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WO2007078599A3 - Functional arrays for high throughput characterization of gene expression regulatory elements - Google Patents

Functional arrays for high throughput characterization of gene expression regulatory elements Download PDF

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Publication number
WO2007078599A3
WO2007078599A3 PCT/US2006/046920 US2006046920W WO2007078599A3 WO 2007078599 A3 WO2007078599 A3 WO 2007078599A3 US 2006046920 W US2006046920 W US 2006046920W WO 2007078599 A3 WO2007078599 A3 WO 2007078599A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
regulatory elements
gene expression
high throughput
expression regulatory
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/US2006/046920
Other languages
French (fr)
Other versions
WO2007078599A8 (en
WO2007078599A9 (en
WO2007078599A2 (en
Inventor
Nathan D Trinklein
Shelley F Aldred
Sara J Cooper
Richard M Myers
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.)
Leland Stanford Junior University
Original Assignee
Leland Stanford Junior University
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
Priority claimed from US11/636,385 external-priority patent/US20070161031A1/en
Application filed by Leland Stanford Junior University filed Critical Leland Stanford Junior University
Priority to JP2008545677A priority Critical patent/JP2009519710A/en
Priority to EP06849046A priority patent/EP2021499A4/en
Publication of WO2007078599A2 publication Critical patent/WO2007078599A2/en
Publication of WO2007078599A9 publication Critical patent/WO2007078599A9/en
Anticipated expiration legal-status Critical
Publication of WO2007078599A3 publication Critical patent/WO2007078599A3/en
Publication of WO2007078599A8 publication Critical patent/WO2007078599A8/en
Ceased legal-status Critical Current

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    • 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
    • C12N15/1086—Preparation or screening of expression libraries, e.g. reporter assays
    • 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
    • C12Q1/6897—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids involving reporter genes operably linked to promoters

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biomedical Technology (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Analytical Chemistry (AREA)
  • Plant Pathology (AREA)
  • Immunology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

The present invention provides compositions, kits, assemblies, libraries, arrays, and high throughput methods for large scale structural and functional characterization of gene expression regulatory elements in a genome of an organism, especially in a human genome. In one aspect of the invention, an array of expression constructs is provided, e.ach of the expression constructs comprising: a nucleic acid segment operably linked with a reporter sequence in an expression vector such that expression of the reporter sequence is under the transcriptional control of the nucleic acid segment, the nucleic acid segment varying in the library and having a diversity of at least 50. The nucleic acid segments can be a large library of gene expression regulatory elements such as transcriptional promoters. The present invention can have a wide variety of applications such as in personalized medicine, pharmacogenomics, and correlation of polymorphisms with phenotypic traits.
PCT/US2006/046920 2005-12-16 2006-12-08 Functional arrays for high throughput characterization of gene expression regulatory elements Ceased WO2007078599A2 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
JP2008545677A JP2009519710A (en) 2005-12-16 2006-12-08 Functional arrays for high-throughput characterization of gene expression regulatory elements
EP06849046A EP2021499A4 (en) 2005-12-16 2006-12-08 FUNCTIONAL NETWORKS FOR THE HIGH-FREQUENCY CHARACTERIZATION OF ELEMENTS REGULATING GENE EXPRESSION

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US75092905P 2005-12-16 2005-12-16
US60/750,929 2005-12-16
US76205606P 2006-01-24 2006-01-24
US60/762,056 2006-01-24
US11/636,385 US20070161031A1 (en) 2005-12-16 2006-12-07 Functional arrays for high throughput characterization of gene expression regulatory elements
US11/636,385 2006-12-07

Publications (4)

Publication Number Publication Date
WO2007078599A2 WO2007078599A2 (en) 2007-07-12
WO2007078599A9 WO2007078599A9 (en) 2007-10-04
WO2007078599A3 true WO2007078599A3 (en) 2008-08-28
WO2007078599A8 WO2007078599A8 (en) 2008-10-30

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2006/046920 Ceased WO2007078599A2 (en) 2005-12-16 2006-12-08 Functional arrays for high throughput characterization of gene expression regulatory elements

Country Status (3)

