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Literature DB >> 29553573

Base editing with a Cpf1-cytidine deaminase fusion.

Xiaosa Li^1,2,3, Ying Wang⁴, Yajing Liu^1,2,3, Bei Yang⁵, Xiao Wang^1,2,3, Jia Wei⁴, Zongyang Lu^1,2,3, Yuxi Zhang¹, Jing Wu¹, Xingxu Huang¹, Li Yang⁴, Jia Chen¹.

Abstract

The targeting range of CRISPR-Cas9 base editors (BEs) is limited by their G/C-rich protospacer-adjacent motif (PAM) sequences. To overcome this limitation, we developed a CRISPR-Cpf1-based BE by fusing the rat cytosine deaminase APOBEC1 to a catalytically inactive version of Lachnospiraceae bacterium Cpf1. The base editor recognizes a T-rich PAM sequence and catalyzes C-to-T conversion in human cells, while inducing low levels of indels, non-C-to-T substitutions and off-target editing.

Entities: Gene Species

Mesh：

Substances：

Year: 2018 PMID： 29553573 DOI： 10.1038/nbt.4102

Source DB: PubMed Journal: Nat Biotechnol ISSN： 1087-0156 Impact factor: 54.908

23 in total

1. Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.

Authors: Daan C Swarts; John van der Oost; Martin Jinek
Journal: Mol Cell Date: 2017-04-20 Impact factor: 17.970

2. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion.

Authors: Yuan Zong; Yanpeng Wang; Chao Li; Rui Zhang; Kunling Chen; Yidong Ran; Jin-Long Qiu; Daowen Wang; Caixia Gao
Journal: Nat Biotechnol Date: 2017-02-27 Impact factor: 54.908

3. Highly efficient RNA-guided base editing in mouse embryos.

Authors: Kyoungmi Kim; Seuk-Min Ryu; Sang-Tae Kim; Gayoung Baek; Daesik Kim; Kayeong Lim; Eugene Chung; Sunghyun Kim; Jin-Soo Kim
Journal: Nat Biotechnol Date: 2017-02-27 Impact factor: 54.908

4. In vivo high-throughput profiling of CRISPR-Cpf1 activity.

Authors: Hui K Kim; Myungjae Song; Jinu Lee; A Vipin Menon; Soobin Jung; Young-Mook Kang; Jae W Choi; Euijeon Woo; Hyun C Koh; Jin-Wu Nam; Hyongbum Kim
Journal: Nat Methods Date: 2016-12-19 Impact factor: 28.547

5. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems.

Authors: Keiji Nishida; Takayuki Arazoe; Nozomu Yachie; Satomi Banno; Mika Kakimoto; Mayura Tabata; Masao Mochizuki; Aya Miyabe; Michihiro Araki; Kiyotaka Y Hara; Zenpei Shimatani; Akihiko Kondo
Journal: Science Date: 2016-08-04 Impact factor: 47.728

6. Engineered CRISPR-Cas9 nucleases with altered PAM specificities.

Authors: Benjamin P Kleinstiver; Michelle S Prew; Shengdar Q Tsai; Ved V Topkar; Nhu T Nguyen; Zongli Zheng; Andrew P W Gonzales; Zhuyun Li; Randall T Peterson; Jing-Ruey Joanna Yeh; Martin J Aryee; J Keith Joung
Journal: Nature Date: 2015-06-22 Impact factor: 49.962

7. Repair of naturally occurring mismatches can induce mutations in flanking DNA.

Authors: Jia Chen; Brendan F Miller; Anthony V Furano
Journal: Elife Date: 2014-04-29 Impact factor: 8.140

8. BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks.

Authors: Winston X Yan; Reza Mirzazadeh; Silvano Garnerone; David Scott; Martin W Schneider; Tomasz Kallas; Joaquin Custodio; Erik Wernersson; Yinqing Li; Linyi Gao; Yana Federova; Bernd Zetsche; Feng Zhang; Magda Bienko; Nicola Crosetto
Journal: Nat Commun Date: 2017-05-12 Impact factor: 14.919

9. Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor.

Authors: Lijie Wang; Wei Xue; Lei Yan; Xiaosa Li; Jia Wei; Miaomiao Chen; Jing Wu; Bei Yang; Li Yang; Jia Chen
Journal: Cell Res Date: 2017-08-29 Impact factor: 25.617

10. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions.

Authors: Y Bill Kim; Alexis C Komor; Jonathan M Levy; Michael S Packer; Kevin T Zhao; David R Liu
Journal: Nat Biotechnol Date: 2017-02-13 Impact factor: 54.908

115 in total

Review 1. Single-nucleotide editing: From principle, optimization to application.

Authors: Jinling Tang; Trevor Lee; Tao Sun
Journal: Hum Mutat Date: 2019-09-15 Impact factor: 4.878

2. Genome, Epigenome, and Transcriptome Editing via Chemical Modification of Nucleobases in Living Cells.

Authors: Brodie L Ranzau; Alexis C Komor
Journal: Biochemistry Date: 2018-12-12 Impact factor: 3.162

3. CRISPR-Cas9 and CRISPR-Assisted Cytidine Deaminase Enable Precise and Efficient Genome Editing in Klebsiella pneumoniae.

Authors: Yu Wang; Shanshan Wang; Weizhong Chen; Liqiang Song; Yifei Zhang; Zhen Shen; Fangyou Yu; Min Li; Quanjiang Ji
Journal: Appl Environ Microbiol Date: 2018-11-15 Impact factor: 4.792

Base editing with a Cpf1-cytidine deaminase fusion.

1. Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.

2. Precise base editing in rice, wheat and maize with a Cas9-cytidine deaminase fusion.

3. Highly efficient RNA-guided base editing in mouse embryos.

4. In vivo high-throughput profiling of CRISPR-Cpf1 activity.

5. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems.

6. Engineered CRISPR-Cas9 nucleases with altered PAM specificities.

7. Repair of naturally occurring mismatches can induce mutations in flanking DNA.

8. BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks.

9. Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor.

10. Increasing the genome-targeting scope and precision of base editing with engineered Cas9-cytidine deaminase fusions.

Review 1. Single-nucleotide editing: From principle, optimization to application.

2. Genome, Epigenome, and Transcriptome Editing via Chemical Modification of Nucleobases in Living Cells.

3. CRISPR-Cas9 and CRISPR-Assisted Cytidine Deaminase Enable Precise and Efficient Genome Editing in Klebsiella pneumoniae.

Review 4. Genome Editing with mRNA Encoding ZFN, TALEN, and Cas9.

5. Identifying genome-wide off-target sites of CRISPR RNA-guided nucleases and deaminases with Digenome-seq.

Review 6. Dissecting Tissue-Specific Super-Enhancers by Integrating Genome-Wide Analyses and CRISPR/Cas9 Genome Editing.

7. The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays.

Review 8. Gene therapy for neurological disorders: progress and prospects.

9. Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion.

10. Detect-seq reveals out-of-protospacer editing and target-strand editing by cytosine base editors.