Title:
COMPOSITION FOR MODIFYING NUCLEIC ACID SEQUENCE, AND METHOD FOR MODIFYING TARGET SITE OF NUCLEIC ACID SEQUENCE
Document Type and Number:
WIPO Patent Application WO/2023/038020
Kind Code:
A1
Abstract:
The present invention addresses the problem of providing: a composition for modifying a nucleic acid sequence, which is not dependent on a PAM sequence or a PFS sequence; and a method for modifying a target site of a nucleic acid sequence. The problem can be solved by a composition which is for modifying a nucleic acid sequence and includes RNA and a fusion protein, wherein: the RNA includes a hybridize region capable of hybridizing with a sequence on the 5' side or 3' side of a target site in the nucleic acid sequence, and a guide region for guiding the fusion protein; the guide region includes a recognition region which forms a complex with the fusion protein; and the fusion protein recognizes a recognition region of the RNA and includes a binding domain which forms a complex with the recognition region (with the exception of a binding domain that includes the RNA recognition region of a Cas protein group), and a modified domain for modifying the target site of the nucleic acid sequence.
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Inventors:
NAKAMURA IKUO (JP)
MAKABE SO (JP)
KOBASHI YUICHI (JP)
MORIIZUMI YASUHIRO (JP)
MAKABE SO (JP)
KOBASHI YUICHI (JP)
MORIIZUMI YASUHIRO (JP)
Application Number:
PCT/JP2022/033375
Publication Date:
March 16, 2023
Filing Date:
September 06, 2022
Export Citation:
Assignee:
UNIV CHIBA NAT UNIV CORP (JP)
BEX CO LTD (JP)
BEX CO LTD (JP)
International Classes:
C12N15/09; C07K19/00; C12N15/11; C12N15/12; C12N15/55; C12N15/62
Domestic Patent References:
| WO2019217942A1 | 2019-11-14 | |||
| WO2013058404A1 | 2013-04-25 | |||
| WO2020045281A1 | 2020-03-05 |
Foreign References:
| JP2020510038A | 2020-04-02 | |||
| JP4968498B2 | 2012-07-04 | |||
| JP2013513389A | 2013-04-22 | |||
| JP2015527889A | 2015-09-24 | |||
| JP2016500262A | 2016-01-12 | |||
| JP2016501531A | 2016-01-21 | |||
| JP2016501532A | 2016-01-21 | |||
| JP5266210B2 | 2013-08-21 |
Other References:
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L. LOWDER ET AL.: "Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act 2.0 and mTALE-Act Systems", MOLECULAR PLANT, vol. 11, 2018, pages 245 - 256, XP055577314, DOI: 10.1016/j.molp.2017.11.010
M. BOETTCHER ET AL.: "Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR", MOLECULAR CELL, vol. 58, no. 4, 2015, pages 575 - 85, XP029129109, DOI: 10.1016/j.molcel.2015.04.028
L. LOWDER ET AL.: "A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation", PLANT PHYSIOLOGY, vol. 169, no. 2, 2015, pages 971 - 85, XP055548389, DOI: 10.1104/pp.15.00636
MARINA ET AL.: "Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing", CELL REPORTS, vol. 33, 3 November 2020 (2020-11-03), pages 108350, XP055898294, DOI: 10.1016/j.celrep.2020.108350
K. JENSEN ET AL.: "The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain", PNAS, vol. 97, no. 11, 2000, pages 5740 - 5745
WANG ET AL.: "Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription", NATURE, vol. 454, 3 July 2008 (2008-07-03)
N. SHIINAET ET AL.: "A Novel RNA-Binding Protein in Neuronal RNA Granules: Regulatory Machinery for Local Translation", THE JOURNAL OF NEUROSCIENCE, vol. 25, no. 17, 27 April 2005 (2005-04-27), pages 4420 - 4434
W. ZHANGET ET AL.: "RNA", vol. 8, 2002, CAMBRIDGE UNIVERSITY PRESS, article "Region-specific alternative splicing in the nervous system: Implications for regulation by the RNA-binding protein NAPOR", pages: 671 - 685
