Literature DB >> 27261176

Genome-scale CRISPR pooled screens.

Neville E Sanjana1.   

Abstract

Genome editing technologies such as clustered regularly interspaced short palindromic repeats (CRISPR) systems have ushered in a new era of targeted DNA manipulation. The easy programmability of CRISPR using short oligonucleotides enables rapid synthesis of large-scale libraries for functional genetic screens. Here we present fundamental concepts and methods for pooled CRISPR screens and review biological results from recent genome-scale loss-of-function and gain-of-function screens. We also discuss new frontiers in pooled screens, including novel effector domains for functional screens and applications in the noncoding genome.
Copyright © 2016 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  CRISPR; Cancer; Cas9; Genetic screens; Genome engineering; Noncoding

Mesh:

Substances:

Year:  2016        PMID: 27261176      PMCID: PMC5133192          DOI: 10.1016/j.ab.2016.05.014

Source DB:  PubMed          Journal:  Anal Biochem        ISSN: 0003-2697            Impact factor:   3.365


  36 in total

1.  Genome-wide atlas of gene expression in the adult mouse brain.

Authors:  Ed S Lein; Michael J Hawrylycz; Nancy Ao; Mikael Ayres; Amy Bensinger; Amy Bernard; Andrew F Boe; Mark S Boguski; Kevin S Brockway; Emi J Byrnes; Lin Chen; Li Chen; Tsuey-Ming Chen; Mei Chi Chin; Jimmy Chong; Brian E Crook; Aneta Czaplinska; Chinh N Dang; Suvro Datta; Nick R Dee; Aimee L Desaki; Tsega Desta; Ellen Diep; Tim A Dolbeare; Matthew J Donelan; Hong-Wei Dong; Jennifer G Dougherty; Ben J Duncan; Amanda J Ebbert; Gregor Eichele; Lili K Estin; Casey Faber; Benjamin A Facer; Rick Fields; Shanna R Fischer; Tim P Fliss; Cliff Frensley; Sabrina N Gates; Katie J Glattfelder; Kevin R Halverson; Matthew R Hart; John G Hohmann; Maureen P Howell; Darren P Jeung; Rebecca A Johnson; Patrick T Karr; Reena Kawal; Jolene M Kidney; Rachel H Knapik; Chihchau L Kuan; James H Lake; Annabel R Laramee; Kirk D Larsen; Christopher Lau; Tracy A Lemon; Agnes J Liang; Ying Liu; Lon T Luong; Jesse Michaels; Judith J Morgan; Rebecca J Morgan; Marty T Mortrud; Nerick F Mosqueda; Lydia L Ng; Randy Ng; Geralyn J Orta; Caroline C Overly; Tu H Pak; Sheana E Parry; Sayan D Pathak; Owen C Pearson; Ralph B Puchalski; Zackery L Riley; Hannah R Rockett; Stephen A Rowland; Joshua J Royall; Marcos J Ruiz; Nadia R Sarno; Katherine Schaffnit; Nadiya V Shapovalova; Taz Sivisay; Clifford R Slaughterbeck; Simon C Smith; Kimberly A Smith; Bryan I Smith; Andy J Sodt; Nick N Stewart; Kenda-Ruth Stumpf; Susan M Sunkin; Madhavi Sutram; Angelene Tam; Carey D Teemer; Christina Thaller; Carol L Thompson; Lee R Varnam; Axel Visel; Ray M Whitlock; Paul E Wohnoutka; Crissa K Wolkey; Victoria Y Wong; Matthew Wood; Murat B Yaylaoglu; Rob C Young; Brian L Youngstrom; Xu Feng Yuan; Bin Zhang; Theresa A Zwingman; Allan R Jones
Journal:  Nature       Date:  2006-12-06       Impact factor: 49.962

2.  CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes.

Authors:  Bastiaan Evers; Katarzyna Jastrzebski; Jeroen P M Heijmans; Wipawadee Grernrum; Roderick L Beijersbergen; Rene Bernards
Journal:  Nat Biotechnol       Date:  2016-04-25       Impact factor: 54.908

Review 3.  The evolution of melanoma resistance reveals therapeutic opportunities.

Authors:  Meghna Das Thakur; Darrin D Stuart
Journal:  Cancer Res       Date:  2013-10-04       Impact factor: 12.701

4.  A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition.

Authors:  Steven R Whittaker; Jean-Philippe Theurillat; Eliezer Van Allen; Nikhil Wagle; Jessica Hsiao; Glenn S Cowley; Dirk Schadendorf; David E Root; Levi A Garraway
Journal:  Cancer Discov       Date:  2013-01-03       Impact factor: 39.397

5.  MED12 controls the response to multiple cancer drugs through regulation of TGF-β receptor signaling.

Authors:  Sidong Huang; Michael Hölzel; Theo Knijnenburg; Andreas Schlicker; Paul Roepman; Ultan McDermott; Mathew Garnett; Wipawadee Grernrum; Chong Sun; Anirudh Prahallad; Floris H Groenendijk; Lorenza Mittempergher; Wouter Nijkamp; Jacques Neefjes; Ramon Salazar; Peter Ten Dijke; Hidetaka Uramoto; Fumihiro Tanaka; Roderick L Beijersbergen; Lodewyk F A Wessels; René Bernards
Journal:  Cell       Date:  2012-11-21       Impact factor: 41.582

