Literature DB >> 23045397

Distant activation of transcription: mechanisms of enhancer action.

Olga I Kulaeva1, Ekaterina V Nizovtseva, Yury S Polikanov, Sergei V Ulianov, Vasily M Studitsky.   

Abstract

Enhancers are regulatory DNA sequences that activate transcription over long distances. Recent studies revealed a widespread role of distant activation in eukaryotic gene regulation and in development of various human diseases, including cancer. Genomic and gene-targeted studies of enhancer action revealed novel mechanisms of transcriptional activation over a distance. They include formation of stable, inactive DNA-protein complexes at the enhancer and target promoter before activation, facilitated distant communication by looping of the spacer chromatin-covered DNA, and promoter activation by mechanisms that are different from classic recruiting. These studies suggest the similarity between the looping mechanisms involved in enhancer action on DNA in bacteria and in chromatin of higher organisms.

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Year:  2012        PMID: 23045397      PMCID: PMC3510544          DOI: 10.1128/MCB.01127-12

Source DB:  PubMed          Journal:  Mol Cell Biol        ISSN: 0270-7306            Impact factor:   4.272


  57 in total

1.  Probability of the site juxtaposition determines the rate of protein-mediated DNA looping.

Authors:  Yury S Polikanov; Vladimir A Bondarenko; Vladimir Tchernaenko; Yong I Jiang; Leonard C Lutter; Alexander Vologodskii; Vasily M Studitsky
Journal:  Biophys J       Date:  2007-06-15       Impact factor: 4.033

2.  Rationally designed insulator-like elements can block enhancer action in vitro.

Authors:  Vladimir A Bondarenko; Yong I Jiang; Vasily M Studitsky
Journal:  EMBO J       Date:  2003-09-15       Impact factor: 11.598

3.  Spontaneous access to DNA target sites in folded chromatin fibers.

Authors:  Michael G Poirier; Malte Bussiek; Jörg Langowski; Jonathan Widom
Journal:  J Mol Biol       Date:  2008-04-16       Impact factor: 5.469

4.  TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation.

Authors:  Gabor Papai; Manish K Tripathi; Christine Ruhlmann; Justin H Layer; P Anthony Weil; Patrick Schultz
Journal:  Nature       Date:  2010-06-17       Impact factor: 49.962

5.  Ectopic nuclear reorganisation driven by a Hoxb1 transgene transposed into Hoxd.

Authors:  Céline Morey; Nelly R Da Silva; Marie Kmita; Denis Duboule; Wendy A Bickmore
Journal:  J Cell Sci       Date:  2008-02-05       Impact factor: 5.285

Review 6.  Nuclear organization of the genome and the potential for gene regulation.

Authors:  Peter Fraser; Wendy Bickmore
Journal:  Nature       Date:  2007-05-24       Impact factor: 49.962

7.  Mediator and cohesin connect gene expression and chromatin architecture.

Authors:  Michael H Kagey; Jamie J Newman; Steve Bilodeau; Ye Zhan; David A Orlando; Nynke L van Berkum; Christopher C Ebmeier; Jesse Goossens; Peter B Rahl; Stuart S Levine; Dylan J Taatjes; Job Dekker; Richard A Young
Journal:  Nature       Date:  2010-08-18       Impact factor: 49.962

8.  Widespread transcription at neuronal activity-regulated enhancers.

Authors:  Tae-Kyung Kim; Martin Hemberg; Jesse M Gray; Allen M Costa; Daniel M Bear; Jing Wu; David A Harmin; Mike Laptewicz; Kellie Barbara-Haley; Scott Kuersten; Eirene Markenscoff-Papadimitriou; Dietmar Kuhl; Haruhiko Bito; Paul F Worley; Gabriel Kreiman; Michael E Greenberg
Journal:  Nature       Date:  2010-04-14       Impact factor: 49.962

Review 9.  Genomic views of distant-acting enhancers.

Authors:  Axel Visel; Edward M Rubin; Len A Pennacchio
Journal:  Nature       Date:  2009-09-10       Impact factor: 49.962

10.  H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions.

Authors:  Chunyuan Jin; Chongzhi Zang; Gang Wei; Kairong Cui; Weiqun Peng; Keji Zhao; Gary Felsenfeld
Journal:  Nat Genet       Date:  2009-07-26       Impact factor: 38.330

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  45 in total

1.  Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization.

Authors:  Dianbo Liu; Jose Davila-Velderrain; Zhizhuo Zhang; Manolis Kellis
Journal:  Nucleic Acids Res       Date:  2019-08-22       Impact factor: 16.971

2.  Phospho-ΔNp63α/microRNA network modulates epigenetic regulatory enzymes in squamous cell carcinomas.

Authors:  Edward A Ratovitski
Journal:  Cell Cycle       Date:  2014-01-06       Impact factor: 4.534

Review 3.  Molecular mechanisms of human papillomavirus-related carcinogenesis in head and neck cancer.

Authors:  Farhoud Faraji; Munfarid Zaidi; Carole Fakhry; Daria A Gaykalova
Journal:  Microbes Infect       Date:  2017-06-12       Impact factor: 2.700

4.  DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation.

Authors:  Stefan M Giovan; Andreas Hanke; Stephen D Levene
Journal:  Biopolymers       Date:  2015-09       Impact factor: 2.505

5.  Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping.

Authors:  Stefan M Giovan; Robert G Scharein; Andreas Hanke; Stephen D Levene
Journal:  J Chem Phys       Date:  2014-11-07       Impact factor: 3.488

Review 6.  Towards quantitative analysis of gene regulation by enhancers.

Authors:  Ekaterina V Nizovtseva; Stefjord Todolli; Wilma K Olson; Vasily M Studitsky
Journal:  Epigenomics       Date:  2017-08-11       Impact factor: 4.778

7.  Rainbow Enhancers Regulate Restrictive Transcription in Teleost Green, Red, and Blue Cones.

Authors:  Wei Fang; Chuanyu Guo; Xiangyun Wei
Journal:  J Neurosci       Date:  2017-02-13       Impact factor: 6.167

8.  Nucleosome spacing periodically modulates nucleosome chain folding and DNA topology in circular nucleosome arrays.

Authors:  Mikhail V Bass; Tatiana Nikitina; Davood Norouzi; Victor B Zhurkin; Sergei A Grigoryev
Journal:  J Biol Chem       Date:  2019-01-10       Impact factor: 5.157

Review 9.  Genomic perspectives of transcriptional regulation in forebrain development.

Authors:  Alex S Nord; Kartik Pattabiraman; Axel Visel; John L R Rubenstein
Journal:  Neuron       Date:  2015-01-07       Impact factor: 17.173

Review 10.  Enhancer biology and enhanceropathies.

Authors:  Edwin Smith; Ali Shilatifard
Journal:  Nat Struct Mol Biol       Date:  2014-03       Impact factor: 15.369

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