Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

Genome Biology
Jenny ChenManuel Garber

Abstract

Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation. We present slncky, a lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-sequencing data and further uses evolutionary constraint to prioritize lncRNAs that are likely to be functionally important. Our automated filtering pipeline is comparable to manual curation efforts and more sensitive than previously published computational approaches. Furthermore, we developed a sensitive alignment pipeline for aligning lncRNA loci and propose new evolutionary metrics relevant for analyzing sequence and transcript evolution. Our analysis reveals that evolutionary selection acts in several distinct patterns, and uncovers two notable classes of ...Continue Reading

References

Jan 1, 1990·Molecular and Cellular Biology·C I BrannanS M Tilghman
Jul 27, 2001·Bioinformatics·I KorfM R Brent
May 23, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Lior PachterSimon Cawley
Dec 31, 2005·Nucleic Acids Research·A S HinrichsW J Kent
Oct 3, 2007·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Yinghui GuanJoe W Gray
May 30, 2008·Nature·Tarjei S MikkelsenAlexander Meissner
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
May 12, 2009·Cell Stem Cell·Jacob HannaRudolf Jaenisch
Jan 30, 2010·Bioinformatics·Aaron R Quinlan, Ira M Hall
May 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jacob HannaRudolf Jaenisch
Aug 30, 2011·Nature·Mitchell GuttmanEric S Lander
Oct 14, 2011·Nature·Kerstin Lindblad-TohManolis Kellis
Oct 21, 2011·Nature·David BrawandHenrik Kaessmann
Nov 24, 2011·Genome Research·Andrea PauliAlexander F Schier
Jun 12, 2012·Cell·Shu XiaoSheng Zhong
Sep 8, 2012·Genome Research·Jennifer HarrowTim J Hubbard
Dec 12, 2012·Frontiers in Genetics·Blake C EllisLloyd D Graham
Dec 22, 2012·Science·Jason MerkinChristopher B Burge
Aug 3, 2013·Science·Susan CarpenterKatherine A Fitzgerald
Oct 25, 2013·Nature·Maria C N MarchettoFred H Gage
Nov 22, 2013·Nucleic Acids Research·Kim D PruittJames M Ostell
Nov 26, 2013·Nucleic Acids Research·Donna KarolchikW James Kent
Dec 10, 2013·Nucleic Acids Research·Paul FlicekStephen M J Searle
Jan 17, 2014·Genome Research·Stefan WashietlManuel Garber

❮ Previous
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Citations

May 18, 2016·Genome Biology and Evolution·Kevin G Nyberg, Carlos A Machado
Jul 21, 2016·Wiley Interdisciplinary Reviews. RNA·Anne Nitsche, Peter F Stadler
May 10, 2017·Nature Reviews. Genetics·Alessandra BreschiRoderic Guigó
Dec 6, 2017·Genes·Jing WangYan Guo
Dec 4, 2016·The Journal of Immunology : Official Journal of the American Association of Immunologists·Charles F SpurlockThomas M Aune
Nov 3, 2016·Development·Rotem Ben-Tov Perry, Igor Ulitsky
Aug 7, 2018·Expert Opinion on Drug Discovery·Ilya BlokhinClaes Wahlestedt
Jun 20, 2019·Cardiovascular Research·João P MonteiroAndrew H Baker
Jul 20, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Antonio P CamargoFabio Papes
Sep 6, 2019·American Journal of Respiratory Cell and Molecular Biology·Dinesh DevadossHitendra S Chand
Nov 16, 2019·Nucleic Acids Research·Oleksii BryzghalovIzabela Makałowska
Jan 12, 2020·Toxicological Sciences : an Official Journal of the Society of Toxicology·Kritika Karri, David J Waxman
Aug 27, 2017·RNA·Ildar GainetdinovTatyana Azhikina
Oct 4, 2019·Briefings in Bioinformatics·Meik KunzThomas Dandekar
Sep 8, 2020·Genome Biology·Jordan P LewandowskiJohn L Rinn
May 26, 2017·Frontiers in Genetics·Andrew D L NelsonMark A Beilstein
Nov 6, 2018·Journal of Animal Science and Technology·Jasdeep Kaur DhanoaChandra Sekhar Mukhopadhyay
Mar 23, 2019·BMC Bioinformatics·Maria Beatriz Walter CostaKatja Nowick
Nov 4, 2016·Nature Reviews. Molecular Cell Biology·Jesse M EngreitzMitchell Guttman
May 4, 2017·BMC Bioinformatics·Francisco Avila CobosPieter Mestdagh
Jan 6, 2017·Nucleic Acids Research·Valentin WucherThomas Derrien
Dec 17, 2017·Cancer Metastasis Reviews·Tony GutschnerMartin Pichler
Feb 3, 2019·Non-coding RNA·Shrey GandhiMonika Stoll
Sep 22, 2017·World Journal of Gastroenterology : WJG·Zhao-Shan NiuWen-Hong Wang
Aug 29, 2019·Frontiers in Genetics·Xuan ZhangChangning Liu
Dec 12, 2020·Computational and Structural Biotechnology Journal·Sha HeHao Zhu

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Datasets Mentioned

BETA
BC094334

Methods Mentioned

BETA
RNA-Seq
Knockout
PCR

Software Mentioned

Bowtie
GENCODE
PLAR
FIRRE
RepeatMasker
SiPhy
Transcript
slncky
lastz
PhyloCSF

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