Search Results for: lncrna rinn

The Future of lncRNAs with Dr. John Rinn

from Epigenie.com

John RinnDr. John L. Rinn from Harvard University and the Broad Institute (Harvard and MIT) is a prominent researcher in long non-coding RNAs (lncRNAs) and agreed to sit down and discuss his perspective on the intersection of lncRNA and epigenetics.

EpiGenie: You’ve mentioned that you feel knockout models are going to play a key role in the next phase of lncRNA studies in your lab. Do you see this as the natural progression in the field of long non-coding RNA in general?

Dr. Rinn: I think the field is at the point where it’s growing up. It’s maturing and it’s beginning to set a higher bar. There have been a few mechanistic studies that examine these next steps, but I think the other thing that’s happened in the field is that these lncRNAs are so bizarre that they almost seem like science fiction. So what’s happening now is that because these conclusions are so out there, people expect a higher burden of proof to back some of these claims to balance the excitement.

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Genome-scale strategies to discover and characterize lncRNAs

Annual Review Biochem

The central dogma of gene expression is that DNA is transcribed into messenger RNAs, which in turn serve as the template for protein synthesis. The discovery of extensive transcription of large RNA transcripts that do not code for proteins, termed long noncoding RNAs (lncRNAs), provides an important new perspective on the centrality of RNA in gene regulation.

An emerging theme from multiple model systems is that lncRNAs form extensive networks of ribonucleoprotein (RNP) complexes with numerous chromatin regulators and then target these enzymatic activities to appropriate locations in the genome. Consistent with this notion, lncRNAs can function as modular scaffolds to specify higher-order organization in RNP complexes and in chromatin states. The importance of these modes of regulation is underscored by the newly recognized roles of long RNAs for proper gene control across all kingdoms of life.

  • Rinn JL, Chang HY. (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81, 145-66. [abstract]

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lncRNA expression signatures in response to enterovirus 71 infection

Outbreaks of hand, foot, and mouth disease caused by enterovirus 71 (EV71) have become considerable threats to the health of infants and young children. To identify the cellular long noncoding RNAs (lncRNAs) involved in the host response to EV71 infection, researchers at Southern Medical University, China performed comprehensive lncRNA and mRNA profiling in EV71-infected rhabdomyosarcoma cells through microarray.

They observed the differential expression of more than 4800 lncRNAs during infection. Further analysis showed 160 regulated enhancer-like lncRNA and nearby mRNA pairs, as well as 313 regulated Rinn’s lncRNA. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression and nearby mRNA pairs. The results provided information for further research on the prevention and treatment of EV71 infection, as well as on distinguishing severe and mild EV71 cases.

Yina Z, Guanb D, Fanc Q, Sub J, Zhenga W, Maa W, Keb C.(2012) lncRNA expression signatures in response to enterovirus 71 infection. Biochem and Biophys Res Comm [Epub ahead of print]. [abstract]

 

Outbreaks of hand, foot, and mouth disease caused by enterovirus 71 (EV71) have become considerable threats to the health of infants and young children. To identify the cellular long noncoding RNAs (lncRNAs) involved in the host response to EV71 infection, we performed comprehensive lncRNA and mRNA profiling in EV71-infected rhabdomyosarcoma cells through microarray. We observed the differential expression of more than 4800 lncRNAs during infection. Further analysis showed 160 regulated enhancer-like lncRNA and nearby mRNA pairs, as well as 313 regulated Rinn’s lncRNA [M. Guttman I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte, O. Zuk, B.W. Carey, J.P. Cassady, M.N. Cabili, R. Jaenisch, T.S. Mikkelsen, T. Jacks, N. Hacohen, B.E. Bernstein, M. Kellis, A. Regev, J.L. Rinn, E.S. Lander. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458 (2009) 223–227, A.M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales, K. Thomas, A. Presser, B.E. Bernstein, A. van Oudenaarden, A. Regev, E.S. Lander, J.L. Rinn. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106 (2009) 11667–11672] and nearby mRNA pairs. The results provided information for further research on the prevention and treatment of EV71 infection, as well as on distinguishing severe and mild EV71 cases.

Long Noncoding RNAs: From Evolution to Function (C7)

lncRNA

Long Noncoding RNAs: From Evolution to Function (C7)

Scientific Organizers: Leonard Lipovich, Jeannie T. Lee, John L. Rinn and James (Ben) Brown

March 15—20, 2015

Keystone Resort, Keystone, Colorado, USA

Sponsored by Regeneron Pharmaceuticals, Inc.

** Registration currently unavailable **

Meeting Summary

It has become clear that metazoan genomes are replete with transcription from non-protein-coding regions, generating many long non-coding RNA (lncRNA) transcripts. Recent progress has enabled genome-wide mapping of lncRNAs and has unraveled unifying themes; lncRNAs function as epigenetic regulators, scaffolds, decoys, and enhancers. While these and other themes have been pursued in several meetings, the field has matured in numerous novel directions, and we will leverage these to comprehensively characterize lncRNAs across metazoan genomes. We aim to broaden our horizons with emerging data from humans and model systems, empowered by novel genomic technologies, including RNA-protein interaction mapping (CLIP- and RIP-seq), reverse genetics for lncRNAs not conserved in evolution (RNA sequencing in control and lncRNA-perturbed backgrounds), and proteogenomics to empirically bound the translational output of putative lncRNAomes. These topics have recently amassed diverse insights into RNA biology. The goal of our meeting is to integrate novel findings, enhance previously proposed models of lncRNA function, and generate new testable hypotheses. Our synthesis of RNA structure, function, evolution, and informatics will foster progress in this rapidly growing field.

Program

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Long noncoding RNAs mean more than HOTAIR

rna-world

From Genetic Engineering News by Patricia Fitzpatrick Dimond, Ph.D.

Long noncoding RNA (lncRNAs) can regulate gene expression at epigenetic, transcriptional, and post-transcriptional levels.

Over the past 10 years, scientists say new methods, including deep sequencing and DNA tiling arrays, have enabled the identification and characterization of the human transcriptome. These techniques completely changed our understanding of genome organization and content and revealed that a much larger part of the human genome is transcribed into RNA than was previously assumed—about 70%.

Last year researchers, including Tim Mercer, Ph.D., at the Institute for Molecular Bioscience-University of Queensland, Roche Nimblegen, and John Rinn, Ph.D., and his team in the department of stem cell and regenerative biology at Harvard, reported that “transcriptomic analyses have revealed an ‘unexpected complexity’ to the human transcriptome, the depth and breadth of which exceeds current RNA sequencing capability.”

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