Literature DB >> 23132386

Cis-acting noncoding RNAs: friends and foes.

Sònia Guil1, Manel Esteller.   

Abstract

In recent years, the number and types of known functional noncoding RNAs have increased considerably. A subset of both short- and long-sized species are known to be involved in the cis regulation of target genes located at or near the same genomic locus. Their expression is often coordinated with that of neighboring protein-coding genes, and in many cases, related transcripts can influence each other at one step or another during their biogenesis. Here, we review the current literature, summarizing the existing knowledge about mammalian cis-acting RNAs and their impact on physiological and disease states.

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Year:  2012        PMID： 23132386     DOI： 10.1038/nsmb.2428

Source DB:  PubMed          Journal:  Nat Struct Mol Biol        ISSN： 1545-9985            Impact factor:   15.369


  102 in total

1.  The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and represses RNA polymerase I transcription.

Authors:  Yonggang Zhou; Raffaella Santoro; Ingrid Grummt
Journal:  EMBO J       Date:  2002-09-02       Impact factor: 11.598

Review 2.  Genome-wide transcription and the implications for genomic organization.

Authors:  Philipp Kapranov; Aarron T Willingham; Thomas R Gingeras
Journal:  Nat Rev Genet       Date:  2007-05-08       Impact factor: 53.242

3.  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

4.  The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin.

Authors:  Stéphane Bertani; Silvia Sauer; Eugene Bolotin; Frank Sauer
Journal:  Mol Cell       Date:  2011-09-16       Impact factor: 17.970

Review 5.  Genomic imprinting: the emergence of an epigenetic paradigm.

Authors:  Anne C Ferguson-Smith
Journal:  Nat Rev Genet       Date:  2011-07-18       Impact factor: 53.242

6.  A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition.

Authors:  Manuel Beltran; Isabel Puig; Cristina Peña; José Miguel García; Ana Belén Alvarez; Raúl Peña; Félix Bonilla; Antonio García de Herreros
Journal:  Genes Dev       Date:  2008-03-15       Impact factor: 11.361

7.  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

8.  The reality of pervasive transcription.

Authors:  Michael B Clark; Paulo P Amaral; Felix J Schlesinger; Marcel E Dinger; Ryan J Taft; John L Rinn; Chris P Ponting; Peter F Stadler; Kevin V Morris; Antonin Morillon; Joel S Rozowsky; Mark B Gerstein; Claes Wahlestedt; Yoshihide Hayashizaki; Piero Carninci; Thomas R Gingeras; John S Mattick
Journal:  PLoS Biol       Date:  2011-07-12       Impact factor: 8.029

9.  Natural antisense transcript of natriuretic peptide precursor A (NPPA): structural organization and modulation of NPPA expression.

Authors:  Tarmo Annilo; Katrin Kepp; Maris Laan
Journal:  BMC Mol Biol       Date:  2009-08-11       Impact factor: 2.946

10.  Polycomb CBX7 has a unifying role in cellular lifespan.

Authors:  Jesús Gil; David Bernard; Dolores Martínez; David Beach
Journal:  Nat Cell Biol       Date:  2003-11-30       Impact factor: 28.213
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  173 in total

Review 1.  Unique features of long non-coding RNA biogenesis and function.

Authors:  Jeffrey J Quinn; Howard Y Chang
Journal:  Nat Rev Genet       Date:  2016-01       Impact factor: 53.242

2.  The Small RNA sr8384 Is a Crucial Regulator of Cell Growth in Solventogenic Clostridia.

Authors:  Yunpeng Yang; Huan Zhang; Nannan Lang; Lu Zhang; Changsheng Chai; Huiqi He; Weihong Jiang; Yang Gu
Journal:  Appl Environ Microbiol       Date:  2020-06-17       Impact factor: 4.792

3.  ELF18-INDUCED LONG-NONCODING RNA Associates with Mediator to Enhance Expression of Innate Immune Response Genes in Arabidopsis.

Authors:  Jun Sung Seo; Hai-Xi Sun; Bong Soo Park; Chung-Hao Huang; Shyi-Dong Yeh; Choonkyun Jung; Nam-Hai Chua
Journal:  Plant Cell       Date:  2017-04-11       Impact factor: 11.277

4.  CPF Recruitment to Non-canonical Transcription Termination Sites Triggers Heterochromatin Assembly and Gene Silencing.

Authors:  Tommy V Vo; Jothy Dhakshnamoorthy; Madeline Larkin; Martin Zofall; Gobi Thillainadesan; Vanivilasini Balachandran; Sahana Holla; David Wheeler; Shiv I S Grewal
Journal:  Cell Rep       Date:  2019-07-02       Impact factor: 9.423

Review 5.  All's well that transcribes well: non-coding RNAs and post-stroke brain damage.

Authors:  Raghu Vemuganti
Journal:  Neurochem Int       Date:  2013-08-15       Impact factor: 3.921

Review 6.  Gene regulation by antisense transcription.

Authors:  Vicent Pelechano; Lars M Steinmetz
Journal:  Nat Rev Genet       Date:  2013-11-12       Impact factor: 53.242

7.  Overexpressed in colorectal carcinoma gene (OCC-1) upregulation and APPL2 gene downregulation in breast cancer specimens.

Authors:  Abolfazl Ghalaei; Maryam Kay; Shiva Zarrinfam; Parisa Hoseinpour; Mehrdad Behmanesh; Bahram M Soltani
Journal:  Mol Biol Rep       Date:  2018-09-14       Impact factor: 2.316

8.  Linc-YY1 promotes myogenic differentiation and muscle regeneration through an interaction with the transcription factor YY1.

Authors:  Liang Zhou; Kun Sun; Yu Zhao; Suyang Zhang; Xuecong Wang; Yuying Li; Leina Lu; Xiaona Chen; Fengyuan Chen; Xichen Bao; Xihua Zhu; Lijun Wang; Ling-Yin Tang; Miguel A Esteban; Chi-Chiu Wang; Ralf Jauch; Hao Sun; Huating Wang
Journal:  Nat Commun       Date:  2015-12-11       Impact factor: 14.919

Review 9.  Targeting RNA in mammalian systems with small molecules.

Authors:  Anita Donlic; Amanda E Hargrove
Journal:  Wiley Interdiscip Rev RNA       Date:  2018-05-03       Impact factor: 9.957

10.  Long noncoding RNA derived from CD244 signaling epigenetically controls CD8+ T-cell immune responses in tuberculosis infection.

Authors:  Yang Wang; Huiling Zhong; Xiaodan Xie; Crystal Y Chen; Dan Huang; Ling Shen; Hui Zhang; Zheng W Chen; Gucheng Zeng
Journal:  Proc Natl Acad Sci U S A       Date:  2015-07-06       Impact factor: 11.205
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