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

Profiled regulatory sites useful for gene control Download PDF

Info

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
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
Original Assignee
Regulome Corp
John A Stamatoyannopoulos
Michael Mcarthur
Michael O Dorschner
Michael Hawrylycz
Rich Humbert
George Stamatoyannopoulos
Rhett Alden
James Clendenning
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, John A Stamatoyannopoulos, Michael Mcarthur, Michael O Dorschner, Michael Hawrylycz, Rich Humbert, George Stamatoyannopoulos, Rhett Alden, James Clendenning filed Critical Regulome Corp
Priority to AU2003302777A priority Critical patent/AU2003302777A1/en
Publication of WO2004053106A2 publication Critical patent/WO2004053106A2/en
Publication of WO2004053106A3 publication Critical patent/WO2004053106A3/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
    • C12N15/1072—Differential gene expression library synthesis, e.g. subtracted libraries, differential screening

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 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 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)

Families Citing this family (9)

* 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
WO2005040377A2 (en) 2003-10-24 2005-05-06 Selexis S.A. High efficiency gene transfer and expression in mammalian cells by a multiple transfection procedure of matrix attachment region sequences
US20070031883A1 (en) * 2004-03-04 2007-02-08 Kincaid Robert H Analyzing CGH data to identify aberrations
US7611838B2 (en) 2004-03-04 2009-11-03 Whitehead Institute For Biomedical Research Biologically-active DNA-binding sites and related methods
EP1954835A4 (en) 2005-12-02 2009-07-22 Whitehead Biomedical Inst Methods for mapping signal transduction pathways to gene expression programs
ES2611000T3 (en) 2010-07-27 2017-05-04 Genomic Health, Inc. Method to use gene expression to determine the 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 *

Also Published As

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

Similar Documents

Publication Publication Date Title
Li et al. DNA methylation methods: Global DNA methylation and methylomic analyses
Vidaki et al. Recent progress, methods and perspectives in forensic epigenetics
Han et al. Epigenetic age-predictor for mice based on three CpG sites
Ugozzoli et al. Real-time genotyping with oligonucleotide probes containing locked nucleic acids
Mesner et al. Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription
CA2394229A1 (en) Loci for idiopathic generalized epilepsy, mutations thereof and method using same to assess, diagnose, prognose or treat epilepsy
Glaab et al. A novel assay for allelic discrimination that combines the fluorogenic 5′ nuclease polymerase chain reaction (TaqMan®) and mismatch amplification mutation assay
BR0308134A (en) quick analysis of variations in a genome
Jin et al. A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data—A case study using E2F1
WO2004005458A3 (en) Functional sites
Kaplow et al. A pooling-based approach to mapping genetic variants associated with DNA methylation
Jolma et al. Methods for analysis of transcription factor DNA-binding specificity in vitro
Novroski et al. Expanding beyond the current core STR loci: an exploration of 73 STR markers with increased diversity for enhanced DNA mixture deconvolution
WO2004053106A3 (en) Profiled regulatory sites useful for gene control
Caratti et al. MiSeq FGx sequencing system: a new platform for forensic genetics
US6892141B1 (en) Primer design system
US20020197632A1 (en) Method to find disease-associated SNPs and genes
El-Maarri SIRPH analysis: SNuPE with IP-RP-HPLC for quantitative measurements of DNA methylation at specific CpG sites
CN112280863B (en) Method and kit for targeting drug apatinib effectiveness
Park et al. Enhanced sensitivity of CpG island search and primer design based on predicted CpG island position
CN104830992A (en) Primer and kit for detecting methylenetetrahydrofolate reductase C677T polymorphic sites and PCR (polymerase chain reaction) method of primer and kit
Qiu et al. Quantification of single nucleotide polymorphisms by automated DNA sequencing
Keller et al. Linking variants from genome-wide association analysis to function via transcriptional network analysis
ATE397064T1 (en) GENOMIC AND COMPLETE CDNA SEQUENCES OF HUMAN ADIPOCYTE SPECIFIC APM1 AND BIALLELIC MARKERS THEREOF
EP1136932B1 (en) Primer design system

Legal Events

Date Code Title Description
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 EG 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 NI NO NZ OM PG PH PL PT RO RU SC SD SE SG SK SL SY TJ TM TN TR TT TZ UA UG US UZ VC VN YU ZA ZM ZW

AL Designated countries for regional patents

Kind code of ref document: A2

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

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)
122 Ep: pct application non-entry in european phase
NENP Non-entry into the national phase

Ref country code: JP

WWW Wipo information: withdrawn in national office

Country of ref document: JP