Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

Stephen J Bush; Charity Muriuki; Mary E B McCulloch; Iseabail L Farquhar; Emily L Clark; David A Hume

doi:10.1186/s12711-018-0391-0

Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

Stephen J Bush, Charity Muriuki, Mary E B McCulloch, Iseabail L Farquhar, Emily L Clark, David A Hume

Research output: Contribution to journal › Article › peer-review

Abstract

BACKGROUND: mRNA-like long non-coding RNAs (lncRNAs) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. Thus, in many cases lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNAs, we compared de novo assembled lncRNAs derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNAs assembled in cattle and human. We then combined the novel lncRNAs with the sheep transcriptional atlas to identify co-regulated sets of protein-coding and non-coding loci.

Original language	English
Pages (from-to)	20
Journal	Genetics Selection Evolution
Volume	50
Issue number	1
DOIs	https://doi.org/10.1186/s12711-018-0391-0
Publication status	Published - 24 Apr 2018

Keywords / Materials (for Non-textual outputs)

Journal Article

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10.1186/s12711-018-0391-0

Cross-species inference of long non-coding RNAs ...
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ISP 1 2017/22 Blueprints for Healthy Animals
Watson, M. (Principal Investigator)
Biotechnology and Biological Sciences Research Council
1/04/17 → 31/03/22
Project: Research
Functional Annotation of the Sheep Genome
Hume, D. (Principal Investigator), Archibald, A. (Co-investigator), Morrison, I. (Co-investigator), Summers, K. (Co-investigator) & Watson, M. (Co-investigator)
Biotechnology and Biological Sciences Research Council
16/10/13 → 3/05/17
Project: Research
Future-Proofing the sustainability of the MRC high throughput sequencing hub in Scotland
Blaxter, M. (Principal Investigator)
MRC
1/10/12 → 30/09/14
Project: Research

Cite this

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abstract = "BACKGROUND: mRNA-like long non-coding RNAs (lncRNAs) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. Thus, in many cases lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNAs, we compared de novo assembled lncRNAs derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNAs assembled in cattle and human. We then combined the novel lncRNAs with the sheep transcriptional atlas to identify co-regulated sets of protein-coding and non-coding loci. ",

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doi = "10.1186/s12711-018-0391-0",

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AU - Bush, Stephen J

AU - Muriuki, Charity

AU - McCulloch, Mary E B

AU - Farquhar, Iseabail L

AU - Clark, Emily L

AU - Hume, David A

PY - 2018/4/24

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N2 - BACKGROUND: mRNA-like long non-coding RNAs (lncRNAs) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. Thus, in many cases lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNAs, we compared de novo assembled lncRNAs derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNAs assembled in cattle and human. We then combined the novel lncRNAs with the sheep transcriptional atlas to identify co-regulated sets of protein-coding and non-coding loci.

AB - BACKGROUND: mRNA-like long non-coding RNAs (lncRNAs) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. Thus, in many cases lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNAs, we compared de novo assembled lncRNAs derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNAs assembled in cattle and human. We then combined the novel lncRNAs with the sheep transcriptional atlas to identify co-regulated sets of protein-coding and non-coding loci.

KW - Journal Article

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DO - 10.1186/s12711-018-0391-0

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SP - 20

JO - Genetics Selection Evolution

JF - Genetics Selection Evolution

IS - 1

ER -

Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome

Abstract

Keywords / Materials (for Non-textual outputs)

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Projects

ISP 1 2017/22 Blueprints for Healthy Animals

Functional Annotation of the Sheep Genome

Future-Proofing the sustainability of the MRC high throughput sequencing hub in Scotland

Cite this