Integration of miRNA and mRNA Co-Expression Reveals Potential Regulatory Roles of miRNAs in Developmental and Immunological Processes in Calf Ileum during Early Growth

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.

Influence of Maternal BLV Infection on miRNA and tRF Expression in Calves

“…MicroRNAs have been shown to play a role in early calf development [46,47]. In the current study, differentially expressed miRNAs were found to be dysregulated in calves born to BLV-infected dams.…”

“…Human and mouse orthologs of the four downregulated miRNAs (miR-1, miR-133a, miR-133b, and miR-206) have been shown to play roles in cardiac and skeletal muscle growth and differentiation [45][46][47]. Specifically, miR-1 targets the Hand2 transcription factor as well as HDAC4, which are necessary for cardiac development and muscle growth repression, respectively [48,49].…”

Altered expression of miRNAs and mRNAs reveals the potential regulatory role of miRNAs in the developmental process of early weaned goats

“…Further functional analysis revealed that these miRNA were involved in rumen development, immune regulation, and digestion processes, which were significantly regulated by bta-miR-145 and bta-miR-199a-3p. The authors also compared the miRNA expression profiles in the calf ileum between the two periods, and identified several miRNA-mRNA pairs such as bta-miR-374a-FBXO18, bta-miR-374a-GTPBP3, and bta-miR-374a-GNB2, which played crucial roles in ileum development, and bta-miR-15b-IKBKB, which was involved in immune functions [15]. These studies provided important information suggesting that the altered miRNAs caused by weaning stress were associated with tissue development and the development of the immune system.…”