WO2001068807A8 - Identification of in vivo dna binding loci of chromatin proteins using a tethered nucleotide modification enzyme - Google Patents

Identification of in vivo dna binding loci of chromatin proteins using a tethered nucleotide modification enzyme

Info

Publication number
WO2001068807A8
WO2001068807A8 PCT/US2001/008590 US0108590W WO0168807A8 WO 2001068807 A8 WO2001068807 A8 WO 2001068807A8 US 0108590 W US0108590 W US 0108590W WO 0168807 A8 WO0168807 A8 WO 0168807A8
Authority
WO
WIPO (PCT)
Prior art keywords
dna
identification
vivo
modification
modification enzyme
Prior art date
Application number
PCT/US2001/008590
Other languages
French (fr)
Other versions
WO2001068807A3 (en
WO2001068807A2 (en
Inventor
Steensel Bas Van
Steven Henikoff
Original Assignee
Hutchinson Fred Cancer Res
Steensel Bas Van
Steven Henikoff
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 Hutchinson Fred Cancer Res, Steensel Bas Van, Steven Henikoff filed Critical Hutchinson Fred Cancer Res
Priority to US10/221,865 priority Critical patent/US20030212455A1/en
Priority to AU2001249245A priority patent/AU2001249245A1/en
Publication of WO2001068807A2 publication Critical patent/WO2001068807A2/en
Publication of WO2001068807A8 publication Critical patent/WO2001068807A8/en
Publication of WO2001068807A3 publication Critical patent/WO2001068807A3/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • 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

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Zoology (AREA)
  • General Engineering & Computer Science (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Microbiology (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Cell Biology (AREA)
  • Plant Pathology (AREA)
  • Biophysics (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Peptides Or Proteins (AREA)

Abstract

A novel technique is provided, designated DamID, for the identification of DNA loci that interact in vivo with specific nuclear proteins in eukaryotes. By tethering a DNA modification enzyme, in particular, E. coli DNA adenine methyl transferase (Dam), to a chromatin protein. The DNA modification enzyme (Dam) can be targeted in vivo to the native binding loci of the protein, resulting in local DNA modification. Sites of DNA modification can subsequently be mapped using modification-specific restriction enzymes, antibodies, or DNA array methods. DNA Modification Identification (DamID) has potential for genome-wide mapping of in vivo target binding sites of chromatin proteins in various eukaryotes.
PCT/US2001/008590 2000-03-16 2001-03-16 Identification of in vivo dna binding loci of chromatin proteins using a tethered nucleotide modification enzyme WO2001068807A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
US10/221,865 US20030212455A1 (en) 2000-03-16 2001-03-16 Identification of in vivo dna binding loci of chromatin proteins using a tethered nucleotide modification enzyme
AU2001249245A AU2001249245A1 (en) 2000-03-16 2001-03-16 Identification of in vivo dna binding loci of chromatin proteins using a tethered nucleotide modification enzyme

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US19036200P 2000-03-16 2000-03-16
US60/190,362 2000-03-16
US27284701P 2001-03-01 2001-03-01
US60/272,847 2001-03-01

Publications (3)

Publication Number Publication Date
WO2001068807A2 WO2001068807A2 (en) 2001-09-20
WO2001068807A8 true WO2001068807A8 (en) 2001-12-27
WO2001068807A3 WO2001068807A3 (en) 2004-08-12

Family

ID=26886029

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2001/008590 WO2001068807A2 (en) 2000-03-16 2001-03-16 Identification of in vivo dna binding loci of chromatin proteins using a tethered nucleotide modification enzyme

Country Status (1)

Country Link
WO (1) WO2001068807A2 (en)

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001083732A2 (en) * 2000-04-28 2001-11-08 Sangamo Biosciences, Inc. Databases of regulatory sequences; methods of making and using same
AU5391401A (en) * 2000-04-28 2001-11-12 Sangamo Biosciences Inc Targeted modification of chromatin structure
US7923542B2 (en) 2000-04-28 2011-04-12 Sangamo Biosciences, Inc. Libraries of regulatory sequences, methods of making and using same
US6511808B2 (en) 2000-04-28 2003-01-28 Sangamo Biosciences, Inc. Methods for designing exogenous regulatory molecules
CA2489360C (en) 2002-06-26 2013-01-29 Cold Spring Harbor Laboratory Methods and compositions for determining methylation profiles
ATE550438T1 (en) 2003-10-21 2012-04-15 Orion Genomics Llc METHOD FOR QUANTITATIVELY DETERMINING THE METHYLATION DENSITY IN A DNA LOCUS
US7459274B2 (en) 2004-03-02 2008-12-02 Orion Genomics Llc Differential enzymatic fragmentation by whole genome amplification
US8158801B2 (en) 2005-09-26 2012-04-17 Life Technologies Corporation Violet laser excitable dyes and their method of use
ES2924185T3 (en) 2017-09-25 2022-10-05 Fred Hutchinson Cancer Center High-efficiency in situ profiles targeting the entire genome
WO2024065721A1 (en) * 2022-09-30 2024-04-04 Peking University Methods of determining genome-wide dna binding protein binding sites by footprinting with double stranded dna deaminase

Also Published As

Publication number Publication date
WO2001068807A3 (en) 2004-08-12
WO2001068807A2 (en) 2001-09-20

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