein comprising a transcriptional repressor domain and a DNA binding domain. The transcriptional repressor domain has an amino acid sequence which includes at least a 12 amino acid residue portion of the amino acid sequence of a ubiquitin conjugating enzyme that has transcriptional repressor activity. The DNA
binding domain is preferably a domain which binds sufficiently close to a promoter region of a target gene to allow the ubiquitin conjugating enzyme to repress transcription. Exemplary DNA binding domains include Gal4, LexA and any of the zinc-finger domains. The invention also relates to nucleic acid polymers encoding such a fusion protein, plasmid vectors comprising such nucleic acid polymers and to host cells transformed therewith. The invention is directed as well to a method for producing a fusion protein having a transcriptional repressor domain and a DNA-binding domain. The method comprises: producing a plasmid vector comprising DNA
which encodes the fusion protein described above, transfecting the plasmid vector into a host cell, expressing the fusion protein in the host cell, and, if desired, purifying the expressed fusion protein ~rom the host cell.
In another aspect, the invention is directed to a composition comprising a protein having transcriptional repressor activity and an acceptable carrier, diluent or biochemical delivery agent suitable for introducing the protein into a target cell. The protein has transcriptional repressor activity and has an amino acid sequence which includes at least a 12 amino-acid residue long portion of a ubiquitin conjugating enzyme which has transcriptional repressor activity. The protein derives its transcriptional repressor activity from the included portion of the enzyme. The composition can be used for non-pharmaceutical (ie, non-human) uses, but can also be CA 02230689 l998-02-27 WO 97/081g5 PCT~US96/140~3 a pharmaceutical composition, in which the aforementioned protein is combined with a pharmaceut:ically acceptable carrier, diluent and/or gene therapy delivery agent.
The invention is further directed to a composition suitable for use in introducing a nucleic acid polymer to a cell, whereby the expression product of the nucleic acid polymer is exposed t:o and/or contacts a target gene therein. The composition can be used for pharmaceutical or non-pharmaceutical applications to regulate transcription. The composition comprises a nucleic acid polymer and a gene therapy delivery agent.
When used in a pharmaceutical application, the amount of the nucleic acid polymer or construct: containing the same is su~ficient to, upon expression in a host cell, express a pharmaceutically effective amount of the protein to regulate a target gene in the cell. The nucleic acid polymer is used in conjunction with a pharmaceutically acceptable gene therapy delivery agent. The nucleic acid polymer encodes a protein having transcriptional repressor activity and having an amino acid secluence which includes at least a 12 amino-acid residue long portion of a ubiquitin conjugating enzyme which has transcriptional repressor activity. The included portion of the enzyme confers the repressor activity on the protein. The nucleic acid polymer can, alternatively, have a nucleic acid sequence which i~> complementary to the aforementioned nucleic acid polymers of the composition. The nucleic acid composition can be a virus which has a viral genome that includes the nucleic acid polymer being delivered to the target: gene. The ubiquitin conjugating enzyme used in such a composition is preferably a UBC-9 protein such as, hUBC-9, yUBC-9 or yUBC-9-m. Another pharmaceutical composition comprises a pharmaceutically active amount of the fusion protein set out above and a pharmaceutically acceptable carrier.

CA 02230689 l998-02-27 W O 97/0819~ PCT~US96/14013 The invention is also directed to a method of regulating transcription of a target gene in a cell. The method comprises exposing the target gene to and/or contacting the target gene with a protein having transcriptional repressor activity. The protein has an amino acid sequence which includes at least a 12 amino acid residue portion of the amino acid sequence of a ubiquitin conjugating enzyme having transcriptional repressor activity, such as a UBC-9. A composition which includes the protein or which includes a nucleic acid polymer encoding the protein may be introduced into the cells in a number of ways, including by contacting, infecting or transfecting the target cells with a gene therapy delivery agent such as a virus. The amount of protein to which the gene is exposed is more than the endogenous amount normally present within the cell. The cell can be an eukaryotic cell such as a fungal cell (e.g. a yeast cell), a plant cell, a non-human animal or m~mm~l ian cell or a human cell. The cell can also be a cell which has been infected with a virus wherein the viral genome is exposed to the transcription regulating protein. The invention is also directed to method of modulating neoplastic tissue growth. In the method, neoplastic tissue cells are contacted with a neoplastic-tissue-growth-modulating amount of one of the pharmaceutical compositions set forth above, thereby modulating the growth of the neoplastic tissue. The invention relates as well to a method of inhibiting the proliferation of Wilm's tumor cells. The method comprises introducing into Wilm's tumor cells a Wilm's-tumor-inhibiting amount of a ubiquitin conjugating enzyme or a segment thereof having transcriptional repressor activity, or alternatively, introducing a nucleic acid polymer which encodes such an amount of the enzyme, and preferably co-expressing WT1 therewith.

CA 02230689 l998-02-27 WO 97/08195 PCT~US96~4013 The discoveries described herein provide an important analytical tool for, and a critical link in the - development of methods by which transcriptional repressors or promoters ~ay be made t:o either inhibit or enhance a variety of cell activities in a desired manner.
hUBC-9 and other members or the UBC-9 family can be used, ~or example, in chemotherapy, gene therapy and drug development. Other uses of the invention include its use to regulate the rate of both specific and general gene transcription and the cell cycle, including the control of abnormal expression of genes associated with hl~m~n disease such as those caused by virus, or associated with yeast infections. The invention has use in non-pharmaceutical applications in the yeast, baking and brewing industries, and also in conjunction with enzymatic conversion methods for producing valuable chemical commodities such as essential amino acids. The enzyme, its activities and other features, methods of expressing the enzyme, and methods for its use are described in greater detail below.
Other features and objects of the present invention will be in part apparent to those skilled in the art and in part pointed out hereinafter.

BRIEF DESCRIPTION OF THE DRAWINGS
The invention is further disclosed and illustrated by the accompanying figures. In the earlier U.S. provisional applications from which the present invention claims priority, and in the figures therein, other designations were used to refer to the enzyme hUBC-9. Specifically, the enzyme has been heretofore referred to using the acronym "TRA", "human UBC," and/or hUBC-h.
The present terminology, hUBC-9, has been incorporated to be consistent with the literature. However, each of these designations refers to the same enzyme, hUBC-9, shown in Fig. lB and also depicted in Fig. lA as corresponding to certain nucleotide sequences shown in Fig. lA.
FIG. lA and lB show nucleotide and amino acid sequences for hUBC-9. Figure lA shows the full length 5 nucleotide sequence and the predicted amino acid sequence for two cDNA clones encoding hUBC-9. The vertical line connecting the cytosine at position 792 of the longer form and at position 73 of the shorter form indicates the splice site and origin of common nucleotide sequences of 10 the two alternative spliced mRNA. Figure lB shows a comparison of predicted amino acid sequences of hUBC-9 and yUBC-9.
FIG. 2A and 2B show the results of Northern and Southern blot analyses, respectively. Figure 2A shows 15 Northern blot of hUBC-9 in different human tissues.
Figure 2B shows Southern blot analysis of the hUBC-9 gene.
FIG. 3A and 3B show in vitro binding of WTl and hUBC-9, in Western blot analyses of associated WTl and 20 hUBC-9 proteins. Figure 3A shows blots of eluates taken from matrix-coupled GST-hUBC-9 which had been passed over and incubated with WTl from 293 cell extracts. Figure 3B
shows the results of co-immunoprecipitation of WTl and hUBC-9 from 293 cells co-transfected with WTl and HA-25 tagged hUBC-9 expression vectors.
FIG. 4A and 4B show temperature-sensitive yeast cell cultures at permissive and restrictive temperatures, respectively.
FIG. 5A and 5B show how hUBC-9 enhances the 30 transcriptional repressor activity of WTl in human embryonic kidney cells (293). Figure 5A shows the relative CAT activity when various amounts of WTl and hUBC-9 expression vectors are co-transfected. Figure 5B
illustrates the relative CAT activity of independent 35 assays at different times ~ standard deviation of each.

WO 97/08195 PCT~US96/14013 FIG. 6A and 6B show the transcriptional repressor activity of a hUBC-9/Gal4 DNA binding domain fu~ion protein. Figure 6A shows the expression and reporter vector constructs. Figure 6B shows the relative CAT activity.
FIG. 7A through 7C show the transcriptional repressor activity of hUBC-9, yUBC-9, and yUBC-9-m /Gal4 DNA binding domain fusion proteins. Figure 7A shows the expression and reporter vector constructs. Figure 7B
shows the relative CAT activity for hUBC-9/Gal4 fusion proteins. Figure 7C shows the relati.ve CAT activity for yUBC-9/Gal4 and yUBC-9-m/Gal4 fusion proteins.
FIG. 8 shows the results of GST/hUBC-9 capture assays for TATA binding protein (TBP), transcription factor IIB (TFIIB) and Wilm's tumor ~uppressor gene product, WT1.
FIG. 9A and 9B relate to GST/hUBC-9 capture assays with wild type hTBP and with ~everal mutant TATA
binding proteins, mTBP. In the schematic representations in Fig. 9A, the shaded area of the wild-type hTBP
represents the highly conserved region between species.
The shaded area for the mutant TBP's represents the portion of the TBP deleted. The term " dl x-y" indicates that in the mTBP, residue~ x through y were deleted.
Fig. 9B shows the blots resulting from the various GST/hUBC-9 capture assays.
FIG. lOA through lOD show the results of WT1 turnover experiments done when WT1 is expressed by itself (Fig. lOA), when WT1 is co-expressed with hUBC-9 (Fig.
lOB), when WT1 is expressed in the presence of lactocysteine, a known inhibitor of the proteolytic degradation system (Fig. lOC) and when WT1 is co-expressed with mUBC-9, a C93S mutant of hUBC-9 (Fig. lOD).
FIG. llA and llB relate to gel mobility shift assays that show the interaction between hUBC-9 and the TATA binding protein (TBP). Fig. llA shows the results W O 97/08195 PCT~US96/14013 of assays using hUBC-9 and an end-labeled DNA probe containing the TATA box either (a) without TBP present (columns A1-A3), (b) with TBP present but without TFIIB
present (columns Bl-B3) and (c) with both TBP and TFIIB
present (columns Cl-C3). Fig. llB shows the results of similar assays in which TBP was present with varying amounts of hUBC-9.
FIG. 12A and 12B show the results of transient co-transfection assays using a 5xUAS pSV CAT reporter vector. Fig. 12A shows the relative level of expression of the reporter vector for assays where a GAL4/hUBC-9 fusion protein (pSGhUBC-9) (0 or 10 ~g), TBP (0, 0.5 or 2.5 ~g) and/or TFIIB (5 ~g) were co-expressed in 293 cells in varying combinations. Fig. 12B shows the relative level of expression of the reporter vector where a mutant TBP, TBP~1-138 (0, 2.5 and 5 ~g), and the hUBC-9/Gal4 fusion protein (0, 10 ~g) were co-expressed in various combinations.
FIG. 13 shows the results of transient co-transfection assays using a 5xUAS pSV CAT reporter vectorwhere TBP~1-138 (0, 2.5 and 5 ~g) was co-expressed with WTl (10 ~g) in various combinations.

DETAILED DESCRIPTION OF THE INVENTION
As used herein, the various symbols for amino acids are as set forth in Table 1.

