Literature DB >> 24480293

Enhancer RNAs: the new molecules of transcription.

Fan Lai1, Ramin Shiekhattar2.   

Abstract

In the past few years, technological advances in nucleotide sequencing have culminated in a greater understanding of the complexity of the human transcriptome. Notably, the discovery that distal regulatory elements known as enhancers are transcribed and such enhancer-derived transcripts (eRNAs) serve a critical function in transcriptional activation has added a new dimension to transcriptional regulation. Here we review recent insights into the tissue-specific and temporal-specific gene regulation brought about by the discovery of eRNAs.
Copyright © 2013 Elsevier Ltd. All rights reserved.

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Year:  2014        PMID: 24480293      PMCID: PMC4484728          DOI: 10.1016/j.gde.2013.11.017

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  31 in total

1.  eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci.

Authors:  Kambiz Mousavi; Hossein Zare; Stefania Dell'orso; Lars Grontved; Gustavo Gutierrez-Cruz; Assia Derfoul; Gordon L Hager; Vittorio Sartorelli
Journal:  Mol Cell       Date:  2013-08-29       Impact factor: 17.970

2.  Genome-wide analysis of estrogen receptor binding sites.

Authors:  Jason S Carroll; Clifford A Meyer; Jun Song; Wei Li; Timothy R Geistlinger; Jérôme Eeckhoute; Alexander S Brodsky; Erika Krasnickas Keeton; Kirsten C Fertuck; Giles F Hall; Qianben Wang; Stefan Bekiranov; Victor Sementchenko; Edward A Fox; Pamela A Silver; Thomas R Gingeras; X Shirley Liu; Myles Brown
Journal:  Nat Genet       Date:  2006-10-01       Impact factor: 38.330

3.  Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain.

Authors:  A J Bannister; P Zegerman; J F Partridge; E A Miska; J O Thomas; R C Allshire; T Kouzarides
Journal:  Nature       Date:  2001-03-01       Impact factor: 49.962

4.  Architectural protein subclasses shape 3D organization of genomes during lineage commitment.

Authors:  Jennifer E Phillips-Cremins; Michael E G Sauria; Amartya Sanyal; Tatiana I Gerasimova; Bryan R Lajoie; Joshua S K Bell; Chin-Tong Ong; Tracy A Hookway; Changying Guo; Yuhua Sun; Michael J Bland; William Wagstaff; Stephen Dalton; Todd C McDevitt; Ranjan Sen; Job Dekker; James Taylor; Victor G Corces
Journal:  Cell       Date:  2013-05-23       Impact factor: 41.582

5.  The long noncoding RNA RMST interacts with SOX2 to regulate neurogenesis.

Authors:  Shi-Yan Ng; Gireesh K Bogu; Boon Seng Soh; Lawrence W Stanton
Journal:  Mol Cell       Date:  2013-08-08       Impact factor: 17.970

6.  Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription.

Authors:  Minna U Kaikkonen; Nathanael J Spann; Sven Heinz; Casey E Romanoski; Karmel A Allison; Joshua D Stender; Hyun B Chun; David F Tough; Rab K Prinjha; Christopher Benner; Christopher K Glass
Journal:  Mol Cell       Date:  2013-08-08       Impact factor: 17.970

7.  Highly conserved non-coding sequences are associated with vertebrate development.

Authors:  Adam Woolfe; Martin Goodson; Debbie K Goode; Phil Snell; Gayle K McEwen; Tanya Vavouri; Sarah F Smith; Phil North; Heather Callaway; Krys Kelly; Klaudia Walter; Irina Abnizova; Walter Gilks; Yvonne J K Edwards; Julie E Cooke; Greg Elgar
Journal:  PLoS Biol       Date:  2004-11-11       Impact factor: 8.029

8.  Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation.

