A catalogue of novel bovine long noncoding RNA across 18 tissues

Long non-coding RNA (lncRNA) have been implicated in diverse biological roles including gene regulation and genomic imprinting. Identifying lncRNA in bovine across many differing tissue would contribute to the current repertoire of bovine lncRNA, and help further improve our understanding of the evo...

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Main Authors:	Koufariotis, Lambros T., Chen, Yi-Ping Phoebe, Chamberlain, Amanda, Vander Jagt, Christy, Hayes, Ben J.
Format:	Online
Language:	English
Published:	Public Library of Science 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619662/

id	pubmed-4619662
recordtype	oai_dc
spelling	pubmed-46196622015-10-29 A catalogue of novel bovine long noncoding RNA across 18 tissues Koufariotis, Lambros T. Chen, Yi-Ping Phoebe Chamberlain, Amanda Vander Jagt, Christy Hayes, Ben J. Research Article Long non-coding RNA (lncRNA) have been implicated in diverse biological roles including gene regulation and genomic imprinting. Identifying lncRNA in bovine across many differing tissue would contribute to the current repertoire of bovine lncRNA, and help further improve our understanding of the evolutionary importance and constraints of these transcripts. Additionally, it could aid in identifying sites in the genome outside of protein coding genes where mutations could contribute to variation in complex traits. This is particularly important in bovine as genomic predictions are increasingly used in genetic improvement for milk and meat production. Our aim was to identify and annotate novel long non coding RNA transcripts in the bovine genome captured from RNA Sequencing (RNA-Seq) data across 18 tissues, sampled in triplicate from a single cow. To address the main challenge in identifying lncRNA, namely distinguishing lncRNA transcripts from unannotated genes and protein coding genes, a lncRNA identification pipeline with a number of filtering steps was developed. A total of 9,778 transcripts passed the filtering pipeline. The bovine lncRNA catalogue includes MALAT1 and HOTAIR, both of which have been well described in human and mouse genomes. We attempted to validate the lncRNA in libraries from three additional cows. 726 (87.47%) liver and 1,668 (55.27%) blood class 3 lncRNA were validated with stranded liver and blood libraries respectively. Additionally, this study identified a large number of novel unknown transcripts in the bovine genome with high protein coding potential, illustrating a clear need for better annotations of protein coding genes. Public Library of Science 2015-10-23 /pmc/articles/PMC4619662/ /pubmed/26496443 http://dx.doi.org/10.1371/journal.pone.0141225 Text en © 2015 Koufariotis et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Koufariotis, Lambros T. Chen, Yi-Ping Phoebe Chamberlain, Amanda Vander Jagt, Christy Hayes, Ben J.
spellingShingle	Koufariotis, Lambros T. Chen, Yi-Ping Phoebe Chamberlain, Amanda Vander Jagt, Christy Hayes, Ben J. A catalogue of novel bovine long noncoding RNA across 18 tissues
author_facet	Koufariotis, Lambros T. Chen, Yi-Ping Phoebe Chamberlain, Amanda Vander Jagt, Christy Hayes, Ben J.
author_sort	Koufariotis, Lambros T.
title	A catalogue of novel bovine long noncoding RNA across 18 tissues
title_short	A catalogue of novel bovine long noncoding RNA across 18 tissues
title_full	A catalogue of novel bovine long noncoding RNA across 18 tissues
title_fullStr	A catalogue of novel bovine long noncoding RNA across 18 tissues
title_full_unstemmed	A catalogue of novel bovine long noncoding RNA across 18 tissues
title_sort	catalogue of novel bovine long noncoding rna across 18 tissues
description	Long non-coding RNA (lncRNA) have been implicated in diverse biological roles including gene regulation and genomic imprinting. Identifying lncRNA in bovine across many differing tissue would contribute to the current repertoire of bovine lncRNA, and help further improve our understanding of the evolutionary importance and constraints of these transcripts. Additionally, it could aid in identifying sites in the genome outside of protein coding genes where mutations could contribute to variation in complex traits. This is particularly important in bovine as genomic predictions are increasingly used in genetic improvement for milk and meat production. Our aim was to identify and annotate novel long non coding RNA transcripts in the bovine genome captured from RNA Sequencing (RNA-Seq) data across 18 tissues, sampled in triplicate from a single cow. To address the main challenge in identifying lncRNA, namely distinguishing lncRNA transcripts from unannotated genes and protein coding genes, a lncRNA identification pipeline with a number of filtering steps was developed. A total of 9,778 transcripts passed the filtering pipeline. The bovine lncRNA catalogue includes MALAT1 and HOTAIR, both of which have been well described in human and mouse genomes. We attempted to validate the lncRNA in libraries from three additional cows. 726 (87.47%) liver and 1,668 (55.27%) blood class 3 lncRNA were validated with stranded liver and blood libraries respectively. Additionally, this study identified a large number of novel unknown transcripts in the bovine genome with high protein coding potential, illustrating a clear need for better annotations of protein coding genes.
publisher	Public Library of Science
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4619662/
_version_	1613492696868978688

A catalogue of novel bovine long noncoding RNA across 18 tissues

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