W O 97/08195 PCT~US96J14~13 Table 1: Amino Acid Abbreviations A Ala Alanine B Asx Asparagine or aspartic acid C Cys Cysteine 5 D Asp Aspartic acid E Glu Glutamic acid F Phe Phenylalanine G Gly Glycine H His Histidine 10 I Ile Isoleucine K Lys Lysine L Leu Leucine M Met Methionine N Asn Asparagine 15 P Pro Proline Q Gln Glutamine R Arg Arginine S Ser Serine T Thr Threonine 20 V Val Valine W Trp Tryptophan Y Tyr Tyrosine Z Glx Glutamine or glutamic acid As used herein, a "substant:ially purified"
protein means that the protein is separated from a majority of host cell proteins normal.ly associated with it or that the protein is synthesized in substantially purified form, such synthesis including expression of the protein in a host cell from a nucleic acid polymer exogenously introduced into the cell by any suitable gene-therapy delivery means. A "substantially isolated"
nucleic acid polymer means that the mixture which comprises the nucleic acid polymer of interest is essentially free of a majority of oth,er nucleic acid polymers normally associated with it. A "nucleic acid polymer" includes a polymer of nuclec,tides or nucleotide derivatives or analogs, including ~or example deoxyribonucleotides, ribonucleotides, etc. Genomic DNA, cDNA and mRNA are exemplary nucleic acid polymers. The term ~regulate transcription" is intended to include enhancement and/or repression of transcription. The term "gene" is intended to include both endogenous and W O 97/0819S PCTrUS96/14013 heterologous genes, and specifically, both genomic DNA
which encodes a target protein in a naturally occurring cell, and also cDNA encoding the target protein, wherein the cDNA is a part of a nucleic acid construct such as a plasmid vector or virus which has been introduced into a cell. The contents of each of the references cited herein are being incorporated by reference in their entirety.
The present invention relates to newly discovered human ubiquitin conjugating enzymes, designated hUBC-9, which in addition to having a functional conjugating activity, have an independent transcriptional repressor activity. Both the conjugating and the repressor activities have been found to influence transcription. The conjugating activity of hUBC-9 ~nh~nces tran5cription through degradation of transcription suppressor proteins such as WT1, and possibly, of hUBC-9 itself. The repressor activity of hUBC-9 represses transcription independently of the conjugating activity. For example, hUBC-9 strikingly enhances the function of WT1 as a repressor of gene transcription. The enzyme also acts independently of WT1 to suppress gene transcription itself, particularly when fused to proteins having a DNA binding domain, such as Gal4.
While not being bound to a particular theory, UBC-9 acts as a potent repressor by disrupting the transcriptional initiation complex through specific interactions with the DNA binding region of the TATA
binding protein (TBP). Such interactions are concentration dependent and result in destabilized TPB/DNA interactions and interference with formation of the TFIIB/TBP transcription initiation complex.
Moreover, hUBC-9 can operate in conjunction with other proteins having a repressor effect, such as WT1, to result in a combined repressor effect which is enhanced WO 97/08195 PCT/US96tl4013 relative to the repressor effect of WTl alone or of hUBC-9 alone. Hence, the association o~ hUBC-9 with other repressor proteins, either through protein-protein interactions as with WTl or by positioning hUBC-9 in the vicinity of the promoter as a fusion protein comprising hUBC-9 and a DNA binding domain, such as the domain of Gal4, Lex A, zinc-fingers or others. DNA binding proteins which are fused to hUBC-9 or repressor proteins which specifically interact with hUBC-9 appear to position human UBC-9 to an appropriate site in relation to promoter DNA such that hUBC-9 can interact with the TBP, and thereby reduce transcription initiation.
Moreover, in the combined WT1/hUBC-9 sy~tem, the conjugating activity of hUBC-9 appears to operate in conjunction with hUBC-9's repressor activity by regulating the levels of WTl present in the system. Such regulation of WT1 levels is accomplished through its ubiquitin conjugating activity and the associated ubiquitin-dependent proteolytic pathway. Moreover, the ubiquitin conjugating activity of hUBC-9 and its repressor activity may act at the same time, with hUBC-9 interacting simultaneously with WT1 (via its conjugating activity) and with the TBP (via its repressor activity).
hUBC-9 may also interact with other repressors such as p53 and Rb in a similar manner. Adva}ltageously, inhibition of UBC-9's conjugating activity results in even a greater degree of repression of the transcription initiative.
Moreover, the homologous ubiquitin conjugating enzymes of other eukaryotes, such as yeast (yUBC-9), exhibit the same bifunctional activities as hUBC-9:
transcription repression and ubiquitin conjugation. The highly conserved nature of UBC-9 among species, both in amino acid sequence and in function, suggests a universal role for this family of proteins. Accordingly, many facets of the invention are directed to the family of W O 97/08195 PCTrUS96/14013 proteins which are structurally homologous and functionally equivalent to hUBC-9, this family being collectively referred to herein using the designation UBC-9. UBC-9 includes any such proteins whether they are identified herein or discovered in the future. Aspects of the invention which relate to individual species' proteins are designated herein as hUBC-9 for hllmAnR and yUBC-9 for yeast. Many facets of the invention also relate to other ubiquitin conjugating enzymes other than the UBC-9 enzymes, provided, that such ubiquitin conjugating enzymes have transcriptional repressor activity in addition to their conjugating activity.
The several aspects of the present invention, including the hUBC-9 protein and nucleic acid polymers which encode it, the transcriptional repressor activity of ubiquitin conjugating enzymes such as a UBC-9 enzyme, and the interaction between UBC-9 enzymes and other transcription repressor proteins, especially such proteins having a DNA binding domain, and in particular tumor suppressor proteins such as WT1, collectively enable several practical applications, including both pharmaceutical applications involving hllmAn~ and non-pharmaceutical uses.

hUBC-9 A yeast two hybrid system was used to identify clones encoding the human ubiquitin conjugating (UBC) enzyme of the present invention. (Example 1). Figure lA
shows the complete nucleotide sequences of two independent cDNA clones, designated as Nucleotide Sequence No.'s 1 and 2, which were established from two alternatively spliced mRNAs. The cDNA clones both encode hUBC-9. The amino acid product resulting from transcription and translation of these cDNA clones migrated identically in SDS-containing polyacrylamide gel as a 17 kilodalton protein.
-W O 97/0~195 PCT~US96/140 13 huBc-s has the amino acid se~uence set forth in Figure lB. Based on a comparison with data in Genebank, hUBC-9 is an active human (h) homolo~ of the yeast ubiquitin conjugating enzyme-9, yUBC-9 or E2, the intermediate enzyme in the ubiquitin protein degradation pathway. The hl~m~n U~3C-9 sequence has a 56% amino acid identity overall with yUBC-9, including identical sequences of 9 amino acids in separate regions. The 158 amino acid sequence of hUBC-9 also contains a cysteine residue in precise alignment with the active site cysteine of yeast UBC-9 (boxed, Fig. lB).
Human UBC was expressed in a all human tissues tested, including heart, brain, placenta, lung, smooth muscle, kidney and pancreas tissues. (Example 2).
However, the level of expression varied in different tissues, as demonstrated by the results of a Northern blot experiment shown in Figure 2A. Northern blots of hUBC-9 in different tissues resulted in generally strong hybridization signals of 2.8 and 1.3 kb. However, heart and smooth muscle are seen to express significantly higher levels of transcripts relative to other tissues analyzed, and kidneys appear to expreAs relatively less of the 2.8 kb mRNA isoform.
hUBC-9 is encoded by a single gene, as demonstrated by experiments in which Southern blots of hllm~n genomic DNA were digested with different restriction enzymes and probed with the 1.1 kb fragment of hUBC-g cDNA. (Example 3). Single hybridization signals were seen in digests of PstI and BamH I (Fig.
2B), suggesting that the human UBC gene exists as a single copy gene in the human genome.
hUBC-9 is further characterized by its association with the repressor domain of the Wilm's tumor suppressor gene product, WT1. Human UBC binds to WT1 both in vivo and in vitro. Protein-protein interactions between hU~3C-9 and WT1 were initially demonstrated in the W O 97/08195 PCT~US96/14013 yeast two hybrid system by high levels of i~-galactosidase activity, as shown in Table 1. (Example 1). Additional experiments were carried out to confirm the WT1-human UBC
protein interactions observed in yeast. Human UBC was 5 expressed as a glutathione S-transferase fusion protein (GST-human UBC) in E. coli and coupled to a glutathione matrix. (Example 4). As shown in Figure 3A, when extracts from 293 cells transfected with WT1 expression plasmids were incubated with the GST-human UBC
10 glutathione matrix, eluates analyzed by Western blots probed with an anti-WT1 antibody demonstrated that the GST-human UBC matrix complexed with WT1, whereas the matrix of GST alone did not. In another experiment, extracts of 293 cells transfected with WT1 and a 15 hemagglutinin (HA)-tagged human UBC (HA-human UBC) expression vector were immunoprecipitated with an anti-WTl antibody and analyzed with anti-HA antibody in Western blots. (Example 5). As shown in Figure 3B, HA-tagged hnmAn UBC was identified in WT1 immune complexes 20 from 293 cells co-transfected with both human UBC and WT1 expression vectors but not in 293 cells transfected with human UBC alone.
hUBC-9 also interacts directly with the TATA-binding protein (TBP), as demonstrated by GST capture 25 assays. A GST fusion protein having the full-length hUBC-9 amino acid sequence captured TBP and WT1 selectively over the transcriptional factor TFIIB, which was also present in the asssay. (Fig. 8). Further assays demonstrated that hUBC-9 interacts with the TBP through 30 the highly conserved C-terminal domain of the TBP.
Several mutants of hTBP were constructed. (Fig. 9A). In GST capture assays, GST/hUBC-9 captured wild-type TBP as well as several of the mutant TPB's; however, deletion of the C-terminal region of TBP (amino acid residues 196-35 335) significantly reduced the capture efficiency, anddeletion of a larger portion thereof (amino acid residues WO 97/0819~; PCT/US96~4013 163-335) resulted in no interactions being detectable in the assay. (Fig. 9B). Hence, hUBC-9 specifically interacts with the C-terminal domain which includes amino acids 163-335 of the TATA binding protein. Gel mobility shift assays, discussed below, further confirmed the specificity of the interaction between TBP and hUBC-9.

The hUBC-9 Enzyme has an Active Conjugating ~ctivity hUBC-9 is an active ubiquitin conjugating enzyme, and as such, is a member of a family of ubiquitinating enzymes. Although sorne variation is believed to exist in the precise amino acid sequence of m~mm~l ian ubiquitin conjugating enzymes, the active cysteine residue at position 93 (boxed, Fig. lB) is characteristic of all of the ubiquitin conjugating enzymes discovered to date, and it has been determined that the presence of the active site cysteine is important to the ubiquitin conjugating activity. This cysteine is believed to provide the enzyme with its ability to participate in thioester i-ormation. Hence, human UBC-9, which has 56% sequence identity to yeast UBC-9 and shares the same active cyst:eine site, forms an integral part of the proteolytic proteosome pathway.
To demonstrate that the conserved cysteine residue of hUBC-9 is involved in mono-ubiquitin thioester formation, we used in vitro transcription/translation of the hl~m~n UBC cDNA in the rabbit reticulocyte system, which contains the three coupled enz~es [El E2 E3]
required for protein ubiquitination. Upon testing the product with lM neutral hydroxylamine, a slower migrating protein band was detected, suggesting that human UBC
contains a thioester that was hydrolyzed by hydroxylamine. In another experiment, an anti-ubiquitin antibody recognized the slower migrat:ing band that was sensitive to hydroxylamine in Western blots. In further experiment, we expressed the full-length hUBC-9 cDNA in a yeast carrying a temperature sensitive mutant form of yUBC-9. (Example 6). As shown in Figures 4A and 4B, growth was fully restored to the temperature sensitive (ts) yUBC-9 yeast at the otherwise nonpermissive temperature. The results of these experiments independently and cumulatively establish that the hUBC-9 cDNA encodes an active ubiquitin conjugating enzyme.

