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WO2002059371A3 - Genome-wide location and function of dna binding proteins - Google Patents

Genome-wide location and function of dna binding proteins Download PDF

Info

Publication number
WO2002059371A3
WO2002059371A3 PCT/US2001/050396 US0150396W WO02059371A3 WO 2002059371 A3 WO2002059371 A3 WO 2002059371A3 US 0150396 W US0150396 W US 0150396W WO 02059371 A3 WO02059371 A3 WO 02059371A3
Authority
WO
WIPO (PCT)
Prior art keywords
cell
genome
genomic dna
dna
identifying
Prior art date
Legal status (The legal status 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 status listed.)
Ceased
Application number
PCT/US2001/050396
Other languages
French (fr)
Other versions
WO2002059371B1 (en
WO2002059371A2 (en
Inventor
John Wyrick
Richard A Young
Bing Ren
Francois Robert
Itamar Simon
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Whitehead Institute for Biomedical Research
Original Assignee
Whitehead Institute for Biomedical Research
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 Institute for Biomedical Research filed Critical Whitehead Institute for Biomedical Research
Priority to CA002432346A priority Critical patent/CA2432346A1/en
Priority to EP01994453A priority patent/EP1381692A2/en
Publication of WO2002059371A2 publication Critical patent/WO2002059371A2/en
Anticipated expiration legal-status Critical
Publication of WO2002059371A3 publication Critical patent/WO2002059371A3/en
Publication of WO2002059371B1 publication Critical patent/WO2002059371B1/en
Ceased legal-status Critical Current

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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Analytical Chemistry (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Zoology (AREA)
  • Biomedical Technology (AREA)
  • Biotechnology (AREA)
  • Urology & Nephrology (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Hematology (AREA)
  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • Cell Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Peptides Or Proteins (AREA)

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.
PCT/US2001/050396 2000-12-21 2001-12-21 Genome-wide location and function of dna binding proteins Ceased WO2002059371A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
CA002432346A CA2432346A1 (en) 2000-12-21 2001-12-21 Genome-wide location and function of dna binding proteins
EP01994453A EP1381692A2 (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 true WO2002059371A3 (en) 2003-11-06
WO2002059371B1 WO2002059371B1 (en) 2003-12-18

Family

ID=26945967

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/050396 Ceased 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 (2)

* 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
US9411930B2 (en) * 2013-02-01 2016-08-09 The Regents Of The University Of California Methods for genome assembly and haplotype phasing

Citations (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

Patent Citations (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

Non-Patent Citations (7)

* Cited by examiner, † Cited by third party
Title
BLAT Y ET AL: "Cohesins bind to preferential sites along yeast chromosome III, with differential regulation along arms versus centric region", CELL, CELL PRESS, CAMBRIDGE, NA, US, vol. 98, July 1999 (1999-07-01), pages 2492 - 59, XP002170838, ISSN: 0092-8674 *
HECHT A ET AL: "Spreading of transcriptional repressor SIR3 from telomeric heterochromatin", NATURE, MACMILLAN JOURNALS LTD. LONDON, GB, vol. 383, 5 September 1996 (1996-09-05), pages 92 - 96, XP002170839, ISSN: 0028-0836 *
REID J L ET AL: "Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase.", MOLECULAR CELL. UNITED STATES DEC 2000, vol. 6, no. 6, December 2000 (2000-12-01), pages 1297 - 1307, XP002226334, ISSN: 1097-2765 *
REN B ET AL: "Genome-wide location and function of DNA binding proteins", SCIENCE, AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE,, US, vol. 290, 22 December 2000 (2000-12-22), pages 2306 - 2309, XP002219199, ISSN: 0036-8075 *
See also references of EP1381692A2 *
TAKAHASHI K ET AL: "Application of the chromatin immunoprecipitation method to identify in vivo protein-DNA associations in fission yeast.", SCIENCE'S STKE [ELECTRONIC RESOURCE]: SIGNAL TRANSDUCTION KNOWLEDGE ENVIRONMENT. UNITED STATES 31 OCT 2000, vol. 2000, no. 56, 31 October 2000 (2000-10-31), pages PL1, XP002226335, ISSN: 1525-8882 *
YOSHIOKA TAKESHI ET AL: "Quantitative analysis of the usage of human T cell receptor alpha and beta chain variable regions by reverse dot blot hybridization.", JOURNAL OF IMMUNOLOGICAL METHODS, vol. 201, no. 2, 1997, pages 145 - 155, XP004117412, ISSN: 0022-1759 *

Also Published As

Publication number Publication date
EP1381692A2 (en) 2004-01-21
CA2432346A1 (en) 2002-08-01
WO2002059371B1 (en) 2003-12-18
WO2002059371A2 (en) 2002-08-01

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