Literature DB >> 29300083

Identifying Novel Enhancer Elements with CRISPR-Based Screens.

Jason C Klein1, Wei Chen2, Molly Gasperini1, Jay Shendure1,3.   

Abstract

Enhancers control the spatiotemporal expression of genes and are essential for encoding differentiation and development. Since their discovery more than three decades ago, researchers have largely studied enhancers removed from their genomic context. The recent adaptation of CRISPR/Cas9 to genome editing in higher organisms now allows researchers to perturb and test these elements in their genomic context, through both mutation and epigenetic modulation. In this Perspective, we discuss recent advances in scanning noncoding regions of the genome for enhancer activity using CRISPR-based tools.

Entities:  

Mesh:

Substances:

Year:  2018        PMID: 29300083      PMCID: PMC6218247          DOI: 10.1021/acschembio.7b00778

Source DB:  PubMed          Journal:  ACS Chem Biol        ISSN: 1554-8929            Impact factor:   5.100


  57 in total

Review 1.  Using reporter genes to study cis-regulatory elements.

Authors:  Maria I Arnone; Ivan J Dmochowski; Christian Gache
Journal:  Methods Cell Biol       Date:  2004       Impact factor: 1.441

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

Authors:  Rui Lopes; Gozde Korkmaz; Reuven Agami
Journal:  Nat Rev Mol Cell Biol       Date:  2016-07-06       Impact factor: 94.444

3.  Genome-scale CRISPR-Cas9 knockout screening in human cells.

Authors:  Ophir Shalem; Neville E Sanjana; Ella Hartenian; Xi Shi; David A Scott; Tarjei Mikkelson; Dirk Heckl; Benjamin L Ebert; David E Root; John G Doench; Feng Zhang
Journal:  Science       Date:  2013-12-12       Impact factor: 47.728

4.  Comprehensive single-cell transcriptional profiling of a multicellular organism.

Authors:  Junyue Cao; Jonathan S Packer; Vijay Ramani; Darren A Cusanovich; Chau Huynh; Riza Daza; Xiaojie Qiu; Choli Lee; Scott N Furlan; Frank J Steemers; Andrew Adey; Robert H Waterston; Cole Trapnell; Jay Shendure
Journal:  Science       Date:  2017-08-18       Impact factor: 47.728

5.  Linking disease associations with regulatory information in the human genome.

Authors:  Marc A Schaub; Alan P Boyle; Anshul Kundaje; Serafim Batzoglou; Michael Snyder
Journal:  Genome Res       Date:  2012-09       Impact factor: 9.043

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

7.  Functional annotation of native enhancers with a Cas9-histone demethylase fusion.

Authors:  Nicola A Kearns; Hannah Pham; Barbara Tabak; Ryan M Genga; Noah J Silverstein; Manuel Garber; René Maehr
Journal:  Nat Methods       Date:  2015-03-16       Impact factor: 28.547

8.  GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases.

Authors:  Shengdar Q Tsai; Zongli Zheng; Nhu T Nguyen; Matthew Liebers; Ved V Topkar; Vishal Thapar; Nicolas Wyvekens; Cyd Khayter; A John Iafrate; Long P Le; Martin J Aryee; J Keith Joung
Journal:  Nat Biotechnol       Date:  2014-12-16       Impact factor: 54.908

9.  Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.

Authors:  Jason Ernst; Alexandre Melnikov; Xiaolan Zhang; Li Wang; Peter Rogov; Tarjei S Mikkelsen; Manolis Kellis
Journal:  Nat Biotechnol       Date:  2016-10-03       Impact factor: 54.908

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

View more
  7 in total

Review 1.  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 2.  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 3.  Genome organization in immune cells: unique challenges.

Authors:  Timothy M Johanson; Wing Fuk Chan; Christine R Keenan; Rhys S Allan
Journal:  Nat Rev Immunol       Date:  2019-07       Impact factor: 53.106

Review 4.  Epigenome rewiring in human pluripotent stem cells.

Authors:  Jielin Yan; Danwei Huangfu
Journal:  Trends Cell Biol       Date:  2021-12-23       Impact factor: 20.808

5.  Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair.

Authors:  Wei Chen; Aaron McKenna; Jacob Schreiber; Maximilian Haeussler; Yi Yin; Vikram Agarwal; William Stafford Noble; Jay Shendure
Journal:  Nucleic Acids Res       Date:  2019-09-05       Impact factor: 16.971

6.  SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression.

Authors:  Guojun Hou; Isaac T W Harley; Xiaoming Lu; Tian Zhou; Ning Xu; Chao Yao; Yuting Qin; Ye Ouyang; Jianyang Ma; Xinyi Zhu; Xiang Yu; Hong Xu; Dai Dai; Huihua Ding; Zhihua Yin; Zhizhong Ye; Jun Deng; Mi Zhou; Yuanjia Tang; Bahram Namjou; Ya Guo; Matthew T Weirauch; Leah C Kottyan; John B Harley; Nan Shen
Journal:  Nat Commun       Date:  2021-01-08       Impact factor: 14.919

Review 7.  The role of single-cell genomics in human genetics.

Authors:  Varun K A Sreenivasan; Saranya Balachandran; Malte Spielmann
Journal:  J Med Genet       Date:  2022-07-05       Impact factor: 5.941

  7 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.