The Conjugating Activity of hUBC-9 Regulate~
Transcription.
The human ubiquitin conjugating protein of the present invention is a member of a family of en~ymes which, via their conjugating activity, function to regulate the cell cycle and duplication o~ DNA. It has now been determined, moreover, that the ubiquitin-dependent protease degradation system i5 directly involved in transcriptional regulation. The conjugating activity of hUBC-9 appears to modulate gene transcription by contributing to the degradation of repressor proteins such as WTl, thereby regulating the level of repressor activity.
WTl was shown to be rapidly degraded by the ubiquitin proteosome proteolysis pathway when expressed in rabbit reticulocyte lysates containing the enzymes required for transiting the proteolysis pathway. In a control experiment, cDNA of WTl was added to rabbit reticulocyte lysates that contained El, E2 and E3 enzymes, ubiquitin and the 26S proteosome complex required for protein ubiquitination and degradation. A
distinct band that migrated identically to WTl was observed upon analysis in SDS gels. In an experiment in which cDNAs of both WTl and hUBC-9 were added to the rabbit reticulocyte system, one protein band had a greatly diminished intensity relative to the band observed in the control experiment. Moreover, lower =~

-WO 97/0~195 PCTGUS96/14013 molecular weight immunoreactive species were found and a single, higher apparent molecular weight species was observed which migrated consistent w:Lth monoubiquitin-WT1. These results further confirm t;he interaction between hUBC-9 and WT1, and significantly, demonstrate that WT1 is degraded in a hUB~-9-dependent m~nne~
The effect of the conjugating activity is al~o demonstrated by inhibition of the proteolytic pathway with lactocysteine, a specific inhibitor of protease activity associated with the 26S proteosome complex, with such inhibition causing the half-life of WT1 to increase.
The turnover of WTl was tested in a ~3eries of experiments in which WT1 was (a) expressed in 293 cells alone, (b) co-expressed with hUBC-9, (c) expressed in the presence of lactocysteine, a known inhibitor of the proteolytic degradation system or (d) co-expressed with mUBC-9, a C93S
mutant of hUBC-9. In each case, the cells were treated with cycloheximide, a protein synthe~is inhibitor. Cells harvested at different times were lysed and analyzed by Western blot~ with anti-WT1 antibody. In the control experiment (WT1 alone), the steady st:ate levels of WT1 decreased dramatically upon the addit:ion of the cycloheximide and the half-life of Wl'1 was determined to be about 1 1/2 hours. (Fig. lOA). The half-life of WT1 decreased when co-expressed with hUBC-9. (Fig. lOB).
However, co-treatment of the cells with lactocysteine resulted in a rise in the steady state levels of WT1 by a factor of about 5. (Fig. lOC). Moreover, a similar increase in the amount of WT1 was observed when a WT1 was co-expressed with a mutant hU~3C-9 which lacked ubiquitin conjugating activity due to substitution of serine at the active site cysteine. (Fig. lOD).
WTl-dependent transcription.al repression is in~luenced by the proteosome degradation system. When WT1 was expressed in 293 cells co-transfected with a reporter plasmid and cultured with lactocysteine (50 ~M), W O 97/08195 PCT~US96/14013 a two-fold to three-fold enhancement of repressor activity was observed. Furthermore, the enhancement effect of lactocysteine progressively decreased as the level of expression of WT1 was increased. Lactocysteine was without effect at an upper limiting level of WT1.
The conjugating activity of hUBC-9 and its effect on repression is independently demonstrated by removal of the conjugating activity. In a cotransfection experiment detailed below, it was shown that removal of the ubiquitin conjugating activity by mutation of yUBC-9 at the active cysteine site results in a greater degree of repression activity than yUBC-9 having the active site cysteine. (Example 9).
These experiments demonstrate, individually and cumulatively, that h~3C-9 has conjugating activity which is specific to the WT1 and possibly to other suppressor proteins. The conjugating activity of hU~3C-9 positively influences transcription through degradation of repressors such as WTl, and possibly, of hUBC-9 itself.

UBC's have a Repressor Activity which Suppresses Transcription.
Ubiquitin conjugating enzymes such as hUBC-9 and yUBC-9 have a transcriptional repression activity.
The repression activity of hU~3C-9 enhances the existing repressor activity of WT1 and perhaps other repressor gene products. Moreover, the suppression of gene transcription by human and yeast UBC's themselves become~
significant when these enzymes are fused to or associate via protein-protein interactions with proteins having a DNA binding domain, such as Gal4 or WT1.
The repression activity of hUBC-9 enzyme strikingly enhances the repressor activity of Wilm's tumor suppressor gene product, WT1. The ability of human U~3C to modulate the transcriptional regulatory activity of WT1 was analyzed in cotransfection experiments W0 97/0~195 PCT/US96/~4013 (Bxample 7). As shown in Figure 5A, when human UBC was expressed alone at 15 ~g, without WTI and without being fused to a DNA binding domain, expression of the reporter gene was reduced slightly more than 2-fold (42% relative - 5 activity). When WT1 was expressed a:lone at 10 ~g, expression of the reporter gene was reduced by about a factor of ten (8% relative activity). However, when human UBC was expressed together with WT1, the repressor activity of WT1 was increased by an additional four-fold factor, resulting in a total transcr:iptional repression of about 50-fold (2% relative activity). In additional experiments, essentially identical results were obtained (Fig. 5B). Human UBC significantly enhances the repressor activity of WT1 in vivo when both are expressed at high levels together.
Furthermore, hUBC-9 is itself a potent transcriptional repressor when it is coupled to a functional DNA binding domain recognized by an appropriate promoter element. Human UBC was coupled to the Gal4 DNA binding domain and tested with a promoter containing five upstream Gal4 DNA binding sequences (5 X
UAS) in co-transfection experiments. (Example 8). As shown in Figure 6B, when human UBC WclS tested with the control promoter (lacking 5 X UAS) reporter plasmid to which human UBC was unable to bind, t:he influence of hl]m~n UBC was minimal (66% relative activity). However, human UBC was a powerful transcriptional repressor when it was able to directly bind, via the Gal4 binding domain, to the promoter/reporter construct containing the Gal4 DNA binding sequences. In this case, human UBC
repressed promoter activity by about eight-fold (12%
relative activity), establishing that: human UBC alone is an effective repressor when it binds to an appropriate promoter element. When the above experiment was repeated (Example 9), the h-UBC-9/Gal4 fusion protein again W O 97/08195 PCTrUS96/14013 demonstrated significant repression activity (15%
relative activity), as shown in Figure 7B.
These results strongly support the conclusion that human UBC has transcriptional repressor activity.
The repressor activity of hUBC is particularly significant when hUBC is positioned near the promoter regions, either through protein-protein interactions with other proteins, such as WT1, or through fusion with DNA
binding domains, such as Gal4, both of which appear to tether hllm~n UBC to gene-specific promoter sites.
Other ubiquitin conjugating enzymes, such as yUBC-9, also function efficiently as transcription repressors when fused to a DNA binding domain. Yeast UBC-9 was coupled to the Gal4 DNA binding domain and co-expressed with a reporter vector having five upstreamGal4 DNA binding sequences. (Example 9). As shown in Figure 7C, when co-expressed by itself at 20 ~g, the yUBC-9/Gal4 fusion protein repressed transcription by about three-fold (0.35 relative activity).

The transcriptional repression activity of UBC'~ is independent o~ their conjugating activity.
As noted above, UBC's have, in addition to their ubiquitin conjugating activity, a transcriptional repression activity. Significantly, the repression activity is independent of the conjugating activity, as demonstrated by data showing that yUBC-9-m, a yUBC-9 C93S
mutant which lacks ubiquitin conjugating activity, functions efficiently as transcription repressor when fused to a DNA binding domain. Briefly, a mutant form of yUBC-9 lacking the active site cysteine at position 93 (designated yUBC-9-m), was coupled to the Gal4 DNA
binding domain and co-expressed with a reporter vector having five upstream Gal4 DNA binding sequences.
(Example 9). As shown in Figure 7C, when co-expressed by itself at 20 ~g, the yUBC-9-m/Gal4 fusion protein =

WO 97/0$19~ ~nUS96~ 13 repressed transcription by about five-fold (20% relative activity).
~ Moreover, the independence of U3C repression activity is supported by data showin~ a higher degree of - 5 transcriptional repression for mutant yUBC-9-m than for yUBC-9. Referring to Figure 7C, whereas yUBC-9 expressed alone showed a 35% relative activity, yUBC-9-m expressed alone showed a 20% relative activity --- an increase in repression activity of about 15%. Consistently, when both normal yUBC-9 and mutant yUBC-9-m were co-expressed with the reporter vector in equal (10 ~g) amounts, the degree of transcriptional repression was intermediate (28% relative activity) between the ~alues for the normal or mutant strain alone.
While not being bound by theory, because the yUBC-9-m lacking the active site cysteine was active as a repressor, and further, even more aclive than the normal yUBC-9 having an active site cysteine, the ubiquitin conjugating activity does not appear to be required for the transcription repressor activity. Nonetheless, as discussed above, the conjugating act:ivity of UBC-9 appears to affect and regulate the level of repressor activity. The conjugating activity of hUBC-9 facilitates proteolytic degradation of WT1 and thereby at least partially relieves the repressor effect of WT1.

hUBC-9 Functions as a Repre~sor Thro~gh its Interactions with the TATA B; n~; n~ Protein (TBP) As noted, hUBC-9 interacts with the C-terminal domain of the TATA binding protein (rrBp) in GST capture assays. Gel mobility shift assays confirmed this interaction, and further demonstrated that hUBC-9 appears to suppress transcription by disrupting the binding of TBP to DNA and by disrupting the formation of the transcription initiation complex. This model is consistent with the understanding that the C-terminal of W O 97/08195 PCT~US96/14013 TBP, with which hUBC-9 was shown to interact, contains a "face" which contacts the major groove of DNA. In the assays carried out, an end-labeled DNA probe containing the TATA box was provided an opportunity to complex with various combinations of TBP, TFIIB and hUBC-9. In control experiments in which there was no TBP present, no detectable complex was formed between hUBC-9 and the DNA
probe, between TFIIB and the probe, or between hUBC-9, TFIIB and the probe. (Fig. llA, columns A1, A2 and A3, respectively). In further control experiments, the combination of purified TBP and the DNA probe containing the TATA box resulted in a single readily detectable complex. (Fig. llA, column B1). The addition of TFIIB
strengthened the intensity of the band, as expected based on the reported ability of TFIIB to enhance the binding of TBP to the TATA sequence. (Fig. llA, column C1).
However, when the above assays were repeated using purified hUBC-9 (10 ng, 50 ng) in the systems, hUBC-9 reduced the level of complex formation between TBP and DNA (Fig. llA, columns B2 and B3), and in subsequent experiments, between TBP and DNA in the presence of TFIIB
(Fig. llA, columns C2 and C3). Hence, hUBC-9 destabilizes TBP/DNA binding. The effect of hUBC-9 on the DNA binding ability of TBP was concentration dependent. (Fig. llB).
To further confirm that hUBC-9 interacts in the region of the TBP DNA binding domain, co-transfection assays were performed which demonstrated that high levels of exogenous TBP overcame the repressor activity of hUBC-9. A 5xUAS pSV CAT reporter vector was used in transientassays in which a GAL4/hUBC-9 fusion protein (pSGhUBC-9) (0 or 10 ~g), TBP (0, 0.5 or 2.5 ~g) and/or TFIIB (5 ~g) were co-expressed in 293 cells in varying combinations.
The repressor activity of hUBC-9 was significantly reduced in a concentration-dependent m~nner by the presence of TBP (without TFIIB). (Fig. 12A, columns A, W O 97/08195 PCT~US96/14013 B, C and D). The presence o~ TFIIB in the assay had no effect on hUBC-9 repression (Fig. 12A., columns E and F).
Further experiments were performed to ensure that the observed decrease in repressor activity of hUBC-9 was not, in fact, related to an intrinsic activation of transcription due to expression of TBP. A mutant TBP was constructed which had an amino acid sequence which included the TBP domain which interacted with hUBC-9 in GST capture assays, but which did not include the amino acid residues 1-138. The mutant TPB (0, 2,5 and 5 ~g), referred to herein as TBP~1-138, and the hUBC-9/Gal4 fusion protein (0, 10 ~g) were co-expressed i.n various combinations in transient co-transfection assays similar to those immediately aforementioned. TBP~1-138 lacked the ability to substantially activate the promoter, but effectively relieved the repressor activity of hUBC-9, although to a lesser extent than wild-type TBP. (Fig.
12B). Hence, hUBC-9 is shown to interact with TBP to repress transcription. Moreover, the addition of TBP can effectively titrate hUBC-9 to relieve its repressor activity, and in effect, enhance tran~cription.
In similar-co-transfection assays, mutant TBP, TBP~1-138 effectively relieved the repressor activity of WT1. (Fig. 13). Cumulatively, these results suggest that WT1 effects suppression in co~m~bination with hUBC-9 by positioning hUBC-9 through protein-protein interactions for direct hUBC-9 interaction with the TBP
subunit of the TFIID transcription fartor, thereby destabilizing the TBP/TATA sequence interaction, and more generally, disrupting formation of the transcription initiation complex.

