Title:
COMPOSITIONS AND METHODS FOR MODIFYING GENOMES USING CPF1 OR CSM1
Document Type and Number:
WIPO Patent Application WO/2017/141173
Kind Code:
A3
Abstract:
Compositions and methods for modifying genomic DNA sequences are provided. The methods roduce double-stranded breaks (DSBs) at pre-determined target sites in a genomic DNA sequence, sulting in mutation, insertion, and/or deletion of DNA sequences at the target site(s) in a genome. ompositions comprise DNA constructs comprising nucleotide sequences that encode a Cpf1 or Csm1 rotein operably linked to a promoter that is operable in the cells of interest. The DNA constructs can e used to direct the modification of genomic DNA at pre-determined genomic loci. Methods to use ese DNA constructs to modify genomic DNA sequences are described herein. Additionally, ompositions and methods for modulating the expression of genes are provided. Compositions omprise DNA constructs comprising a promoter that is operable in the cells of interest operably nked to nucleotide sequences that encode a mutated Cpf1 or Csm1 protein with an abolished ability to roduce DSBs, optionally linked to a domain that regulates transcriptional activity. The methods can e used to up- or down-regulate the expression of genes at predetermined genomic loci.
Inventors:
BEGEMANN MATTHEW (US)
GRAY BENJAMIN NEIL (US)
GRAY BENJAMIN NEIL (US)
Application Number:
PCT/IB2017/050845
Publication Date:
November 02, 2017
Filing Date:
February 15, 2017
Export Citation:
Assignee:
BENSON HILL BIOSYSTEMS INC (US)
International Classes:
C12N9/22; C12N15/10; C12N15/62; C12N15/82
Domestic Patent References:
| WO2015071474A2 | 2015-05-21 |
Foreign References:
| US20140356956A1 | 2014-12-04 | |||
| EP3009511A2 | 2016-04-20 |
Other References:
ROBERT D. FAGERLUND ET AL: "The Cpf1 CRISPR-Cas protein expands genome-editing tools", GENOME BIOLOGY, vol. 523, no. 1, 17 December 2015 (2015-12-17), GB, pages 481, XP055271439, ISSN: 1465-6906, DOI: 10.1186/s13059-015-0824-9
BERND ZETSCHE ET AL: "Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System", CELL, vol. 163, no. 3, 1 October 2015 (2015-10-01), US, pages 759 - 771, XP055267511, ISSN: 0092-8674, DOI: 10.1016/j.cell.2015.09.038
SERGEY SHMAKOV ET AL: "Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems", MOLECULAR CELL., vol. 60, no. 3, 1 November 2015 (2015-11-01), US, pages 385 - 397, XP055267512, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2015.10.008
NICOLE RUSK: "Genomics: New kid on the CRISPR block", NATURE METHODS, vol. 12, no. 12, 1 December 2015 (2015-12-01), pages 1117 - 1117, XP055271447, ISSN: 1548-7091, DOI: 10.1038/nmeth.3680
DATABASE UniProt [online] 20 January 2016 (2016-01-20), "RecName: Full=CRISPR-associated endonuclease Cpf1 {ECO:0000303|PubMed:26422227}; EC=3.1.-.-; AltName: Full=FnCpf1 {ECO:0000303|PubMed:26422227};", XP002770633, retrieved from EBI accession no. UNIPROT:A0Q7Q2 Database accession no. A0Q7Q2
DATABASE UniProt [online] 5 October 2010 (2010-10-05), "SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:EFI70750.1};", XP002773449, retrieved from EBI accession no. UNIPROT:D8E0G1 Database accession no. D8E0G1
THE NORTH AMERICAN CONSORTIUM FOR RUMEN BACTERIA ET AL: "Comparative Genome Analysis ofand: Insights into Their Environmental Niche", MICROBIAL ECOLOGY, SPRINGER-VERLAG, NE, vol. 60, no. 4, 29 June 2010 (2010-06-29), pages 721 - 729, XP019858682, ISSN: 1432-184X, DOI: 10.1007/S00248-010-9692-8
DATABASE UniProt [online] 26 November 2014 (2014-11-26), "SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:KFO67988.1};", XP002773450, retrieved from EBI accession no. UNIPROT:A0A091FC75 Database accession no. A0A091FC75
TAE-YANG JUNG ET AL: "Crystal Structure of the Csm1 Subunit of the Csm Complex and Its Single-Stranded DNA-Specific Nuclease Activity", STRUCTURE, vol. 23, no. 4, 1 April 2015 (2015-04-01), AMSTERDAM, NL, pages 782 - 790, XP055403999, ISSN: 0969-2126, DOI: 10.1016/j.str.2015.01.021
BERND ZETSCHE ET AL: "Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System", CELL, vol. 163, no. 3, 1 October 2015 (2015-10-01), US, pages 759 - 771, XP055267511, ISSN: 0092-8674, DOI: 10.1016/j.cell.2015.09.038
SERGEY SHMAKOV ET AL: "Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems", MOLECULAR CELL., vol. 60, no. 3, 1 November 2015 (2015-11-01), US, pages 385 - 397, XP055267512, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2015.10.008
NICOLE RUSK: "Genomics: New kid on the CRISPR block", NATURE METHODS, vol. 12, no. 12, 1 December 2015 (2015-12-01), pages 1117 - 1117, XP055271447, ISSN: 1548-7091, DOI: 10.1038/nmeth.3680
DATABASE UniProt [online] 20 January 2016 (2016-01-20), "RecName: Full=CRISPR-associated endonuclease Cpf1 {ECO:0000303|PubMed:26422227}; EC=3.1.-.-; AltName: Full=FnCpf1 {ECO:0000303|PubMed:26422227};", XP002770633, retrieved from EBI accession no. UNIPROT:A0Q7Q2 Database accession no. A0Q7Q2
DATABASE UniProt [online] 5 October 2010 (2010-10-05), "SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:EFI70750.1};", XP002773449, retrieved from EBI accession no. UNIPROT:D8E0G1 Database accession no. D8E0G1
THE NORTH AMERICAN CONSORTIUM FOR RUMEN BACTERIA ET AL: "Comparative Genome Analysis ofand: Insights into Their Environmental Niche", MICROBIAL ECOLOGY, SPRINGER-VERLAG, NE, vol. 60, no. 4, 29 June 2010 (2010-06-29), pages 721 - 729, XP019858682, ISSN: 1432-184X, DOI: 10.1007/S00248-010-9692-8
DATABASE UniProt [online] 26 November 2014 (2014-11-26), "SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:KFO67988.1};", XP002773450, retrieved from EBI accession no. UNIPROT:A0A091FC75 Database accession no. A0A091FC75
TAE-YANG JUNG ET AL: "Crystal Structure of the Csm1 Subunit of the Csm Complex and Its Single-Stranded DNA-Specific Nuclease Activity", STRUCTURE, vol. 23, no. 4, 1 April 2015 (2015-04-01), AMSTERDAM, NL, pages 782 - 790, XP055403999, ISSN: 0969-2126, DOI: 10.1016/j.str.2015.01.021
Attorney, Agent or Firm:
BUCK, B. Logan (US)
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