Literature DB >> 28978770

Emerging Properties and Functional Consequences of Noncoding Transcription.

Ryan Ard1, Robin C Allshire2,3, Sebastian Marquardt4.   

Abstract

Eukaryotic genomes are rich in transcription units encoding "long noncoding RNAs" (lncRNAs). The purpose of all this transcription is unclear since most lncRNAs are quickly targeted for destruction during synthesis or shortly thereafter. As debates continue over the functional significance of many specific lncRNAs, support grows for the notion that the act of transcription rather than the RNA product itself is functionally important in many cases. Indeed, this alternative mechanism might better explain how low-abundance lncRNAs transcribed from noncoding DNA function in organisms. Here, we highlight some of the recently emerging features that distinguish coding from noncoding transcription and discuss how these differences might have important implications for the functional consequences of noncoding transcription.
Copyright © 2017 by the Genetics Society of America.

Keywords:  RNA Polymerase II transcription; chromatin; gene regulation; long noncoding RNA (lncRNA); nascent transcription; noncoding transcription; transcription cycle; transcriptional interference

Mesh:

Substances:

Year:  2017        PMID: 28978770      PMCID: PMC5629311          DOI: 10.1534/genetics.117.300095

Source DB:  PubMed          Journal:  Genetics        ISSN: 0016-6731            Impact factor:   4.562


  108 in total

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Review 2.  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

Review 3.  "Cat's Cradling" the 3D Genome by the Act of LncRNA Transcription.

Authors:  Marta Melé; John L Rinn
Journal:  Mol Cell       Date:  2016-06-02       Impact factor: 17.970

Review 4.  Evolution to the rescue: using comparative genomics to understand long non-coding RNAs.

Authors:  Igor Ulitsky
Journal:  Nat Rev Genet       Date:  2016-08-30       Impact factor: 53.242

5.  Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription.

Authors:  Michael J Carrozza; Bing Li; Laurence Florens; Tamaki Suganuma; Selene K Swanson; Kenneth K Lee; Wei-Jong Shia; Scott Anderson; John Yates; Michael P Washburn; Jerry L Workman
Journal:  Cell       Date:  2005-11-18       Impact factor: 41.582

6.  Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex.

Authors:  Michael-Christopher Keogh; Siavash K Kurdistani; Stephanie A Morris; Seong Hoon Ahn; Vladimir Podolny; Sean R Collins; Maya Schuldiner; Kayu Chin; Thanuja Punna; Natalie J Thompson; Charles Boone; Andrew Emili; Jonathan S Weissman; Timothy R Hughes; Brian D Strahl; Michael Grunstein; Jack F Greenblatt; Stephen Buratowski; Nevan J Krogan
Journal:  Cell       Date:  2005-11-18       Impact factor: 41.582

7.  Distinct RNA degradation pathways and 3' extensions of yeast non-coding RNA species.

Authors:  Sebastian Marquardt; Dane Z Hazelbaker; Stephen Buratowski
Journal:  Transcription       Date:  2011-05

8.  Nuclear stability and transcriptional directionality separate functionally distinct RNA species.

Authors:  Robin Andersson; Peter Refsing Andersen; Eivind Valen; Leighton J Core; Jette Bornholdt; Mette Boyd; Torben Heick Jensen; Albin Sandelin
Journal:  Nat Commun       Date:  2014-11-12       Impact factor: 14.919

9.  Extensive transcriptional heterogeneity revealed by isoform profiling.

Authors:  Vicent Pelechano; Wu Wei; Lars M Steinmetz
Journal:  Nature       Date:  2013-04-24       Impact factor: 49.962

Review 10.  Considerations when investigating lncRNA function in vivo.

Authors:  Andrew R Bassett; Asifa Akhtar; Denise P Barlow; Adrian P Bird; Neil Brockdorff; Denis Duboule; Anne Ephrussi; Anne C Ferguson-Smith; Thomas R Gingeras; Wilfried Haerty; Douglas R Higgs; Eric A Miska; Chris P Ponting
Journal:  Elife       Date:  2014-08-14       Impact factor: 8.140

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  21 in total

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Journal:  Methods Mol Biol       Date:  2021

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Authors:  Yu Wang; Ning Liu; Ming-Yue Li; Mao-Fang Du
Journal:  Am J Transl Res       Date:  2021-03-15       Impact factor: 4.060

3.  Intergenic RNA mainly derives from nascent transcripts of known genes.

Authors:  Jernej Ule; Nicholas M Luscombe; Federico Agostini; Julian Zagalak; Jan Attig
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4.  Efficient termination of nuclear lncRNA transcription promotes mitochondrial genome maintenance.

Authors:  Dorine Jeanne Mariëtte du Mee; Maxim Ivanov; Joseph Paul Parker; Stephen Buratowski; Sebastian Marquardt
Journal:  Elife       Date:  2018-03-05       Impact factor: 8.140

5.  Long noncoding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease, and RNAi in fission yeast.

Authors:  Sophie R Atkinson; Samuel Marguerat; Danny A Bitton; Maria Rodríguez-López; Charalampos Rallis; Jean-François Lemay; Cristina Cotobal; Michal Malecki; Pawel Smialowski; Juan Mata; Philipp Korber; François Bachand; Jürg Bähler
Journal:  RNA       Date:  2018-06-18       Impact factor: 4.942

6.  Nutrient-dependent control of RNA polymerase II elongation rate regulates specific gene expression programs by alternative polyadenylation.

Authors:  Carlo Yague-Sanz; Yann Vanrobaeys; Ronan Fernandez; Maxime Duval; Marc Larochelle; Jude Beaudoin; Julien Berro; Simon Labbé; Pierre-Étienne Jacques; François Bachand
Journal:  Genes Dev       Date:  2020-06-04       Impact factor: 11.361

7.  H19 induced by oxidative stress confers temozolomide resistance in human glioma cells via activating NF-κB signaling.

Authors:  Shibo Duan; Ming Li; Zhifeng Wang; Longlong Wang; Yongjie Liu
Journal:  Onco Targets Ther       Date:  2018-10-02       Impact factor: 4.147

8.  Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

Authors:  Mathys Grapotte; Manu Saraswat; Chloé Bessière; Christophe Menichelli; Jordan A Ramilowski; Jessica Severin; Yoshihide Hayashizaki; Masayoshi Itoh; Michihira Tagami; Mitsuyoshi Murata; Miki Kojima-Ishiyama; Shohei Noma; Shuhei Noguchi; Takeya Kasukawa; Akira Hasegawa; Harukazu Suzuki; Hiromi Nishiyori-Sueki; Martin C Frith; Clément Chatelain; Piero Carninci; Michiel J L de Hoon; Wyeth W Wasserman; Laurent Bréhélin; Charles-Henri Lecellier
Journal:  Nat Commun       Date:  2021-06-02       Impact factor: 14.919

9.  Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation.

Authors:  Peter Kindgren; Ryan Ard; Maxim Ivanov; Sebastian Marquardt
Journal:  Nat Commun       Date:  2018-11-01       Impact factor: 14.919

10.  Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions.

Authors:  Alex C Tuck; Kedar Nath Natarajan; Greggory M Rice; Jason Borawski; Fabio Mohn; Aneliya Rankova; Matyas Flemr; Alice Wenger; Razvan Nutiu; Sarah Teichmann; Marc Bühler
Journal:  Life Sci Alliance       Date:  2018-07-31
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