Producing hUBC-9 The nucleotide sequence encoding the m~mm~lian or yeast or other UBC enzyme, or active portion thereof, is cloned into an expression vector w3ing known W O 97/08195 PCTrUS96/14013 procedures. Briefly, specific nucleotide sequences in the vector are cleaved by site-specific restriction enzymes such as NcoI and HindIII. Then, after optional alkaline phosphatase treatment of the vector, the vector and a target fragment comprising the nucleotide sequence of interest are ligated together with the resulting insertion of the target codons in place adjacent to desired control and expression sequences. The particular vector employed will depend in part on the type of host cell chosen for use in gene expression. Typically, a host-compatible plasmid will be used containing genes for markers such as ampicillin or tetracycline resistance, and also containing suitable promoter and terminator sequences. A preferred plasmid into which the recombinant DNA expression sequence of the present invention may been ligated is plasmid pET. A pET plasmid which expresses human UBC-9 has been deposited in GeneBank, Ascession No.'s ~L66818 and ~166867.
The plasmid comprising the DNA expression sequence for the UBC enzymes of the present invention may then be expressed in a host cell. Bacteria, e.g., various strains of E. coli, and yeast, e.g., Baker's yeast, are most frequently used as host cells for expression of mAmm~lian UBC enzymes, although techniques for using more complex cells are known. See, e.g., procedures for using plant cells described by Depicker, A., et al., 1982. E. coli host strain X7029, wild-type F-, having deletion X74 covering the lac operon is utilized in a preferred embodiment of the present inven-tion. A host cell is transformed using a protocoldesigned specifically for the particular host cell. For E. coli, a calcium treatment produces the transformation.
(Cohen, S.N., 1972). Alternatively and more efficiently, electroporation of salt-free E. coli is performed according to the method of Dower et al., 1988. After transformation, the transformed hosts are selected from CA 02230689 l998-02-27 W O 97/08195 PCTJUS96J14~13 other bacteria based on characterist:ics acq~ired from the expression vector, such as ampicillin resistance, and then the transformed colonies of bacteria are further screened for the ability to give rise to high levels of isopropylthiogalactoside (IPTG)-induced thermostable DNA
polymerase activity. Colonies of transformed E. coli are then grown in large quantity and expression of mAmmAlian UBC enzyme is induced for isolation and purification.
Example 4 details the expression of human ~3C in bacteria as a GST-fusion protein. Example 6 details the expression of a temperature-sensiti~e yeast UBC strain in yeast.
Although a variety of purification technigues are known, all involve the steps of disruption of the E.
coli cells, inactivation and ,e..l~vdl of native proteins and precipitation of nucleic acids. The enzyme is separated by taking advantage of such characteristics as its weight (centrifugation), size (dialysis, gel-filtration chromatography), or charge (ion-exchange chromatography). Generally, combinations of these techniques are employed together in the purification process. In a preferred process for purifying mAmmAlian UBC enzyme, the E. coli cells are weakened using lysozyme and the cells are lysed and nearly all native proteins are denatured by heating the cell suspension rapidly to 80 ~C and incubating at 80-81 ~C for 20 minutes. The suspension is then cooled and centrifuged to precipitate the denatured proteins. The supernatant (containing mAmmAlian UBC enzyme) then undergoes a high-salt polyethylene-imine treatment to precipitate nucleic acids. Centrifugation of the extract removes the nucleic acids and mAmmAlian UBC enzyme is concentrated by use of ammonium sulfate precipitation before chromatography, preferably on a heparin-agarose colu~mn. Preferably, the purified enzyme is at least 60% (w/w) of the protein of a preparation. Even more preferably, the protein is provided as a homogeneous preparation.

Compositions The ubiquitin conjugating enzymes disclosed herein as having transcription repression activity (e.g.
hUBC-9, yUBC-9 and y-UBC9-m), as well as other ubiquitin conjugating enzymes having such an activity, or segments thereof, may be combined with an acceptable carrier, diluent or delivery agent to form a useful composition.
The composition has both pharmaceutical (ie, human) and non-pharmaceutical applications. In either case, the protein used in the composition has transcriptional repressor activity. The amino acid sequence of the protein includes at least a 12 amino acid portion of a ubiquitin conjugating protein such as a UBC-9 which has a transcription repression activity. The amino acid sequence of the protein preferably includes at least a segment of hUBC-9 or yUBC-9. An active-site mutant of a ubiquitin conjugating enzyme, such as a cys93 mutant of hUBC-9, whereby such a mutant lacks its ubiquitin conjugating activity, or a segment thereof, can also be used as the protein. A mutant in which a serine residue replaces the cysteine residue is preferred. In an alternative method for removing the ubiquitin conjugating activity from the composition, the composition can further include a biochemical inhibitor suitable for inhibiting the active site cysteine of the ubiquitin conjugating enzyme. An exemplary suitable inhibitor in n-ethyl-maleimide. The protein in the composition may have only transcriptional repressor activity, or have such an activity as well as ubiquitin conjugating activity. In use, the composition may further comprise one or more other proteins, including for example a second protein having transcriptional repressor activity, such as WT1. The composition may also comprise other W O 97/08195 PCT~US96/140~3 proteins having a DNA binding domain with which the ubiquitin conjugating enzyme or segment thereof interacts. Moreover, the protein used in the composition may be a fusion protein which has a amino acid sequence that includes a DNA binding domain and a transcriptional repressor domain. The repressor domain of the fusion protein preferably includes at least a 12 amino acid segment of a ubiquitin conjugating enzyme having transcriptional repressor activity. The DN~ binding domain is preferably a domain which binds to or interacts with or otherwise associates with a region of a gene which is sufficiently close to the promotor region to allow the ubiquitin conjugating enzy~e or segment thereof to interact with the promoter region, and particularly, with the TATA binding protein at the TATA binding site.
Such domains include the amino acid se~uences of the Gal4 domain, the LexA domain, and the many zinc-finger domains.
For pharmaceutical compositions, the protein is combined with a pharmaceutically acceptable carrier, diluent or gene therapy delivery agent, and a pharmaceutically active amount of the protein is used in the composition. The amount is preferably an amount that is effective to achieve modulation or regulation or suppression of gene transcription of a target gene.
While smaller or larger amounts may be suitable in particular applications, the pharmaceutically active amount of the protein is preferably an amount sufficient to increase the concentration of the protein in the cell of the target gene being regulated b~y a factor ranging from about 1% to about 1000% relative to the amount of the protein which is endogenous to the cell. The increase in concentration more preferably ranges from about 10~ to about 100%. Where the protein in the pharmaceutical composition is a segment of a ubiquitin conjugating enzyme having transcript:i.onal repressor W O 97/08195 PCT~US96/14013 activity, the amount is taken relative to the endogenous amount of the ubiquitin conjugating enzyme in its natural full-sequence state. The particular dosage administered for a particular pharmaceutical application, while preferably consistent with the aforementioned amounts, will be dependent upon the age, health, and weight of the recipient, type of concurrent treatment, if any, frequency of treatment, the nature of the effect desired, and whether a localized tissue or system-wide effect is being sought. For treatment of Wilm's tumor, a tumor-inhibiting amount is to be administered. Similarly, for regulating or modulating or suppressing any particular neoplastic tissue growth, an effective amount to achieve such regulation, modulation or suppression determined by the factors outlined above, is to be applied. The amount of protein used in a non-pharmaceutical application may be in a range similar to that for pharmaceutical compositions, but may also include amounts outside this range.
The nucleic acid polymers which encode a ubiquitin conjugating enzyme such as a UBC-9 having transcriptional repressor activity, or which encode a segment thereof, can be used in a nucleic acid composition in combination with a gene therapy delivery agent. As used herein, the term gene therapy relates to operations and/or manipulations affecting both human and non-human genes, whether such operations are in-vivo or ex-vivo in nature. More specifically, the composition preferably comprises a nucleic acid polymer that encodes a protein which has transcriptional repressor activity.
The transcriptional repressor protein has an amino acid se~uence which includes at least a portion of the amino acid sequence of a ubiquitin conjugating enzyme having transcriptional repressor activity, with the included portion being at least about 12 amino acid residues in length. Alternatively, the nucleic acid polymer can have -WO 97/0~195 PC'r~US96/1401 a nucleotide sequence complementary to the nucleic acid sequence of the immediately aforementioned nucleic acid polymer. The ubiquitin conjugating enzyme can be a UBC-9 such as hUBC-9, or a segment thereof~ or a mutant thereof lacking ubiquitin conjugating activity. The composition may further comprise or be used in conjunction with a biochemical inhibitor of the ubiquitin conjugating activity of the ubiquitin conjugating enzyme. The nucleic acid polymer can also encode a fusion protein such as the aforementioned fusion protein described in connection with the above-described protein composition.
For pharmaceutical use, thle nucleic acid composition compri~es a pharmaceutically effective amount of the nucleic acid and a pharmaceutically acceptable gene therapy delivery means. The amount of nucleic acid required will vary depending on the type of cell, the effect being sought and on the delivlery system used to introduce the nucleic acid polymer into a target cell.
In general, the amount of nucleic acid polymer is preferably an amount sufficient to, upon expression in the target cell, result in an amount of protein sufficient to regulate or modulate or repress transcription of the target gene. Preferably, the amount is sufficient to increase the concentration of the protein in the cell of the target ge:ne being regulated by a factor ranging from about 1% to about 1000% relative to the amount of the protein which is endogenous to the cell of the gene being regulated. The increase in concentration more preferably ranges from about 10% to about 100%. Where the nucleic acid polymer of the agent encodes a protein which is a segment of a ubiquitin conjugating enzyme having transcriptional repressor activity, the amount is taken relative to the endogenous amount of the ubiquitin conjugating enzyme in its natural full-sequence state.

