No-nonsense functions for long noncoding RNAs.
Takashi Nagano,Peter Fraser +1 more
TLDR
The mysterious secrets of long noncoding RNAs, often referred to as the Dark Matter of the genome, are gradually coming to light as several recent papers dig deep to reveal surprisingly complex and diverse functions.About:
This article is published in Cell.The article was published on 2011-04-15 and is currently open access. It has received 790 citations till now. The article focuses on the topics: Genome.read more
Citations
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A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?
TL;DR: It is proposed that this "competing endogenous RNA" (ceRNA) activity forms a large-scale regulatory network across the transcriptome, greatly expanding the functional genetic information in the human genome and playing important roles in pathological conditions, such as cancer.
Journal ArticleDOI
Genome Regulation by Long Noncoding RNAs
John L. Rinn,Howard Y. Chang +1 more
TL;DR: Long noncoding RNAs (lncRNAs) as discussed by the authors form extensive networks of ribonucleoprotein (RNP) complexes with numerous chromatin regulators and then target these enzymatic activities to appropriate locations in the genome.
Journal ArticleDOI
The multilayered complexity of ceRNA crosstalk and competition
TL;DR: Understanding this novel RNA crosstalk will lead to significant insight into gene regulatory networks and have implications in human development and disease.
Journal ArticleDOI
A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA
Marcella Cesana,Davide Cacchiarelli,Ivano Legnini,Tiziana Santini,Olga Sthandier,Mauro Chinappi,Anna Tramontano,Anna Tramontano,Irene Bozzoni +8 more
TL;DR: It is demonstrated that linc-MD1 exerts the same control over differentiation timing in human myoblasts, and that its levels are strongly reduced in Duchenne muscle cells, indicating that the ceRNA network plays an important role in muscle differentiation.
A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response
Maite Huarte,Mitchell Guttman,Mitchell Guttman,David M. Feldser,Manuel Garber,Magdalena J. Koziol,Magdalena J. Koziol,Daniela Kenzelmann-Broz,Ahmad M. Khalil,Ahmad M. Khalil,Or Zuk,Ido Amit,Michal Rabani,Laura D. Attardi,Aviv Regev,Aviv Regev,Eric S. Lander,Eric S. Lander,Eric S. Lander,Tyler Jacks,John L. Rinn,John L. Rinn +21 more
TL;DR: In this paper, the identification of lincRNAs (lincRNA-p21) that serve as a repressor in p53-dependent transcriptional responses was reported, and the observed transcriptional repression was mediated through the physical association with hnRNP-K at repressed genes and regulation of p53 mediates apoptosis.
References
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Journal ArticleDOI
Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
John L. Rinn,Michael Kertesz,Jordon K. Wang,Sharon L. Squazzo,Xiao Xu,Samantha A. Brugmann,L. Henry Goodnough,Jill A. Helms,Peggy J. Farnham,Eran Segal,Howard Y. Chang +10 more
TL;DR: The transcriptional landscape of the four human HOX loci is characterized at five base pair resolution in 11 anatomic sites and 231 HOX ncRNAs are identified that extend known transcribed regions by more than 30 kilobases, suggesting transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance.
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Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
Miao-Chih Tsai,Ohad Manor,Yue Wan,Nima Mosammaparast,Jordon K. Wang,Fei Lan,Yang Shi,Eran Segal,Howard Y. Chang +8 more
TL;DR: The results suggest that lincRNAs may serve as scaffolds by providing binding surfaces to assemble select histone modification enzymes, thereby specifying the pattern of histone modifications on target genes.
Journal ArticleDOI
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
Ahmad M. Khalil,Mitchell Guttman,Maite Huarte,Manuel Garber,Arjun Raj,Dianali Rivea Morales,Kelly Thomas,Aviva Presser,Bradley E. Bernstein,Alexander van Oudenaarden,Aviv Regev,Eric S. Lander,John L. Rinn +12 more
TL;DR: A model in which some lincRNAs guide chromatin-modifying complexes to specific genomic loci to regulate gene expression is proposed, and it is shown that siRNA-mediated depletion of certain linc RNAs associated with PRC2 leads to changes in gene expression.
Journal ArticleDOI
Widespread transcription at neuronal activity-regulated enhancers
Tae Kyung Kim,Martin Hemberg,Jesse M. Gray,Allen M. Costa,Daniel M. Bear,Jing Wu,David A. Harmin,Michael W. Laptewicz,Kellie Barbara-Haley,Scott Kuersten,Eirene Markenscoff-Papadimitriou,Eirene Markenscoff-Papadimitriou,Dietmar Kuhl,Haruhiko Bito,Paul F. Worley,Gabriel Kreiman,Michael E. Greenberg +16 more
TL;DR: It is revealed that a widespread mechanism of enhancer activation involves RNAPII binding and eRNA synthesis, which occurs specifically at enhancers that are actively engaged in promoting mRNA synthesis.
Journal ArticleDOI
A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response
Maite Huarte,Mitchell Guttman,Mitchell Guttman,David M. Feldser,Manuel Garber,Magdalena J. Koziol,Magdalena J. Koziol,Daniela Kenzelmann-Broz,Ahmad M. Khalil,Ahmad M. Khalil,Or Zuk,Ido Amit,Michal Rabani,Laura D. Attardi,Aviv Regev,Aviv Regev,Eric S. Lander,Eric S. Lander,Eric S. Lander,Tyler Jacks,John L. Rinn,John L. Rinn +21 more
TL;DR: A model whereby transcription factors activate lincRNAs that serve as key repressors by physically associating with repressive complexes and modulate their localization to sets of previously active genes is proposed.
Related Papers (5)
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Mitchell Guttman,Ido Amit,Manuel Garber,Courtney French,Michael F. Lin,David M. Feldser,Maite Huarte,Maite Huarte,Or Zuk,Bryce W. Carey,John P. Cassady,Moran N. Cabili,Rudolf Jaenisch,Tarjei S. Mikkelsen,Tyler Jacks,Nir Hacohen,Bradley E. Bernstein,Bradley E. Bernstein,Manolis Kellis,Manolis Kellis,Aviv Regev,John L. Rinn,John L. Rinn,John L. Rinn,Eric S. Lander +24 more