WO1999045021A1 - Genes regules par le cycle cellulaire - Google Patents

Genes regules par le cycle cellulaire Download PDF

Info

Publication number
WO1999045021A1
WO1999045021A1 PCT/US1999/004705 US9904705W WO9945021A1 WO 1999045021 A1 WO1999045021 A1 WO 1999045021A1 US 9904705 W US9904705 W US 9904705W WO 9945021 A1 WO9945021 A1 WO 9945021A1
Authority
WO
WIPO (PCT)
Prior art keywords
probes
cell cycle
genes
yeast
regulated
Prior art date
Application number
PCT/US1999/004705
Other languages
English (en)
Inventor
Raymond J. Cho
Michael J. Campbell
Lisa Wodicka
David J. Lockhart
Ronald W. Davis
Original Assignee
Affymetrix, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Affymetrix, Inc. filed Critical Affymetrix, Inc.
Priority to AU28921/99A priority Critical patent/AU2892199A/en
Publication of WO1999045021A1 publication Critical patent/WO1999045021A1/fr

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/37—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from fungi
    • C07K14/39—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from fungi from yeasts
    • C07K14/395—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from fungi from yeasts from Saccharomyces

Definitions

  • the events of DNA replication, chromosome segregation, and mitosis define a fundamental periodicity in eukaryotic cell cycle. Precise coordination of the unidirectional transitions between these stages is critical to cell integrity and survival.
  • Each of said probes comprises at least 12 nucleotides. Greater than 50 % of the probes in the set comprise portions of yeast genes which are cell cycle regulated. Cell cycle regulated yeast genes are defined as genes whose expression varies by more than 2-fold during the cell cycle of yeast.
  • a method for identifying compounds which affect the cell cycle of yeast.
  • Synchronized yeast cells are contacted with a test compound.
  • RNA is isolated from the yeast cells.
  • the amount of particular mRNA species in the RNA isolated from the yeast cells is determined using a set of polynucleotide probes. Each of said probes comprises at least 12 nucleotides. Greater than 50 % of the probes in the set comprise portions of yeast genes which are cell cycle regulated.
  • Cell cycle regulated yeast genes are defined as genes whose expression varies by more than 2-fold during the cell cycle of yeast.
  • a test compound is identified as a candidate drug if it is found to affect the amount of the particular mRNA species.
  • RNA from synchronized yeast cells is isolated.
  • the amount of particular mRNA species in the RNA isolated from the yeast cells is determined using probes.
  • Each of said probes comprises at least 12 nucleotides.
  • Greater than 50 % of the probes in the set comprise portions of yeast genes which are cell cycle regulated.
  • Cell cycle regulated yeast genes are defined as genes whose expression varies by more than 2-fold during the cell cycle of yeast. The relative amounts of the particular mRNA species determined is characteristic of phase of cell cycle of the yeast.
  • Fig. la Phase contrast photographs of yeast cells in various phases of the cell cycle as indicated.
  • Fig. lb Graph of the percentage of cells that are unbudded (purple) small budded (yellow) , and large budded (green) versus time.
  • Fig. lc Graph of the percentage of cells that are premitotic (red), mitotic (blue) and postmitotic (green) versus time. At 110 minutes, virtually all cells completed mitosis.
  • Fig.2 Close-up views of high-density oligonucleotide arrays containing 25-mer probes for nearly every gene in the Saccharomyces cerevisiae genome, following hybridization with labeled cDNA from synchronized cells.
  • the first column shows array features containing probes to the CJNl gene (highlighted in red) from different time points.
  • the second column shows array features containing probes to the YML027w open reading frame. Transcript levels for both genes reached their maxima during late G, phase.
  • transcripts which peaked in both late G ! and G 2 yellow
  • transcripts which peaked in both S and M red
  • Fig. 4 b transcripts which peaked singly in S
  • transcripts which peaked singly in M green
  • Fig.4c transcripts for the CLNl, CLN2, CLBl, and CLB2 cyclin genes Fig. Ad transcripts for MCM genes (mustard)
  • transcripts for genes involved in DNA replication blue
  • Figs. 5_ ⁇ -5o Phenotypic categorization of mRNAs which are regulated with the cell cycle.
  • Fig. 6 Functional classifications of cell cycle-dependent transcripts which display cell cycle-specific periodicity. Biological functions of characterized genes were determined from the published literature and the MIPS database. Transcripts which peaked twice in one cell cycle are also listed.