W O 97/08195 PCTrUS96/14013 Gene therapy delivery agents are used to introduce the nucleic acid polymer into target cells or to enhance the uptake of the nucleic acid polymer by the target cells. Several approaches for introducing the nucleic acid polymer into the cell and effecting expression thereof are known and practiced by those of skill in the art. (Mulligan, R., The Basic Science of Gene Therapy, SCIENCE, Vol. 260, pp.926-32 (1993)). In one approach, the nucleic acid polymer of the composition may be combined, complexed, coupled or fused with a delivery agent which introduces the nucleic acid polymer into a human cell in vivo. For example, the nucleic acid may be combined with a lipophilic cationic compound, which may be in the form of liposomes. The use of liposomes to introduce genes or other pharmaceutically active ingredients into cells is taught, for example, in U.S. Pat. Nos. 4,397,355 and 4,394,448. Alternatively, said nucleic acid may be combined with a lipophilic carrier such as any one of a number of sterols including cholesterol, cholate and deoxycholic acid. A preferred sterol is cholesterol. Additionally, the nucleic acid may be conjugated to a peptide that is ingested by cells.
Examples of useful peptides include peptide hormones or antibodies. By choosing a peptide that is selectively taken up by Wilm's tumor or other neoplastic cells, specific delivery of the nucleic acid may be effected.
The nucleic acid may be covalently bound to the peptide via methods well known in the art. The peptide of choice may then be attached to the activated enzyme via an amino and sulfydryl reactive hetero bifunctional reagent. The latter is bound to a cysteine residue present in the peptide. Upon exposure of target cells to the nucleic acid bound to the peptide, the nucleic acid is endocytosed and is rendered available for modulation of gene transcription. The nucleic acid polymer of the present invention can also be delivered to specific WO 97/0~195 PCT/US96J14013 tissues using a DNA-antibody conjugate, such as is described in U.S. Patent No. 5,428,132 to Hirsch et al.
Other gene therapy delivery agents used to introduce sense or antisense nucleic acid polymers such as DNA and RNA into human cells are disclosed in U.S. Patent No.
5,460,831 to Gelman et al. and U.S. Patent No. 5,433,946 to Allen et al.
In an alternative approach, the gene therapy delivery agent is a construct having cDNA which includes the nucleic acid polymer and which can be expressed in a host cell. Such a construct is infected or transfected into the cell and expresses the ubiquitin conjugating enzyme having transcriptional repressor activity in the cell. For example, the composition can be a virus having a viral genome which comprises the mlcleic acid polymer of the agent or which is complexed to the nucleic acid polymer of the agent. Such methods are taught, for example, in U.S. Patent No. 5,252,47'3 to Srivastava, U.S.
Patent No.'s 5,521,291 and 5,547,932 to Birnstiel et al., U.S. Patent No. 5,512,421 to Burns et al., U.S. Patent No. 5,240,846 to Collins et al., U.S. Patent No.
5,112,767 to Roy-Burman et al. and U.S. Patent No.
5,543,328 to McClelland et al.
In yet another approach, the gene therapy delivery agent is a human cell. The nucleic acid polymer of the composition is inserted into a human cell in vitro and the cell comprising the nucleic acid polymer is then introduced into the body. The encoded ubiquitin conjugating enzyme is then expressed by the cells in vivo. Such a method is taught for example, in U.S.
Patent No. 5,399,346 to Anderson et al.
The composition comprising the nucleic acid polymer and the pharmaceutical compositions comprising the protein of the present invention may be administered by any means that achieve their intended purpose. For example, administration may be by parenteral, subcutaneous, intravenous, intramuscular, intraperitoneal, or transdermal routes. Formulations for parenteral administration can include aqueous solutions of the composition or pharmaceutical composition in water-soluble form, for example, water-soluble salts. In addition, suspensions of the active compounds in oily injection suspensions may be administered. Suitable lipophilic solvents or vehicles include fatty oils, for example, sesame oil, or synthetic fatty acid esters, for example, sodium carboxymethyl cellulose, sorbitol, and/or dextran. Optionally, the suspension may also contain stabilizers. The particular gene therapy delivery agent used in the composition of the present invention and the determination of optimal ranges of effective amounts of each component is within capacities of a person of skill in the art of the art.
The pharmaceutical compositions of the present invention can be used in a variety of pharmaceutical and non-pharmaceutical applications. In general, gene transcription in cells can be regulated, enhanced or repressed, by controlling the concentration of UBC-9 and/or of TBP to which a target gene is exposed or in which a target gene comes in contact. In particular, repression of transcription can be carried out in a gene-specific manner by positioning the UBC enzymes near thepromoter regions of various genes, for example, by fusion of a UBC-9 repressor domain with a gene-specific DNA
binding domain, or alternatively, by protein-protein interactions between UBC-9 and proteins associated with the promoter region or involved with transcription initiation, such as WTl, TBP, or others.
A variety of cells can be used in the present invention. Eukaryotic cells are particularly preferred, as naturally occurring eukaryotic cells contain genes having promoter regions which include a TATA box. hUBC-9 or other UBC-9's or other ubiquitin conjugating enzymes WO 97/08~95 PCT~US96/14013 having transcriptional repressor activity or segments thereof which are at least about 12 amino acid residues in length can disrupt the TATA binding protein's role in transcription initiation in such genes. For example, the cells can be ~ungal cells (e.g. yeast cells), plant cells, non-human animal cells, non-human m~m~l ian cells and hllmAn cells. Non-eukaryotic cells such as E. Coli can also be used where the cells comprise genetically engineered nucleic acid polymer const:ructs which include a promoter region which involves TBP for initiation of transcription.
The function of repressor gene products such as WT1 can be strikingly enhanced by such an approach, allowing for control of transcription of genes promoters on which WT1 is known to operate, such as IGF-II, PDGF A-chain, CSF-l and IGF-R or others later discovered. The regulation of transcription can also be controlled by localized inhibition of the conjugating activity of U~3C-9, for example, through a 93cys mutant: enzyme lacking such activity, or through agents which inhibit the active cite cysteine or which otherwise interrupt: the proteolytic degradation pathway in a specific manner. The regulation of transcription is particularly useful in medical treatment, diagnostic and research applications. For example, UBC-9 can be used in therapeutic compositions for inhibiting neoplastic tissue growth by itself, or in combination with known tumor suppressor proteins such as WT1. It is particularly suited to treating Wilm's tumors and to treating the other types of tumors with which WT1 suppressor gene is associated, incluating for example leukemia and mesothelioma. It can also be useful in controlling any number of human diseases which are causally linked to an overabundance of a certain protein.
The gene from which the overabundant protein is expressed could be exposed to a U~3C-9 or other ubiaruitin conjugating enzymes which have repressor activity to -decrease the amount of overabundant protein expressed.
In certain circumstances, the repressor activity of a UBC-9 or of other ubiquitin conjugating enzymes could be applied to effect an increase in the expression of a particular protein of interest. An increase in a protein of interest can be effected through a "rebound"
mechanism, where the increase therein is a result of a natural biochemical mechanism following a decrease in the amount of a second protein present in the system. The decrease in the amount of the second protein is accomplished according to the methods of the present invention directed to the gene which encodes that protein. Another significant application of the present invention includes the treatment of a human viral infection. This application would include exposing the viral genome of human virus, and particularly, the promoter region of the genome, to a ubiquitin conjugating enzyme having transcriptional repressor activity. By suppressing transcription of a viral genome, the virus may be killed or at least controlled. The invention could also be used to kill or at least help control yeast infections.
Moreover, transcription regulation is useful in a variety of non-human, non-pharmaceutical applications.
The invention could, for example, be used for the treatment of animals or of particular animal diseases much as described above. The present invention is also useful for treating plant diseases resulting from overabundant expression, and may have other plant applications as well.
In another set of non-therapeutic applications, hUBC-9 may be used to develop animal-based models or in -vitro assays. For example, an animal having a selective protein deficiency can be developed by administering the pharmaceutical composition or the biochemical agent of the present invention to an animal whereby transcription WO 97/08195 PCT/US96/140~3 of a target gene encoding the proteirl of interest is repressed by the repressor activity of a UBC-9 or other ubiquitin conjugating enzyme having a repressor activity.
An alternative application could inc:lude an in-vitro comparative assay in which the effect of hUBC-9 on a culture of neoplastic cells or other cells of interest (e.g. 293 cells) is used as a standa:rd against which the effect of other potential anti-cance:r agents could be evaluated.
Enzymatic conversion processes, in which chemicals are commercially produced llsing enzymes expressed in cells can also take advantage of the present invention. Exemplary bioconversion processes include the yeast-catalyzed processes associated with the brewing and baking industries, and as well as the commercial production of a variety of carboxylic acids, including essential amino acids or analogs thereof, from amides or nitriles. The invention can also be used in bioconversion processes which are inlegral to bioremediation measures being carried out to effect environmental cleanup. The cells used in such enzymatic conversion processes can be eukaryot:ic cells or non-eukaryotic cells, such as genetically engineered E. coli cells. Other uses and applications of the several aspects of the invention will be apparent to those skilled in the art.
The following examples illustrate the principles and advantages of the invention.

EXAMPLES
All molecular biological manipulations used in carrying out the experiments upon which the following examples are based were performed using methods known in the art, as described, for example, in Sambrook et al., Molecular Cloninq, A Laboratory Manual, Cold Springs Harbor Laboratory Press, Cold Springs Harbor, NY (1989).

W O 97/08195 PCT~US96/14013 Example 1: Isolatlon of hUBC-9 The repressor domain (residues 85-179) within the N-terminal region of each of the alternative splice variants of WTl were previously mapped and identified as functioning independently as a potent repressor when fused to a Gal4 binding domain. (Wang, Z-Y., et al.
1993). This repressor domain was also shown to block the repressor function o~ WT1 if expressed independently without a functional DNA binding domain, suggesting that the repressor domain lacking DNA binding activity competed with WT1 for an interactive nuclear factor needed for WT1 to function as transcription repressor.
(Wang, Z-Y., et al., 1995).
The interactive factor, now identified as hUBC-9, was isolated by using a yeast two hybrid screen. Avector, LexADB-WT-N, was constructed by coupling residues 85-179 of human WT1 with the Lex DNA binding domain. To construct pLexADB/WT-N, a cDNA fragment encoding the negative regulating domain (residues 85-179) of WT1 was obtained by digestion of the plasmid pSGWT-N with XbaI, blunt ended with Klenow fragment and the EcoRI digestion, and cloned into EcoRI and SmaI treated vector pStopll6, which was modified from plasmid pBTM116 by introducing stop codons in each of three reading frames within the polylinker region.
The vector expressed a fusion protein with the LexA DNA binding (DB) domain and the negative regulatory domain of WT1 (WTN) as "bait". Yeast strain L40 was used in library screening. L40 was transformed with pLexADB/WT-N and then with the Gal4 activation domain fused with human placenta cDNA library (Clontech, CA) as recommended by the manufacturer. Two million yeast transformants were screened. Positive colonies on His-plates were further tested for ~-Galactosidase activity with a filter assay. Positive clones were tested for specificity with a LexADB/lamin C hybrid, LexADB/WT-INS

