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Literature DB >> 27381243

Applying CRISPR-Cas9 tools to identify and characterize transcriptional enhancers.

Rui Lopes¹, Gozde Korkmaz¹, Reuven Agami^1,2.

Abstract

The development of the CRISPR-Cas9 system triggered a revolution in the field of genome engineering. Initially, the use of this system was focused on the study of protein-coding genes but, recently, a number of CRISPR-Cas9-based tools have been developed to study non-coding transcriptional regulatory elements. These technological advances offer unprecedented opportunities for elucidating the functions of enhancers in their endogenous context. Here, we discuss the application, current limitations and future development of CRISPR-Cas9 systems to identify and characterize enhancer elements in a high-throughput manner.

Mesh：

Year: 2016 PMID： 27381243 DOI： 10.1038/nrm.2016.79

Source DB: PubMed Journal: Nat Rev Mol Cell Biol ISSN： 1471-0072 Impact factor: 94.444

101 in total

1. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity.

Authors: F Ann Ran; Patrick D Hsu; Chie-Yu Lin; Jonathan S Gootenberg; Silvana Konermann; Alexandro E Trevino; David A Scott; Azusa Inoue; Shogo Matoba; Yi Zhang; Feng Zhang
Journal: Cell Date: 2013-08-29 Impact factor: 41.582

2. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells.

Authors: Xuebing Wu; David A Scott; Andrea J Kriz; Anthony C Chiu; Patrick D Hsu; Daniel B Dadon; Albert W Cheng; Alexandro E Trevino; Silvana Konermann; Sidi Chen; Rudolf Jaenisch; Feng Zhang; Phillip A Sharp
Journal: Nat Biotechnol Date: 2014-04-20 Impact factor: 54.908

3. Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element.

Authors: Marc R Mansour; Brian J Abraham; Lars Anders; Alla Berezovskaya; Alejandro Gutierrez; Adam D Durbin; Julia Etchin; Lee Lawton; Stephen E Sallan; Lewis B Silverman; Mignon L Loh; Stephen P Hunger; Takaomi Sanda; Richard A Young; A Thomas Look
Journal: Science Date: 2014-11-13 Impact factor: 47.728

4. Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin.

Authors: Daria Shlyueva; Christoph Stelzer; Daniel Gerlach; J Omar Yáñez-Cuna; Martina Rath; Łukasz M Boryń; Cosmas D Arnold; Alexander Stark
Journal: Mol Cell Date: 2014-03-27 Impact factor: 17.970

Review 5. High-throughput functional genomics using CRISPR-Cas9.

Authors: Ophir Shalem; Neville E Sanjana; Feng Zhang
Journal: Nat Rev Genet Date: 2015-04-09 Impact factor: 53.242

6. Activation of proto-oncogenes by disruption of chromosome neighborhoods.

Authors: Denes Hnisz; Abraham S Weintraub; Daniel S Day; Anne-Laure Valton; Rasmus O Bak; Charles H Li; Johanna Goldmann; Bryan R Lajoie; Zi Peng Fan; Alla A Sigova; Jessica Reddy; Diego Borges-Rivera; Tong Ihn Lee; Rudolf Jaenisch; Matthew H Porteus; Job Dekker; Richard A Young
Journal: Science Date: 2016-03-03 Impact factor: 47.728

7. Genome-wide mapping of in vivo protein-DNA interactions.

Authors: David S Johnson; Ali Mortazavi; Richard M Myers; Barbara Wold
Journal: Science Date: 2007-05-31 Impact factor: 47.728

8. 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

9. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.

Authors: Baohui Chen; Luke A Gilbert; Beth A Cimini; Joerg Schnitzbauer; Wei Zhang; Gene-Wei Li; Jason Park; Elizabeth H Blackburn; Jonathan S Weissman; Lei S Qi; Bo Huang
Journal: Cell Date: 2013-12-19 Impact factor: 41.582

10. RNA-guided gene activation by CRISPR-Cas9-based transcription factors.

Authors: Pablo Perez-Pinera; D Dewran Kocak; Christopher M Vockley; Andrew F Adler; Ami M Kabadi; Lauren R Polstein; Pratiksha I Thakore; Katherine A Glass; David G Ousterout; Kam W Leong; Farshid Guilak; Gregory E Crawford; Timothy E Reddy; Charles A Gersbach
Journal: Nat Methods Date: 2013-07-25 Impact factor: 28.547

25 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

2. The effect of chromatin states on cancer: big data lead the way.

Authors: Xufeng Chen; Iannis Aifantis
Journal: Lancet Haematol Date: 2018-06 Impact factor: 18.959

Review 3. Specialized Subpopulations of Deep-Layer Pyramidal Neurons in the Neocortex: Bridging Cellular Properties to Functional Consequences.

Authors: Arielle Baker; Brian Kalmbach; Mieko Morishima; Juhyun Kim; Ashley Juavinett; Nuo Li; Nikolai Dembrow
Journal: J Neurosci Date: 2018-05-21 Impact factor: 6.167

Review 4. Identifying Novel Enhancer Elements with CRISPR-Based Screens.

Authors: Jason C Klein; Wei Chen; Molly Gasperini; Jay Shendure
Journal: ACS Chem Biol Date: 2018-01-10 Impact factor: 5.100

Review 5. 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

Review 6. Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement.

Authors: Qiang Li; Manoj Sapkota; Esther van der Knaap
Journal: Hortic Res Date: 2020-03-15 Impact factor: 6.793