Literature DB >> 31988385

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

Molly Gasperini1, Jacob M Tome1, Jay Shendure2,3,4,5.   

Abstract

The human gene catalogue is essentially complete, but we lack an equivalently vetted inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers have been nominated via biochemical annotations; however, only a handful of these have been validated and confidently linked to their target genes. Here we review emerging technologies for discovering, characterizing and validating human enhancers at scale. We furthermore propose a new framework for operationally defining enhancers that accommodates the heterogeneous and complementary results that are emerging from reporter assays, biochemical measurements and CRISPR screens.

Entities:  

Mesh:

Year:  2020        PMID: 31988385      PMCID: PMC7845138          DOI: 10.1038/s41576-019-0209-0

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  238 in total

Review 1.  Topology of mammalian developmental enhancers and their regulatory landscapes.

Authors:  Wouter de Laat; Denis Duboule
Journal:  Nature       Date:  2013-10-24       Impact factor: 49.962

2.  Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome.

Authors:  R C Hardison; J Oeltjen; W Miller
Journal:  Genome Res       Date:  1997-10       Impact factor: 9.043

3.  Chromosomal subunits in active genes have an altered conformation.

Authors:  H Weintraub; M Groudine
Journal:  Science       Date:  1976-09-03       Impact factor: 47.728

4.  Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9.

Authors:  Gozde Korkmaz; Rui Lopes; Alejandro P Ugalde; Ekaterina Nevedomskaya; Ruiqi Han; Ksenia Myacheva; Wilbert Zwart; Ran Elkon; Reuven Agami
Journal:  Nat Biotechnol       Date:  2016-01-11       Impact factor: 54.908

5.  Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data.

Authors:  Hannah A Pliner; Jonathan S Packer; José L McFaline-Figueroa; Darren A Cusanovich; Riza M Daza; Delasa Aghamirzaie; Sanjay Srivatsan; Xiaojie Qiu; Dana Jackson; Anna Minkina; Andrew C Adey; Frank J Steemers; Jay Shendure; Cole Trapnell
Journal:  Mol Cell       Date:  2018-08-02       Impact factor: 17.970

6.  Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits.

Authors:  Jacob C Ulirsch; Satish K Nandakumar; Li Wang; Felix C Giani; Xiaolan Zhang; Peter Rogov; Alexandre Melnikov; Patrick McDonel; Ron Do; Tarjei S Mikkelsen; Vijay G Sankaran
Journal:  Cell       Date:  2016-06-02       Impact factor: 41.582

7.  Intragenic Enhancers Attenuate Host Gene Expression.

Authors:  Senthilkumar Cinghu; Pengyi Yang; Justin P Kosak; Amanda E Conway; Dhirendra Kumar; Andrew J Oldfield; Karen Adelman; Raja Jothi
Journal:  Mol Cell       Date:  2017-10-05       Impact factor: 17.970

8.  Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding.

Authors:  Dominic Schmidt; Michael D Wilson; Benoit Ballester; Petra C Schwalie; Gordon D Brown; Aileen Marshall; Claudia Kutter; Stephen Watt; Celia P Martinez-Jimenez; Sarah Mackay; Iannis Talianidis; Paul Flicek; Duncan T Odom
Journal:  Science       Date:  2010-04-08       Impact factor: 47.728

9.  Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation.

Authors:  Kristel M Dorighi; Tomek Swigut; Telmo Henriques; Natarajan V Bhanu; Benjamin S Scruggs; Nataliya Nady; Christopher D Still; Benjamin A Garcia; Karen Adelman; Joanna Wysocka
Journal:  Mol Cell       Date:  2017-05-05       Impact factor: 17.970

10.  Functional footprinting of regulatory DNA.

Authors:  Jeff Vierstra; Andreas Reik; Kai-Hsin Chang; Sandra Stehling-Sun; Yuanyue Zhou; Sarah J Hinkley; David E Paschon; Lei Zhang; Nikoletta Psatha; Yuri R Bendana; Colleen M O'Neil; Alexander H Song; Andrea K Mich; Pei-Qi Liu; Gary Lee; Daniel E Bauer; Michael C Holmes; Stuart H Orkin; Thalia Papayannopoulou; George Stamatoyannopoulos; Edward J Rebar; Philip D Gregory; Fyodor D Urnov; John A Stamatoyannopoulos
Journal:  Nat Methods       Date:  2015-08-31       Impact factor: 28.547

View more
  74 in total

Review 1.  CRISPR technologies for precise epigenome editing.

Authors:  Muneaki Nakamura; Yuchen Gao; Antonia A Dominguez; Lei S Qi
Journal:  Nat Cell Biol       Date:  2021-01-08       Impact factor: 28.824

Review 2.  Genomic resources for dissecting the role of non-protein coding variation in gene-environment interactions.

Authors:  Daniel Levings; Kirsten E Shaw; Sarah E Lacher
Journal:  Toxicology       Date:  2020-05-22       Impact factor: 4.221

Review 3.  In search of lost time: Enhancers as modulators of timing in lymphocyte development and differentiation.

Authors:  Jonathan M Chu; Nicholas A Pease; Hao Yuan Kueh
Journal:  Immunol Rev       Date:  2021-03-18       Impact factor: 12.988

4.  Accurate prediction of cis-regulatory modules reveals a prevalent regulatory genome of humans.

Authors:  Pengyu Ni; Zhengchang Su
Journal:  NAR Genom Bioinform       Date:  2021-06-17

Review 5.  Modulating gene regulation to treat genetic disorders.

Authors:  Navneet Matharu; Nadav Ahituv
Journal:  Nat Rev Drug Discov       Date:  2020-10-05       Impact factor: 84.694

Review 6.  Genomic enhancers in cardiac development and disease.

Authors:  Chukwuemeka G Anene-Nzelu; Mick C J Lee; Wilson L W Tan; Albert Dashi; Roger S Y Foo
Journal:  Nat Rev Cardiol       Date:  2021-08-11       Impact factor: 32.419

Review 7.  The essential but enigmatic regulatory role of HERVH in pluripotency.

Authors:  Corinne E Sexton; Richard L Tillett; Mira V Han
Journal:  Trends Genet       Date:  2021-07-30       Impact factor: 11.639

Review 8.  Evolutionary genetics of skin pigmentation in African populations.

Authors:  Yuanqing Feng; Michael A McQuillan; Sarah A Tishkoff
Journal:  Hum Mol Genet       Date:  2021-04-26       Impact factor: 6.150

9.  Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning.

Authors:  Zeynep Kalender Atak; Ibrahim Ihsan Taskiran; Jonas Demeulemeester; Christopher Flerin; David Mauduit; Liesbeth Minnoye; Gert Hulselmans; Valerie Christiaens; Ghanem-Elias Ghanem; Jasper Wouters; Stein Aerts
Journal:  Genome Res       Date:  2021-04-08       Impact factor: 9.043

Review 10.  Adeno-associated virus gene replacement for recessive inner ear dysfunction: Progress and challenges.

Authors:  Charles Askew; Wade W Chien
Journal:  Hear Res       Date:  2020-03-18       Impact factor: 3.208

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.