W~ 97~8195 PCT~US96/14~13 (containing residues 250-266 of WT1), LexADB/WT-N, and the LexADB vector alone. Plasmids reactive only with plexADB/WT-N were recovered from yeast and used to transform HB101 via electroporation and selected on leu~, amp~ minimal media. 65 positive clones were identified in the initial screening.
The 65 positive plasmids recovered were re-introduced to yeast to re-check specificity and for quantitation of ~-gal activity. ~-ga.lactosidase activity units are shown, in Table 2, for the DNA-binding domain fusion partner coupled with the vector alone and with the vector fused with hUBC-9 fused with the Gal4 activation domain. Table 2 shows the binding specificity of hUBC-9 to the negative regulatory domain of WT1 in the yeast two hybrid system.
Table 2 - Bindinq Specificity of hUBC-s in Two-Hybrid sYstem *-Galactosidase activity DNA-binding 20 domain fusion partner Vector hUBC-9 Vector alone: N.D. 0.2_0.1 +WT 85-179: 0.3_0.2 57.9_16.2 +WT 250-266: 0.2+0.2 0.3_0.2 +T.~m;n C: 0.3_0.1 1.5_0.5 Eleven positive clones which remained specific to WT1 were sequenced using dideoxy NTPs and sequenase 2.0 according to the manufacturer's specifications (U.S.
Biochemical). Sequence analysis and homology searches were performed using GCG program (GCG, Madison, WI).
Each of the inserts was in the same reading frame as the Gal4 activation domain. Seven of these plasmids encoded the same protein that we designated human UBC. The insert of the longest cDNA clone detected transcripts of approximately 2.8 and 1.3 kb in Northern blot analysis.
To seek full-length cDNAs, we rescreened a human placenta cDNA library with probes obtained with the two hybrid screen and isolated eight independent clones after tertiary screening. Five clones contained a 1.1 kb DNA fragment, one contained a 1.8 kb DNA fragment and two clones contained small DNA fragments that were not further analyzed. The 1.8 kb cDNA and 1.1 kb cDNA were fully sequenced. The two clones share the same sequences within the coding region and 3' end but alternative splicing appears to introduce a long 5' untranslated region (5' UTR) upstream of the translation initiation site of the longer cDNA isoform. Multiple start and stop codons were identified in all three reading frames within the long 5' UTR, indicating that the protein product of the longer transcript may be under strict translational regulation. In vitro transcription/translation of both mRNAs produced the same size protein but the longer cDNA
clone expressed less than 20% of the protein product than was expressed from the shorter mRNA (data not shown), confirming that the long 5' UTR sharply reduces translation efficiency. Because the 5' UTR of the long form contains multiple intervening start and stop codons in all three reading frames (Fig. lA), it seems likely that the presence of these codons may negatively regulate the rate of translation in the longer mRNA isoform.
In control experiments, LexADB-WT-N failed to activate transcription of reporter genes containing LexA
binding sites in yeast when analyzed alone.

ExamPle 2: Northern Blot AnalYsis of Human Tissues A human tissue Northern blot (Clontech, CA) was probed with 1.1 kb hUBC-9 cDNA, according to the manufacturer/s recommendation. Figure 2A shows the Northern blots of hUBC-9 in different human tissues.
Each lane contained 2 ~g poly A' RNA from heart (H), brain (B), placenta (Pl), lung (Li), smooth muscle (SM), kidney (K), pancreas (Pa). The ~-actin cDNA was used to probe WO 97/08195 PCTAUS96J~4013 the same blot as control. The size markers are indicated on the left side of the blot.

ExamPle 3: Analvsis of Human Genomic DNA for hU~3C-9 Gene 10 ~g of human genomic DNA (Promega, Madison WI) were digested with Hind III (H), EcoRI (E), Bgl II
(Bg), or BamHI (B). The digested DN~ was separated by electrophoresis on 1% agarose gel and Southern blot was performed with the full-length 1.1 kb hU~3C-9 CDNA as probe. Figure 2B shows the Southern blot analysis of the h~3C-9 gene.

Exam~le 4: Expression of GST-hUBC-9 Fusion Protein in E. col i Briefly, hUBC-9 was fused with glutathione S-transferase (GST) by expression in bacteria as a GST-hUBC-9 fusion protein. GST-hUBC-9 and GST were independently coupled to a reduced g:l.utathione sepharose matrix and washed extensively. Extracts from 293 cells which had been transfected with vectors expressing WT1 and various WT1 domains were then passed over the columns, and after incubating and washing, eluates were obtained. The eluates were separated by SDS-PAGE, transferred to nitrocellulose filter for immunoblotting, and analyzed by Western blot using anti-WT1 (1:500) and anti-IgG coupled with peroxidase. The blot was visualized by color fluorography.
To construct GST-hUBC-9, p~3S-hUBC-9 was digested with EcoRI and the 1.1-kb insert was subcloned into the EcoRl site of the pGEX-KG vector containing GST
in frame. E.coli strain DH5~ was transformed with GST-hUBC-9 and GST-hUBC-9 waq extracted and purified on glutathione-sepharose beads. GST ancl GST-hU.3C-9 fusion protein were independently bound to glutathione-Sepharose beads and washed extensively.

W O 97/08195 PCT~US96/14013 WTl and various domains thereof were expressed in 293 cells as previously described (Wang et al., 1993).
Extracts were made from 2X106 293 (human embryonic kidney cell) cells transfected with CMV promoter driven expression vectors encoding full length and the WT1~1-84, WT1~1-294, and WT1~297-429 domains of WTl.
In vitro binding assays were performed by incubating the extracts with the sepharose beads containing 2-3 ~g of GST and GST-hUBC-9 in lysis buffer (50 mM Tris (pH 7.4), 150 mM NaCl, 5 mM EDTA, 0.1~ NP-40, 50 mM NaF, 1 mM PMSF, 1 ~g leupeptin/ml, 1 ~g antipain/ml) for 2-3 hours at room temperature.
Complexes were washed extensively with lysis buffer and lysis buffer with 0.5M NaCl, boiled in SDS PAGE loading buffer (1% SDS, 10~ ~-mercaptoethanol), and run on 5%
SDS-polyacylamide gels. Gels were transferred to nitrocellulose membranes (SOSNC) and immunoblotted with polyclonal anti-WTl antibodies SC089 and SC189 (Santa Cruz, CA), which recognize the N-terminal and C-terminal domains of WTl, respectively. Following the addition of an alkaline phosphatase-conjugated secondary antibody, bound WTl protein was visualized with 5-bromo-4-chloro-3-indolyphosphate toluidinium and nitro blue tetrazolium (BCIP, NBT; Promega, Madison, WI).
Figure 3A shows the in vitro binding of WTl and hUBC-9. The left column shows the cell lysate control results with the arrow indicating WTl at the expected estimated molecular mass of 14kd. The right column shows the GST control results. The middle column shows the results for the GST-hUBC-9 fusion protein with the associated arrows indicating binding between WTl and the GST-hUBC-9 matrix. Because no similar binding was observed between WTl and the GST control matrix, these results demonstrate that WTl binds to or associates with hUBC-9.

WO 97/0~195 PCT/US96/14013 Example 5: Cell Cotransfection with WT1 and HA-taqqed Human UBC
An expression vector encoding the influenza virus hemagglutinin (HA) tagged hUBC-9 was constructed by cloning the 1.1 k~ EcoRI fragment of hUBC-9 into the EcoRI site of expression vector pGCN (REF) in frame with a cDNA fragment encoding the HA peptide.
293 cells were cotransfected with WT1 and HA-tagged hUBC-9 expression plasmids. Cellular lysates were prepared and the extracts were immunoprecipitated with either anti-WT1 antibody or a nonspecific rabbit polyclonal antibody (anti-Gal4DB). WT1 associated proteins were separated on 15% SDS-PA~E and blotted. The blot was then analyzed by probing with anti-HA monoclonal antibody which recognized the HA tagged hUBC-9.
Figure 3B shows the results of the co-immunoprecipitation of WT1 and hUBC-9.

Exam~le 6: Co-ExPression of hUBC-9 with ts YUBC-9 Yeast strain W9432 (MATa, ubc9-~ TRP1, pSE362[ARS1, CEN4, HIS3]-ubc9-1) is isogenic to W303 except for carrying a replacement of ~he genomic yUBC-9 coding sequence by the TRP1 marker and a plasmid-borne copy of the temperature ~ensitive yUBC-9-1 allele (1.5 kb Xbal-Sspl fragment).
hUBC-9 cDNA (1.1 kb EcoRI fragment) and yUBC-9 gene (0.6 kb EcoRI-XbaI fragment) were each fused to the GAL1 promoter in vectors p416GAL1 (ARSH4, CEN6, URA3) and pSE936 (ARS1, CEN4, URA3), respectively.
Referring to Figures 4A and 4B, the temperature-sensitive yeast strain (W9432) was independently transformed with the hUBC-9 (Row 1) and yUBC-9 (Row 4) control vectors (p416G~L1 and pSE936, respectively) and with a construct expressing hUBC-9 cDNA
(Row 2) or the yUBC-9 gene (Row 3). 'To compare growth of these strains, cells were spotted in a dilution series on galactose-containing plates and incubated for 3.5 days at the permissive temperatures (23 ~C) or 2 days at the restrictive temperature (34 ~C).

Example 7: hU~3C-9 / WT1 Co-transfection Experiments 293 cells were co-transfected by calcium phosphate/DNA precipitation with hUBC-9 and WT1 expression constructs under the control of the CMV
promoter and with a PDGF A-chain promoter driven CAT
reporter plasmid.
The total amount of CMV promoter sequence transfected into each dish was equalized in each transfection by the addition of vector DNA. Transfection efficiency were standardized by co-transfection of a CMV
promoter driven ~B-galactosidase reporter construct. All experiments were repeated at least three times.
Figure 5A shows the results of the CAT assay and ~B-galactosidase assays. CAT activity was quantitated by scintillation counting of excised sections of TLC
plates. Figure 5B shows the relative CAT activity values from different assays at different times, including the standard deviation of each. The experiments demonstrate that hUBC-9 ~nh~nces the transcriptional repressor activity of WT1 in human embryonic kidney cell (293 cell).

Exam~le 8: hl~}3C-9-Gal4 Cotransfection Assay hUBC-9 was coupled to the Gal4 DNA binding domain and evaluated for its effect on transcription in a reporter system.
Referring to Figure 6A, a control expression vector, pSG424, was constructed with a SV40 promoter driven Gal4 DNA binding domain. A fusion protein expression vector, pSG-hUBC-9, was constructed with full length cDNA of hUBC-9 fused with Gal4 DNA binding domain driven by SV40 promoter. pSG-hUBC-9 was constructed by WO 97/08195 PCT/US96~1401~

inserting an EcoR1 DNA fragment containing full length of hUBC-9 cDNA into the EcoRl site of expresslon vector pSG424. Reporter plasmids pSV CAT and 5XUAS pSV CAT were provided by Dr. S. Weintraub (Washin~ton University at St. Louis). The pSV CAT plasmid included a SV40 promoter fused with CAT reporter gene (Promega, Madison, WI). The 5xUAS pSV CAT plasmid included a pSV CAT plasmid with additional 5 copies of the Gal4 bind:ing sites upstream of the SV40 promoter.
Co-transfection experiments were done in which each of the expression vectors were cotransfected with each of the reporter plasmids. 5 ~g of reporter plasmid DNA were used in each transfection w:ith various amounts of expression plasmids. Figure 6B shows the results of CAT and ~-galactosidase as~ays, performed as described above (Example 7), for different amollnts of expression plasmids, as indicated. CAT activity is shown as CAT
activity relative to the control alone.

