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WO2004053106A3 - Profiled regulatory sites useful for gene control - Google Patents

Profiled regulatory sites useful for gene control Download PDF

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Publication number
WO2004053106A3
WO2004053106A3 PCT/US2003/040070 US0340070W WO2004053106A3 WO 2004053106 A3 WO2004053106 A3 WO 2004053106A3 US 0340070 W US0340070 W US 0340070W WO 2004053106 A3 WO2004053106 A3 WO 2004053106A3
Authority
WO
WIPO (PCT)
Prior art keywords
regulatory
chromatin
methods
quantitative
profiling
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/US2003/040070
Other languages
French (fr)
Other versions
WO2004053106A2 (en
Inventor
John A Stamatoyannopoulos
Michael Mcarthur
Michael O Dorschner
Michael Hawrylycz
Rich Humbert
George Stamatoyannopoulos
Rhett Alden
James Clendenning
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.)
Regulome Corp
Original Assignee
Regulome Corp
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 Regulome Corp filed Critical Regulome Corp
Priority to AU2003302777A priority Critical patent/AU2003302777A1/en
Publication of WO2004053106A2 publication Critical patent/WO2004053106A2/en
Anticipated expiration legal-status Critical
Publication of WO2004053106A3 publication Critical patent/WO2004053106A3/en
Ceased legal-status Critical Current

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
    • C12N15/1072—Differential gene expression library synthesis, e.g. subtracted libraries, differential screening

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  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Biomedical Technology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Plant Pathology (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The invention provides methods for quantitative profiling of chromatin sensitivity to a DNA modifying agent. The invention also relates to methods for identifying regulatory sites in a genomic locus and to methods for determining chromatin architecture in a genomic locus. Regulatory site profiles associated with specific genes are particularly useful for discovery of medicinal agents, other genomic sequences involved in gene regulation, and regulatory mechanisms that are involved in health and disease. The regulatory sequence profiles also are highly valuable when used by computer programs for comparing known and unknown genetic sequences by a large variety of experimental and computer manipulations. Figure 1 is a schematic illustration of an embodiment of high-throughput quantitative chromatin profiling of hypersensitive sites using quantitative PCR (HSqPCR).
PCT/US2003/040070 2002-12-05 2003-12-05 Profiled regulatory sites useful for gene control Ceased WO2004053106A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2003302777A AU2003302777A1 (en) 2002-12-05 2003-12-05 Profiled regulatory sites useful for gene control

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US43159702P 2002-12-05 2002-12-05
US60/431,597 2002-12-05
US49217103P 2003-08-01 2003-08-01
US60/492,171 2003-08-01

Publications (2)

Publication Number Publication Date
WO2004053106A2 WO2004053106A2 (en) 2004-06-24
WO2004053106A3 true WO2004053106A3 (en) 2006-09-08

Family

ID=32511586

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2003/040070 Ceased WO2004053106A2 (en) 2002-12-05 2003-12-05 Profiled regulatory sites useful for gene control

Country Status (2)

Country Link
AU (1) AU2003302777A1 (en)
WO (1) WO2004053106A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10669562B2 (en) 2003-10-24 2020-06-02 Selexis S.A. High efficiency gene transfer and expression in mammalian cells by a multiple transfection procedure of MAR sequences

Families Citing this family (8)

* 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
ATE437233T1 (en) 2001-01-26 2009-08-15 Selexis Sa MATRIX ATTACHMENT REGIONS AND METHOD OF USE THEREOF
US20040191779A1 (en) * 2003-03-28 2004-09-30 Jie Zhang Statistical analysis of regulatory factor binding sites of differentially expressed genes
WO2005088306A2 (en) * 2004-03-04 2005-09-22 Whitehead Institute For Biomedical Research Biologically-active dna-binding sites and related methods
US20070031883A1 (en) * 2004-03-04 2007-02-08 Kincaid Robert H Analyzing CGH data to identify aberrations
WO2007064898A2 (en) 2005-12-02 2007-06-07 Whitehead Institute For Biomedical Research Methods for mapping signal transduction pathways to gene expression programs
MX338883B (en) 2010-07-27 2016-05-04 Genomic Health Inc Method for using gene expression to determine prognosis of prostate cancer.
WO2014121104A1 (en) * 2013-01-31 2014-08-07 The Regents Of The University Of California Pooled genetic perturbation effects

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020081603A1 (en) * 2000-04-28 2002-06-27 Alan Wolffe Databases of regulatory sequences; methods of making and using same

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20020081603A1 (en) * 2000-04-28 2002-06-27 Alan Wolffe Databases of regulatory sequences; methods of making and using same

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
MCARTHUR ET AL.: "Quantification of DNaseI sensitivity by real-time PCR: quantitative analysis of DNaseI-hypersensitivity of the mouse beta-globin LCR", JOURNAL OF MOLECULAR BIOLOGY, vol. 313, no. 1, October 2001 (2001-10-01), pages 27 - 34, XP004466186 *
YANG ET AL: "Normalization for cDNA micrarray data: a robust composite method addressing single and multiple slide systematic variation", NUCLEIC ACIDS RESEARCH, vol. 30, no. 4, February 2002 (2002-02-01), pages E15 (PAGES 1-10), XP002242805 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10669562B2 (en) 2003-10-24 2020-06-02 Selexis S.A. High efficiency gene transfer and expression in mammalian cells by a multiple transfection procedure of MAR sequences

Also Published As

Publication number Publication date
WO2004053106A2 (en) 2004-06-24
AU2003302777A1 (en) 2004-06-30
AU2003302777A8 (en) 2004-06-30

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