  • Fig. 7 Major functional groups of cell cycle-de pendent transcripts. ORF loci and names are listed for some genes detected as periodically transcribed by visual inspection of mRNA fluctuation patterns. Bioche mical functions were determined from the published literature and the MIPS database. Some of these transcriptional periodicities have been previously described.
  • Fig. 8 Upstream regulatory elements in cell cycle-dependent transcription. Known and putative regulatory sequences and their frequency of occurrence in genes which display cell cycle-dependent mRNA Auction. Frequencey of occurrence is also shown for a random set of 300 genes from the yeast genome which do not show periodic mRNA Auction. Percent of genes in each category containing the regulatory sequence is listed in parentheses.
  • the probes for each gene or mRNA may comprise at least 10, 12, 14, 16, 18, 20, 22, or 25 nucleotides, and are typically single stranded. Double stranded probes can also be used.
  • the probes may comprise sense or antisense sequences, so long as they are derived from transcribed portions of the genome.
  • the probes may be DNA or RNA and can also contain nucleotide analogues or non-nucleotide moieties, such as radiolabels, fluorescent labels, enzymes, etc.
  • At least 50% of the probes in the sets comprise portions of genes whose expression varies by more than 2-fold during the cell cycle of yeast. Preferably at least 60, 75, 90, 95, 97, or 98 percent of the probes in the sets are from such cell cycle varying genes.
  • the probes which are not such genes may be controls for hybridization, which are irrelevant or mismatched at one or more nucleotides.
  • the sets may be of various sizes, depending on the purpose for which they are to be used. Typically the sets comprise at least 10, 20, 30, 40, 50, 100, 200, 300, 313, or 355 probes.
  • the sets of probes can be used for any type of nucleic acid hybridization reactions known in the art. They may be used for solution hybridization or on a solid phase.
  • RNA Ribonucleic acid
  • cDNA Ribonucleic acid
  • Solid phases which may be used include microtiter dishes, arrays, filter blots, etc.
  • One particularly useful type of solid support is an array in which the probes are synthesized onto discrete locations on the solid support. See, e.g., Chee et al, Science 274, 610-614 (1996).
  • Such arrays can contain many discrete probes in a very small area, for example greater than 1,000 or 10,000 in an area of 1.6 cm 2 .
  • synchronized cells be used in the practice of the present invention. Cells can be synchronized using any techniques known in the art, including the use of conditional mutations and/or changes in the growth conditions of the cells.
  • Test compounds which can be tested using the sets of probes of the present invention may be, for example, simple organic or inorganic compounds, natural or synthetic polymers, proteins, oligonucleotides, polypeptides, semisynthetic derivatives of natural products, natural product extracts. Mixtures of compounds or test substances may be tested, as can libraries of test compounds. Combinatorial libraries of compounds may be used, as can libraries of cloned nucleic acids or proteins they produce. Any substances which can be contacted with yeast cells can be tested. Similarly, forms of radiation can be tested for their effects using the sets of probes of the present invention.
  • test compounds may be those which are being screened for toxic, mutagenic, carcinogenic, or therapeutic value.
  • Compounds or treatments which cause a change in the pattern of expression of the monitored genes are potentially useful to alter cell cycle of eukaryotes. Such treatments may be useful as antifungal agents.
  • Such assays may also be useful as prescreens for identifying anti-cancer or anti-viral therapies.
  • the amount of hybridization of a test sample of RNA or DNA to a set of probes can be determined using any or the techniques or methods which are known in the art.
  • the test sample can be labeled with a radiolabel or a fluorescent label.
  • the amount of the label can be quantitated using appropriate instrumentation, such as a scintillation counter, an X-ray film, a fluorimeter.
  • the amount of hybridization of the sets of probes to the samples collected from cells before and after treatment with a test compound, or treated and untreated can be readily compared.
  • transcript levels could result from the shift between the restrictive and permissive temperatures and from the state of cell cycle arrest.
  • analysis was focused on data from cdc28-13 time points taken more than forty minutes past the point of release from arrest.
