Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets

Oncotarget
R WeikardChrista Kuehn

Abstract

Long noncoding RNAs (lncRNAs) emerged as important regulatory component of mechanisms involved in gene expression, chromatin modification and epigenetic processes, but they are rarely annotated in the bovine genome. Our study monitored the jejunum transcriptome of German Holstein calves fed two different milk diets using transcriptome sequencing (RNA-seq). To identify potential lncRNAs within the pool of unknown transcripts, four bioinformatic lncRNA prediction tools were applied. The intersection of the alignment-free lncRNA prediction tools (CNCI, PLEK and FEELnc) predicted 1,812 lncRNA transcripts concordantly comprising a catalogue of 1,042 putative lncRNA loci expressed in the calves' intestinal mucosa. Nine lncRNA loci were differentially expressed (DE lncRNAs) between both calf groups. To elucidate their biological function, we applied a systems biology approach that combines weighted gene co-expression network analysis with functional enrichment and biological pathway analysis. Four DE lncRNAs were found to be strongly correlated with a gene network module (GNM) enriched for genes from canonical pathways of remodeling of epithelial adherens junction, tight junction and integrin signaling. Another DE lncRNA was strongly ...Continue Reading

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Citations

Nov 15, 2018·Annual Review of Animal Biosciences·Elisabetta GiuffraUNKNOWN FAANG Consortium
Feb 7, 2020·Animal : an International Journal of Animal Bioscience·H M HammonC Koch
May 10, 2020·Animal : an International Journal of Animal Bioscience·B Kosinska-SelbiJ Szyda
Nov 18, 2018·International Journal of Molecular Sciences·Eveline M Ibeagha-AwemuNathalie Bissonnette
Feb 23, 2021·Computational and Structural Biotechnology Journal·Nida Amin, Jana Seifert
Jul 2, 2021·Frontiers in Genetics·Praveen Krishna ChitneediBeatriz Gutiérrez-Gil

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Methods Mentioned

BETA
RNA-seq
ubiquitination
scraping

Software Mentioned

Cuffdiff2
edgeR
linux
Ensembl
Cufflinks
Tophat2
FEELnc
BLAST
CNCI
Ensembl Biomart

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