Authors:  Wenbo Li; Dimple Notani; Qi Ma; Bogdan Tanasa; Esperanza Nunez; Aaron Yun Chen; Daria Merkurjev; Jie Zhang; Kenneth Ohgi; Xiaoyuan Song; Soohwan Oh; Hong-Sook Kim; Christopher K Glass; Michael G Rosenfeld
Journal:  Nature       Date:  2013-06-02       Impact factor: 49.962

9.  Enhancer transcripts mark active estrogen receptor binding sites.

Authors:  Nasun Hah; Shino Murakami; Anusha Nagari; Charles G Danko; W Lee Kraus
Journal:  Genome Res       Date:  2013-05-01       Impact factor: 9.043

10.  lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs.

Authors:  Liuqing Yang; Chunru Lin; Chunyu Jin; Joy C Yang; Bogdan Tanasa; Wenbo Li; Daria Merkurjev; Kenneth A Ohgi; Da Meng; Jie Zhang; Christopher P Evans; Michael G Rosenfeld
Journal:  Nature       Date:  2013-08-14       Impact factor: 49.962

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  28 in total

1.  Long noncoding RNA MRUL promotes ABCB1 expression in multidrug-resistant gastric cancer cell sublines.

Authors:  Ying Wang; Dexin Zhang; Kaichun Wu; Qingchuan Zhao; Yongzhan Nie; Daiming Fan
Journal:  Mol Cell Biol       Date:  2014-06-23       Impact factor: 4.272

Review 2.  From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease.

Authors:  Miao Sun; W Lee Kraus
Journal:  Endocr Rev       Date:  2014-11-26       Impact factor: 19.871

3.  Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs.

Authors:  Nasun Hah; Chris Benner; Ling-Wa Chong; Ruth T Yu; Michael Downes; Ronald M Evans
Journal:  Proc Natl Acad Sci U S A       Date:  2015-01-06       Impact factor: 11.205

4.  Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly.

Authors:  Sreejith J Nair; Lu Yang; Dario Meluzzi; Soohwan Oh; Feng Yang; Meyer J Friedman; Susan Wang; Tom Suter; Ibraheem Alshareedah; Amir Gamliel; Qi Ma; Jie Zhang; Yiren Hu; Yuliang Tan; Kenneth A Ohgi; Ranveer Singh Jayani; Priya R Banerjee; Aneel K Aggarwal; Michael G Rosenfeld
Journal:  Nat Struct Mol Biol       Date:  2019-03-04       Impact factor: 15.369

Review 5.  A Phase Separation Model for Transcriptional Control.

Authors:  Denes Hnisz; Krishna Shrinivas; Richard A Young; Arup K Chakraborty; Phillip A Sharp
Journal:  Cell       Date:  2017-03-23       Impact factor: 41.582

Review 6.  Mechanisms of Nucleosome Dynamics In Vivo.

Authors:  Steven Henikoff
Journal:  Cold Spring Harb Perspect Med       Date:  2016-09-01       Impact factor: 6.915

Review 7.  Functions of long noncoding RNAs in the nucleus.

Authors:  Bin Yu; Ge Shan
Journal:  Nucleus       Date:  2016-04-25       Impact factor: 4.197

8.  Inferring a role for methylation of intergenic DNA in the regulation of genes aberrantly expressed in precursor B-cell acute lymphoblastic leukemia.

Authors:  Md Almamun; Olha Kholod; Alexei J Stuckel; Benjamin T Levinson; Nathan T Johnson; Gerald L Arthur; J Wade Davis; Kristen H Taylor
Journal:  Leuk Lymphoma       Date:  2017-01-17

Review 9.  The state of play in higher eukaryote gene annotation.

Authors:  Jonathan M Mudge; Jennifer Harrow
Journal:  Nat Rev Genet       Date:  2016-10-24       Impact factor: 53.242

10.  The distal upstream promoter in Ly49 genes, Pro1, is active in mature NK cells and T cells, does not require TATA boxes, and displays enhancer activity.

Authors:  Frances Gays; Sally Taha; Colin G Brooks
Journal:  J Immunol       Date:  2015-04-29       Impact factor: 5.422

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