Literature DB >> 26986719

Spatial Organization of Epigenomes.

Jonathan Christopher Dubé1, Xue Qing David Wang1, Josée Dostie1.   

Abstract

The role of genome architecture in transcription regulation has become the focus of an increasing number of studies over the past decade. Chromatin organization can have a significant impact on gene expression by promoting or restricting the physical proximity between regulatory DNA elements. Given that any change in chromatin state has the potential to alter DNA folding and the proximity between control elements, the spatial organization of chromatin is inherently linked to its molecular composition. In this review, we explore how modulators of chromatin state and organization might keep gene expression in check. We discuss recent findings and present some of the less well-studied aspects of spatial genome organization such as chromatin dynamics and regulation by non-coding RNAs.

Keywords:  Chromatin organization; Chromosome conformation capture; Epigenetics; Gene expression; Non-coding RNAs

Year:  2016        PMID: 26986719      PMCID: PMC4723270          DOI: 10.1007/s40610-016-0028-4

Source DB:  PubMed          Journal:  Curr Mol Biol Rep        ISSN: 2198-6428


  103 in total

1.  The Polycomb Ezh2 methyltransferase regulates muscle gene expression and skeletal muscle differentiation.

Authors:  Giuseppina Caretti; Monica Di Padova; Bruce Micales; Gary E Lyons; Vittorio Sartorelli
Journal:  Genes Dev       Date:  2004-11-01       Impact factor: 11.361

2.  The energy landscapes and motions of proteins.

Authors:  H Frauenfelder; S G Sligar; P G Wolynes
Journal:  Science       Date:  1991-12-13       Impact factor: 47.728

Review 3.  Discovering genome regulation with 3C and 3C-related technologies.

Authors:  Sylvain D Ethier; Hisashi Miura; Josée Dostie
Journal:  Biochim Biophys Acta       Date:  2011-12-20

4.  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 5.  The 3D genome in transcriptional regulation and pluripotency.

Authors:  David U Gorkin; Danny Leung; Bing Ren
Journal:  Cell Stem Cell       Date:  2014-06-05       Impact factor: 24.633

6.  A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Authors:  Suhas S P Rao; Miriam H Huntley; Neva C Durand; Elena K Stamenova; Ivan D Bochkov; James T Robinson; Adrian L Sanborn; Ido Machol; Arina D Omer; Eric S Lander; Erez Lieberman Aiden
Journal:  Cell       Date:  2014-12-11       Impact factor: 41.582

7.  Yin Yang 1 is a critical regulator of B-cell development.

Authors:  Huifei Liu; Marc Schmidt-Supprian; Yujiang Shi; Elias Hobeika; Natasha Barteneva; Hassan Jumaa; Roberta Pelanda; Michael Reth; Jane Skok; Klaus Rajewsky; Yang Shi
Journal:  Genes Dev       Date:  2007-05-15       Impact factor: 11.361

8.  The transcriptional landscape of the mammalian genome.

Authors:  P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728

9.  Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins.

Authors:  Jennifer C Harr; Teresa Romeo Luperchio; Xianrong Wong; Erez Cohen; Sarah J Wheelan; Karen L Reddy
Journal:  J Cell Biol       Date:  2015-01-05       Impact factor: 10.539

10.  Recruitment to the nuclear periphery can alter expression of genes in human cells.

Authors:  Lee E Finlan; Duncan Sproul; Inga Thomson; Shelagh Boyle; Elizabeth Kerr; Paul Perry; Bauke Ylstra; Jonathan R Chubb; Wendy A Bickmore
Journal:  PLoS Genet       Date:  2008-03-21       Impact factor: 5.917

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