Literature DB >> 24105322

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts.

Sarah Geisler1, Jeff Coller.   

Abstract

The increased application of transcriptome-wide profiling approaches has led to an explosion in the number of documented long non-coding RNAs (lncRNAs). While these new and enigmatic players in the complex transcriptional milieu are encoded by a significant proportion of the genome, their functions are mostly unknown. Early discoveries support a paradigm in which lncRNAs regulate transcription via chromatin modulation, but new functions are steadily emerging. Given the biochemical versatility of RNA, lncRNAs may be used for various tasks, including post-transcriptional regulation, organization of protein complexes, cell-cell signalling and allosteric regulation of proteins.

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Year:  2013        PMID: 24105322      PMCID: PMC4852478          DOI: 10.1038/nrm3679

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN: 1471-0072            Impact factor:   94.444


  123 in total

Review 1.  Metabolic enzymes that bind RNA: yet another level of cellular regulatory network?

Authors:  Joanna Cieśla
Journal:  Acta Biochim Pol       Date:  2006-01-12       Impact factor: 2.149

2.  A starvation-induced noncoding RNA modulates expression of Dicer-regulated genes.

Authors:  Sabine Hellwig; Brenda L Bass
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-22       Impact factor: 11.205

Review 3.  Horizontal transfer of RNAs: exosomes as mediators of intercellular communication.

Authors:  Saraswathi Ramachandran; Viswanathan Palanisamy
Journal:  Wiley Interdiscip Rev RNA       Date:  2011-10-19       Impact factor: 9.957

4.  A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.

Authors:  Kevin C Wang; Yul W Yang; Bo Liu; Amartya Sanyal; Ryan Corces-Zimmerman; Yong Chen; Bryan R Lajoie; Angeline Protacio; Ryan A Flynn; Rajnish A Gupta; Joanna Wysocka; Ming Lei; Job Dekker; Jill A Helms; Howard Y Chang
Journal:  Nature       Date:  2011-03-20       Impact factor: 49.962

5.  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

6.  Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase.

Authors:  Mohammad Ali Faghihi; Farzaneh Modarresi; Ahmad M Khalil; Douglas E Wood; Barbara G Sahagan; Todd E Morgan; Caleb E Finch; Georges St Laurent; Paul J Kenny; Claes Wahlestedt
Journal:  Nat Med       Date:  2008-06-29       Impact factor: 53.440

7.  Yeast telomerase RNA: a flexible scaffold for protein subunits.

Authors:  David C Zappulla; Thomas R Cech
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-28       Impact factor: 11.205

Review 8.  Molecular recognition and function of riboswitches.

Authors:  Alexander Serganov; Dinshaw J Patel
Journal:  Curr Opin Struct Biol       Date:  2012-05-12       Impact factor: 6.809

9.  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

10.  The GENCODE pseudogene resource.

Authors:  Baikang Pei; Cristina Sisu; Adam Frankish; Cédric Howald; Lukas Habegger; Xinmeng Jasmine Mu; Rachel Harte; Suganthi Balasubramanian; Andrea Tanzer; Mark Diekhans; Alexandre Reymond; Tim J Hubbard; Jennifer Harrow; Mark B Gerstein
Journal:  Genome Biol       Date:  2012-09-26       Impact factor: 13.583

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  609 in total

1.  A BRCA1-interacting lncRNA regulates homologous recombination.

Authors:  Vivek Sharma; Simran Khurana; Nard Kubben; Kotb Abdelmohsen; Philipp Oberdoerffer; Myriam Gorospe; Tom Misteli
Journal:  EMBO Rep       Date:  2015-09-27       Impact factor: 8.807

Review 2.  Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain.

Authors:  Julieta Aprea; Federico Calegari
Journal:  EMBO J       Date:  2015-10-29       Impact factor: 11.598

3.  A novel long non-coding RNA in the rheumatoid arthritis risk locus TRAF1-C5 influences C5 mRNA levels.

Authors:  T C Messemaker; M Frank-Bertoncelj; R B Marques; A Adriaans; A M Bakker; N Daha; S Gay; T W Huizinga; R E M Toes; H M M Mikkers; F Kurreeman
Journal:  Genes Immun       Date:  2015-12-17       Impact factor: 2.676

Review 4.  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

5.  RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes.

Authors:  Heeyoun Bunch; Brian P Lawney; Adam Burkholder; Duanduan Ma; Xiaofeng Zheng; Shmulik Motola; David C Fargo; Stuart S Levine; Yaoyu E Wang; Guang Hu
Journal:  Genomics       Date:  2016-07-16       Impact factor: 5.736

6.  Stable C0T-1 repeat RNA is abundant and is associated with euchromatic interphase chromosomes.

Authors:  Lisa L Hall; Dawn M Carone; Alvin V Gomez; Heather J Kolpa; Meg Byron; Nitish Mehta; Frank O Fackelmayer; Jeanne B Lawrence
Journal:  Cell       Date:  2014-02-27       Impact factor: 41.582

7.  Integrative Transcriptome Analyses of Metabolic Responses in Mice Define Pivotal LncRNA Metabolic Regulators.

Authors:  Ling Yang; Ping Li; Wenjing Yang; Xiangbo Ruan; Kurtis Kiesewetter; Jun Zhu; Haiming Cao
Journal:  Cell Metab       Date:  2016-09-22       Impact factor: 27.287

8.  Quantitative Proteomics Analysis Reveals Novel Insights into Mechanisms of Action of Long Noncoding RNA Hox Transcript Antisense Intergenic RNA (HOTAIR) in HeLa Cells.

Authors:  Peng Zheng; Qian Xiong; Ying Wu; Ying Chen; Zhuo Chen; Joy Fleming; Ding Gao; Lijun Bi; Feng Ge
Journal:  Mol Cell Proteomics       Date:  2015-03-11       Impact factor: 5.911

9.  RNA-seq analysis identifies key long non-coding RNAs connected to the pathogenesis of alcohol-associated head and neck squamous cell carcinoma.

Authors:  Vicky Yu; Pranav Singh; Elham Rahimy; Hao Zheng; Selena Z Kuo; Elizabeth Kim; Jessica Wang-Rodriguez; Weg M Ongkeko
Journal:  Oncol Lett       Date:  2016-08-08       Impact factor: 2.967

10.  Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer.

Authors:  Haiyang Guo; Musaddeque Ahmed; Fan Zhang; Cindy Q Yao; SiDe Li; Yi Liang; Junjie Hua; Fraser Soares; Yifei Sun; Jens Langstein; Yuchen Li; Christine Poon; Swneke D Bailey; Kinjal Desai; Teng Fei; Qiyuan Li; Dorota H Sendorek; Michael Fraser; John R Prensner; Trevor J Pugh; Mark Pomerantz; Robert G Bristow; Mathieu Lupien; Felix Y Feng; Paul C Boutros; Matthew L Freedman; Martin J Walsh; Housheng Hansen He
Journal:  Nat Genet       Date:  2016-08-15       Impact factor: 38.330

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