WO2003095608A3 - Dna microarrays comprising active chromatin elements and comprehensive profiling therewith - Google Patents

Dna microarrays comprising active chromatin elements and comprehensive profiling therewith Download PDF

Info

Publication number
WO2003095608A3
WO2003095608A3 PCT/US2002/015032 US0215032W WO03095608A3 WO 2003095608 A3 WO2003095608 A3 WO 2003095608A3 US 0215032 W US0215032 W US 0215032W WO 03095608 A3 WO03095608 A3 WO 03095608A3
Authority
WO
WIPO (PCT)
Prior art keywords
therewith
dna microarrays
active chromatin
chromatin elements
comprehensive profiling
Prior art date
Application number
PCT/US2002/015032
Other languages
French (fr)
Other versions
WO2003095608A2 (en
Inventor
Michael Mcarthur
Original Assignee
Stamatoyannopoulos John A
Michael Mcarthur
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 Stamatoyannopoulos John A, Michael Mcarthur filed Critical Stamatoyannopoulos John A
Priority to EP02807414A priority Critical patent/EP1407053A4/en
Priority to JP2004503602A priority patent/JP2005519635A/en
Priority to CA002460679A priority patent/CA2460679A1/en
Priority to AU2002367838A priority patent/AU2002367838A1/en
Priority to US10/319,440 priority patent/US20030170689A1/en
Priority to US10/375,404 priority patent/US20040014086A1/en
Publication of WO2003095608A2 publication Critical patent/WO2003095608A2/en
Publication of WO2003095608A3 publication Critical patent/WO2003095608A3/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
    • C12N15/102—Mutagenizing nucleic acids
    • 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
    • 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
    • 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
    • C12N2830/00—Vector systems having a special element relevant for transcription
    • C12N2830/80—Vector systems having a special element relevant for transcription from vertebrates
    • C12N2830/85—Vector systems having a special element relevant for transcription from vertebrates mammalian
    • 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
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips

Abstract

Methods are disclosed for the construction of and interrogation of DNA arrays containing Active Chromatin Elements, and, thereby active genetic regulatory sequences.. Further methods are disclosed for interrogation of such arrays in order to reveal the pattern of genetic regulatory activity within any given cell or tissue type under a variety of conditions.
PCT/US2002/015032 2001-05-11 2002-05-13 Dna microarrays comprising active chromatin elements and comprehensive profiling therewith WO2003095608A2 (en)

Priority Applications (6)

Application Number Priority Date Filing Date Title
EP02807414A EP1407053A4 (en) 2001-05-11 2002-05-13 Dna microarrays comprising active chromatin elements and comprehensive profiling therewith
JP2004503602A JP2005519635A (en) 2001-05-11 2002-05-13 DNA microarray containing active chromatin elements and comprehensive profiling using the same
CA002460679A CA2460679A1 (en) 2001-05-11 2002-05-13 Dna microarrays comprising active chromatin elements and comprehensive profiling therewith
AU2002367838A AU2002367838A1 (en) 2001-05-11 2002-05-13 DNA microarrays comprising active chromatin elements and comprehensive profiling therewith
US10/319,440 US20030170689A1 (en) 2001-05-11 2002-12-12 DNA microarrays comprising active chromatin elements and comprehensive profiling therewith
US10/375,404 US20040014086A1 (en) 2001-05-11 2003-02-27 Regulome arrays

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US29003601P 2001-05-11 2001-05-11
US60/290,036 2001-05-11

Related Child Applications (2)

Application Number Title Priority Date Filing Date
US10/319,440 Continuation-In-Part US20030170689A1 (en) 2001-05-11 2002-12-12 DNA microarrays comprising active chromatin elements and comprehensive profiling therewith
US10/375,404 Continuation-In-Part US20040014086A1 (en) 2001-05-11 2003-02-27 Regulome arrays

Publications (2)

Publication Number Publication Date
WO2003095608A2 WO2003095608A2 (en) 2003-11-20
WO2003095608A3 true WO2003095608A3 (en) 2004-02-12

