Using CRISPR to understand and manipulate gene regulation

被引：14

作者：

Akinci, Ersin ^{[1
,2
,3
]}

Hamilton, Marisa C. ^{[1
,2
]}

Khowpinitchai, Benyapa ^{[1
,2
]}

Sherwood, Richard, I ^{[1
,2
,4
]}

机构：

[1] Brigham & Womens Hosp, Div Genet, Dept Med, Boston, MA 02115 USA

[2] Harvard Med Sch, Boston, MA 02115 USA

[3] Akdeniz Univ, Fac Agr, Dept Agr Biotechnol, TR-07070 Antalya, Turkey

[4] Hubrecht Inst, NL-3584 CT Utrecht, Netherlands

来源：

DEVELOPMENT | 2021年 / 148卷 / 09期

基金：

美国国家卫生研究院;

关键词：

CRISPR screening; CRISPR-Cas9; Disease modeling; Epigenetics; Gene regulation; PLURIPOTENT STEM-CELLS; TRANSCRIPTION FACTORS; COMPUTATIONAL FRAMEWORK; CELLULAR IDENTITY; CAS9; NUCLEASES; GENOMIC DNA; BETA-CELL; ENHANCER; CHROMATIN; IDENTIFICATION;

D O I：

10.1242/dev.182667

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Understanding how genes are expressed in the correct cell types and at the correct level is a key goal of developmental biology research. Gene regulation has traditionally been approached largely through observational methods, whereas perturbational approaches have lacked precision. CRISPR-Cas9 has begun to transform the study of gene regulation, allowing for precise manipulation of genomic sequences, epigenetic functionalization and gene expression. CRISPR-Cas9 technology has already led to the discovery of new paradigms in gene regulation and, as new CRISPR-based tools and methods continue to be developed, promises to transform our knowledge of the gene regulatory code and our ability to manipulate cell fate. Here, we discuss the current and future application of the emerging CRISPR toolbox toward predicting gene regulatory network behavior, improving stem cell disease modeling, dissecting the epigenetic code, reprogramming cell fate and treating diseases of gene dysregulation.

引用

页数：16

共 182 条

[91] Functional Classification and Experimental Dissection of Long Noncoding RNAs [J].

Kopp, Florian ;

Mendell, Joshua T. .

CELL, 2018, 172 (03) :393-407

[92] A CRISPR-Cas9 screen identifies essential CTCF anchor sites for estrogen receptor-driven breast cancer cell proliferation [J].

Korkmaz, Gozde ;

Manber, Zohar ;

Lopes, Rui ;

Prekovic, Stefan ;

Schuurman, Karianne ;

Kim, Yongsoo ;

Teunissen, Hans ;

Flach, Koen ;

de Wit, Elzo ;

Galli, Giorgio G. ;

Zwart, Wilbert ;

Elkon, Ran ;

Agami, Reuven .

NUCLEIC ACIDS RESEARCH, 2019, 47 (18) :9557-9572

[93] Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9 [J].

Korkmaz, Gozde ;

Lopes, Rui ;

Ugalde, Alejandro P. ;

Nevedomskaya, Ekaterina ;

Han, Ruiqi ;

Myacheva, Ksenia ;

Zwart, Wilbert ;

Elkon, Ran ;

Agami, Reuven .

NATURE BIOTECHNOLOGY, 2016, 34 (02) :192-+

[94] Integrative analysis of 111 reference human epigenomes [J].

Kundaje, Anshul ;

Meuleman, Wouter ;

Ernst, Jason ;

Bilenky, Misha ;

Yen, Angela ;

Heravi-Moussavi, Alireza ;

Kheradpour, Pouya ;

Zhang, Zhizhuo ;

Wang, Jianrong ;

Ziller, Michael J. ;

Amin, Viren ;

Whitaker, John W. ;

Schultz, Matthew D. ;

Ward, Lucas D. ;

Sarkar, Abhishek ;

Quon, Gerald ;

Sandstrom, Richard S. ;

Eaton, Matthew L. ;

Wu, Yi-Chieh ;

Pfenning, Andreas R. ;

Wang, Xinchen ;

Claussnitzer, Melina ;

