Abstract
This study aimed to investigate the potential regulatory roles of miRNAs in calf ileum developmental transition from the pre- to the post-weaning period. For this purpose, ileum tissues were collected from eight calves at the pre-weaning period and another eight calves at the post-weaning period and miRNA expression characterized by miRNA sequencing, followed by functional analyses. A total of 388 miRNAs, including 81 novel miRNAs, were identified. A total of 220 miRNAs were differentially expressed (DE) between the two periods. The potential functions of DE miRNAs in ileum development were supported by significant enrichment of their target genes in gene ontology terms related to metabolic processes and transcription factor activities or pathways related to metabolism (peroxisomes), vitamin digestion and absorption, lipid and protein metabolism, as well as intracellular signaling. Integration of DE miRNAs and DE mRNAs revealed several DE miRNA-mRNA pairs with crucial roles in ileum development (bta-miR-374a—FBXO18, bta-miR-374a—GTPBP3, bta-miR-374a—GNB2) and immune function (bta-miR-15b—IKBKB). This is the first integrated miRNA-mRNA analysis exploring the potential roles of miRNAs in calf ileum growth and development during early life.
Highlights
MicroRNAs are small (~22 nucleotides) endogenous RNA molecules that regulate gene expression post-transcriptionally by targeting principally the 30 untranslated region (30 UTR) of genes and to some extend the 50 UTR, introns and coding region of mRNAs [1]
MiRNA sequencing of 16 libraries generated a total of 185,458,022 reads
Mapped reads belonging to other RNA species, tRNA (3,153,316 (2.1%)), rRNA (480,099 (0.3%)), snRNA (236,118 (0.2%)) and snoRNA (1,620,029 (1.1%)) were discarded
Summary
MicroRNAs (miRNAs) are small (~22 nucleotides) endogenous RNA molecules that regulate gene expression post-transcriptionally by targeting principally the 30 untranslated region (30 UTR) of genes and to some extend the 50 UTR, introns and coding region of mRNAs [1]. They play key roles in a wide range of biological processes [2]. Several ileum miRNAs are reported to play important roles in host responses to Mycobacterium avium subspecies paratuberculosis infection, such as the role of bta-miR-196b in the proliferation of endothelial cells and bta-miR-146b in bacteria recognition and regulation of the inflammatory response [22]
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