6.  Genome-wide CRISPR-Cas9 Screens Reveal Loss of Redundancy between PKMYT1 and WEE1 in Glioblastoma Stem-like Cells.

Authors:  Chad M Toledo; Yu Ding; Pia Hoellerbauer; Ryan J Davis; Ryan Basom; Emily J Girard; Eunjee Lee; Philip Corrin; Traver Hart; Hamid Bolouri; Jerry Davison; Qing Zhang; Justin Hardcastle; Bruce J Aronow; Christopher L Plaisier; Nitin S Baliga; Jason Moffat; Qi Lin; Xiao-Nan Li; Do-Hyun Nam; Jeongwu Lee; Steven M Pollard; Jun Zhu; Jeffery J Delrow; Bruce E Clurman; James M Olson; Patrick J Paddison
Journal:  Cell Rep       Date:  2015-12-07       Impact factor: 9.423

7.  A Genome-wide CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Screen Identifies NEK7 as an Essential Component of NLRP3 Inflammasome Activation.

Authors:  Jonathan L Schmid-Burgk; Dhruv Chauhan; Tobias Schmidt; Thomas S Ebert; Julia Reinhardt; Elmar Endl; Veit Hornung
Journal:  J Biol Chem       Date:  2015-11-09       Impact factor: 5.157

8.  Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains.

Authors:  Junwei Shi; Eric Wang; Joseph P Milazzo; Zihua Wang; Justin B Kinney; Christopher R Vakoc
Journal:  Nat Biotechnol       Date:  2015-05-11       Impact factor: 54.908

9.  BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis.

Authors:  Matthew C Canver; Elenoe C Smith; Falak Sher; Luca Pinello; Neville E Sanjana; Ophir Shalem; Diane D Chen; Patrick G Schupp; Divya S Vinjamur; Sara P Garcia; Sidinh Luc; Ryo Kurita; Yukio Nakamura; Yuko Fujiwara; Takahiro Maeda; Guo-Cheng Yuan; Feng Zhang; Stuart H Orkin; Daniel E Bauer
Journal:  Nature       Date:  2015-09-16       Impact factor: 49.962

10.  Saturation editing of genomic regions by multiplex homology-directed repair.

Authors:  Gregory M Findlay; Evan A Boyle; Ronald J Hause; Jason C Klein; Jay Shendure
Journal:  Nature       Date:  2014-09-04       Impact factor: 49.962

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  30 in total

Review 1.  From Reductionism to Holism: Toward a More Complete View of Development Through Genome Engineering.

Authors:  Rebecca K Delker; Richard S Mann
Journal:  Adv Exp Med Biol       Date:  2017       Impact factor: 2.622

2.  Future directions for high-throughput splicing assays in precision medicine.

Authors:  Christy L Rhine; Christopher Neil; David T Glidden; Kamil J Cygan; Alger M Fredericks; Jing Wang; Nephi A Walton; William G Fairbrother
Journal:  Hum Mutat       Date:  2019-08-17       Impact factor: 4.878

3.  Comprehensive Genome-wide Perturbations via CRISPR Adaptation Reveal Complex Genetics of Antibiotic Sensitivity.

Authors:  Wenyan Jiang; Panos Oikonomou; Saeed Tavazoie
Journal:  Cell       Date:  2020-02-27       Impact factor: 41.582

Review 4.  [Development of CRISPR technology and its application in bone and cartilage tissue engineering].

Authors:  Guo Chen; Du Cheng; Bin Chen
Journal:  Nan Fang Yi Ke Da Xue Xue Bao       Date:  2019-12-30

Review 5.  Lysosomal acid lipase and lipid metabolism: new mechanisms, new questions, and new therapies.

Authors:  Hanrui Zhang
Journal:  Curr Opin Lipidol       Date:  2018-06       Impact factor: 4.776

Review 6.  Research on CRISPR/system in major cancers and its potential in cancer treatments.

Authors:  Z Liu; Z Liao; Y Chen; L Zhou; W Huangting; H Xiao
Journal:  Clin Transl Oncol       Date:  2020-07-15       Impact factor: 3.405

7.  Phenomics-Based Quantification of CRISPR-Induced Mosaicism in Zebrafish.

Authors:  Claire J Watson; Adrian T Monstad-Rios; Rehaan M Bhimani; Charlotte Gistelinck; Andy Willaert; Paul Coucke; Yi-Hsiang Hsu; Ronald Y Kwon
Journal:  Cell Syst       Date:  2020-03-18       Impact factor: 10.304

8.  Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies.

Authors:  Theodore L Roth; P Jonathan Li; Franziska Blaeschke; Jasper F Nies; Ryan Apathy; Cody Mowery; Ruby Yu; Michelle L T Nguyen; Youjin Lee; Anna Truong; Joseph Hiatt; David Wu; David N Nguyen; Daniel Goodman; Jeffrey A Bluestone; Chun Jimmie Ye; Kole Roybal; Eric Shifrut; Alexander Marson
Journal:  Cell       Date:  2020-04-16       Impact factor: 41.582

Review 9.  High-Throughput Approaches to Pinpoint Function within the Noncoding Genome.

Authors:  Antonino Montalbano; Matthew C Canver; Neville E Sanjana
Journal:  Mol Cell       Date:  2017-10-05       Impact factor: 17.970

Review 10.  Research Techniques Made Simple: CRISPR Genetic Screens.

Authors:  Auke B C Otten; Bryan K Sun
Journal:  J Invest Dermatol       Date:  2020-04       Impact factor: 8.551

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