High-throughput functional genomics using CRISPR-Cas9

被引：872

作者：

Shalem, Ophir ^{[1
]}

Sanjana, Neville E.

Zhang, Feng

机构：

[1] Broad Inst MIT & Harvard, Cambridge Ctr 7, Cambridge, MA 02142 USA

来源：

NATURE REVIEWS GENETICS | 2015年 / 16卷 / 05期

基金：

美国国家卫生研究院; 美国国家科学基金会;

关键词：

SEQUENCE-SPECIFIC CONTROL; LENTIVIRAL RNAI LIBRARY; CANCER GENE DISCOVERY; DOUBLE-STRANDED-RNA; HUMAN-CELLS; IN-VIVO; SHRNA LIBRARIES; TARGET DNA; CAENORHABDITIS-ELEGANS; NUCLEASE SPECIFICITY;

D O I：

10.1038/nrg3899

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Forward genetic screens are powerful tools for the discovery and functional annotation of genetic elements. Recently, the RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas9 nuclease has been combined with genome-scale guide RNA libraries for unbiased, phenotypic screening. In this Review, we describe recent advances using Cas9 for genome-scale screens, including knockout approaches that inactivate genomic loci and strategies that modulate transcriptional activity. We discuss practical aspects of screen design, provide comparisons with RNA interference (RNAi) screening, and outline future applications and challenges.

引用

页码：299 / 311

页数：13

共 127 条

[1] Microhomology-based choice of Cas9 nuclease target sites [J].

Bae, Sangsu ;

Kweon, Jiyeon ;

Kim, Heon Seok ;

Kim, Jin-Soo .

NATURE METHODS, 2014, 11 (07) :705-706

[2] MicroRNAs: Genomics, biogenesis, mechanism, and function (Reprinted from Cell, vol 116, pg 281-297, 2004) [J].

Bartel, David P. .

CELL, 2007, 131 (04) :11-29

[3] A Systematic Mammalian Genetic Interaction Map Reveals Pathways Underlying Ricin Susceptibility [J].

Bassik, Michael C. ;

Kampmann, Martin ;

Lebbink, Robert Jan ;

Wang, Shuyi ;

Hein, Marco Y. ;

Poser, Ina ;

Weibezahn, Jimena ;

Horlbeck, Max A. ;

Chen, Siyuan ;

Mann, Matthias ;

Hyman, Anthony A. ;

LeProust, Emily M. ;

McManus, Michael T. ;

Weissman, Jonathan S. .

CELL, 2013, 152 (04) :909-922

[4]

Bassik MC, 2009, NAT METHODS, V6, P443, DOI [10.1038/NMETH.1330, 10.1038/nmeth.1330]

[5] A large-scale RNAi screen in human cells identifies new components of the p53 pathway [J].

Berns, K ;

Hijmans, EM ;

Mullenders, J ;

Brummelkamp, TR ;

Velds, A ;

Heimerikx, M ;

Kerkhoven, RM ;

Madiredjo, M ;

Nijkamp, W ;

Weigelt, B ;

Agami, R ;

Ge, W ;

Cavet, G ;

Linsley, PS ;

Beijersbergen, RL ;

Bernards, R .

NATURE, 2004, 428 (6981) :431-437

[6] RNAi screens in mice identify physiological regulators of oncogenic growth [J].

Beronja, Slobodan ;

Janki, Peter ;

Heller, Evan ;

Lien, Wen-Hui ;

Keyes, Brice E. ;

Oshimori, Naoki ;

Fuchs, Elaine .

NATURE, 2013, 501 (7466) :185-+

[7] Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system [J].

Bikard, David ;

Jiang, Wenyan ;

Samai, Poulami ;

Hochschild, Ann ;

Zhang, Feng ;

Marraffini, Luciano A. .

NUCLEIC ACIDS RESEARCH, 2013, 41 (15) :7429-7437

[8] 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets [J].

Birmingham, A ;

Anderson, EM ;

Reynolds, A ;

Ilsley-Tyree, D ;

Leake, D ;

Fedorov, Y ;

Baskerville, S ;

Maksimova, E ;

Robinson, K ;

Karpilow, J ;

Marshall, WS ;

Khvorova, A .

NATURE METHODS, 2006, 3 (03) :199-204

[9] Statistical methods for analysis of high-throughput RNA interference screens [J].

Birmingham, Amanda ;

Selfors, Laura M. ;

Forster, Thorsten ;

Wrobel, David ;

Kennedy, Caleb J. ;

Shanks, Emma ;

Santoyo-Lopez, Javier ;

Dunican, Dara J. ;

Long, Aideen ;

Kelleher, Dermot ;

Smith, Queta ;

Beijersbergen, Roderick L. ;

Ghazal, Peter ;

Shamu, Caroline E. .

NATURE METHODS, 2009, 6 (08) :569-575

[10] Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin [J].

Bolotin, A ;

Ouinquis, B ;

Sorokin, A ;

Ehrlich, SD .

MICROBIOLOGY-SGM, 2005, 151 :2551-2561

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