Literature DB >> 22337053

Modular regulatory principles of large non-coding RNAs.

Mitchell Guttman1, John L Rinn.   

Abstract

It is clear that RNA has a diverse set of functions and is more than just a messenger between gene and protein. The mammalian genome is extensively transcribed, giving rise to thousands of non-coding transcripts. Whether all of these transcripts are functional is debated, but it is evident that there are many functional large non-coding RNAs (ncRNAs). Recent studies have begun to explore the functional diversity and mechanistic role of these large ncRNAs. Here we synthesize these studies to provide an emerging model whereby large ncRNAs might achieve regulatory specificity through modularity, assembling diverse combinations of proteins and possibly RNA and DNA interactions.

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Year:  2012        PMID: 22337053      PMCID: PMC4197003          DOI: 10.1038/nature10887

Source DB:  PubMed          Journal:  Nature        ISSN: 0028-0836            Impact factor:   49.962


  99 in total

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2.  Ripples from neighbouring transcription.

Authors:  Miki Ebisuya; Takuya Yamamoto; May Nakajima; Eisuke Nishida
Journal:  Nat Cell Biol       Date:  2008-09       Impact factor: 28.824

3.  Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation.

Authors:  Radha Raman Pandey; Tanmoy Mondal; Faizaan Mohammad; Stefan Enroth; Lisa Redrup; Jan Komorowski; Takashi Nagano; Debora Mancini-Dinardo; Chandrasekhar Kanduri
Journal:  Mol Cell       Date:  2008-10-24       Impact factor: 17.970

4.  Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Authors:  Ali Mortazavi; Brian A Williams; Kenneth McCue; Lorian Schaeffer; Barbara Wold
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

5.  Divergent transcription from active promoters.

Authors:  Amy C Seila; J Mauro Calabrese; Stuart S Levine; Gene W Yeo; Peter B Rahl; Ryan A Flynn; Richard A Young; Phillip A Sharp
Journal:  Science       Date:  2008-12-04       Impact factor: 47.728

Review 6.  MicroRNAs: target recognition and regulatory functions.

Authors:  David P Bartel
Journal:  Cell       Date:  2009-01-23       Impact factor: 41.582

7.  Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome.

Authors:  Jing Zhao; Bryan K Sun; Jennifer A Erwin; Ji-Joon Song; Jeannie T Lee
Journal:  Science       Date:  2008-10-31       Impact factor: 47.728

8.  The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin.

Authors:  Takashi Nagano; Jennifer A Mitchell; Lionel A Sanz; Florian M Pauler; Anne C Ferguson-Smith; Robert Feil; Peter Fraser
Journal:  Science       Date:  2008-11-06       Impact factor: 47.728

9.  Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription.

Authors:  Xiangting Wang; Shigeki Arai; Xiaoyuan Song; Donna Reichart; Kun Du; Gabriel Pascual; Paul Tempst; Michael G Rosenfeld; Christopher K Glass; Riki Kurokawa
Journal:  Nature       Date:  2008-05-28       Impact factor: 49.962

Review 10.  Differentiating protein-coding and noncoding RNA: challenges and ambiguities.

Authors:  Marcel E Dinger; Ken C Pang; Tim R Mercer; John S Mattick
Journal:  PLoS Comput Biol       Date:  2008-11-28       Impact factor: 4.475

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  983 in total

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Review 2.  Endogenous viruses: insights into viral evolution and impact on host biology.

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Journal:  Nat Rev Genet       Date:  2012-03-16       Impact factor: 53.242

3.  "Snorkeling" for missing players in cancer.

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Journal:  J Clin Invest       Date:  2012-07-02       Impact factor: 14.808

4.  Understanding the photophysics of the spinach-DFHBI RNA aptamer-fluorogen complex to improve live-cell RNA imaging.

Authors:  Kyu Young Han; Benjamin J Leslie; Jingyi Fei; Jichuan Zhang; Taekjip Ha
Journal:  J Am Chem Soc       Date:  2013-12-10       Impact factor: 15.419

5.  Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm.

Authors:  Supatcha Lertampaiporn; Chinae Thammarongtham; Chakarida Nukoolkit; Boonserm Kaewkamnerdpong; Marasri Ruengjitchatchawalya
Journal:  Nucleic Acids Res       Date:  2014-04-25       Impact factor: 16.971

Review 6.  Encoding activities of non-coding RNAs.

Authors:  Yanan Pang; Chuanbin Mao; Shanrong Liu
Journal:  Theranostics       Date:  2018-03-28       Impact factor: 11.556

7.  Long noncoding RNA SPRY4-IT1 is upregulated in esophageal squamous cell carcinoma and associated with poor prognosis.

Authors:  Hai-Wei Xie; Qing-Quan Wu; Bin Zhu; Fang-Jun Chen; Lv Ji; Su-Qing Li; Chun-Mei Wang; Yu-Suo Tong; Lei Tuo; Ming Wu; Zhi-Hua Liu; Jin Lv; Wei-Hong Shi; Xiu-Feng Cao
Journal:  Tumour Biol       Date:  2014-05-09

8.  CEBPA-mediated upregulation of the lncRNA PLIN2 promotes the development of chronic myelogenous leukemia via the GSK3 and Wnt/β-catenin signaling pathways.

Authors:  Chengming Sun; Shuping Luan; Guili Zhang; Na Wang; Huiyuan Shao; Caifu Luan
Journal:  Am J Cancer Res       Date:  2017-05-01       Impact factor: 6.166

9.  Insertion of an Alu element in a lncRNA leads to primate-specific modulation of alternative splicing.

Authors:  Shanshan Hu; Xiaolin Wang; Ge Shan
Journal:  Nat Struct Mol Biol       Date:  2016-10-03       Impact factor: 15.369

Review 10.  Long noncoding RNAs in innate and adaptive immunity.

Authors:  Katherine A Fitzgerald; Daniel R Caffrey
Journal:  Curr Opin Immunol       Date:  2013-12-22       Impact factor: 7.486

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