High-resolution interrogation of functional elements in the noncoding genome

被引：209

作者：

Sanjana, Neville E. ^{[1
,2
,4
,5
]}

Wright, Jason ^{[1
,2
,4
,5
]}

Zheng, Kaijie ^{[1
,2
]}

Shalem, Ophir ^{[1
,2
]}

Fontanillas, Pierre ^{[1
]}

Joung, Julia ^{[1
,2
]}

Cheng, Christine ^{[1
,3
]}

Regev, Aviv ^{[1
,3
]}

Zhang, Feng ^{[1
,2
]}

机构：

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

[2] MIT, Dept Biol Engn, Dept Brain & Cognit Sci, McGovern Inst Brain Res, Cambridge, MA 02139 USA

[3] MIT, Dept Biol, Howard Hughes Med Inst, David H Koch Inst Integrat Canc Biol, 77 Massachusetts Ave, Cambridge, MA 02142 USA

[4] NYU, New York Genome Ctr, 550 1St Ave, New York, NY 10012 USA

[5] NYU, Dept Biol, 550 1St Ave, New York, NY 10012 USA

来源：

SCIENCE | 2016年 / 353卷 / 6307期

关键词：

TRANSCRIPTION FACTOR-BINDING; DISSECTION; ENHANCERS; CHROMATIN; SITES; MODEL;

D O I：

10.1126/science.aaf7613

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The noncoding genome affects gene regulation and disease, yet we lack tools for rapid identification and manipulation of noncoding elements. We developed a CRISPR screen using similar to 18,000 single guide RNAs targeting >700 kilobases surrounding the genes NF1, NF2, and CUL3, which are involved in BRAF inhibitor resistance in melanoma. We find that noncoding locations that modulate drug resistance also harbor predictive hallmarks of noncoding function. With a subset of regions at the CUL3 locus, we demonstrate that engineered mutations alter transcription factor occupancy and long-range and local epigenetic environments, implicating these sites in gene regulation and chemotherapeutic resistance. Through our expansion of the potential of pooled CRISPR screens, we provide tools for genomic discovery and for elucidating biologically relevant mechanisms of gene regulation.

引用

页码：1545 / 1549

页数：6

共 25 条

[1] Genomic Classification of Cutaneous Melanoma [J].

Akbani, Rehan ;

Akdemir, Kadir C. ;

Aksoy, B. Arman ;

Albert, Monique ;

Ally, Adrian ;

Amin, Samirkumar B. ;

Arachchi, Harindra ;

Arora, Arshi ;

Auman, J. Todd ;

Ayala, Brenda ;

Baboud, Julien ;

Balasundaram, Miruna ;

Balu, Saianand ;

Barnabas, Nandita ;

Bartlett, John ;

Bartlett, Pam ;

Bastian, Boris C. ;

Baylin, Stephen B. ;

Behera, Madhusmita ;

Belyaev, Dmitry ;

Benz, Christopher ;

Bernard, Brady ;

Beroukhim, Rameen ;

Bir, Natalie ;

Black, Aaron D. ;

Bodenheimer, Tom ;

Boice, Lori ;

Boland, Genevieve M. ;

Bono, Riccardo ;

Bootwalla, Moiz S. ;

Bosenberg, Marcus ;

Bowen, Jay ;

Bowlby, Reanne ;

Bristow, Christopher A. ;

Brockway-Lunardi, Laura ;

Brooks, Denise ;

Brzezinski, Jakub ;

Bshara, Wiam ;

Buda, Elizabeth ;

Burns, William R. ;

Butterfield, Yaron S. N. ;

Button, Michael ;

Calderone, Tiffany ;

Cappellini, Giancarlo Antonini ;

Carter, Candace ;

Carter, Scott L. ;

Cherney, Lynn ;

Cherniack, Andrew D. ;

Chevalier, Aaron ;

Chin, Lynda .

CELL, 2015, 161 (07) :1681-1696

[2] The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans [J].