  • a database of potential gene promoter sequences was created by extracting the 500 bp upstream of the translational start site of every gene in the genome. This data set was then searched for hexanucleotide and hepanucleotide sequences that occurred with disproportionate frequency in the upstream regions of one set of cell cycle-regulated genes. The nucleotides surrounding these short sequences were visually inspected to determine a longer consensus sequence. For example, the sequence 5' GTAAACA 3' was found upstream of nearly 40% of the genes induced in G 2 and M, but upstream of less than 20% of genes induced at other times. After visual inspection of several G 2 and M gene promoter regions, this sequence was expanded to 5' AAAANGTAAACAA 3'. A search of non-coding sequence revealed that this sequence was found upstream of 14% of genes induced in G 2 , but upstream of less than 1% of other genes in the genome (Table 3). Another method of identifying candidate regulatory elements is examination of
  • G 2 and M regulatory elements may be responsible for periodicity of mRNA abundance during these phases.
  • G 2 and M regulatory elements maybe relatively rare, but highly specific in determining periodicity of transcript levels.
  • regulatory sequences that affect transcription during these periods may be highly degenerate. Both methods described for identifying candidate regulatory elements
  • telomeric or centromeric gene location was positioned directly adjacent to another gene induced in the same cell cycle phase (Fig. 3).
  • the proportion of cell cycle regulated genes which would occupy adjacent positions by random chance is less than 3%. More than half of these gene pairs were transcribed divergently on opposite strands, many with fewer than 1500 bp bases separating their 5' ends.
  • Periodic mRNA fluctuation was also observed in functional classifications of genes not previously associated with the cell cycle.
  • transcripts for the FAA1, FAA3, and ELOl enzymes which participate in fatty acid biosynthesis, peaked during G,.
  • Many of the nuclear-encoded mitochondrial enzymes required for glycolysis and oxidative phosphorylation were induced in early G, with very similar patterns of mRNA fluctuation. None of the transcripts for these mitochondrial genes peaked outside of G,.
  • transcripts of both proteolytic effectors and substrates were examined for periodic changes in transcript levels. No periodic Auctuation was observed for any transcripts encoding constituents of the anaphase promoting complex (APC) or ubiquitin-dependent degradation pathway, which are involved in the proteolytic
  • mRNA and protein expression patterns may provide clues to the function of previously uncharacterized genes.
  • mRNA regulation is a strong indicator of biological function in the cell cycle, and it is likely that many of the uncharacterized genes in this screen have functions related to the cell cycle.
  • periodicity of mRNA abundance was observed in fewer than 25% of all known CDC genes and genes known to be involved in mitosis, DNA replication, or other cell cycle-specific biological roles.
  • poly(A)+RNA was purified from total RNA with an
  • Oligotex dT-column selection step (Qiagen, Chatsworth, CA). Purified poly(A)+
  • dT21 primer 10 mMDTT, 1st Strand Buffer (Gibco Life Technologies, Gaithersburg,
  • RNA and primer were annealed for 10 min at 65°C, and the reaction was incubated at 42°C for 60 min.
  • RNASE H RNASE H
  • E. coli DNA polymerase I Gibco
  • E. coli DNA ligase New England Biolabs, Beverly, MA
  • the 600 :1 reaction volume was incubated at 16°C for 180 min.
  • 30 units of T4 DNA polymerase (Gibco) were added to each reaction for 5 min at 16°C.
  • Reactions were extracted with an equal volume of phenolxhloroform.
  • Phase-Lock Gel (5 Prime-3 Prime, Inc., Boulder, CO) was used for all organic extractions to increase
  • Double-stranded cDNA was ethanol precipitated and resuspended in 30 :1 of distilled water. cDNA was fragmented to an average length of 50 bp with addition of 3.5 :1 One-Phor-All buffer (Pharmacia Biotech, Piscataway, NJ), 2.2 :1 25 mM CoCl 2 (Boehringer Mannheim, Indianapolis, IN), and 0.15 units DNAse I (Gibco).
  • 16 contains the cdcl5-2 allele (kindly provided by K. Nasmyth).
  • Strain K3445 was grown overnight in YPAD (yeast extract/adenine/peptone/glucose, Difco Laboratories, Detroit, MI) at 25°C to a density of 8.0 10 6 cells/ml and divided into 50 ml aliquots. All samples were transferred to a 37°C shaking waterbath for 165 min. The cell cycle was reinitiated by moving the flasks to a 25°C shaking waterbath. Every 10 min, one 50 ml sample was
  • Hybridizations were carried out at 42°C for 14 to 16 hr with
  • biotinylated DNA was fiuorescently labeled by incubating with 2 :g/ml
  • the arrays were read at a resolution of 7.5 :m using especially designed