Liu, Yaping ;

Coarfa, Cristian ;

Harris, R. Alan ;

Shoresh, Noam ;

Epstein, Charles B. ;

Gjoneska, Elizabeta ;

Leung, Danny ;

Xie, Wei ;

Hawkins, R. David ;

Lister, Ryan ;

Hong, Chibo ;

Gascard, Philippe ;

Mungall, Andrew J. ;

Moore, Richard ;

Chuah, Eric ;

Tam, Angela ;

Canfield, Theresa K. ;

Hansen, R. Scott ;

Kaul, Rajinder ;

Sabo, Peter J. ;

Bansal, Mukul S. ;

Carles, Annaick ;

Dixon, Jesse R. ;

Farh, Kai-How ;

Feizi, Soheil ;

Karlic, Rosa ;

Kim, Ah-Ram ;

Kulkarni, Ashwinikumar .

NATURE, 2015, 518 (7539) :317-330

[95] The Human Transcription Factors [J].

Lambert, Samuel A. ;

Jolma, Arttu ;

Campitelli, Laura F. ;

Das, Pratyush K. ;

Yin, Yimeng ;

Albu, Mihai ;

Chen, Xiaoting ;

Taipale, Jussi ;

Hughes, Timothy R. ;

Weirauch, Matthew T. .

CELL, 2018, 172 (04) :650-665

[96] Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility [J].

Lareau, Caleb A. ;

Duarte, Fabiana M. ;

Chew, Jennifer G. ;

Kartha, Vinay K. ;

Burkett, Zach D. ;

Kohlway, Andrew S. ;

Pokholok, Dmitry ;

Aryee, Martin J. ;

Steemers, Frank J. ;

Lebofsky, Ronald ;

Buenrostro, Jason D. .

NATURE BIOTECHNOLOGY, 2019, 37 (08) :916-+

[97] Genome-wide CRISPR-KO Screen Uncovers mTORC1-Mediated Gsk3 Regulation in Naive Pluripotency Maintenance and Dissolution [J].

Li, Meng ;

Yu, Jason S. L. ;

Tilgner, Katarzyna ;

Ong, Swee Hoe ;

Koike-Yusa, Hiroko ;

Yusa, Kosuke .

CELL REPORTS, 2018, 24 (02) :489-502

[98] Genome-scale screens identify JNK-JUN signaling as a barrier for pluripotency exit and endoderm differentiation [J].

Li, Qing V. ;

Dixon, Gary ;

Verma, Nipun ;

Rosen, Bess P. ;

Gordillo, Miriam ;

Luo, Renhe ;

Xu, Chunlong ;

Wang, Qiong ;

Soh, Chew-Li ;

Yang, Dapeng ;

Crespo, Miguel ;

Shukla, Abhijit ;

Xiang, Qing ;

Dundar, Friederike ;

Zumbo, Paul ;

Witkin, Matthew ;

Koche, Richard ;

Betel, Doron ;

Chen, Shuibing ;

Massague, Joan ;

Garippa, Ralph ;

Evans, Todd ;

Beer, Michael A. ;

Huangfu, Danwei .

NATURE GENETICS, 2019, 51 (06) :999-+

[99] MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens [J].

Li, Wei ;

Xu, Han ;

Xiao, Tengfei ;

Cong, Le ;

Love, Michael I. ;

Zhang, Feng ;

Irizarry, Rafael A. ;

Liu, Jun S. ;

Brown, Myles ;

Liu, X. Shirley .

GENOME BIOLOGY, 2014, 15 (12) :554

[100] CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming [J].

Liu, Yanxia ;

Yu, Chen ;

Daley, Timothy Patrick ;

Wang, Fangyuan ;

Cao, William S. ;

Bhate, Salil ;

Lin, Xueqiu ;

Still, Chris, II ;

Liu, Honglei ;

Zhao, Dehua ;

Wang, Haifeng ;

Xie, Xinmin S. ;

Ding, Sheng ;

Wong, Wing Hung ;

Wernig, Marius ;

Qi, Lei S. .

CELL STEM CELL, 2018, 23 (05) :758-+

← 5 6 7 8 9 10 11 12 13 14 →