Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development

Scientific Reports
Weimin ZhaoKui Li

Abstract

Long intergenic non-coding RNAs (lincRNAs) play important roles in many cellular processes. Here, we present the first systematic identification and characterization of lincRNAs in fetal porcine skeletal muscle. We obtained a total of 55.02 million 90-bp paired-end reads and assembled 54,550 transcripts using cufflinks. We developed a pipeline to identify 570 multi-exon lincRNAs by integrating a set of previous approaches. These putative porcine lincRNAs share many characteristics with mammalian lincRNAs, such as a relatively short length, small number of exons and low level of sequence conservation. We found that the porcine lincRNAs were preferentially located near genes mediating transcriptional regulation rather than those with developmental functions. We further experimentally analyzed the features of a conserved mouse lincRNA gene and found that isoforms 1 and 4 of this lincRNA were enriched in the cell nucleus and were associated with polycomb repressive complex 2 (PRC2). Our results provide a catalog of fetal porcine lincRNAs for further experimental investigation of the functions of these genes in the skeletal muscle developmental process.

References

Jan 1, 1990·Molecular and Cellular Biology·C I BrannanS M Tilghman
Jun 1, 1973·Journal of Animal Science·C R AshmoreL Doerr
Aug 1, 1973·Journal of Animal Science·H J Swatland
Jan 11, 1996·Nature·G D PennyN Brockdorff
Feb 22, 2001·Science·J C VenterX Zhu
Dec 26, 2001·Nucleic Acids Research·Alex BatemanErik L L Sonnhammer
Jan 10, 2003·Nucleic Acids Research·Sam Griffiths-JonesSean R Eddy
Oct 22, 2004·Nature·UNKNOWN International Human Genome Sequencing Consortium
Nov 3, 2004·Genes & Development·Giuseppina CarettiVittorio Sartorelli
Mar 9, 2005·Journal of Animal Science·E KanisJ A M van Arendonk
Mar 26, 2005·Science·Jill ChengThomas R Gingeras
Jul 7, 2005·Journal of Muscle Research and Cell Motility·Marinus F W Te PasMarco H Pool
Mar 28, 2007·Genome Research·Jasmina PonjavicGerton Lunter
May 19, 2007·Science·Philipp KapranovThomas R Gingeras
Jun 3, 2008·Nature Methods·Ali MortazaviBarbara Wold
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Feb 26, 2009·Cell·Chris P PontingWolf Reik
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
Jul 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Ahmad M KhalilJohn L Rinn
Feb 5, 2010·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Bang XiaoKui Li
Mar 25, 2010·Animal Genetics·B ZhouJ Y Wang
Aug 4, 2010·Cell Research·Susan C WuYi Zhang
Oct 5, 2010·Cell·Ulf Andersson ØromRamin Shiekhattar
Dec 21, 2010·Nature Cell Biology·Yuntao S MaoDavid L Spector
Feb 1, 2011·Bioinformatics·Robert Schmieder, Robert Edwards
Aug 30, 2011·Nature·Mitchell GuttmanEric S Lander
Nov 10, 2011·BMC Genomics·Anna Esteve-CodinaMiguel Pérez-Enciso
Nov 15, 2011·Nature Biotechnology·Tim R MercerJohn L Rinn
Nov 24, 2011·Genome Research·Andrea PauliAlexander F Schier
Sep 8, 2012·Genome Research·Jennifer HarrowTim J Hubbard

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Citations

May 20, 2015·Biochemical and Biophysical Research Communications·Cong TaoKui Li
Feb 10, 2017·Animal Science Journal = Nihon Chikusan Gakkaihō·Baosong XingJing Wang
Mar 5, 2016·Biology of Reproduction·Maoliang RanZhaohui Li
Jun 30, 2018·International Journal of Molecular Sciences·Marta MajewskaMariusz Krzysztof Majewski
Feb 27, 2018·Physiological Reports·Ana I Hernandez CorderoArimantas Lionikas
Sep 13, 2016·Animal Genetics·R WeikardC Kuehn
Jul 26, 2018·Animals : an Open Access Journal From MDPI·Qing LiCaihong Wei
Oct 20, 2018·Journal of Animal Science and Biotechnology·Monika RuszkowskaRenata E Ciereszko
Mar 8, 2019·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Jing Xiang CuiYong Qing Zeng
Feb 16, 2017·BMC Genomics·Xiaoxiao GaoYunhai Zhang

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Methods Mentioned

BETA
RNA-seq
immunoprecipitation
PCR

Software Mentioned

TopHat
BLASTN
Cufflinks
Galaxy
Ensembl
cutadapt
RepeatMasker
Ensemble
7500 System ( SDS )
HMMER

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