[go: up one dir, main page]

WO2019023291A3 - Compositions and methods for making and decoding paired-guide rna libraries and uses thereof - Google Patents

Compositions and methods for making and decoding paired-guide rna libraries and uses thereof Download PDF

Info

Publication number
WO2019023291A3
WO2019023291A3 PCT/US2018/043588 US2018043588W WO2019023291A3 WO 2019023291 A3 WO2019023291 A3 WO 2019023291A3 US 2018043588 W US2018043588 W US 2018043588W WO 2019023291 A3 WO2019023291 A3 WO 2019023291A3
Authority
WO
WIPO (PCT)
Prior art keywords
paired
decoding
compositions
making
methods
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/US2018/043588
Other languages
French (fr)
Other versions
WO2019023291A2 (en
Inventor
Xiaole LIU
Myles Brown
Jingyu PENG
Tengfei XIAO
Wei Li
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.)
Dana Farber Cancer Institute Inc
Original Assignee
Dana Farber Cancer Institute Inc
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 Dana Farber Cancer Institute Inc filed Critical Dana Farber Cancer Institute Inc
Publication of WO2019023291A2 publication Critical patent/WO2019023291A2/en
Publication of WO2019023291A3 publication Critical patent/WO2019023291A3/en
Anticipated expiration legal-status Critical
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
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPR]
    • 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
    • C12N2320/00—Applications; Uses
    • C12N2320/10—Applications; Uses in screening processes
    • C12N2320/12—Applications; Uses in screening processes in functional genomics, i.e. for the determination of gene function
    • 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
    • C12N2330/00—Production
    • C12N2330/30—Production chemically synthesised
    • C12N2330/31—Libraries, arrays

Landscapes

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

Abstract

The present disclosure relates to compositions and methods for making and decoding paired-guide RNA (pgRNA) libraries using the Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR) system, and using the resulting pgRNA/CRISPR libraries to identify genetic interactions or functional non-coding elements.
PCT/US2018/043588 2017-07-25 2018-07-25 Compositions and methods for making and decoding paired-guide rna libraries and uses thereof Ceased WO2019023291A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762536870P 2017-07-25 2017-07-25
US62/536,870 2017-07-25

Publications (2)

Publication Number Publication Date
WO2019023291A2 WO2019023291A2 (en) 2019-01-31
WO2019023291A3 true WO2019023291A3 (en) 2019-04-25

Family

ID=63312445

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2018/043588 Ceased WO2019023291A2 (en) 2017-07-25 2018-07-25 Compositions and methods for making and decoding paired-guide rna libraries and uses thereof

Country Status (1)

Country Link
WO (1) WO2019023291A2 (en)

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12460201B2 (en) 2019-07-16 2025-11-04 Massachusetts Institute Of Technology Methods of multiplexing CRISPR

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3597741A1 (en) 2012-04-27 2020-01-22 Duke University Genetic correction of mutated genes
US9828582B2 (en) 2013-03-19 2017-11-28 Duke University Compositions and methods for the induction and tuning of gene expression
WO2016130600A2 (en) 2015-02-09 2016-08-18 Duke University Compositions and methods for epigenome editing
EP3362571A4 (en) 2015-10-13 2019-07-10 Duke University GENOMIC ENGINEERING WITH TYPE I CRISPRISMS IN EUKARYOTIC CELLS
WO2017095967A2 (en) 2015-11-30 2017-06-08 Duke University Therapeutic targets for the correction of the human dystrophin gene by gene editing and methods of use
US20190127713A1 (en) 2016-04-13 2019-05-02 Duke University Crispr/cas9-based repressors for silencing gene targets in vivo and methods of use
JP7490211B2 (en) 2016-07-19 2024-05-27 デューク ユニバーシティ Therapeutic Applications of CPF1-Based Genome Editing
EP4125350A4 (en) * 2020-04-27 2024-04-03 Duke University TARGETED GENOMIC INTEGRATION TO RESTORE A NEUROFIBROMIN CODING SEQUENCE IN NEUROFIBROMATOSIS TYPE 1 (NF1)
AU2021405456A1 (en) * 2020-12-25 2023-07-13 LogoMix, Inc. Method for causing large-scale deletions in genomic dna and method for analyzing genomic dna
WO2022167421A1 (en) * 2021-02-02 2022-08-11 Limagrain Europe Linkage of a distal promoter to a gene of interest by gene editing to modify gene expression