D. SHARMAL ET AL.: "The kinetic landscape of an RNA-binding protein in cells", NATURE, vol. 591, 4 March 2021 (2021-03-04)
P. BIELLI ET AL.: "The RNA-binding protein Sam68 is a multifunctional player in human cancer", ENDOCRINE-RELATED CANCER, vol. 18, 2011, pages R91 - R102
M. HALLIER ET AL.: "The Transcription Factor Spi-l/PU.1 Binds RNA and Interferes with the RNA-binding Protein p54nrb", THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 271, no. 19, 1996, pages 11177 - 11181
M. HAFNER ET AL.: "Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP", CELL, vol. 141, 2010, pages 129 - 141, XP055293783, DOI: 10.1016/j.cell.2010.03.009
T. SAKUMA ET AL.: "Repeating pattern of non-RVD variations in DNA-binding modules enhances TALEN activity", SCIENTIFIC REPORTS, vol. 3, 2013, XP055594242, DOI: 10.1038/srep03379
M. JINEK ET AL.: "A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity", SCIENCE, vol. 337, 2012, pages 816 - 821, XP055229606, DOI: 10.1126/science.1225829
S. MORITA ET AL.: "Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions", NATURE BIOTECHNOLOGY, vol. 34, 2016, pages 1060 - 1065, XP055459997, DOI: 10.1038/nbt.3658
C. LI ET AL.: "Expanded base editing in rice and wheat using a Cas9-adenosine deaminase fusion", GENOME BIOLOGY, vol. 19, 2018, XP055655088, DOI: 10.1186/s13059-018-1443-z
A. KOMOR ET AL.: "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage", NATURE, vol. 533, 2016, pages 420 - 424, XP093078921, DOI: 10.1038/nature17946
L. LOWDER ET AL.: "Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act 2.0 and mTALE-Act Systems", MOLECULAR PLANT, vol. 11, 2018, pages 245 - 256, XP055577314, DOI: 10.1016/j.molp.2017.11.010
M. BOETTCHER ET AL.: "Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR", MOLECULAR CELL, vol. 58, no. 4, 2015, pages 575 - 85, XP029129109, DOI: 10.1016/j.molcel.2015.04.028
L. LOWDER ET AL.: "A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation", PLANT PHYSIOLOGY, vol. 169, no. 2, 2015, pages 971 - 85, XP055548389, DOI: 10.1104/pp.15.00636
MARINA ET AL.: "Evaluation of Engineered CRISPR-Cas-Mediated Systems for Site-Specific RNA Editing", CELL REPORTS, vol. 33, 3 November 2020 (2020-11-03), pages 108350, XP055898294, DOI: 10.1016/j.celrep.2020.108350
K. JENSEN ET AL.: "The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain", PNAS, vol. 97, no. 11, 2000, pages 5740 - 5745
WANG ET AL.: "Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription", NATURE, vol. 454, 3 July 2008 (2008-07-03)
N. SHIINAET ET AL.: "A Novel RNA-Binding Protein in Neuronal RNA Granules: Regulatory Machinery for Local Translation", THE JOURNAL OF NEUROSCIENCE, vol. 25, no. 17, 27 April 2005 (2005-04-27), pages 4420 - 4434
W. ZHANGET ET AL.: "RNA", vol. 8, 2002, CAMBRIDGE UNIVERSITY PRESS, article "Region-specific alternative splicing in the nervous system: Implications for regulation by the RNA-binding protein NAPOR", pages: 671 - 685
D. SHARMAL ET AL.: "The kinetic landscape of an RNA-binding protein in cells", NATURE, vol. 591, 4 March 2021 (2021-03-04)
P. BIELLI ET AL.: "The RNA-binding protein Sam68 is a multifunctional player in human cancer", ENDOCRINE-RELATED CANCER, vol. 18, 2011, pages R91 - R102
M. HALLIER ET AL.: "The Transcription Factor Spi-l/PU.1 Binds RNA and Interferes with the RNA-binding Protein p54nrb", THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 271, no. 19, 1996, pages 11177 - 11181
M. HAFNER ET AL.: "Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP", CELL, vol. 141, 2010, pages 129 - 141, XP055293783, DOI: 10.1016/j.cell.2010.03.009
Attorney, Agent or Firm:
MATSUMOTO Seiji (JP)
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