Family

ID=29420206

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2002/015032 WO2003095608A2 (en) 2001-05-11 2002-05-13 Dna microarrays comprising active chromatin elements and comprehensive profiling therewith

Country Status (6)

Country Link
US (1) US20030170689A1 (en)
EP (1) EP1407053A4 (en)
JP (1) JP2005519635A (en)
AU (1) AU2002367838A1 (en)
CA (1) CA2460679A1 (en)
WO (1) WO2003095608A2 (en)

Families Citing this family (20)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001084148A2 (en) * 2000-04-28 2001-11-08 Sangamo Biosciences, Inc. Pharmacogenomics and identification of drug targets by reconstruction of signal transduction pathways based on sequences of accessible regions
US20040014086A1 (en) * 2001-05-11 2004-01-22 Regulome Corporation Regulome arrays
WO2003058193A2 (en) * 2001-07-02 2003-07-17 The Board Of Trustees Of The Leland Stanford Junior University Microarrays for cell phenotyping and manipulation
US20110151438A9 (en) * 2001-11-19 2011-06-23 Affymetrix, Inc. Methods of Analysis of Methylation
US20050003369A1 (en) * 2002-10-10 2005-01-06 Affymetrix, Inc. Method for depleting specific nucleic acids from a mixture
WO2005118873A2 (en) * 2004-05-28 2005-12-15 Cemines, Inc. Compositions and methods for detecting open chromatin and for genome-wide chromatin state profiling
GB0419419D0 (en) * 2004-09-01 2004-10-06 Medical Res Council Method
WO2006119264A2 (en) * 2005-04-29 2006-11-09 The Regents Of The University Of California Antibodies against histone modifications for clinical diagnosis and prognosis of cancer
US20060292585A1 (en) * 2005-06-24 2006-12-28 Affymetrix, Inc. Analysis of methylation using nucleic acid arrays
US7901882B2 (en) 2006-03-31 2011-03-08 Affymetrix, Inc. Analysis of methylation using nucleic acid arrays
US9273309B2 (en) * 2006-08-24 2016-03-01 University Of Massachusetts Mapping of genomic interactions
US8076070B2 (en) * 2008-08-06 2011-12-13 University Of Southern California Genome-wide chromosome conformation capture
US10526641B2 (en) * 2014-08-01 2020-01-07 Dovetail Genomics, Llc Tagging nucleic acids for sequence assembly
GB2554572B (en) 2015-03-26 2021-06-23 Dovetail Genomics Llc Physical linkage preservation in DNA storage
JP7441003B2 (en) 2016-02-23 2024-02-29 ダブテイル ゲノミクス エルエルシー Generation of phased read sets and haplotype phasing for genome assembly
SG11201810088SA (en) 2016-05-13 2018-12-28 Dovetail Genomics Llc Recovering long-range linkage information from preserved samples
US20190234874A1 (en) 2016-07-19 2019-08-01 Altius Institute For Biomedical Sciences Methods for fluorescence imaging microscopy
CN106987629B (en) * 2017-03-31 2021-01-15 上海市第一妇婴保健院 Method for detecting nucleosome arrangement on genome at single cell level
GB2581152A (en) * 2019-02-05 2020-08-12 Univ Oxford Innovation Ltd Production of 3C library
CN112973592B (en) * 2019-12-16 2022-12-09 天津大学 High-throughput DNA synthesis device and method based on array type ink-jet printing

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5610053A (en) * 1993-04-07 1997-03-11 The United States Of America As Represented By The Department Of Health And Human Services DNA sequence which acts as a chromatin insulator element to protect expressed genes from cis-acting regulatory sequences in mammalian cells
US6165709A (en) * 1997-02-28 2000-12-26 Fred Hutchinson Cancer Research Center Methods for drug target screening

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5972608A (en) * 1997-08-27 1999-10-26 University Of Massachusetts Assays and reagents for chromatin remodeling enzymes and their modulators

