Journal ArticleDOI
RNA decay machines: the exosome.
Aleksander Chlebowski,Michal Lubas,Michal Lubas,Michal Lubas,Torben Heick Jensen,Andrzej Dziembowski,Andrzej Dziembowski +6 more
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TLDR
This review is focused on the most comprehensively described yeast and human exosomes, and shall point out similarities or dissimilarities to prokaryotic complexes and proteins where appropriate.About:
This article is published in Biochimica et Biophysica Acta.The article was published on 2013-06-01. It has received 225 citations till now. The article focuses on the topics: Exosome Multienzyme Ribonuclease Complex & Exosome complex.read more
Citations
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RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity.
Evangelos Pefanis,Jiguang Wang,Gerson Rothschild,Junghyun Lim,David Kazadi,Jianbo Sun,Alexander J. Federation,Jaime Chao,Oliver Elliott,Zhi-Ping Liu,Aris N. Economides,James E. Bradner,Raul Rabadan,Uttiya Basu +13 more
TL;DR: It is proposed that the RNA exosome protects divergently transcribed lncRNA expressing enhancers by resolving deleterious transcription-coupled secondary DNA structures, while also regulating long-range super-enhancer chromosomal interactions important for cellular function.
Journal ArticleDOI
The regulation and functions of the nuclear RNA exosome complex
TL;DR: Novel, previously unappreciated functions of the nuclear exosome are introduced and discussed, including in transcription regulation and in the maintenance of genome stability.
Journal ArticleDOI
The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality
Aditya Radhakrishnan,Ying Hsin Chen,Sophie G. Martin,Najwa Alhusaini,Rachel Green,Jeff Coller +5 more
TL;DR: It is established that the DEAD-box protein Dhh1p is a sensor of codon optimality that targets an mRNA for decay, and mRNAs whose translation elongation rate is slowed by inclusion of non-optimal codons are specifically degraded in a DHH1p-dependent manner.
Journal ArticleDOI
Stable Pausing by RNA Polymerase II Provides an Opportunity to Target and Integrate Regulatory Signals
Telmo Henriques,Daniel A. Gilchrist,Sergei Nechaev,Michael Bern,Ginger W. Muse,Adam B. Burkholder,David C. Fargo,Karen Adelman +7 more
TL;DR: It is demonstrated that paused elongation complexes can be remarkably stable, with half-lives exceeding 15 min at genes with inefficient pause release, and proposed that stable pausing of polymerase provides a temporal window of opportunity for recruitment of factors to modulate gene expression and that the nascent tssRNA represents an appealing target for these interactions.
Journal ArticleDOI
Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs.
Margarita Schlackow,Takayuki Nojima,Tomás Gomes,Ashish Dhir,Maria Carmo-Fonseca,Nick J. Proudfoot +5 more
TL;DR: In this paper, the authors define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells, based on a range of nascent transcriptomic approaches applied to different nuclear fractions, including mammalian native elongating transcript sequencing.
References
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Journal ArticleDOI
Global analysis of protein localization in budding yeast
Won-Ki Huh,James V. Falvo,Luke C. Gerke,Adam S. Carroll,Russell W. Howson,Jonathan S. Weissman,Erin K. O'Shea +6 more
TL;DR: The construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells.
Journal ArticleDOI
Initial genome sequencing and analysis of multiple myeloma
Michael A Chapman,Michael S. Lawrence,Jonathan J Keats,Kristian Cibulskis,Carrie Sougnez,Anna C. Schinzel,Christina L. Harview,Jean Philippe Brunet,Gregory J. Ahmann,Mazhar Adli,Mazhar Adli,Kenneth C. Anderson,Kristin G. Ardlie,Daniel Auclair,Angela Baker,P. Leif Bergsagel,Bradley E. Bernstein,Bradley E. Bernstein,Bradley E. Bernstein,Yotam Drier,Yotam Drier,Rafael Fonseca,Stacey Gabriel,Craig C. Hofmeister,Sundar Jagannath,Andrzej Jakubowiak,Amrita Krishnan,Joan Levy,Ted Liefeld,Sagar Lonial,Scott Mahan,Bunmi Mfuko,Stefano Monti,Louise M. Perkins,Robb Onofrio,Trevor J. Pugh,S. Vincent Rajkumar,Alex H. Ramos,David S. Siegel,Andrey Sivachenko,A. Keith Stewart,Suzanne Trudel,Ravi Vij,Douglas Voet,Wendy Winckler,Todd Zimmerman,John D. Carpten,Jeff Trent,William C. Hahn,William C. Hahn,Levi A. Garraway,Levi A. Garraway,Matthew Meyerson,Matthew Meyerson,Eric S. Lander,Eric S. Lander,Eric S. Lander,Gad Getz,Todd R. Golub +58 more
TL;DR: The massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs indicates that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.
Initial genome sequencing and analysis of multiple myeloma
Michael A Chapman,Michael S. Lawrence,Jonathan J Keats,Kristian Cibulskis,Carrie Sougnez,Anna C. Schinzel,Christina L. Harview,Jean Philippe Brunet,Gregory J. Ahmann,Mazhar Adli,Mazhar Adli,Kenneth C. Anderson,Kristin G. Ardlie,Daniel Auclair,Angela Baker,P. Leif Bergsagel,Bradley E. Bernstein,Bradley E. Bernstein,Bradley E. Bernstein,Yotam Drier,Yotam Drier,Rafael Fonseca,Stacey Gabriel,Craig C. Hofmeister,Sundar Jagannath,Andrzej Jakubowiak,Amrita Krishnan,Joan Levy,Ted Liefeld,Sagar Lonial,Scott Mahan,Bunmi Mfuko,Stefano Monti,Louise M. Perkins,Robb Onofrio,Trevor J. Pugh,S. Vincent Rajkumar,Alex H. Ramos,David S. Siegel,Andrey Sivachenko,A. Keith Stewart,Suzanne Trudel,Ravi Vij,Douglas Voet,Wendy Winckler,Todd Zimmerman,John D. Carpten,Jeff Trent,William C. Hahn,William C. Hahn,Levi A. Garraway,Levi A. Garraway,Matthew Meyerson,Matthew Meyerson,Eric S. Lander,Eric S. Lander,Eric S. Lander,Gad Getz,Todd R. Golub +58 more
TL;DR: In this paper, a massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs was reported, and several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set.
Journal ArticleDOI
The Exosome: A Conserved Eukaryotic RNA Processing Complex Containing Multiple 3′→5′ Exoribonucleases
TL;DR: The exosome constitutes a highly conserved eukaryotic RNA processing complex in S. cerevisiae that is required for 3' processing of the 5.8S rRNA.
Journal ArticleDOI
AU binding proteins recruit the exosome to degrade ARE-containing mRNAs.
Ching Yi Chen,Roberto Gherzi,Shao En Ong,Edward L. Chan,Reinout Raijmakers,Ger J.M. Pruijn,Georg Stoecklin,Christoph Moroni,Matthias Mann,Michael Karin +9 more
TL;DR: Using a cell-free RNA decay system, it is demonstrated that the mammalian exosome is required for rapid degradation of ARE-containing RNAs but not for poly(A) shortening.