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Literature DB >> 22223044

Initiating RNA polymerase II and TIPs as hallmarks of enhancer activity and tissue-specificity.

Abstract

In past years, many efforts were invested to define epigenetic features associated with enhancers of transcription. We propose that both transcription initiation and the H3K4me3 histone modification are among the best hallmarks of active enhancers in several primary tissues and extend the concept of large transcription initiation platforms (TIPs).

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Year: 2011 PMID： 22223044 PMCID： PMC3265787 DOI： 10.4161/trns.2.6.18747

Source DB: PubMed Journal: Transcription ISSN： 2154-1272

25 in total

1. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.

Authors: Nathaniel D Heintzman; Rhona K Stuart; Gary Hon; Yutao Fu; Christina W Ching; R David Hawkins; Leah O Barrera; Sara Van Calcar; Chunxu Qu; Keith A Ching; Wei Wang; Zhiping Weng; Roland D Green; Gregory E Crawford; Bing Ren
Journal: Nat Genet Date: 2007-02-04 Impact factor: 38.330

Review 2. Genome-wide RNA polymerase II: not genes only!

Authors: Frederic Koch; Frederic Jourquin; Pierre Ferrier; Jean-Christophe Andrau
Journal: Trends Biochem Sci Date: 2008-05-06 Impact factor: 13.807

3. Combinatorial patterns of histone acetylations and methylations in the human genome.

Authors: Zhibin Wang; Chongzhi Zang; Jeffrey A Rosenfeld; Dustin E Schones; Artem Barski; Suresh Cuddapah; Kairong Cui; Tae-Young Roh; Weiqun Peng; Michael Q Zhang; Keji Zhao
Journal: Nat Genet Date: 2008-06-15 Impact factor: 38.330

4. H3K4 tri-methylation provides an epigenetic signature of active enhancers.

Authors: Aleksandra Pekowska; Touati Benoukraf; Joaquin Zacarias-Cabeza; Mohamed Belhocine; Frederic Koch; Hélène Holota; Jean Imbert; Jean-Christophe Andrau; Pierre Ferrier; Salvatore Spicuglia
Journal: EMBO J Date: 2011-08-16 Impact factor: 11.598

5. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling.

Authors: Vladimir R Ramirez-Carrozzi; Daniel Braas; Dev M Bhatt; Christine S Cheng; Christine Hong; Kevin R Doty; Joshua C Black; Alexander Hoffmann; Michael Carey; Stephen T Smale
Journal: Cell Date: 2009-07-10 Impact factor: 41.582

6. Histone modifications at human enhancers reflect global cell-type-specific gene expression.

Authors: Nathaniel D Heintzman; Gary C Hon; R David Hawkins; Pouya Kheradpour; Alexander Stark; Lindsey F Harp; Zhen Ye; Leonard K Lee; Rhona K Stuart; Christina W Ching; Keith A Ching; Jessica E Antosiewicz-Bourget; Hui Liu; Xinmin Zhang; Roland D Green; Victor V Lobanenkov; Ron Stewart; James A Thomson; Gregory E Crawford; Manolis Kellis; Bing Ren
Journal: Nature Date: 2009-03-18 Impact factor: 49.962

7. Stalled Hox promoters as chromosomal boundaries.

Authors: Vivek S Chopra; Jessica Cande; Joung-Woo Hong; Michael Levine
Journal: Genes Dev Date: 2009-06-10 Impact factor: 11.361

8. ChIP-seq accurately predicts tissue-specific activity of enhancers.

Authors: Axel Visel; Matthew J Blow; Zirong Li; Tao Zhang; Jennifer A Akiyama; Amy Holt; Ingrid Plajzer-Frick; Malak Shoukry; Crystal Wright; Feng Chen; Veena Afzal; Bing Ren; Edward M Rubin; Len A Pennacchio
Journal: Nature Date: 2009-02-12 Impact factor: 49.962

9. Jmjd3 contributes to the control of gene expression in LPS-activated macrophages.

Authors: Francesca De Santa; Vipin Narang; Zhei Hwee Yap; Betsabeh Khoramian Tusi; Thomas Burgold; Liv Austenaa; Gabriele Bucci; Marieta Caganova; Samuele Notarbartolo; Stefano Casola; Giuseppe Testa; Wing-Kin Sung; Chia-Lin Wei; Gioacchino Natoli
Journal: EMBO J Date: 2009-09-24 Impact factor: 11.598

10. BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

Authors: Chunlei Wu; Camilo Orozco; Jason Boyer; Marc Leglise; James Goodale; Serge Batalov; Christopher L Hodge; James Haase; Jeff Janes; Jon W Huss; Andrew I Su
Journal: Genome Biol Date: 2009-11-17 Impact factor: 13.583

22 in total

Review 1. Transcription regulation by distal enhancers: who's in the loop?

Authors: Ralph Stadhouders; Anita van den Heuvel; Petros Kolovos; Ruud Jorna; Kris Leslie; Frank Grosveld; Eric Soler
Journal: Transcription Date: 2012-07-01

2. PLZF regulates CCR6 and is critical for the acquisition and maintenance of the Th17 phenotype in human cells.

Authors: Satya P Singh; Hongwei H Zhang; Hsinyi Tsang; Paul J Gardina; Timothy G Myers; Vijayaraj Nagarajan; Chang Hoon Lee; Joshua M Farber
Journal: J Immunol Date: 2015-04-01 Impact factor: 5.422

3. Suppression of Enhancer Overactivation by a RACK7-Histone Demethylase Complex.

Authors: Hongjie Shen; Wenqi Xu; Rui Guo; Bowen Rong; Lei Gu; Zhentian Wang; Chenxi He; Lijuan Zheng; Xin Hu; Zhen Hu; Zhi-Ming Shao; Pengyuan Yang; Feizhen Wu; Yujiang Geno Shi; Yang Shi; Fei Lan
Journal: Cell Date: 2016-04-07 Impact factor: 41.582

Review 4. Preparing the first responders: building the inflammatory transcriptome from the ground up.

Authors: Inez Rogatsky; Karen Adelman
Journal: Mol Cell Date: 2014-04-24 Impact factor: 17.970

Review 5. Characterization of noncoding regulatory DNA in the human genome.

Authors: Ran Elkon; Reuven Agami
Journal: Nat Biotechnol Date: 2017-08-08 Impact factor: 54.908

Review 6. Chromatin remodeling effects on enhancer activity.

Authors: Estela García-González; Martín Escamilla-Del-Arenal; Rodrigo Arzate-Mejía; Félix Recillas-Targa
Journal: Cell Mol Life Sci Date: 2016-03-30 Impact factor: 9.261

7. Selective inhibition of CTCF binding by iAs directs TET-mediated reprogramming of 5-hydroxymethylation patterns in iAs-transformed cells.

Authors: Matthew Rea; Tyler Gripshover; Yvonne Fondufe-Mittendorf
Journal: Toxicol Appl Pharmacol Date: 2017-11-22 Impact factor: 4.219