Oncotarget

Research Papers:

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

Rosemarie Weikard _, Frieder Hadlich, Harald M. Hammon, Doerte Frieten, Caroline Gerbert, Christian Koch, Georg Dusel and Christa Kuehn

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Oncotarget. 2018; 9:21052-21069. https://doi.org/10.18632/oncotarget.24898

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Abstract

Rosemarie Weikard1, Frieder Hadlich1, Harald M. Hammon1, Doerte Frieten2, Caroline Gerbert3, Christian Koch3, Georg Dusel2 and Christa Kuehn1,4

1Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany

2University of Applied Sciences, Bingen, Germany

3Educational and Research Centre for Animal Husbandry, Hofgut Neumühle, Münchweiler, Germany

4Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany

Correspondence to:

Rosemarie Weikard, email: weikard@fbn-dummerstorf.de

Keywords: long noncoding RNA; transcriptome; jejunum; pre-weaning calf; nutrition

Received: December 09, 2017    Accepted: February 25, 2018    Published: April 20, 2018

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 correlated with a GNM enriched for genes associated with energy metabolism and maintaining of cellular homeostasis with a focus on mitochondrial processes.

Our data suggest that these DE lncRNAs may play potential regulatory roles in modulating biological processes associated with energy metabolism pathways and cellular signaling processes affecting the barrier function of intestinal epithelial cells of calves in response to different feeding regimens in the pre-weaning period.


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