Example 9: hUF3C-9, YUBC-9 and YUBC-9-m Gal4 Fusion Proteins hUBC-9, yUBC-9 and yUBC-9-m (a mutant yUBC-9 with serine in place of the active site cy~teine) were independently coupled to a Gal4 DNA binding domain and evaluated for effect on transcription in a reporter sy~tem.
Referring to Figure 7A, control expression vector, pSG424, and hUBC-9/Gal4 fusion protein expression vector, pSG-hUBC-9, were constructed as described above (Example 8). A yUBC-9/Gal4 expressic)n vector, pSG-yUBC-9, was constructed by inserting an EcoR1 DNA fragmentcontaining full length of yUBC-9 cDN~ into the EcoRI site of expression vector pSG424. A yUBC-9-m/Gal4 expression vector, pSG-yUBC-9-m, was constructed by digestion of pUC19-yUBC9-m plasmid with HindIII, blunted with Klenow fragment, and then digested by EcoRI and cloned into WO 97/08195 PCTrUS96/14013 EcoRI-SmaI digested pSG424 plasmid. The reporter plasmids, depicted in Figure 7A, were as obtained described above (Example 8).
The results of CAT and ~-galactosidase assays, performed as discussed above (Example 7), for cotransfection experiments are shown in Figure 7B and 7C
for human and yeast UBC's, respectively. 5 ~g of reporter plasmid DNA were used in each transfection with various amounts of expression plasmids, as indicated.
In light of the detailed description of the invention and the examples presented above, it can be appreciated that the several objects of the invention are achieved. The explanations and illustrations presented herein are intended to acquaint others skilled in the art with the invention, its principles, and its practical application. Those skilled in the art may adapt and apply the invention in its numerous forms, as may be best suited to the requirements of a particular use.
Accordingly, the specific embodiments of the present invention as set forth are not intended as being exhaustive or limiting of the invention.

W~ 97~0819~ PCTAUS96/14013 BIBLIOGRAPHY
Cohen, S.N., 1972: Proc. Natl. Acad. Sci.
69:2110 (1972) Depicker, A., et al., 1982: J. Mol. APpl. Gen.
(1982) 1:561.
Dower et al. (1988), Nucleic Acids Research 16:6127-6145.
Goeble, M.G., et al., 1988: The yeast cell cycle gene CDC34 encodes a ubiquitin-conjugating enzyme.
Science, 1988. 241 (4871): p. 1331-5 Seufert, W. et. al., 1995: Role of a ubiquitin-conjugating enzyme in degradation of S- and M-phase cyclins. Nature, 1995. 373(6509): p. 78-81.
Wang, Z-Y., et al., 1995: WTl, the Wilms~ tu~or suppressor gene product, represses transcription through an interactive nuclear protein. Oncogene, 1995. 10: p.
1243-1247].
Wang, Z-Y., et al., 1993: Identification of a single-stranded DNA-binding protein that interacts with an Sl nuclease-sensitive region in the platelet-derived growth factor A-chain gene promoter. J. Biol. Chem., 1993a 268 (No. 14, May 15), p. 9172, p. 10681-10685.
.

Claims (86)

WE CLAIM:

1. An substantially purified protein selected from the group consisting of:
(a) hUBC-9, and (b) a protein having an amino acid sequence which includes the amino acid sequence of hUBC-9.

2. An substantially purified protein selected from the group consisting of (a) a protein having ubiquitin conjugating activity or transcriptional repressor activity, and having an amino acid sequence which includes a portion of the amino acid sequence of hUBC-9, the included portion being at least about 12 amino acid residues in length and conferring the conjugating or repressor activity on the protein, and (b) a protein having transcriptional repressor activity and having at least about 65% sequence identity to hUBC-9.

3. The protein of claim 2 wherein the protein has transcriptional repressor activity.

4. The protein of claim 2 wherein the protein has transcriptional repressor activity and lacks ubiquitin conjugating activity.

5. The protein of claim 2 wherein the protein has transcriptional repressor activity and is a C93 mutant of hUBC-9, whereby the mutated hUBC-9 protein lacks ubiquitin conjugating activity.

6. The protein of claim 2 wherein the protein has transcriptional repressor activity and ubiquitin conjugating activity.

7. A substantially isolated nucleic acid polymer selected from the group consisting of:
(a) a nucleic acid polymer encoding hUBC-9; and (c) a nucleic acid polymer having a nucleotide sequence complementary to the nucleic acid sequence of a nucleic acid polymer encoding hUBC-9.

8. The nucleic acid polymer of claim 7 wherein the nucleic acid polymer has a nucleotide sequence selected from the group consisting of:
(a) Nucleotide Sequence No. 1, Fig. 1A;
(b) Nucleotide Sequence No. 2, Fig. 1A;
(c) a nucleotide sequence which includes the sequence from position 88 to position 564 of Nucleotide Sequence No. 2, Fig. 1A; and (d) a nucleotide sequence complementary to the nucleotide sequence set forth in (a), (b) or (c).

9. A substantially isolated nucleic acid polymer, the nucleic acid polymer being selected from the group consisting of:
(a) a nucleic acid polymer encoding a protein having ubiquitin conjugating activity or transcriptional repressor activity, the encoded protein having an amino acid sequence which includes a portion of the amino acid sequence of hUBC-9, the included portion being at least about 12 amino acid residues in length and conferring the conjugating or repressor activity on the protein; and (b) a nucleic acid polymer having a nucleotide sequence complementary to the nucleotide sequence of the nucleic acid polymer recited in (a).

10. The nucleic acid polymer of claim 9 wherein the nucleic acid polymer has a nucleotide sequence which includes a portion of a nucleotide sequence selected from a group consisting of: (a) Nucleotide Sequence No. 1, Fig. 1A; (b) Nucleotide Sequence No. 2, Fig. 1A; (c) a nucleotide sequence which includes the sequence from position 88 to position 564 of Nucleotide Sequence No. 2, Fig. 1A; and (d) a nucleotide sequence complementary to the nucleotide sequence set forth in (a), (b) or (c), the included portion being at least about 36 nucleotide residues in length and encoding an amino acid sequence which confers the conjugating or repressor activity on the encoded protein.

11. The nucleic acid polymer of claim 9 wherein the encoded protein has transcriptional repressor activity.

12. The nucleic acid polymer of claim 9 wherein the encoded protein has transcriptional repressor activity and does not have ubiquitin conjugating activity.

13. The nucleic acid polymer of claim 9 wherein the encoded protein has transcriptional repressor activity and ubiquitin conjugating activity.

14. A substantially isolated nucleic acid polymer, the nucleic acid polymer being at least about 36 nucleotide residues in length and encoding a protein which has transcriptional repressor activity, wherein:
(a) the encoded protein has at least about 65%
sequence identity to hUBC-9 or mUBC9; or (b) the nucleic acid polymer hybridizes to a nucleic acid polymer complementary to a nucleic acid polymer selected from the group consisting of: (i) a nucleic acid polymer encoding hUBC-9; (ii) Nucleotide Sequence No. 1, Fig. 1A; (iii) Nucleotide Sequence No. 2, Fig. 1A; (iv) a nucleotide sequence which includes the sequence from position 88 to position 564 of Nucleotide Sequence No. 2, Fig. 1A; and (v) a nucleic acid polymer encoding a protein having ubiquitin conjugating activity or transcriptional repressor activity, the encoded protein having an amino acid sequence which includes a portion of the amino acid sequence of hUBC-9, the included portion being at least about 12 amino acid residues in length and conferring the conjugating or repressor activity on the protein.

15. The nucleic acid polymer of claim 14 wherein the encoded protein has transcriptional repressor activity and lacks ubiquitin conjugating activity.

16. A method for producing hUBC-9 or a protein having an amino acid sequence which includes the amino acid sequence hUBC-9 or a portion of thereof, the included portion being at least about 12 amino acid residues in length and conferring ubiqutin conjugating or transcriptional repressor activity on the protein, the method comprising producing a plasmid vector comprising DNA, the DNA encoding a protein selected from the group consisting of: (i) hUBC-9, (ii) a protein having an amino acid sequence which includes the amino acid sequence of hUBC-9; and (iii) a protein having ubiquitin conjugating activity or transcriptional repressor activity, and having an amino acid sequence which includes a portion of the amino acid sequence of hUBC-9, the included portion being at least about 12 amino acid residues in length and conferring the conjugating or repressor activity on the protein, transfecting the plasmid vector into a host cell, and expressing the protein in the host cell.

17. A plasmid vector comprising DNA, the DNA
comprising a deoxyribonucleic acid polymer which encodes a protein selected from the group consisting of:
(a) hUBC-9, (b) a protein having an amino acid sequence which includes the amino acid sequence of hUBC-9, (c) a protein having ubiquitin conjugating activity or transcriptional repressor activity, and having an amino acid sequence which includes a portion of the amino acid sequence of hUBC-9, the included portion being at least about 12 amino acid residues in length and conferring the conjugating or repressor activity on the protein, (d) a protein having transcriptional repressor activity and having at least about 65% sequence identity to hUBC-9, and (e) a fusion protein having transcriptional repressor activity, the fusion protein comprising a DNA
binding domain and a transcriptional repressor domain, the transcriptional repressor domain having an amino acid sequence which includes at least a portion of the amino acid sequence of a ubiquitin conjugating enzyme having transcriptional repressor activity, the included portion being at least about 12 amino acid residues in length and conferring the repressor activity on the fusion protein.

18. The plasmid vector of claim 17 wherein the deoxyribonucleic acid polymer has a nucleotide sequence selected from the group consisting of:
(a) Nucleotide Sequence No. 1, Fig. 1A;
(b) Nucleotide Sequence No. 2, Fig. 1A; and (c) a nucleotide sequence which includes the sequence from position 88 to position 564 of Nucleotide Sequence No. 2, Fig. 1A.

19. A host cell transformed with a plasmid vector comprising DNA, the DNA comprising a deoxyribonucleic acid polymer which encodes a protein selected from the group consisting of:
(a) hUBC-9, (b) a protein having an amino acid sequence which includes the amino acid sequence of hUBC-9, (c) a protein having ubiquitin conjugating activity or transcriptional repressor activity, and having an amino acid sequence which includes a portion of the amino acid sequence of hUBC-9, the included portion being at least about 12 amino acid residues in length and conferring the conjugating or repressor activity on the protein, (d) a protein having transcriptional repressor activity and having at least about 65% sequence identity to hUBC-9, and (e) a fusion protein having transcriptional repressor activity, the fusion protein comprising a DNA
binding domain and a transcriptional repressor domain, the transcriptional repressor domain having an amino acid sequence which includes at least a portion of the amino acid sequence of a ubiquitin conjugating enzyme having transcriptional repressor activity, the included portion being at least about 12 amino acid residues in length and conferring the repressor activity on the fusion protein.

20. The host cell of claim 19 wherein the deoxyribonucleic acid polymer has a nucleotide sequence selected from the group consisting of:
(a) Nucleotide Sequence No. 1, Fig. 1A;
(b) Nucleotide Sequence No. 2, Fig. 1A; and (c) a nucleotide sequence which includes the sequence from position 88 to position 564 of Nucleotide Sequence No. 2, Fig. 1A.

21. A host cell co-transfected with first and second plasmid vectors each comprising DNA, the DNA of the first vector comprising a deoxyribonucleic acid polymer encoding transcriptional repressor protein, the DNA of the second vector comprising a deoxyribonucleic acid polymer encoding an adapter protein, the adapter protein having transcriptional repressor activity and an amino acid sequence which includes at least a portion of the amino acid sequence of a ubiquitin conjugating enzyme having transcriptional repressor activity, the included portion being at least about 12 amino acid residues in length and conferring the repressor activity on the adapter protein.

22. The host cell of claim 21 wherein the ubiquitin conjugating enzyme has transcriptional repressor activity and a mutated active site cysteine residue, whereby the mutated enzyme lacks ubiquitin conjugating activity.