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150225730A1 (en) * 2014-02-12 2015-08-13 Dna2.0, Inc. Methods for generating libraries with co-varying regions of polynuleotides for genome modification
WO2016130697A1 (en) * 2015-02-11 2016-08-18 Memorial Sloan Kettering Cancer Center Methods and kits for generating vectors that co-express multiple target molecules
WO2017069829A2 (en) * 2015-07-31 2017-04-27 The Trustees Of Columbia University In The City Of New York High-throughput strategy for dissecting mammalian genetic interactions
WO2017122096A1 (en) * 2016-01-15 2017-07-20 Astrazeneca Ab Gene modification assays

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4683202A (en) 1985-03-28 1987-07-28 Cetus Corporation Process for amplifying nucleic acid sequences
US4683195A (en) 1986-01-30 1987-07-28 Cetus Corporation Process for amplifying, detecting, and/or-cloning nucleic acid sequences
WO2014093694A1 (en) 2012-12-12 2014-06-19 The Broad Institute, Inc. Crispr-cas nickase systems, methods and compositions for sequence manipulation in eukaryotes
US8697359B1 (en) 2012-12-12 2014-04-15 The Broad Institute, Inc. CRISPR-Cas systems and methods for altering expression of gene products
DK2898075T3 (en) 2012-12-12 2016-06-27 Broad Inst Inc CONSTRUCTION AND OPTIMIZATION OF IMPROVED SYSTEMS, PROCEDURES AND ENZYME COMPOSITIONS FOR SEQUENCE MANIPULATION
EP4570817A3 (en) 2012-12-12 2025-09-24 The Broad Institute Inc. Crispr-cas component systems, methods and compositions for sequence manipulation

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150225730A1 (en) * 2014-02-12 2015-08-13 Dna2.0, Inc. Methods for generating libraries with co-varying regions of polynuleotides for genome modification
WO2016130697A1 (en) * 2015-02-11 2016-08-18 Memorial Sloan Kettering Cancer Center Methods and kits for generating vectors that co-express multiple target molecules
WO2017069829A2 (en) * 2015-07-31 2017-04-27 The Trustees Of Columbia University In The City Of New York High-throughput strategy for dissecting mammalian genetic interactions
WO2017122096A1 (en) * 2016-01-15 2017-07-20 Astrazeneca Ab Gene modification assays

Non-Patent Citations (9)