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5610053A (en) * 1993-04-07 1997-03-11 The United States Of America As Represented By The Department Of Health And Human Services DNA sequence which acts as a chromatin insulator element to protect expressed genes from cis-acting regulatory sequences in mammalian cells
US6165709A (en) * 1997-02-28 2000-12-26 Fred Hutchinson Cancer Research Center Methods for drug target screening

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See also references of EP1407053A4 *

Also Published As

Publication number Publication date
CA2460679A1 (en) 2003-11-20
EP1407053A2 (en) 2004-04-14
EP1407053A4 (en) 2004-09-29
AU2002367838A1 (en) 2003-11-11
WO2003095608A2 (en) 2003-11-20
JP2005519635A (en) 2005-07-07
US20030170689A1 (en) 2003-09-11

Similar Documents

Publication Publication Date Title
WO2003095608A3 (en) Dna microarrays comprising active chromatin elements and comprehensive profiling therewith
EP2333099A3 (en) Enzymes having alpha amylase activity and methods of use thereof
TWI365766B (en) Catalysts having enhanced stability, efficiency and/or activity for alkylene oxide production
WO1999051731A3 (en) Maize histone deacetylases and their use
MXPA03008484A (en) Aryl and biaryl compounds having mch modulatory activity.
WO2004052080A3 (en) Regulome arrays
DK0691980T3 (en) 7-deazapurine-modifying oligonucleotides
IN2014DN02483A (en)
AU2001241078A1 (en) Alpha-amylase activity inhibitors
WO2001002019A3 (en) Control of gene expression
IL136232A0 (en) Measurements of enzymatic activity in a single, individual cell in population
WO1999004038A3 (en) Biallelic markers for use in constructing a high density disequilibrium map of the human genome
ATE432341T1 (en) 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASES FROM PLANTS
EP1849868A3 (en) Plant defensins
ATE412056T1 (en) NUCLEIC ACID MOLECULES ENCODING ENZYMES POSSESSING FRUCTOSYL TRANSFERASE ACTIVITY AND THEIR USE
PL359409A1 (en) Compounds useful for the preparation of medicaments with phosphodiesterase iv inhibitory activity
FR2791360B1 (en) INDUCTIBLE PROMOTER, COMTII, CHIMERIC GENE COMPRISING SAME AND TRANSFORMED PLANTS
WO2003026390A3 (en) Plant reproduction polynucleotides and methods of use
Brookes Hard cell, soft cell
AU2003282564A8 (en) Gene profiling of single or multiple cells
EP1707630A4 (en) Antisense oligonucleotide having anticancerous activity
AU2001271111A1 (en) Human prothrombin kringle with endothelial cell growth inhibitory activity, vector and host thereof
ITRM20010670A1 (en) RECOMBINANT PLANTS AND DNA BUILT.
DE29910595U1 (en) Electrochemical sensor for determining the number and the physiological state of activity of cells or organisms, especially microorganisms
NO992819D0 (en) DNA elements for use in genetic engineering

Legal Events

Date Code Title Description
WWE Wipo information: entry into national phase

Ref document number: 10319440

Country of ref document: US

WWE Wipo information: entry into national phase

Ref document number: 2004503602

Country of ref document: JP

WWE Wipo information: entry into national phase

Ref document number: 2460679

Country of ref document: CA

AK Designated states

Kind code of ref document: A2

Designated state(s): AE AG AL AM AT AU AZ BA BB BG BR BY BZ CA CH CN CO CR CU CZ DE DK DM DZ EC EE ES FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MA MD MG MK MN MW MX MZ NO NZ PL PT RO RU SD SE SG SI SK SL TJ TM TR TT TZ UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW MZ SD SL SZ TZ UG ZM ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE TR BF BJ CF CG CI CM GA GN GQ GW ML MR NE SN TD TG

WWE Wipo information: entry into national phase

Ref document number: 2002367838

Country of ref document: AU

WWE Wipo information: entry into national phase

Ref document number: 2002807414

Country of ref document: EP

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

WWP Wipo information: published in national office

Ref document number: 2002807414

Country of ref document: EP