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.
Highlights
Long noncoding RNAs are loci located in genomic regions, which are antisense, intronic, intergenic or overlapping with regard to proteincoding loci
Identification and functional characterization of Long noncoding RNAs (lncRNAs) atlases fits the aim of the international global network for Functional Annotation of Animal Genomes (FAANG), which is to identify and functionally annotate novel regulatory elements in domesticated animal genomes with a focus on biologically important representative tissues to generate a link between genome and phenome [25, 26]
We identified nine lncRNAs that displayed different expression pattern in pre-weaning calves in response to different milk supply, and we predicted potential biological roles for DE lncRNAs in cellular signaling and metabolic processes associated with the different nutritional challenge of the calves
Summary
Long noncoding RNAs (lncRNAs) are loci located in genomic regions, which are antisense, intronic, intergenic or overlapping with regard to proteincoding loci. LncRNAs turned out to be functionally associated with specific developmental stages in cells and tissues, the pathogenesis of various diseases (e.g., tumor growth, mental and neurogenerative disorders, www.oncotarget.com cardiovascular pathologies), the susceptibility to infection and other environmental challenges and with metabolic disorders (e.g., obesity, diabetes) [1,2,3,4,5,6,7,8,9,10,11,12,13] In these remarkably distinct biological processes, dysfunctions and conditions, lncRNAs were found to be involved in a broad range of mechanisms regulating gene expression, genomic imprinting, chromatin modification and epigenetic processes [14,15,16]. Identification and functional characterization of lncRNA atlases fits the aim of the international global network for Functional Annotation of Animal Genomes (FAANG), which is to identify and functionally annotate novel regulatory elements in domesticated animal genomes with a focus on biologically important representative tissues to generate a link between genome and phenome [25, 26]
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