WO2002059371B1 - Genome-wide location and function of dna binding proteins - Google Patents

Genome-wide location and function of dna binding proteins

Info

Publication number
WO2002059371B1
WO2002059371B1 PCT/US2001/050396 US0150396W WO02059371B1 WO 2002059371 B1 WO2002059371 B1 WO 2002059371B1 US 0150396 W US0150396 W US 0150396W WO 02059371 B1 WO02059371 B1 WO 02059371B1
Authority
WO
WIPO (PCT)
Prior art keywords
genes
cell
cell cycle
identifying
genome
Prior art date
Application number
PCT/US2001/050396
Other languages
French (fr)
Other versions
WO2002059371A2 (en
WO2002059371A3 (en
Inventor
John Wyrick
Richard A Young
Bing Ren
Francois Robert
Itamar Simon
Original Assignee
Whitehead Biomedical Inst
John Wyrick
Richard A Young
Bing Ren
Francois Robert
Itamar Simon
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 Whitehead Biomedical Inst, John Wyrick, Richard A Young, Bing Ren, Francois Robert, Itamar Simon filed Critical Whitehead Biomedical Inst
Priority to EP01994453A priority Critical patent/EP1381692A2/en
Priority to CA002432346A priority patent/CA2432346A1/en
Publication of WO2002059371A2 publication Critical patent/WO2002059371A2/en
Publication of WO2002059371A3 publication Critical patent/WO2002059371A3/en
Publication of WO2002059371B1 publication Critical patent/WO2002059371B1/en

Links

Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection

Abstract

The present invention relates to a method of identifying a region (one or more) of a genome of a cell to which a protein of interest binds. In the methods described herein, DNA binding protein of a cell is linked (e.g., covalently crosslinked) to genomic DNA of a cell. The genomic DNA to which the DNA binding protein is linked is removed and combined or contacted with DNA comprising a sequence complementary to genomic DNA of the cell under conditions in which hybridization between the identified genomic DNA and the sequence complementary to genomic DNA occurs. Region(s) of hybridization are region(s) of the genome of the cell to which the protein of binds. A method of identifying a set of genes where cell cycle regulator binding correlates with gene expression and of identifying genomic targets of cell cycle transcription activators in living cells is also encompassed.

Claims

AMENDED CLAIMS[received by the International Bureau on 12 March 2003 (12.03.03); original claims 1-14 replaced by amended claims 1-3 (1 page)]
1. A method of identifying a set of genes, the members of which are genes for which cell cycle regulator binding correlates with gene expression, comprising:
(a) identifying a set of genes that is bound in vivo by at least one cell cycle regulator in a selected cell type;
(b) comparing the set of genes identified in (a) with genes whose expression levels vary in a periodic manner during the cell cycle of the selected cell type; and
(c) identifying genes that are bound by one or more of the cell cycle regulators, thus identifying a set of genes, the members of which are genes whose expression levels vary in a periodic manner during the cell cycle and are bound by at least one cell cycle regulator, wherein the set identified in (c) is referred to as a set of genes, the members of which are genes for which cell cycle regulator binding correlates with gene expression.
2. The method of claim 1, wherein the selected cell type is a yeast cell.
3. The method of claim 2, wherein the at least one cell cycle regulator is at least one of the nine known yeast cell cycle transcriptional activators.
PCT/US2001/050396 2000-12-21 2001-12-21 Genome-wide location and function of dna binding proteins WO2002059371A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
EP01994453A EP1381692A2 (en) 2000-12-21 2001-12-21 Genome-wide location and function of dna binding proteins
CA002432346A CA2432346A1 (en) 2000-12-21 2001-12-21 Genome-wide location and function of dna binding proteins

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US25745500P 2000-12-21 2000-12-21
US60/257,455 2000-12-21
US32362001P 2001-09-20 2001-09-20
US60/323,620 2001-09-20

Publications (3)

Publication Number Publication Date
WO2002059371A2 WO2002059371A2 (en) 2002-08-01
WO2002059371A3 WO2002059371A3 (en) 2003-11-06
WO2002059371B1 true WO2002059371B1 (en) 2003-12-18

Family

ID=26945967

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/050396 WO2002059371A2 (en) 2000-12-21 2001-12-21 Genome-wide location and function of dna binding proteins

Country Status (3)

Country Link
EP (1) EP1381692A2 (en)
CA (1) CA2432346A1 (en)
WO (1) WO2002059371A2 (en)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP2006078313A (en) * 2004-09-09 2006-03-23 Hitachi Software Eng Co Ltd Protein binding position identifying method

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001016378A2 (en) * 1999-09-01 2001-03-08 Whitehead Institute For Biomedical Research Chromosome-wide analysis of protein-dna interactions

Also Published As

Publication number Publication date
WO2002059371A2 (en) 2002-08-01
CA2432346A1 (en) 2002-08-01
EP1381692A2 (en) 2004-01-21
WO2002059371A3 (en) 2003-11-06

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