Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

被引：313

作者：

Korkmaz, Gozde ^{[1
]}

Lopes, Rui ^{[1
]}

Ugalde, Alejandro P. ^{[1
]}

Nevedomskaya, Ekaterina ^{[2
]}

Han, Ruiqi ^{[1
]}

Myacheva, Ksenia ^{[1
]}

Zwart, Wilbert ^{[2
]}

Elkon, Ran ^{[1
]}

Agami, Reuven ^{[1
,3
]}

机构：

[1] Netherlands Canc Inst, Div Biol Stress Response, Amsterdam, Netherlands

[2] Netherlands Canc Inst, Div Mol Pathol, Amsterdam, Netherlands

[3] Rotterdam Univ, Erasmus MC, Rotterdam, Netherlands

来源：

NATURE BIOTECHNOLOGY | 2016年 / 34卷 / 02期

关键词：

HUMAN-CELLS; BREAST-CANCER; P53; TRANSCRIPTION; MECHANISMS; ALIGNMENT; THERAPY; BINDING; CAS9; RNAS;

D O I：

10.1038/nbt.3450

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Systematic identification of noncoding regulatory elements has, to date, mainly relied on large-scale reporter assays that do not reproduce endogenous conditions. We present two distinct CRISPR-Cas9 genetic screens to identify and characterize functional enhancers in their native context. Our strategy is to target Cas9 to transcription factor binding sites in enhancer regions. We identified several functional enhancer elements and characterized the role of two of them in mediating p53 (TP53) and ERa (ESR1) gene regulation. Moreover, we show that a genomic CRISPR-Cas9 tiling screen can precisely map functional domains within enhancer elements. Our approach expands the utility of CRISPR-Cas9 to elucidate the functions of the noncoding genome

引用

页码：192 / +

页数：10

共 38 条

[1] Distinct initiation and maintenance mechanisms cooperate to induce G1 cell cycle arrest in response to DNA damage [J].

Agami, R ;

Bernards, R .

CELL, 2000, 102 (01) :55-66

[2] HTSeq-a Python']Python framework to work with high-throughput sequencing data [J].

Anders, Simon ;

Pyl, Paul Theodor ;

Huber, Wolfgang .

BIOINFORMATICS, 2015, 31 (02) :166-169

[3] Cyclin D1 in breast cancer pathogenesis [J].

Arnold, A ;

Papanikolaou, A .

JOURNAL OF CLINICAL ONCOLOGY, 2005, 23 (18) :4215-4224

[4] Can predictive biomarkers in breast cancer guide adjuvant endocrine therapy? [J].

Beelen, Karin ;

Zwart, Wilbert ;

Linn, Sabine C. .

NATURE REVIEWS CLINICAL ONCOLOGY, 2012, 9 (09) :529-541

[5] Distinct p53 genomic binding patterns in normal and cancer-derived human cells [J].

Botcheva, Krassimira ;

McCorkle, Sean R. ;

McCombie, W. R. ;

Dunn, John J. ;

Anderson, Carl W. .

CELL CYCLE, 2011, 10 (24) :4237-4249

[6] BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis [J].

Canver, Matthew C. ;

Smith, Elenoe C. ;

Sher, Falak ;

Pinello, Luca ;

Sanjana, Neville E. ;

Shalem, Ophir ;

Chen, Diane D. ;

Schupp, Patrick G. ;

Vinjamur, Divya S. ;

Garcia, Sara P. ;

Luc, Sidinh ;

Kurita, Ryo ;

Nakamura, Yukio ;

Fujiwara, Yuko ;

Maeda, Takahiro ;

Yuan, Guo-Cheng ;

Zhang, Feng ;

Orkin, Stuart H. ;

Bauer, Daniel E. .

NATURE, 2015, 527 (7577) :192-+

[7] Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease [J].

Cho, Seung Woo ;

Kim, Sojung ;

Kim, Jong Min ;

Kim, Jin-Soo .

NATURE BIOTECHNOLOGY, 2013, 31 (03) :230-232

[8] Ensembl 2015 [J].

Cunningham, Fiona ;

Amode, M. Ridwan ;

Barrell, Daniel ;

Beal, Kathryn ;

Billis, Konstantinos ;

Brent, Simon ;

Carvalho-Silva, Denise ;

Clapham, Peter ;

Coates, Guy ;

Fitzgerald, Stephen ;

Gil, Laurent ;

Giron, Carlos Garcia ;

Gordon, Leo ;

Hourlier, Thibaut ;

Hunt, Sarah E. ;

Janacek, Sophie H. ;

Johnson, Nathan ;

Juettemann, Thomas ;

Kaehaeri, Andreas K. ;

Keenan, Stephen ;

Martin, Fergal J. ;

Maurel, Thomas ;

McLaren, William ;

Murphy, Daniel N. ;

Nag, Rishi ;

Overduin, Bert ;

Parker, Anne ;

Patricio, Mateus ;

Perry, Emily ;

Pignatelli, Miguel ;

Riat, Harpreet Singh ;

Sheppard, Daniel ;

Taylor, Kieron ;

Thormann, Anja ;

Vullo, Alessandro ;

Wilder, Steven P. ;

Zadissa, Amonida ;

Aken, Bronwen L. ;

Birney, Ewan ;

Harrow, Jennifer ;

Kinsella, Rhoda ;

Muffato, Matthieu ;

Ruffier, Magali ;

Searle, Stephen M. J. ;

Spudich, Giulietta ;

Trevanion, Stephen J. ;

Yates, Andy ;

Zerbino, Daniel R. ;

Flicek, Paul .

NUCLEIC ACIDS RESEARCH, 2015, 43 (D1) :D662-D669

[9] BRD7 is a candidate tumour suppressor gene required for p53 function [J].

Drost, Jarno ;

Mantovani, Fiamma ;

Tocco, Francesca ;

Elkon, Ran ;

Comel, Anna ;

Holstege, Henne ;

Kerkhoven, Ron ;

Jonkers, Jos ;

Voorhoeve, P. Mathijs ;

Agami, Reuven ;

Del Sal, Giannino .

NATURE CELL BIOLOGY, 2010, 12 (04) :380-U189

[10] WAF1, A POTENTIAL MEDIATOR OF P53 TUMOR SUPPRESSION [J].

ELDEIRY, WS ;

TOKINO, T ;

VELCULESCU, VE ;

LEVY, DB ;

PARSONS, R ;

TRENT, JM ;

LIN, D ;

MERCER, WE ;

KINZLER, KW ;

VOGELSTEIN, B .

CELL, 1993, 75 (04) :817-825

← 1 2 3 4 →