Literature DB >> 30323312

Base editing: precision chemistry on the genome and transcriptome of living cells.

Holly A Rees1,2,3, David R Liu4,5,6.   

Abstract

RNA-guided programmable nucleases from CRISPR systems generate precise breaks in DNA or RNA at specified positions. In cells, this activity can lead to changes in DNA sequence or RNA transcript abundance. Base editing is a newer genome-editing approach that uses components from CRISPR systems together with other enzymes to directly install point mutations into cellular DNA or RNA without making double-stranded DNA breaks. DNA base editors comprise a catalytically disabled nuclease fused to a nucleobase deaminase enzyme and, in some cases, a DNA glycosylase inhibitor. RNA base editors achieve analogous changes using components that target RNA. Base editors directly convert one base or base pair into another, enabling the efficient installation of point mutations in non-dividing cells without generating excess undesired editing by-products. In this Review, we summarize base-editing strategies to generate specific and precise point mutations in genomic DNA and RNA, highlight recent developments that expand the scope, specificity, precision and in vivo delivery of base editors and discuss limitations and future directions of base editing for research and therapeutic applications.

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Year:  2018        PMID: 30323312      PMCID: PMC6535181          DOI: 10.1038/s41576-018-0059-1

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  159 in total

Review 1.  Regulation of ion channel/neurotransmitter receptor function by RNA editing.

Authors:  Peter H Seeburg; Jochen Hartner
Journal:  Curr Opin Neurobiol       Date:  2003-06       Impact factor: 6.627

2.  CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations.

Authors:  Cem Kuscu; Mahmut Parlak; Turan Tufan; Jiekun Yang; Karol Szlachta; Xiaolong Wei; Rashad Mammadov; Mazhar Adli
Journal:  Nat Methods       Date:  2017-06-05       Impact factor: 28.547

3.  Knockout mice created by TALEN-mediated gene targeting.

Authors:  Young Hoon Sung; In-Jeoung Baek; Duk Hyoung Kim; Jisun Jeon; Jaehoon Lee; Kyunghee Lee; Daewon Jeong; Jin-Soo Kim; Han-Woong Lee
Journal:  Nat Biotechnol       Date:  2013-01       Impact factor: 54.908

Review 4.  Site-directed RNA editing with antagomir deaminases--a tool to study protein and RNA function.

Authors:  Paul Vogel; Thorsten Stafforst
Journal:  ChemMedChem       Date:  2014-06-20       Impact factor: 3.466

Review 5.  Functions and regulation of RNA editing by ADAR deaminases.

Authors:  Kazuko Nishikura
Journal:  Annu Rev Biochem       Date:  2010       Impact factor: 23.643

6.  Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells.

Authors:  Yunqing Ma; Jiayuan Zhang; Weijie Yin; Zhenchao Zhang; Yan Song; Xing Chang
Journal:  Nat Methods       Date:  2016-10-10       Impact factor: 28.547

7.  Efficient introduction of specific homozygous and heterozygous mutations using CRISPR/Cas9.

Authors:  Dominik Paquet; Dylan Kwart; Antonia Chen; Andrew Sproul; Samson Jacob; Shaun Teo; Kimberly Moore Olsen; Andrew Gregg; Scott Noggle; Marc Tessier-Lavigne
Journal:  Nature       Date:  2016-04-27       Impact factor: 49.962

8.  A-to-I editing in the miRNA seed region regulates target mRNA selection and silencing efficiency.

Authors:  Hideaki Kume; Kimihiro Hino; Josephine Galipon; Kumiko Ui-Tei
Journal:  Nucleic Acids Res       Date:  2014-07-23       Impact factor: 16.971

9.  Internal modification of U2 small nuclear (sn)RNA occurs in nucleoli of Xenopus oocytes.

Authors:  Y T Yu; M D Shu; A Narayanan; R M Terns; M P Terns; J A Steitz
Journal:  J Cell Biol       Date:  2001-03-19       Impact factor: 10.539

10.  In vivo base editing of post-mitotic sensory cells.

Authors:  Wei-Hsi Yeh; Hao Chiang; Holly A Rees; Albert S B Edge; David R Liu
Journal:  Nat Commun       Date:  2018-06-05       Impact factor: 14.919