* Cited by examiner, † Cited by third party
Title
ALAN S L WONG ET AL: "Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 113, no. 9, 10 February 2016 (2016-02-10), pages 2544 - 2549, XP002775745, ISSN: 0027-8424, [retrieved on 20160216], DOI: 10.1073/PNAS.1517883113 *
CARLOS PULIDO-QUETGLAS ET AL: "Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion", PLOS COMPUTATIONAL BIOLOGY, vol. 13, no. 3, 2 March 2017 (2017-03-02), pages e1005341, XP055545792, DOI: 10.1371/journal.pcbi.1005341 *
DOW LUKAS E ET AL: "Inducible in vivo genome editing with CRISPR-Cas9", NATURE BIOTECHNOLOGY, vol. 33, no. 4, 18 February 2015 (2015-02-18), pages 390, XP055266912 *
FADI J NAJM ET AL: "Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens", NATURE BIOTECHNOLOGY, vol. 36, no. 2, 18 December 2017 (2017-12-18), pages 179 - 189, XP055545881, ISSN: 1087-0156, DOI: 10.1038/nbt.4048 *
GASPERINI MOLLY ET AL: "CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions", AMERICAN JOURNAL OF HUMAN GENETICS, vol. 101, no. 2, 14 July 2017 (2017-07-14), pages 192 - 205, XP085148255, ISSN: 0002-9297, DOI: 10.1016/J.AJHG.2017.06.010 *
JIAN CAO ET AL: "An easy and efficient inducible CRISPR/Cas9 platform with improved specificity for multiple gene targeting", NUCLEIC ACIDS RESEARCH, vol. 44, no. 19, 25 July 2016 (2016-07-25), pages e149, XP055544423, ISSN: 0305-1048, DOI: 10.1093/nar/gkw660 *
JOANA A. VIDIGAL ET AL: "Rapid and efficient one-step generation of paired gRNA CRISPR-Cas9 libraries", NATURE COMMUNICATIONS, vol. 6, no. 1, 17 August 2015 (2015-08-17), XP055541465, DOI: 10.1038/ncomms9083 *
KABADI AMI M ET AL: "Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector", NUCLEIC ACIDS RESEARCH, vol. 42, no. 19, 13 August 2014 (2014-08-13), XP055177310 *
KYUHO HAN ET AL: "Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions", NATURE BIOTECHNOLOGY, vol. 35, no. 5, 20 March 2017 (2017-03-20), pages 463 - 474, XP055544433, ISSN: 1087-0156, DOI: 10.1038/nbt.3834 *

Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US12460201B2 (en) 2019-07-16 2025-11-04 Massachusetts Institute Of Technology Methods of multiplexing CRISPR

Also Published As

Publication number Publication date
WO2019023291A2 (en) 2019-01-31

Similar Documents

Publication Publication Date Title
WO2019023291A3 (en) Compositions and methods for making and decoding paired-guide rna libraries and uses thereof
WO2017181107A3 (en) Modified cpf1 mrna, modified guide rna, and uses thereof
WO2015191693A3 (en) Method for gene editing
WO2016057951A3 (en) Crispr oligonucleotides and gene editing
WO2017117349A3 (en) Cell separation devices, systems, and methods
WO2017031360A8 (en) Capture of nucleic acids using a nucleic acid-guided nuclease-based system
WO2014204727A9 (en) Functional genomics using crispr-cas systems, compositions methods, screens and applications thereof
WO2018109174A3 (en) Il-11 antibodies
WO2018094356A3 (en) Compositions and methods for target nucleic acid modification
EP4400597A3 (en) Novel rna-guided nucleases and uses thereof
EP4524255A3 (en) Methods and compositions for nucleic acid analysis
WO2016100951A3 (en) Crispr-based compositions and methods of use
WO2018109170A3 (en) Il-11ra antibodies
EP4538390A3 (en) Methods and compositions for analyzing nucleic acid
EP3775272A4 (en) Methods, systems, and compositions for counting nucleic acid molecules
HK1257295A1 (en) Compositions and methods for immunooncology
WO2017070626A3 (en) Respiratory virus vaccines
EP4403638A3 (en) Novel crispr enzymes and systems
MX2017009506A (en) Crispr hybrid dna/rna polynucleotides and methods of use.
WO2017180694A8 (en) Cas9 fusion molecules, gene editing systems, and methods of use thereof
WO2018175636A3 (en) Compositions and methods for immunooncology
EP3252172A3 (en) Fast hybridization for next generation sequencing target enrichment
WO2016110453A8 (en) A crispr-cas system for a filamentous fungal host cell
EP4545544A3 (en) Modified crispr rna and modified single crispr rna and uses thereof
WO2015160895A3 (en) Modified transposases for improved insertion sequence bias and increased dna input tolerance

Legal Events

Date Code Title Description
NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 18758989

Country of ref document: EP

Kind code of ref document: A2