WO2005118873A3 - Compositions and methods for detecting open chromatin and for genome-wide chromatin state profiling - Google Patents

Compositions and methods for detecting open chromatin and for genome-wide chromatin state profiling Download PDF

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Publication number
WO2005118873A3
WO2005118873A3 PCT/US2005/019150 US2005019150W WO2005118873A3 WO 2005118873 A3 WO2005118873 A3 WO 2005118873A3 US 2005019150 W US2005019150 W US 2005019150W WO 2005118873 A3 WO2005118873 A3 WO 2005118873A3
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WO
WIPO (PCT)
Prior art keywords
methods
chromatin
arrays
compositions
detecting open
Prior art date
Application number
PCT/US2005/019150
Other languages
French (fr)
Other versions
WO2005118873A2 (en
Inventor
Toomas Neuman
Original Assignee
Cemines Inc
Toomas Neuman
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 Cemines Inc, Toomas Neuman filed Critical Cemines Inc
Publication of WO2005118873A2 publication Critical patent/WO2005118873A2/en
Publication of WO2005118873A3 publication Critical patent/WO2005118873A3/en

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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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes

Abstract

Methods and compositions are provided for detecting open chromatin in genomic DNA, including oligonucleotide arrays useful for detecting open chromatin and generating chromatin state profiles for biological samples. The invention further concerns the use of such arrays in diagnostic and prognostic methods, as well as in methods of monitoring treatment and evaluating the response of cells and patients to candidate or established therapeutic agents. The invention also concerns the use of such arrays for the provision of pharmacogenomic data useful in methods of tailoring treatment to individuals. The invention additionally concerns the use of such arrays for the identification of chromatin state profiles representative of cell types or cell states, which may be used to evidence cell types or cell states.
PCT/US2005/019150 2004-05-28 2005-05-31 Compositions and methods for detecting open chromatin and for genome-wide chromatin state profiling WO2005118873A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US57547804P 2004-05-28 2004-05-28
US60/575,478 2004-05-28

Publications (2)

Publication Number Publication Date
WO2005118873A2 WO2005118873A2 (en) 2005-12-15
WO2005118873A3 true WO2005118873A3 (en) 2006-02-23

Family

ID=35463473

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2005/019150 WO2005118873A2 (en) 2004-05-28 2005-05-31 Compositions and methods for detecting open chromatin and for genome-wide chromatin state profiling

Country Status (1)

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WO (1) WO2005118873A2 (en)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2988673A1 (en) 2015-06-24 2016-12-29 Oxford Biodynamics Limited Epigenetic chromosome interactions

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030170689A1 (en) * 2001-05-11 2003-09-11 Rexagen Corporation DNA microarrays comprising active chromatin elements and comprehensive profiling therewith
US20040014086A1 (en) * 2001-05-11 2004-01-22 Regulome Corporation Regulome arrays

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030170689A1 (en) * 2001-05-11 2003-09-11 Rexagen Corporation DNA microarrays comprising active chromatin elements and comprehensive profiling therewith
US20040014086A1 (en) * 2001-05-11 2004-01-22 Regulome Corporation Regulome arrays
WO2004052080A2 (en) * 2002-12-12 2004-06-24 Regulome Corporation Regulome arrays

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
CARTER N.P. ET AL: "Applications of Genomic Microarrays to Explore Human Chromosome Structure and Function", HUMAN MOLECULAR GENETICS, vol. 13, no. 2, October 2004 (2004-10-01), pages R297 - R302, XP002994745 *
URNOV F.D.: "Chromatin Remodeling as a Guide to Transcriptional Regulatory Networks in Mammals", JOURNAL OF CELLULAR BIOCHEM., vol. 88, no. 4, 2003, pages 684 - 694, XP002994743 *
WIDLAK P.: "DNA Microarrays, A Novel Approach in Studies of Chromatin Structure", ACTA BIOCHIMICA POLONICA, vol. 51, no. 1, 2004, pages 1 - 8, XP002994744 *

Also Published As

Publication number Publication date
WO2005118873A2 (en) 2005-12-15

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