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Mycology (AREA)
  • Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Medicinal Chemistry (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Microbiology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

On sait que la progression dans le cycle des cellules eucaryotes est régulé par les fluctuations périodiques des niveaux d'expression de nombreux gènes qui l'accompagnent. L'invention concerne ainsi al caractérisation transgénomique des niveaux de transcription de l'ARN messager pendant le cycle cellulaire de la levure Saccharomyces cerevisae pendant la gemmation. On a trouvé une périodicité liée au cycle cellulaire dans le cas de 422 transcriptions sur 6.220 transcriptions étudiées. Moins du quart des 422 gènes identifiés dans notre base d'étude ont déjà été impliqués dans des activités spécifiques de périodes du cycle cellulaire, et plus de 40 % d'entre eux ne présentent aucun rôle biologique connu. On a même découvert qu'environ 30 % de ces 422 gènes sont directement adjacents d'autres gènes faisant preuve d'induction dans la même phase du cycle cellulaire, ce qui fait penser à un mécanisme d'organisation chromosomique au niveau de la régulation globale de l'ARN messager. L'analyse des régions en amont de ces gènes montre que la majeure partie de la transcription liée au cycle cellulaire est commandée par des éléments favorisant et renforçant préalablement on caractérisés. Une analyse statistique des fréquences des nucléotides dans les régions amont des gènes de co-induction a permis d'identifier des éléments régulateurs candidats fonction du cycle cellulaire.
PCT/US1999/004705 1998-03-03 1999-03-03 Genes regules par le cycle cellulaire WO1999045021A1 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU28921/99A AU2892199A (en) 1998-03-03 1999-03-03 Cell cycle regulated genes

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US7665898P 1998-03-03 1998-03-03
US60/076,658 1998-03-03

Publications (1)

Publication Number Publication Date
WO1999045021A1 true WO1999045021A1 (fr) 1999-09-10

Family

ID=22133420

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1999/004705 WO1999045021A1 (fr) 1998-03-03 1999-03-03 Genes regules par le cycle cellulaire

Country Status (2)

Country Link
AU (1) AU2892199A (fr)
WO (1) WO1999045021A1 (fr)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002022866A2 (fr) * 2000-09-11 2002-03-21 Pika Weihenstephan Gmbh Procede et kit d'essai pour analyser une matiere contenant de l'acide nucleique

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5698686A (en) * 1994-10-20 1997-12-16 Arch Development Corporation Yeast telomerase compositions
US5801236A (en) * 1994-03-18 1998-09-01 Myriad Genetics, Inc. Probes for MTS1 gene and polynucleotides encoding mutant MTS1 genes

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5801236A (en) * 1994-03-18 1998-09-01 Myriad Genetics, Inc. Probes for MTS1 gene and polynucleotides encoding mutant MTS1 genes
US5698686A (en) * 1994-10-20 1997-12-16 Arch Development Corporation Yeast telomerase compositions

