Literature DB >> 24290031

Long noncoding RNAs: fresh perspectives into the RNA world.

Lin Yang1, John E Froberg1, Jeannie T Lee2.   

Abstract

Large-scale mapping of transcriptomes has revealed significant levels of transcriptional activity within both unannotated and annotated regions of the genome. Interestingly, many of the novel transcripts demonstrate tissue-specific expression and some level of sequence conservation across species, but most have low protein-coding potential. Here, we describe progress in identifying and characterizing long noncoding RNAs (lncRNAs) and review how these transcripts interact with other biological molecules to regulate diverse cellular processes. We also preview emerging techniques that will help advance the discovery and characterization of novel transcripts. Finally, we discuss the role of lncRNAs in disease and therapeutics.
Copyright © 2013 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  Long noncoding RNA; epigenetics; next-generation sequencing; therapeutics

Mesh:

Substances:

Year:  2013        PMID: 24290031      PMCID: PMC3904784          DOI: 10.1016/j.tibs.2013.10.002

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  103 in total

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2.  Jpx RNA activates Xist by evicting CTCF.

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Journal:  Cell       Date:  2013-06-20       Impact factor: 41.582

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

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Journal:  Mol Cell       Date:  2011-09-16       Impact factor: 17.970

Review 4.  Understanding the transcriptome through RNA structure.

Authors:  Yue Wan; Michael Kertesz; Robert C Spitale; Eran Segal; Howard Y Chang
Journal:  Nat Rev Genet       Date:  2011-08-18       Impact factor: 53.242

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

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Journal:  Genes Dev       Date:  2008-03-15       Impact factor: 11.361

6.  Most "dark matter" transcripts are associated with known genes.

Authors:  Harm van Bakel; Corey Nislow; Benjamin J Blencowe; Timothy R Hughes
Journal:  PLoS Biol       Date:  2010-05-18       Impact factor: 8.029

7.  Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription.

Authors:  Minna U Kaikkonen; Nathanael J Spann; Sven Heinz; Casey E Romanoski; Karmel A Allison; Joshua D Stender; Hyun B Chun; David F Tough; Rab K Prinjha; Christopher Benner; Christopher K Glass
Journal:  Mol Cell       Date:  2013-08-08       Impact factor: 17.970

8.  The transcriptional landscape of the mammalian genome.

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9.  Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression.

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Journal:  Nat Biotechnol       Date:  2011-07-31       Impact factor: 54.908

10.  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

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  157 in total

Review 1.  Noncoding RNAs and pancreatic cancer.

Authors:  Juan-Fei Peng; Yan-Yan Zhuang; Feng-Ting Huang; Shi-Neng Zhang
Journal:  World J Gastroenterol       Date:  2016-01-14       Impact factor: 5.742

Review 2.  Transcriptome complexity in cardiac development and diseases--an expanding universe between genome and phenome.

Authors:  Chen Gao; Yibin Wang
Journal:  Circ J       Date:  2014-04-22       Impact factor: 2.993

3.  Technologies to probe functions and mechanisms of long noncoding RNAs.

Authors:  Ci Chu; Robert C Spitale; Howard Y Chang
Journal:  Nat Struct Mol Biol       Date:  2015-01       Impact factor: 15.369

Review 4.  Long non-coding RNAs (lncRNAs) and their transcriptional control of inflammatory responses.

Authors:  Nicholas W Mathy; Xian-Ming Chen
Journal:  J Biol Chem       Date:  2017-06-14       Impact factor: 5.157

Review 5.  The crosstalk between long non-coding RNAs and PI3K in cancer.

Authors:  Leonidas Benetatos; Evangelos Voulgaris; Georgios Vartholomatos
Journal:  Med Oncol       Date:  2017-02-07       Impact factor: 3.064

Review 6.  Noncoding RNAs: Regulators of the Mammalian Transcription Machinery.

Authors:  Tess M Eidem; Jennifer F Kugel; James A Goodrich
Journal:  J Mol Biol       Date:  2016-02-23       Impact factor: 5.469

Review 7.  Connecting the dots: chromatin and alternative splicing in EMT.

Authors:  Jessica A Warns; James R Davie; Archana Dhasarathy
Journal:  Biochem Cell Biol       Date:  2015-07-07       Impact factor: 3.626

8.  Two deletions overlapping a distant FOXF1 enhancer unravel the role of lncRNA LINC01081 in etiology of alveolar capillary dysplasia with misalignment of pulmonary veins.

Authors:  Przemyslaw Szafranski; Avinash V Dharmadhikari; Jennifer A Wambach; Chris T Towe; Frances V White; R Mark Grady; Pirooz Eghtesady; F Sessions Cole; Gail Deutsch; Partha Sen; Paweł Stankiewicz
Journal:  Am J Med Genet A       Date:  2014-05-19       Impact factor: 2.802

9.  Long non-coding RNA ANRIL regulates inflammatory responses as a novel component of NF-κB pathway.

Authors:  Xiao Zhou; Xiaorui Han; Ann Wittfeldt; Jingzhi Sun; Chujun Liu; Xiaoxia Wang; Li-Ming Gan; Huiqing Cao; Zicai Liang
Journal:  RNA Biol       Date:  2016       Impact factor: 4.652

10.  Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA.

Authors:  Robert D Bell; Xiaochun Long; Mingyan Lin; Jan H Bergmann; Vivek Nanda; Sarah L Cowan; Qian Zhou; Yu Han; David L Spector; Deyou Zheng; Joseph M Miano
Journal:  Arterioscler Thromb Vasc Biol       Date:  2014-02-27       Impact factor: 8.311

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