Title:
METHOD FOR INDUCING DELETION IN GENOMIC DNA
Document Type and Number:
WIPO Patent Application WO/2020/122104
Kind Code:
A1
Abstract:
A method for producing a genomic DNA in which a deletion of more than 100 nucleotides has been induced in a target region of a genomic DNA, said method including a step in which a type I CRISPR-associated complex for antiviral defense (type I Cascade complex), CRISPR RNA (crRNA), and a Cas3 protein are brought into contact with a genomic DNA.
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Inventors:
HOTTA AKITSU (JP)
OKUZAKI YUYA (JP)
XU HUAIGENG (JP)
GEE PETER DAVID (JP)
KITA YUTO (JP)
MASHIMO TOMOJI (JP)
YOSHIMI KAZUTO (JP)
OKUZAKI YUYA (JP)
XU HUAIGENG (JP)
GEE PETER DAVID (JP)
KITA YUTO (JP)
MASHIMO TOMOJI (JP)
YOSHIMI KAZUTO (JP)
Application Number:
PCT/JP2019/048426
Publication Date:
June 18, 2020
Filing Date:
December 11, 2019
Export Citation:
Assignee:
UNIV KYOTO (JP)
UNIV OSAKA (JP)
UNIV OSAKA (JP)
International Classes:
C12N15/09; C12N5/10
Domestic Patent References:
| WO2017066497A2 | 2017-04-20 | |||
| WO2018225858A1 | 2018-12-13 | |||
| WO2019039417A1 | 2019-02-28 | |||
| WO2019246555A1 | 2019-12-26 | |||
| WO2018179578A1 | 2018-10-04 |
Foreign References:
| JP2018231649A | 2018-12-11 | |||
| US201962938346P | 2019-11-21 |
Other References:
H MORISAKA, S SANO , J TAKEDA : "490 Genome editing in mammalian cells by cascade and Cas3", JOURNAL OF INVESTIGATIVE DERMATOLOGY, vol. 137, no. 5, 1 May 2017 (2017-05-01), pages S84, XP055720152, DOI: 10.1016/j.jid.2017.02.510
MORISAKA HIROYUKI , SANO SHIGETOSHI, TAKEDA JUNJI: "Genome editing in mammalian cells by Cascade and Cas3", PROGRAMS AND ABSTRACTS OF 42TH ANNUAL ACADEMIC CONFERENCE AND GENERAL CONFERENCE OF THE JAPANESE SOCIETY FOR INVESTIGATE DERMATOLOGY, 2 November 2017 (2017-11-02), pages 1 - 3, XP009517845
DOLAN ADAM E.; HOU ZHONGGANG; XIAO YIBEI; GRAMELSPACHER MAX J.; HEO JAEWON; HOWDEN SARA E.; FREDDOLINO PETER L.; KE AILONG; ZHANG : "Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas", MOLECULAR CELL, ELSEVIER, AMSTERDAM, NL, vol. 74, no. 5, 6 June 2019 (2019-06-06), AMSTERDAM, NL, pages 936 - 950+5, XP085709103, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2019.03.014
CAMERON PETER; COONS MARY M.; KLOMPE SANNE E.; LIED ALEXANDRA M.; SMITH STEPHEN C.; VIDAL BASTIEN; DONOHOUE PAUL D.; ROTSTEIN TOME: "Harnessing type I CRISPR- Cas systems for genome engineering in human cells", NATURE BIOTECHNOLOGY, vol. 37, no. 12, 18 November 2019 (2019-11-18), pages 1471 - 1477, XP036954221, ISSN: 1087-0156, DOI: 10.1038/s41587-019-0310-0
HIROYUKI MORISAKA , KAZUTO YOSHIMI , YUGA OKUZAKI , PETER GEE , YAYOI KUNIHIRO , EKASIT SONPHO , HUAIGENG XU , NORIKO SASAKAWA , Y: "CRISPR-Cas3 induces broad and unidirectional genome editing in human cells", NATURE COMMUNICATIONS, vol. 10, no. 1, 1 December 2019 (2019-12-01), pages 1 - 13, XP055720163, DOI: 10.1038/s41467-019-13226-x
MOHANRAJU PRARTHANA, MAKAROVA KIRA S., ZETSCHE BERND, ZHANG FENG, KOONIN EUGENE V., VAN DER OOST JOHN: "Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems", SCIENCE, vol. 353, no. 6299, 2016, pages 1 - 14, XP055791785, ISSN: 0036-8075, DOI: 10.1126/science.aad5147
