WO2001016378A3 - Chromosome-wide analysis of protein-dna interactions - Google Patents

Chromosome-wide analysis of protein-dna interactions Download PDF

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Publication number
WO2001016378A3
WO2001016378A3 PCT/US2000/024358 US0024358W WO0116378A3 WO 2001016378 A3 WO2001016378 A3 WO 2001016378A3 US 0024358 W US0024358 W US 0024358W WO 0116378 A3 WO0116378 A3 WO 0116378A3
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WO
WIPO (PCT)
Prior art keywords
protein
cell
genomic dna
dna
chromosome
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/US2000/024358
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French (fr)
Other versions
WO2001016378A2 (en
WO2001016378A9 (en
Inventor
John Wyrick
Richard A Young
Bing Ren
Francois Robert
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 CA002383928A priority Critical patent/CA2383928A1/en
Priority to JP2001520923A priority patent/JP2003508066A/en
Priority to DE60045796T priority patent/DE60045796D1/en
Priority to AT00959909T priority patent/ATE503843T1/en
Priority to EP00959909A priority patent/EP1220949B1/en
Priority to DE2000959909 priority patent/DE00959909T1/en
Publication of WO2001016378A2 publication Critical patent/WO2001016378A2/en
Anticipated expiration legal-status Critical
Publication of WO2001016378A3 publication Critical patent/WO2001016378A3/en
Publication of WO2001016378A9 publication Critical patent/WO2001016378A9/en
Ceased legal-status Critical Current

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    • 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
    • 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
    • C12Q1/6804—Nucleic acid analysis using immunogens
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors
    • 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
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Wood Science & Technology (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • Urology & Nephrology (AREA)
  • Pathology (AREA)
  • Biomedical Technology (AREA)
  • Hematology (AREA)
  • Food Science & Technology (AREA)
  • Cell Biology (AREA)
  • Medicinal Chemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (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 decribed 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 binds.
PCT/US2000/024358 1999-09-01 2000-09-01 Chromosome-wide analysis of protein-dna interactions Ceased WO2001016378A2 (en)

Priority Applications (6)

Application Number Priority Date Filing Date Title
CA002383928A CA2383928A1 (en) 1999-09-01 2000-09-01 Chromosome-wide analysis of protein-dna interactions
JP2001520923A JP2003508066A (en) 1999-09-01 2000-09-01 Whole chromosome analysis of protein-DNA interactions
DE60045796T DE60045796D1 (en) 1999-09-01 2000-09-01 TOTAL CHROMOSOME ANALYSIS OF PROTEIN-DNS INTERACTIONS
AT00959909T ATE503843T1 (en) 1999-09-01 2000-09-01 WHOLE CHROMOSOME ANALYSIS OF PROTEIN-DNA INTERACTIONS
EP00959909A EP1220949B1 (en) 1999-09-01 2000-09-01 Chromosome-wide analysis of protein-dna interactions
DE2000959909 DE00959909T1 (en) 1999-09-01 2000-09-01 TOTAL CHROMOSOME ANALYSIS OF PROTEIN-DNS INTERACTIONS

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US15197299P 1999-09-01 1999-09-01
US60/151,972 1999-09-01

Publications (3)

Publication Number Publication Date
WO2001016378A2 WO2001016378A2 (en) 2001-03-08
WO2001016378A3 true WO2001016378A3 (en) 2002-05-02
WO2001016378A9 WO2001016378A9 (en) 2002-11-28

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/024358 Ceased WO2001016378A2 (en) 1999-09-01 2000-09-01 Chromosome-wide analysis of protein-dna interactions

Country Status (7)

Country Link
US (1) US6410243B1 (en)
EP (1) EP1220949B1 (en)
JP (1) JP2003508066A (en)
AT (1) ATE503843T1 (en)
CA (1) CA2383928A1 (en)
DE (2) DE60045796D1 (en)
WO (1) WO2001016378A2 (en)

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US7470507B2 (en) 1999-09-01 2008-12-30 Whitehead Institute For Biomedical Research Genome-wide location and function of DNA binding proteins

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WO2004024084A2 (en) * 2002-09-12 2004-03-25 Massachusetts Institute Of Technology Rb pahtway and chromatin remodeling genes that antagonize let-60 ras signaling
US20060099713A1 (en) * 2002-10-01 2006-05-11 Buck Institute Targeted-assisted iterative screening (tais):a novel screening format for large molecular repertoires
US20040161779A1 (en) * 2002-11-12 2004-08-19 Affymetrix, Inc. Methods, compositions and computer software products for interrogating sequence variations in functional genomic regions
US20040115794A1 (en) * 2002-12-12 2004-06-17 Affymetrix, Inc. Methods for detecting transcriptional factor binding sites
US7750908B2 (en) * 2003-04-04 2010-07-06 Agilent Technologies, Inc. Focus plus context viewing and manipulation of large collections of graphs
JP2007524399A (en) 2003-07-03 2007-08-30 ザ・レジェンツ・オブ・ザ・ユニバーシティ・オブ・カリフォルニア Genomic mapping of functional DNA elements and cellular proteins
US8222005B2 (en) * 2003-09-17 2012-07-17 Agency For Science, Technology And Research Method for gene identification signature (GIS) analysis
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EP1721012A2 (en) * 2004-03-04 2006-11-15 Whitehead Institute For Biomedical Research Biologically-active dna-binding sites and related methods
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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7470507B2 (en) 1999-09-01 2008-12-30 Whitehead Institute For Biomedical Research Genome-wide location and function of DNA binding proteins

Also Published As

Publication number Publication date
EP1220949A2 (en) 2002-07-10
ATE503843T1 (en) 2011-04-15
CA2383928A1 (en) 2001-03-08
JP2003508066A (en) 2003-03-04
WO2001016378A2 (en) 2001-03-08
DE00959909T1 (en) 2005-11-10
DE60045796D1 (en) 2011-05-12
EP1220949B1 (en) 2011-03-30
WO2001016378A9 (en) 2002-11-28
US6410243B1 (en) 2002-06-25

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