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  363 in total

1.  Precise, predictable multi-nucleotide deletions in rice and wheat using APOBEC-Cas9.

Authors:  Shengxing Wang; Yuan Zong; Qiupeng Lin; Huawei Zhang; Zhuangzhuang Chai; Dandan Zhang; Kunling Chen; Jin-Long Qiu; Caixia Gao
Journal:  Nat Biotechnol       Date:  2020-06-29       Impact factor: 54.908

2.  BEAT: A Python Program to Quantify Base Editing from Sanger Sequencing.

Authors:  Li Xu; Yakun Liu; Renzhi Han
Journal:  CRISPR J       Date:  2019-07-18

3.  Real-time observation of Cas9 postcatalytic domain motions.

Authors:  Yanbo Wang; John Mallon; Haobo Wang; Digvijay Singh; Myung Hyun Jo; Boyang Hua; Scott Bailey; Taekjip Ha
Journal:  Proc Natl Acad Sci U S A       Date:  2020-12-21       Impact factor: 11.205

4.  Sequence-specific prediction of the efficiencies of adenine and cytosine base editors.

Authors:  Myungjae Song; Hui Kwon Kim; Sungtae Lee; Younggwang Kim; Sang-Yeon Seo; Jinman Park; Jae Woo Choi; Hyewon Jang; Jeong Hong Shin; Seonwoo Min; Zhejiu Quan; Ji Hun Kim; Hoon Chul Kang; Sungroh Yoon; Hyongbum Henry Kim
Journal:  Nat Biotechnol       Date:  2020-07-06       Impact factor: 54.908

5.  Development and Characterization of a Modular CRISPR and RNA Aptamer Mediated Base Editing System.

Authors:  Juan Carlos Collantes; Victor M Tan; Huiting Xu; Melany Ruiz-Urigüen; Amer Alasadi; Jingjing Guo; Hanlin Tao; Chi Su; Katarzyna M Tyc; Tommaso Selmi; John J Lambourne; Jennifer A Harbottle; Jesse Stombaugh; Jinchuan Xing; Ceri M Wiggins; Shengkan Jin
Journal:  CRISPR J       Date:  2021-02

Review 6.  Gene therapy using haematopoietic stem and progenitor cells.

Authors:  Giuliana Ferrari; Adrian J Thrasher; Alessandro Aiuti
Journal:  Nat Rev Genet       Date:  2020-12-10       Impact factor: 53.242

7.  Discrimination of single-point mutations in unamplified genomic DNA via Cas9 immobilized on a graphene field-effect transistor.

Authors:  Sarah Balderston; Jeffrey J Taulbee; Elizabeth Celaya; Kandace Fung; Amanda Jiao; Kasey Smith; Reza Hajian; Giedrius Gasiunas; Simonas Kutanovas; Daehwan Kim; Jonathan Parkinson; Kenneth Dickerson; Juan-José Ripoll; Regis Peytavi; Hsiang-Wei Lu; Francie Barron; Brett R Goldsmith; Philip G Collins; Irina M Conboy; Virginijus Siksnys; Kiana Aran
Journal:  Nat Biomed Eng       Date:  2021-04-05       Impact factor: 25.671

Review 8.  Precision Control of CRISPR-Cas9 Using Small Molecules and Light.

Authors:  Soumyashree A Gangopadhyay; Kurt J Cox; Debasish Manna; Donghyun Lim; Basudeb Maji; Qingxuan Zhou; Amit Choudhary
Journal:  Biochemistry       Date:  2019-01-22       Impact factor: 3.162

9.  In vivo HSPC gene therapy with base editors allows for efficient reactivation of fetal γ-globin in β-YAC mice.

Authors:  Chang Li; Aphrodite Georgakopoulou; Arpit Mishra; Sucheol Gil; R David Hawkins; Evangelia Yannaki; André Lieber
Journal:  Blood Adv       Date:  2021-02-23

Review 10.  CRISPR-Based Therapeutic Genome Editing: Strategies and In Vivo Delivery by AAV Vectors.

Authors:  Dan Wang; Feng Zhang; Guangping Gao
Journal:  Cell       Date:  2020-04-02       Impact factor: 41.582

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