EDZER. WESTRA; PAULB.G. VANERP; TIM KNNE; SHIPEY WONG; RAYMONDH.J. STAALS; CHRISTELL.C. SEEGERS; SANDER BOLLEN; MATTHIJSM. JORE; E: "CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3", MOLECULAR CELL, vol. 46, no. 5, 16 March 2012 (2012-03-16), pages 595 - 605, XP028522152, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2012.03.018
HIDETO MATSUI, NAOKO FUJIMOTO, NORIKO SASAKAWA, YASUHIDE OHINATA, MIDORI SHIMA, SHINYA YAMANAKA, MITSUHIKO SUGIMOTO, AKITSU HOTTA: "Delivery of full-length factor VIII using a piggyBac transposon vector to correct a mouse model of hemophilia A", PLOS ONE, vol. 9, no. 8, e104957, 15 August 2014 (2014-08-15), pages 1 - 10, XP055467838, DOI: 10.1371/journal.pone.0104957
ISHIDA K. ET AL.: "Site-specific randomization of the endogenous genome by a regulatable CRISPR-Cas9 piggyBac system in human cells", SCI REP., vol. 8, no. 1, 2018, pages 310
MALI P. ET AL.: "RNA-guided human genome engineering via Cas9", SCIENCE, vol. 339, no. 6121, 2013, pages 823 - 826, XP055469277, DOI: 10.1126/science.1232033
"NCBI", Database accession no. NP_417241.1
TANAKA A. ET AL.: "Efficient and reproducible myogenic differentiation from human iPS cells: prospects for modeling Myoshi Myopathy in vitro", PLOS ONE, vol. 8, no. 4, 2013, pages e61540, XP055544983, DOI: 10.1371/journal.pone.0061540
LI H. L. ET AL.: "Precise correction of the Dystrophin gene in Duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9", STEM CELL REPORTS, vol. 4, no. 1, 2015, pages 143 - 154, XP055541946, DOI: 10.1016/j.stemcr.2014.10.013
HAYES R. P. ET AL.: "Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli", NATURE, vol. 530, no. 7591, 2016, pages 499 - 503
HOCHSTRASSER M. L. ET AL.: "CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference", PROC NATL ACAD SCI U S A, vol. 111, no. 18, 2014, pages 6618 - 6623, XP055752880, DOI: 10.1073/pnas.1405079111
WESTRA E. R.: "CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3", MOL CELL, vol. 46, no. 5, 2012, pages 595 - 605, XP028522152, DOI: 10.1016/j.molcel.2012.03.018
See also references of EP 3896158A4
MORISAKA HIROYUKI , SANO SHIGETOSHI, TAKEDA JUNJI: "Genome editing in mammalian cells by Cascade and Cas3", PROGRAMS AND ABSTRACTS OF 42TH ANNUAL ACADEMIC CONFERENCE AND GENERAL CONFERENCE OF THE JAPANESE SOCIETY FOR INVESTIGATE DERMATOLOGY, 2 November 2017 (2017-11-02), pages 1 - 3, XP009517845
DOLAN ADAM E.; HOU ZHONGGANG; XIAO YIBEI; GRAMELSPACHER MAX J.; HEO JAEWON; HOWDEN SARA E.; FREDDOLINO PETER L.; KE AILONG; ZHANG : "Introducing a Spectrum of Long-Range Genomic Deletions in Human Embryonic Stem Cells Using Type I CRISPR-Cas", MOLECULAR CELL, ELSEVIER, AMSTERDAM, NL, vol. 74, no. 5, 6 June 2019 (2019-06-06), AMSTERDAM, NL, pages 936 - 950+5, XP085709103, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2019.03.014