Country Link
EP (1) EP2021499A4 (en)
JP (1) JP2009519710A (en)
WO (1) WO2007078599A2 (en)

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US10501749B2 (en) 2013-03-14 2019-12-10 Monsanto Technology Llc Plant regulatory elements derived from medicago truncatula 3′UTR sequences, and uses thereof
US12447172B2 (en) 2018-11-09 2025-10-21 Universite Paris-Saclay Use of the miR-27a-5p microRNA for treating Clostridium difficile-induced bowel inflammation

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US9163259B2 (en) * 2012-05-04 2015-10-20 Novartis Ag Viral vectors for the treatment of retinal dystrophy
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WO2015143385A1 (en) * 2014-03-21 2015-09-24 Life Technologies Corporation Multi-copy reference assay
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KR101791296B1 (en) 2014-04-17 2017-10-27 제주대학교 산학협력단 Expression cassette and vector with genes related Alzheimer's disease and transgenic cell line made from it
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WO2016149455A2 (en) * 2015-03-17 2016-09-22 The General Hospital Corporation The rna interactome of polycomb repressive complex 1 (prc1)
US20180187190A1 (en) * 2015-06-12 2018-07-05 Erasmus University Medical Center Rotterdam New crispr assays
AU2016326657B2 (en) 2015-09-25 2019-10-24 Context Biopharma, Inc. Methods of making onapristone intermediates
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AU2017248659B2 (en) 2016-04-15 2022-08-11 The Trustees Of The University Of Pennsylvania Gene therapy for treating hemophilia A
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WO2018111104A1 (en) * 2016-12-14 2018-06-21 Erasmus University Medical Center Rotterdam Use of human crispr sequences in diagnostics
US11920149B2 (en) 2017-03-27 2024-03-05 Vrije Universiteit Brussel Diaphragm-specific nucleic acid regulatory elements and methods and use thereof
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AU2018275549B2 (en) * 2017-05-31 2024-12-19 The University Of North Carolina At Chapel Hill Optimized human clotting factor IX gene expression cassettes and their use
RU2671156C1 (en) * 2017-08-21 2018-10-29 Общество с ограниченной ответственностью "Центр Генетики и Репродуктивной Медицины "ГЕНЕТИКО" Method of preimplantation genetic diagnostics of type 1 spinal muscular atrophy
EP3714070B1 (en) 2017-11-20 2021-12-29 Turun yliopisto A novel cip2a variant and uses thereof
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KR20200128112A (en) 2018-02-28 2020-11-11 유니버시티 오브 피츠버그-오브 더 커먼웰쓰 시스템 오브 하이어 에듀케이션 Modular system for gene and protein delivery based on AAV
US12274733B2 (en) 2018-09-28 2025-04-15 President And Fellows Of Harvard College Cellular reprogramming to reverse aging and promote organ and tissue regeneration
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WO2020092614A1 (en) 2018-10-31 2020-05-07 Rutgers, The State University Of New Jersey Gramc: genome-scale reporter assay method for cis-regulatory modules
US20220073905A1 (en) * 2018-12-28 2022-03-10 University Of Pittsburgh - Of The Commonwealth System Of Higher Education Methods and materials for single cell transcriptome-based development of aav vectors and promoters
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WO2024110770A1 (en) * 2022-11-22 2024-05-30 INSERM (Institut National de la Santé et de la Recherche Médicale) A new promoter for retinal pigment epithelium (rpe) targeted gene therapy
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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10501749B2 (en) 2013-03-14 2019-12-10 Monsanto Technology Llc Plant regulatory elements derived from medicago truncatula 3′UTR sequences, and uses thereof
US12447172B2 (en) 2018-11-09 2025-10-21 Universite Paris-Saclay Use of the miR-27a-5p microRNA for treating Clostridium difficile-induced bowel inflammation

Also Published As

Publication number Publication date
EP2021499A4 (en) 2010-02-17
WO2007078599A8 (en) 2008-10-30
WO2007078599A9 (en) 2007-10-04
EP2021499A2 (en) 2009-02-11
JP2009519710A (en) 2009-05-21
WO2007078599A2 (en) 2007-07-12

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