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
O'CONNOR P. M., ET AL.: "CHARACTERIZATION OF THE P53 TUMOR SUPPRESSOR PATHWAY IN CELL LINES OF THE NATIONAL CANCER INSTITUTE ANTICANCER DRUG SCREEN AND CORRELATIONS WITH THE GROWTH-INHIBITORY POTENCY OF 123 ANTICANCER AGENTS.", CANCER RESEARCH, AMERICAN ASSOCIATION FOR CANCER RESEARCH, US, vol. 57., no. 19., 1 October 1997 (1997-10-01), US, pages 4285 - 4300., XP002920858, ISSN: 0008-5472 *
PLOCHOCKA-ZULINSKA D., RASMUSSEN G., RASMUSSEN C.: "REGULATION OF CALCINEURIN GENE EXPRESSION IN SCHIZOSACCHAROMYCES POMBE.", JOURNAL OF BIOLOGICAL CHEMISTRY, AMERICAN SOCIETY FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY, US, vol. 270., no. 42., 20 October 1999 (1999-10-20), US, pages 24794 - 24797., XP002920857, ISSN: 0021-9258 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002022866A2 (fr) * 2000-09-11 2002-03-21 Pika Weihenstephan Gmbh Procede et kit d'essai pour analyser une matiere contenant de l'acide nucleique
WO2002022866A3 (fr) * 2000-09-11 2003-06-05 Pika Weihenstephan Gmbh Procede et kit d'essai pour analyser une matiere contenant de l'acide nucleique

Also Published As

Publication number Publication date
AU2892199A (en) 1999-09-20

Similar Documents

Publication Publication Date Title
Cho et al. A genome-wide transcriptional analysis of the mitotic cell cycle
Cohen et al. Monitoring cellular responses to Listeria monocytogenes with oligonucleotide arrays
Duff et al. Transgenic mouse models of Alzheimer's disease: how useful have they been for therapeutic development?
EP0743989B1 (fr) Procédé d'identifcation des genes exprimés differentes
EP3828285B1 (fr) Transposition en une chromatine endogène permettant l'épigénomique personnelle
Cawley et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
Kruse et al. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution
WO1998026098B1 (fr) Procede de mesure de concentrations relatives en acides nucleique dans un melange complexe et extraction de sequences specifiques
Satterthwaite et al. Differential gene expression in coronary arteries from patients presenting with ischemic heart disease: further evidence for the inflammatory basis of atherosclerosis
JP2004504059A (ja) 転写された遺伝子を分析、及び同定するための方法、及びフインガープリント法
JP2003245072A (ja) シグナル伝達経路の決定
Rafalski et al. New experimental and computational approaches to the analysis of gene expression.
EP1255859A2 (fr) Genes specifiques de tissu a signification diagnostique
Kapranov et al. Beyond expression profiling: next generation uses of high density oligonucleotide arrays
Cox Applications of nylon membrane arrays to gene expression analysis
JPH10510981A (ja) ヌクレオチド配列を特性決定するための方法、装置及び組成物
JP2002335999A (ja) ユニバーサルアレイを用いる遺伝子発現のモニター
US6509153B1 (en) Genetic markers of toxicity preparation and uses
Gardiner et al. Design, production, and utilization of long oligonucleotide microarrays for expression analysis in maize
WO1999045021A1 (fr) Genes regules par le cycle cellulaire
JP2004524801A (ja) Ａｒｅ含有遺伝子の発現を同定および分析するための方法
JP2001509017A (ja) イーストトランスクリプトームのキャラクタリゼーション
Scott et al. P2P‐R expression is genetically coregulated with components of the translation machinery and with PUM2, a translational repressor that associates with the P2P‐R mRNA
Ando et al. Efficient construction of cDNA microarrays utilizing normalized cDNA libraries of Arabidopsis thaliana
Nguyen et al. DNA microarrays

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A1

Designated state(s): AL AM AT AU AZ BA BB BG BR BY CA CH CN CU CZ DE DK EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT UA UG US UZ VN YU ZW

AL Designated countries for regional patents

Kind code of ref document: A1

Designated state(s): GH GM KE LS MW SD SL SZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
NENP Non-entry into the national phase

Ref country code: KR

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

122 Ep: pct application non-entry in european phase