CAMERON PETER; COONS MARY M.; KLOMPE SANNE E.; LIED ALEXANDRA M.; SMITH STEPHEN C.; VIDAL BASTIEN; DONOHOUE PAUL D.; ROTSTEIN TOME: "Harnessing type I CRISPR- Cas systems for genome engineering in human cells", NATURE BIOTECHNOLOGY, vol. 37, no. 12, 18 November 2019 (2019-11-18), pages 1471 - 1477, XP036954221, ISSN: 1087-0156, DOI: 10.1038/s41587-019-0310-0
HIROYUKI MORISAKA , KAZUTO YOSHIMI , YUGA OKUZAKI , PETER GEE , YAYOI KUNIHIRO , EKASIT SONPHO , HUAIGENG XU , NORIKO SASAKAWA , Y: "CRISPR-Cas3 induces broad and unidirectional genome editing in human cells", NATURE COMMUNICATIONS, vol. 10, no. 1, 1 December 2019 (2019-12-01), pages 1 - 13, XP055720163, DOI: 10.1038/s41467-019-13226-x
MOHANRAJU PRARTHANA, MAKAROVA KIRA S., ZETSCHE BERND, ZHANG FENG, KOONIN EUGENE V., VAN DER OOST JOHN: "Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems", SCIENCE, vol. 353, no. 6299, 2016, pages 1 - 14, XP055791785, ISSN: 0036-8075, DOI: 10.1126/science.aad5147
EDZER. WESTRA; PAULB.G. VANERP; TIM KNNE; SHIPEY WONG; RAYMONDH.J. STAALS; CHRISTELL.C. SEEGERS; SANDER BOLLEN; MATTHIJSM. JORE; E: "CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3", MOLECULAR CELL, vol. 46, no. 5, 16 March 2012 (2012-03-16), pages 595 - 605, XP028522152, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2012.03.018
HIDETO MATSUI, NAOKO FUJIMOTO, NORIKO SASAKAWA, YASUHIDE OHINATA, MIDORI SHIMA, SHINYA YAMANAKA, MITSUHIKO SUGIMOTO, AKITSU HOTTA: "Delivery of full-length factor VIII using a piggyBac transposon vector to correct a mouse model of hemophilia A", PLOS ONE, vol. 9, no. 8, e104957, 15 August 2014 (2014-08-15), pages 1 - 10, XP055467838, DOI: 10.1371/journal.pone.0104957
ISHIDA K. ET AL.: "Site-specific randomization of the endogenous genome by a regulatable CRISPR-Cas9 piggyBac system in human cells", SCI REP., vol. 8, no. 1, 2018, pages 310
MALI P. ET AL.: "RNA-guided human genome engineering via Cas9", SCIENCE, vol. 339, no. 6121, 2013, pages 823 - 826, XP055469277, DOI: 10.1126/science.1232033
"NCBI", Database accession no. NP_417241.1
TANAKA A. ET AL.: "Efficient and reproducible myogenic differentiation from human iPS cells: prospects for modeling Myoshi Myopathy in vitro", PLOS ONE, vol. 8, no. 4, 2013, pages e61540, XP055544983, DOI: 10.1371/journal.pone.0061540
LI H. L. ET AL.: "Precise correction of the Dystrophin gene in Duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR-Cas9", STEM CELL REPORTS, vol. 4, no. 1, 2015, pages 143 - 154, XP055541946, DOI: 10.1016/j.stemcr.2014.10.013
HAYES R. P. ET AL.: "Structural basis for promiscuous PAM recognition in type I-E Cascade from E. coli", NATURE, vol. 530, no. 7591, 2016, pages 499 - 503
HOCHSTRASSER M. L. ET AL.: "CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference", PROC NATL ACAD SCI U S A, vol. 111, no. 18, 2014, pages 6618 - 6623, XP055752880, DOI: 10.1073/pnas.1405079111
WESTRA E. R.: "CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3", MOL CELL, vol. 46, no. 5, 2012, pages 595 - 605, XP028522152, DOI: 10.1016/j.molcel.2012.03.018
See also references of EP 3896158A4
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TANAI Sumio et al. (JP)
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