Ardlie, Kristin G. ;

DeLuca, David S. ;

Segre, Ayellet V. ;

Sullivan, Timothy J. ;

Young, Taylor R. ;

Gelfand, Ellen T. ;

Trowbridge, Casandra A. ;

Maller, Julian B. ;

Tukiainen, Taru ;

Lek, Monkol ;

Ward, Lucas D. ;

Kheradpour, Pouya ;

Iriarte, Benjamin ;

Meng, Yan ;

Palmer, Cameron D. ;

Esko, Tonu ;

Winckler, Wendy ;

Hirschhorn, Joel N. ;

Kellis, Manolis ;

MacArthur, Daniel G. ;

Getz, Gad ;

Shabalin, Andrey A. ;

Li, Gen ;

Zhou, Yi-Hui ;

Nobel, Andrew B. ;

Rusyn, Ivan ;

Wright, Fred A. ;

Lappalainen, Tuuli ;

Ferreira, Pedro G. ;

Ongen, Halit ;

Rivas, Manuel A. ;

Battle, Alexis ;

Mostafavi, Sara ;

Monlong, Jean ;

Sammeth, Michael ;

Mele, Marta ;

Reverter, Ferran ;

Goldmann, Jakob M. ;

Koller, Daphne ;

Guigo, Roderic ;

McCarthy, Mark I. ;

Dermitzakis, Emmanouil T. ;

Gamazon, Eric R. ;

Im, Hae Kyung ;

Konkashbaev, Anuar ;

Nicolae, Dan L. ;

Cox, Nancy J. ;

Flutre, Timothee ;

Wen, Xiaoquan ;

Stephens, Matthew .

SCIENCE, 2015, 348 (6235) :648-660

[3]

Buenrostro JD, 2013, NAT METHODS, V10, P1213, DOI [10.1038/NMETH.2688, 10.1038/nmeth.2688]

[4] 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-+

[5] Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis [J].

Chen, Sidi ;

Sanjana, Neville E. ;

Zheng, Kaijie ;

Shalem, Ophir ;

Lee, Kyungheon ;

Shi, Xi ;

Scott, David A. ;

Song, Jun ;

Pan, Jen Q. ;

Weissleder, Ralph ;

Lee, Hakho ;

Zhang, Feng ;

Sharp, Phillip A. .

CELL, 2015, 160 (06) :1246-1260

[6] Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites [J].

Crawford, GE ;

Holt, IE ;

Mullikin, JC ;

Tai, D ;

Green, ED ;

Wolfsberg, TG ;

Collins, FS .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (04) :992-997

[7] Capturing chromosome conformation [J].

Dekker, J ;

Rippe, K ;

Dekker, M ;

Kleckner, N .

SCIENCE, 2002, 295 (5558) :1306-1311

[8] An integrated encyclopedia of DNA elements in the human genome [J].

Dunham, Ian ;

Kundaje, Anshul ;

Aldred, Shelley F. ;

Collins, Patrick J. ;

Davis, CarrieA. ;

Doyle, Francis ;

Epstein, Charles B. ;

Frietze, Seth ;

Harrow, Jennifer ;

Kaul, Rajinder ;

Khatun, Jainab ;

Lajoie, Bryan R. ;

Landt, Stephen G. ;

Lee, Bum-Kyu ;

Pauli, Florencia ;

Rosenbloom, Kate R. ;

Sabo, Peter ;

Safi, Alexias ;

Sanyal, Amartya ;

Shoresh, Noam ;

Simon, Jeremy M. ;

Song, Lingyun ;

Trinklein, Nathan D. ;

Altshuler, Robert C. ;

Birney, Ewan ;

Brown, James B. ;

Cheng, Chao ;

Djebali, Sarah ;

Dong, Xianjun ;

Dunham, Ian ;

Ernst, Jason ;

Furey, Terrence S. ;

Gerstein, Mark ;

Giardine, Belinda ;

Greven, Melissa ;

Hardison, Ross C. ;

Harris, Robert S. ;

Herrero, Javier ;

Hoffman, Michael M. ;

Iyer, Sowmya ;

Kellis, Manolis ;

Khatun, Jainab ;

Kheradpour, Pouya ;

Kundaje, Anshul ;

Lassmann, Timo ;

Li, Qunhua ;

Lin, Xinying ;

Marinov, Georgi K. ;

Merkel, Angelika ;

Mortazavi, Ali .

NATURE, 2012, 489 (7414) :57-74

[9] A hidden Markov Model approach to variation among sites in rate of evolution [J].

Felsenstein, J ;

Churchill, GA .

MOLECULAR BIOLOGY AND EVOLUTION, 1996, 13 (01) :93-104

[10] Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome [J].

Heintzman, Nathaniel D. ;

Stuart, Rhona K. ;

Hon, Gary ;

Fu, Yutao ;

Ching, Christina W. ;

Hawkins, R. David ;

Barrera, Leah O. ;

Van Calcar, Sara ;

Qu, Chunxu ;

Ching, Keith A. ;

Wang, Wei ;

Weng, Zhiping ;

Green, Roland D. ;

Crawford, Gregory E. ;

Ren, Bing .

NATURE GENETICS, 2007, 39 (03) :311-318

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