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Literature DB >> 25418744

A shared architecture for promoters and enhancers.

Abstract

A new study detects unstable nascent RNAs and uncovers thousands of transcription initiation sites in promoters and enhancers. Detailed analysis shows that these initiation sites have a similar architecture and that they are differentiated by post-transcriptional regulation rather than transcription initiation.

Mesh：

Substances：
RNA

Year: 2014 PMID： 25418744 DOI： 10.1038/ng.3152

Source DB: PubMed Journal: Nat Genet ISSN： 1061-4036 Impact factor: 38.330

7 in total

1. ChromHMM: automating chromatin-state discovery and characterization.

Authors: Jason Ernst; Manolis Kellis
Journal: Nat Methods Date: 2012-02-28 Impact factor: 28.547

2. Transcriptional noise and the fidelity of initiation by RNA polymerase II.

Authors: Kevin Struhl
Journal: Nat Struct Mol Biol Date: 2007-02 Impact factor: 15.369

3. Unamplified cap analysis of gene expression on a single-molecule sequencer.

Authors: Mutsumi Kanamori-Katayama; Masayoshi Itoh; Hideya Kawaji; Timo Lassmann; Shintaro Katayama; Miki Kojima; Nicolas Bertin; Ai Kaiho; Noriko Ninomiya; Carsten O Daub; Piero Carninci; Alistair R R Forrest; Yoshihide Hayashizaki
Journal: Genome Res Date: 2011-05-19 Impact factor: 9.043

Review 4. Noncoding transcription at enhancers: general principles and functional models.

Authors: Gioacchino Natoli; Jean-Christophe Andrau
Journal: Annu Rev Genet Date: 2012-08-16 Impact factor: 16.830

5. Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.

Authors: William S Kruesi; Leighton J Core; Colin T Waters; John T Lis; Barbara J Meyer
Journal: Elife Date: 2013-06-18 Impact factor: 8.140

6. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.

Authors: Leighton J Core; André L Martins; Charles G Danko; Colin T Waters; Adam Siepel; John T Lis
Journal: Nat Genet Date: 2014-11-10 Impact factor: 38.330

7. An atlas of active enhancers across human cell types and tissues.

Authors: Robin Andersson; Claudia Gebhard; Michael Rehli; Albin Sandelin; Irene Miguel-Escalada; Ilka Hoof; Jette Bornholdt; Mette Boyd; Yun Chen; Xiaobei Zhao; Christian Schmidl; Takahiro Suzuki; Evgenia Ntini; Erik Arner; Eivind Valen; Kang Li; Lucia Schwarzfischer; Dagmar Glatz; Johanna Raithel; Berit Lilje; Nicolas Rapin; Frederik Otzen Bagger; Mette Jørgensen; Peter Refsing Andersen; Nicolas Bertin; Owen Rackham; A Maxwell Burroughs; J Kenneth Baillie; Yuri Ishizu; Yuri Shimizu; Erina Furuhata; Shiori Maeda; Yutaka Negishi; Christopher J Mungall; Terrence F Meehan; Timo Lassmann; Masayoshi Itoh; Hideya Kawaji; Naoto Kondo; Jun Kawai; Andreas Lennartsson; Carsten O Daub; Peter Heutink; David A Hume; Torben Heick Jensen; Harukazu Suzuki; Yoshihide Hayashizaki; Ferenc Müller; Alistair R R Forrest; Piero Carninci
Journal: Nature Date: 2014-03-27 Impact factor: 49.962

7 in total

A shared architecture for promoters and enhancers.

1. ChromHMM: automating chromatin-state discovery and characterization.

2. Transcriptional noise and the fidelity of initiation by RNA polymerase II.

3. Unamplified cap analysis of gene expression on a single-molecule sequencer.

Review 4. Noncoding transcription at enhancers: general principles and functional models.

5. Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation.

6. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers.

7. An atlas of active enhancers across human cell types and tissues.

Review 1. Architectural and Functional Commonalities between Enhancers and Promoters.

2. Discriminative identification of transcriptional responses of promoters and enhancers after stimulus.

3. High-throughput functional comparison of promoter and enhancer activities.

4. TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers.

5. Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data.

Review 6. Non-Coding RNA: Sequence-Specific Guide for Chromatin Modification and DNA Damage Signaling.

Review 7. Progress and challenges in bioinformatics approaches for enhancer identification.