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Literature DB >> 27423542

CRISPR Screens to Discover Functional Noncoding Elements.

Abstract

A major challenge in genomics is to identify functional elements in the noncoding genome. Recently, pooled clustered regularly interspersed palindromic repeat (CRISPR) mutagenesis screens of noncoding regions have emerged as a novel method for finding elements that impact gene expression and phenotype/disease-relevant biological processes. Here we review and compare different approaches for high-throughput dissection of noncoding elements.

Entities: CellLine Chemical Disease Gene Species

Keywords: CRISPR; Cas9; enhancer; functional genomics; gene regulation; noncoding

Mesh：

Substances：
RNA, Untranslated

Year: 2016 PMID： 27423542 PMCID： PMC4992445 DOI： 10.1016/j.tig.2016.06.004

Source DB: PubMed Journal: Trends Genet ISSN： 0168-9525 Impact factor: 11.639

17 in total

1. The ENCODE project: missteps overshadowing a success.

Authors: Sean R Eddy
Journal: Curr Biol Date: 2013-04-08 Impact factor: 10.834

Review 2. Development and applications of CRISPR-Cas9 for genome engineering.

Authors: Patrick D Hsu; Eric S Lander; Feng Zhang
Journal: Cell Date: 2014-06-05 Impact factor: 41.582

3. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis.

Authors: Sidi Chen; Neville E Sanjana; Kaijie Zheng; Ophir Shalem; Kyungheon Lee; Xi Shi; David A Scott; Jun Song; Jen Q Pan; Ralph Weissleder; Hakho Lee; Feng Zhang; Phillip A Sharp
Journal: Cell Date: 2015-03-05 Impact factor: 41.582

4. Genome-wide association study shows BCL11A associated with persistent fetal hemoglobin and amelioration of the phenotype of beta-thalassemia.

Authors: Manuela Uda; Renzo Galanello; Serena Sanna; Guillaume Lettre; Vijay G Sankaran; Weimin Chen; Gianluca Usala; Fabio Busonero; Andrea Maschio; Giuseppe Albai; Maria Grazia Piras; Natascia Sestu; Sandra Lai; Mariano Dei; Antonella Mulas; Laura Crisponi; Silvia Naitza; Isadora Asunis; Manila Deiana; Ramaiah Nagaraja; Lucia Perseu; Stefania Satta; Maria Dolores Cipollina; Carla Sollaino; Paolo Moi; Joel N Hirschhorn; Stuart H Orkin; Gonçalo R Abecasis; David Schlessinger; Antonio Cao
Journal: Proc Natl Acad Sci U S A Date: 2008-02-01 Impact factor: 11.205

5. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE.

Authors: Dan Graur; Yichen Zheng; Nicholas Price; Ricardo B R Azevedo; Rebecca A Zufall; Eran Elhaik
Journal: Genome Biol Evol Date: 2013 Impact factor: 3.416

6. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay.

Authors: Alexandre Melnikov; Anand Murugan; Xiaolan Zhang; Tiberiu Tesileanu; Li Wang; Peter Rogov; Soheil Feizi; Andreas Gnirke; Curtis G Callan; Justin B Kinney; Manolis Kellis; Eric S Lander; Tarjei S Mikkelsen
Journal: Nat Biotechnol Date: 2012-02-26 Impact factor: 54.908

Review 7. Defining functional DNA elements in the human genome.

Authors: Manolis Kellis; Barbara Wold; Michael P Snyder; Bradley E Bernstein; Anshul Kundaje; Georgi K Marinov; Lucas D Ward; Ewan Birney; Gregory E Crawford; Job Dekker; Ian Dunham; Laura L Elnitski; Peggy J Farnham; Elise A Feingold; Mark Gerstein; Morgan C Giddings; David M Gilbert; Thomas R Gingeras; Eric D Green; Roderic Guigo; Tim Hubbard; Jim Kent; Jason D Lieb; Richard M Myers; Michael J Pazin; Bing Ren; John A Stamatoyannopoulos; Zhiping Weng; Kevin P White; Ross C Hardison
Journal: Proc Natl Acad Sci U S A Date: 2014-04-21 Impact factor: 12.779

8. 8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage.

Authors: Chris M Rands; Stephen Meader; Chris P Ponting; Gerton Lunter
Journal: PLoS Genet Date: 2014-07-24 Impact factor: 5.917

9. An integrated encyclopedia of DNA elements in the human genome.

Authors:
Journal: Nature Date: 2012-09-06 Impact factor: 49.962

10. Integrative analysis of 111 reference human epigenomes.

Authors: Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal: Nature Date: 2015-02-19 Impact factor: 69.504

15 in total

1. CRISPR/Cas9-mediated deletion of lncRNA Gm26878 in the distant Foxf1 enhancer region.

Authors: Przemyslaw Szafranski; Justyna A Karolak; Denise Lanza; Marzena Gajęcka; Jason Heaney; Paweł Stankiewicz
Journal: Mamm Genome Date: 2017-04-12 Impact factor: 2.957

Review 2. Human gene essentiality.

Authors: István Bartha; Julia di Iulio; J Craig Venter; Amalio Telenti
Journal: Nat Rev Genet Date: 2017-10-30 Impact factor: 53.242

Review 3. Towards a comprehensive catalogue of validated and target-linked human enhancers.

Authors: Molly Gasperini; Jacob M Tome; Jay Shendure
Journal: Nat Rev Genet Date: 2020-01-27 Impact factor: 53.242

Review 4. Enhancer redundancy in development and disease.

Authors: Evgeny Z Kvon; Zeba Wunderlich; Rachel Waymack; Mario Gad
Journal: Nat Rev Genet Date: 2021-01-12 Impact factor: 53.242

5. Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change.

Authors: Pejman Mohammadi; Stephane E Castel; Andrew A Brown; Tuuli Lappalainen
Journal: Genome Res Date: 2017-10-11 Impact factor: 9.043

Review 6. Functional interrogation of non-coding DNA through CRISPR genome editing.

Authors: Matthew C Canver; Daniel E Bauer; Stuart H Orkin
Journal: Methods Date: 2017-03-10 Impact factor: 3.608

7. A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome.

Authors: Thierry Bertomeu; Jasmin Coulombe-Huntington; Andrew Chatr-Aryamontri; Karine G Bourdages; Etienne Coyaud; Brian Raught; Yu Xia; Mike Tyers
Journal: Mol Cell Biol Date: 2017-12-13 Impact factor: 4.272