23. The host cell of claim 21 wherein the ubiquitin conjugating enzyme is UBC-9.

24. The host cell of claim 21 wherein the ubiquitin conjugating enzyme is hUBC-9 or yUBC-9.

25. The host cell of claim 21 wherein the ubiquitin conjugating enzyme is hUBC-9.

26. The host cell of claim 21 wherein the transcriptional repressor protein is WT1.

27. The host cell of claim 21 wherein the transcriptional repressor protein is WT1 and the adapter protein is UBC-9.

28. The host cell of claim 21 wherein the adapter protein is (a) a ubiquitin conjugating enzyme having transcriptional repressor activity or (b) a ubiquitin conjugating enzyme having transcriptional repressor activity and having a mutated active site cysteine residue, whereby the mutated enzyme lacks ubiquitin conjugating activity.

29. The host cell of claim 28 wherein the ubiquitin conjugating enzyme is UBC-9.

30. The host cell of claim 28 wherein the ubiquitin conjugating enzyme is hUBC-9 or yUBC-9.

31. The host cell of claim 28 wherein the ubiquitin conjugating enzyme is hUBC-9.

32. The host cell of claim 28 wherein the transcriptional repressor protein is WT1.

33. The host cell of claim 28 wherein the transcriptional repressor protein is WT1 and the adapter protein is UBC-9.

34. A fusion protein having transcriptional repressor activity, the fusion protein comprising a DNA
binding domain and a transcriptional repressor domain, the transcriptional repressor domain having an amino acid sequence which includes at least a portion of the amino acid sequence of a ubiquitin conjugating enzyme having transcriptional repressor activity, the included portion being at least about 12 amino acid residues in length and conferring the repressor activity on the fusion protein.

35. The fusion protein of claim 34 wherein the ubiquitin conjugating enzyme has transcriptional repressor activity and a mutated active site cysteine residue, whereby the mutated enzyme lacks ubiquitin conjugating activity.

36. The fusion protein of claim 34 wherein the ubiquitin conjugating enzyme is UBC-9.

37. The fusion protein of claim 34 wherein the ubiquitin conjugating enzyme is hUBC-9 or yUBC-9.

38. The fusion protein of claim 34 wherein the ubiquitin conjugating enzyme is hUBC-9.

39. The fusion protein of claim 34 wherein the amino acid sequence of the transcriptional repressor domain includes the amino acid sequence of (a) a ubiquitin conjugating enzyme having transcriptional repressor activity or (b) a ubiquitin conjugating enzyme having transcriptional repressor activity and having a mutated active site cysteine residue, whereby the mutated enzyme lacks ubiquitin conjugating activity.

40. The fusion protein of claim 39 wherein the ubiquitin conjugating enzyme is UBC-9.

41. The fusion protein of claim 39 wherein the ubiquitin conjugating enzyme is hUBC-9 or yUBC-9.

42. The fusion protein of claim 39 wherein the ubiquitin conjugating enzyme is hUBC-9.

43. The fusion protein of claim 34 wherein the DNA binding domain has an amino acid sequence which includes the amino acid sequence of a domain selected from the group consisting of Ga14, LexA or a zinc-finger domain.

44. A nucleic acid polymer encoding the fusion protein of claim 34.

45. A composition comprising a protein having transcriptional repressor activity, the protein having an amino acid sequence which includes at least a portion of the amino acid sequence of a ubiquitin conjugating enzyme having transcriptional repressor activity, the included portion being at least about 12 amino acid residues in length and conferring the repressor activity on the protein, and a carrier, diluent or delivery agent.

46. The composition of claim 45 wherein the composition is a pharmaceutical composition comprising an amount of the protein effective to regulate transcription of a target gene in a cell, and a pharmaceutically acceptable carrier, diluent or gene therapy delivery agent.

47. The composition of claim 45 wherein the ubiquitin conjugating enzyme has a mutated active site cysteine residue, whereby the mutated enzyme lacks ubiquitin conjugating activity.

48. The composition of claim 45 further comprising a biochemical inhibitor suitable for inhibiting the active site cysteine of the protein, whereby the protein lacks ubiquitin conjugating activity.

49. The composition of claim 45 wherein the ubiquitin conjugating enzyme is UBC-9.

50. The composition of claim 45 wherein the ubiquitin conjugating enzyme is yUBC-9 or hUBC-9.

51. The composition of claim 45 wherein the ubiquitin conjugating enzyme is hUBC-9.

52. The composition of claim 45 wherein the amino acid sequence of the transcriptional repressor protein includes the amino acid sequence of a ubiquitin conjugating enzyme having transcriptional repressor activity.

53. The composition of claim 45 further comprising a second protein having transcriptional repressor activity.

54. The composition of claim 45 further comprising WT1.

55. The composition of claim 45 wherein the transcriptional repressor protein is a fusion protein, the fusion protein comprising a DNA binding domain and a transcriptional repressor domain, the transcriptional repressor domain having an amino acid sequence which includes at least a portion of the amino acid sequence of (a) a ubiquitin conjugating enzyme having transcriptional repressor activity, or (b) a ubiquitin conjugating enzyme having transcriptional repressor activity and a mutated active site cysteine residue, whereby the mutated enzyme lacks ubiquitin conjugating activity, the included portion being at least about 12 amino acid residues in length and conferring the repressor activity on the protein.

56. A composition suitable for use in gene therapy, the agent comprising a nucleic acid polymer selected from the group consisting of: (a) a nucleic acid polymer encoding a protein having transcriptional repressor activity, the protein having an amino acid sequence which includes at least a portion of the amino acid sequence of a ubiquitin conjugating enzyme having transcriptional repressor activity, the included portion being at least about 12 amino acid residues in length and conferring the repressor activity on the protein; and (b) a nucleic acid polymer having a nucleotide sequence complementary to the nucleic acid sequence of the nucleic acid polymer set forth in (a), and a gene therapy delivery agent.

57. The composition of claim 56 wherein the composition is a pharmaceutical composition and comprises an amount of nucleic acid polymer sufficient, upon introduction of the nucleic acid polymer into a host cell, to express an amount of a transcriptional repressor protein effective to regulate transcription of a target gene in the cell, and a pharmaceutically acceptable gene therapy delivery agent.

58. The composition of claim 56 wherein the ubiquitin conjugating enzyme has a mutated active site cysteine residue, whereby the mutated enzyme lacks ubiquitin conjugating activity.

59. The composition of claim 56 further comprising a biochemical inhibitor suitable for inhibiting the active site cysteine of the protein, whereby the protein lacks ubiquitin conjugating activity.

60. The composition of claim 56 wherein the ubiquitin conjugating enzyme is a UBC-9.

61. The composition of claim 56 wherein the nucleic acid polymer encodes a fusion protein having transcriptional repressor activity, the fusion protein comprising a DNA binding domain and a transcriptional repressor domain, the transcriptional repressor domain having an amino acid sequence which includes at least a portion of the amino acid sequence of (a) a ubiquitin conjugating enzyme having transcriptional repressor activity or (b) a ubiquitin conjugating enzyme having transcriptional repressor activity and a mutated active site cysteine residue, whereby the mutated enzyme lacks ubiquitin conjugating activity, the included portion being at least about 12 amino acid residues in length and conferring the repressor activity on the protein.

62. The composition of claim 56 wherein the nucleic acid polymer has a nucleotide sequence selected from the group consisting of:
(a) Nucleotide Sequence No. 1, Fig. 1A;
(b) Nucleotide Sequence No. 2, Fig. 1A;
(c) a nucleotide sequence which includes the sequence from position 88 to position 564 of Nucleotide Sequence No. 2, Fig. 1A; and (d) a nucleotide sequence complementary to the nucleotide sequence set forth in paragraph (a), (b) or (c).

63. The composition of claim 56 wherein the composition comprises a virus having a viral genome comprising the nucleic acid polymer.

64. The composition of claim 63 wherein the viral genome comprises a nucleic acid polymer having a nucleotide sequence selected from the group consisting of:
(a) Nucleotide Sequence No. 1, Fig. 1A;
(b) Nucleotide Sequence No. 2, Fig. 1A;

(c) a nucleotide sequence which includes the sequence from position 88 to position 564 of Nucleotide Sequence No. 2, Fig. 1A; and (d) a nucleotide sequence complementary to the nucleotide sequence set forth in paragraph (a), (b) or (c).

65. The composition of claim 63 wherein the ubiquitin conjugating enzyme is UBC-9.

66. A method for suppressing transcription of a gene in a cell, the method comprising exposing the gene to a substantially purified protein, the protein having transcriptional repressor activity and an amino acid sequence which includes at least a portion of the amino acid sequence of a ubiquitin conjugating enzyme having transcriptional repressor activity, the included portion being at least about 12 amino acid residues in length and conferring the repressor activity on the protein.

67. The method of claim 66 wherein the ubiquitin conjugating enzyme has a mutated active site cysteine residue, whereby the mutated enzyme lacks ubiquitin conjugating activity.

68. The method of claim 66 wherein the ubiqutin conjugating enzyme is a UBC-9.

69. The method of claim 66 wherein the gene is exposed to the protein by introducing the protein into the cell.

70. The method of claim 66 wherein the gene is exposed to the protein by introducing a nucleic acid polymer which encodes the protein into the cell.

71. The method of claim 66 wherein the cell is transfected with a plasmid vector having a DNA
comprising a deoxyribonucleic acid polymer which encodes the protein.

72. The method of claim 66 wherein the cell is infected with a virus having a genome comprising a nucleic acid polymer which (a) encodes the protein or (b) has a nucleotide sequence complementary to the nucleic acid sequence of the nucleic acid polymer set forth in (a).

73. The method of claim 66 wherein the cell is cotransfected with a first plasmid vector having a first DNA and second plasmid vector having a second DNA, the first DNA comprising a deoxyribonucleic acid polymer which encodes the protein, the second DNA comprising a nucleic acid polymer which encodes WT1, and wherein the DNA's are expressed in the cell.

74. The method of claim 66 wherein the protein is a fusion protein comprising a DNA binding domain and transcriptional repressor domain, the transcriptional repressor domain having an amino acid sequence which includes at least a portion of the amino acid sequence of (a) a ubiquitin conjugating enzyme having transcriptional repressor activity or (b) a ubiquitin conjugating enzyme having transcriptional repressor activity and a mutated active site cysteine residue, whereby the mutated enzyme lacks ubiquitin conjugating activity, the included portion of the amino acid sequence being at least about 12 amino acid residues in length and conferring the repressor activity on the protein.

75. The method of claim 66 wherein the cell is infected with a virus having a viral genome and the gene to which the protein is exposed is viral genome, whereby transcription of the viral genome is repressed.

76. The method of claim 66 wherein the cell is a eukaryotic cell.

77. The method of claim 66 wherein the cell is a fungal cell.

78. The method of claim 66 wherein the cell is a yeast cell.

79. The method of claim 66 wherein the cell is a plant cell.

80. The method of claim 66 wherein the cell is a non-human animal cell.

81. The method of claim 66 wherein the cell is a non-human mammalian cell.

82. The method of claim 66 wherein the cell is a human cell.

83. The method of claim 82 wherein the human cell is exposed to the protein by contacting, infecting or transfecting the cell with a composition comprising a nucleic acid polymer which encodes the protein and a pharmaceutically acceptable carrier, diluent or gene therapy delivery agent.

84. The method of claim 82 wherein the human cell is a neoplastic tissue cell.

85. The method of claim 82 wherein the human cell is a Wilm's tumor cell, and administering the composition inhibits proliferation of the tumor cell.

86. A method for regulating transcription of a gene in a cell, the method comprising exposing the gene to an substantially purified protein having ubiquitin conjugating activity or transcriptional repressor activity, the protein having an amino acid sequence which includes at least a portion of the amino acid sequence of hUBC-9, the included portion being at least about 12 amino acid residues in length and conferring the repressor activity on the protein.