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Literature DB >> 20373265

Transcriptional gene silencing through epigenetic changes mediated by non-coding RNAs.

Abstract

Chromatin remodeling guided by non-coding RNA (ncRNA) contributes mechanistically to the establishment of chromatin structure and to the maintenance of epigenetic memory. Various ncRNAs have been identified as regulators of chromatin structure and gene expression. The widespread occurrence of antisense transcription in eukaryotes emphasizes the prevalence of gene regulation by natural antisense transcripts. Recently, antisense ncRNAs have been implicated in the silencing of tumor suppressor genes through epigenetic remodeling events. Characterization of the antisense RNAs involved in the development or maintenance of oncogenic states may define ncRNAs as early biomarkers for the emergence of cancer, and could have a significant impact on the development of tools for disease diagnosis and treatment. In this review, current knowledge on the mechanisms of ncRNA-mediated transcriptional gene silencing in humans is discussed, and parallels between the establishment of a silent chromatin state mediated by siRNAs and long antisense ncRNAs are highlighted.

Entities: CellLine Chemical Disease Gene Species

Mesh：

Substances：

Year: 2010 PMID： 20373265 PMCID： PMC2861437

Source DB: PubMed Journal: Curr Opin Mol Ther ISSN： 1464-8431

99 in total

1. DNA methyltransferase Dnmt1 associates with histone deacetylase activity.

Authors: F Fuks; W A Burgers; A Brehm; L Hughes-Davies; T Kouzarides
Journal: Nat Genet Date: 2000-01 Impact factor: 38.330

2. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin.

Authors: Antoine H F M Peters; Stefan Kubicek; Karl Mechtler; Roderick J O'Sullivan; Alwin A H A Derijck; Laura Perez-Burgos; Alexander Kohlmaier; Susanne Opravil; Makoto Tachibana; Yoichi Shinkai; Joost H A Martens; Thomas Jenuwein
Journal: Mol Cell Date: 2003-12 Impact factor: 17.970

Review 3. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins.

Authors: Leonie Ringrose; Renato Paro
Journal: Annu Rev Genet Date: 2004 Impact factor: 16.830

4. Crucial role of antisense transcription across the Xist promoter in Tsix-mediated Xist chromatin modification.

Authors: Tatsuya Ohhata; Yuko Hoki; Hiroyuki Sasaki; Takashi Sado
Journal: Development Date: 2007-12-05 Impact factor: 6.868

5. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors: Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal: Nature Date: 2007-06-14 Impact factor: 49.962

6. Promoter-targeted siRNAs induce gene silencing of simian immunodeficiency virus (SIV) infection in vitro.

Authors: Heidi G W Lim; Kazuo Suzuki; David A Cooper; Anthony D Kelleher
Journal: Mol Ther Date: 2008-01-29 Impact factor: 11.454

Review 7. Epigenetic changes in cancer.

Authors: Kirsten Grønbaek; Christoffer Hother; Peter A Jones
Journal: APMIS Date: 2007-10 Impact factor: 3.205

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

Review 9. Small RNAs in transcriptional gene silencing and genome defence.

Authors: Danesh Moazed
Journal: Nature Date: 2009-01-22 Impact factor: 49.962

Review 10. The genetic signatures of noncoding RNAs.

Authors: John S Mattick
Journal: PLoS Genet Date: 2009-04-24 Impact factor: 5.917

43 in total

Review 1. The redox basis of epigenetic modifications: from mechanisms to functional consequences.

Authors: Anthony R Cyr; Frederick E Domann
Journal: Antioxid Redox Signal Date: 2011-02-05 Impact factor: 8.401

2. Transcriptional gene silencing of HIV-1 through promoter targeted RNA is highly specific.

Authors: Kazuo Suzuki; Takaomi Ishida; Makoto Yamagishi; Chantelle Ahlenstiel; Sanjay Swaminathan; Katharine Marks; Daniel Murray; Erin M McCartney; Michael R Beard; Marina Alexander; Damian F J Purcell; David A Cooper; Toshiki Watanabe; Anthony D Kelleher
Journal: RNA Biol Date: 2011-11-01 Impact factor: 4.652

Transcriptional gene silencing through epigenetic changes mediated by non-coding RNAs.

1. DNA methyltransferase Dnmt1 associates with histone deacetylase activity.

2. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin.

Review 3. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins.

4. Crucial role of antisense transcription across the Xist promoter in Tsix-mediated Xist chromatin modification.

5. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

6. Promoter-targeted siRNAs induce gene silencing of simian immunodeficiency virus (SIV) infection in vitro.

Review 7. Epigenetic changes in cancer.

8. The transcriptional landscape of the mammalian genome.

Review 9. Small RNAs in transcriptional gene silencing and genome defence.

Review 10. The genetic signatures of noncoding RNAs.

Review 1. The redox basis of epigenetic modifications: from mechanisms to functional consequences.

2. Transcriptional gene silencing of HIV-1 through promoter targeted RNA is highly specific.

Review 3. Noisy silence: non-coding RNA and heterochromatin formation at repetitive elements.

Review 4. Diabetic embryopathy: a role for the epigenome?

Review 5. Chromatin structure of pluripotent stem cells and induced pluripotent stem cells.

Review 6. RITS-connecting transcription, RNA interference, and heterochromatin assembly in fission yeast.

7. High expression of CAI2, a 9p21-embedded long noncoding RNA, contributes to advanced-stage neuroblastoma.

Review 8. The theory of RNA-mediated gene evolution.

Review 9. CRISPR/Cas9: molecular tool for gene therapy to target genome and epigenome in the treatment of lung cancer.

10. A potential suppressive effect of natural antisense IL-1β RNA on lipopolysaccharide-induced IL-1β expression.