33  Profiling miRNA transcripts in the equine hindgut by quantitative PCR

Abstract

Gastrointestinal (GI) homeostasis in a horse results from dynamic interactions between a horse's gut physiology and the microbes in the various compartments. MicroRNAs (miRNA), single-stranded 20–22 basepair RNA molecules involved in post-transcriptional control of gene expression, have been implicated as an essential mechanism for control of gastrointestinal physiology and communication between host and microbe. Researchers have described how host-derived miRNAs influence microbial communities' composition in the GI. We have recently described how the pelvic flexure separates distinct microbial populations in the equine hindgut and subsequently have wondered if equine miRNA transcripts expressed by GI tissues could have a role in maintaining this separation. Investigations to characterize miRNAs' expression profile and other non-coding RNAs in the equine GI tract are limited. To address this, it is critical that we first know something about the expression of non-coding transcripts in the equine GI. This study investigated miRNA expression in tissues of the hindgut surrounding the pelvic flexure. RNA was isolated from the intestinal epithelium of 3 4-year-old American Quarter Horses collected from the right and left ventral colon (VC), pelvic flexure (PF), and right and left dorsal colon (DC). The miRNA transcripts were reverse transcribed using the miScript II RT kit, and relative abundance was quantified using the miScript SYBR Green PCR kit and primer sets for 286 annotated mature equine miRNAs. Biological replicates were pooled, and differential expression was determined following normalization by the delta Ct = Ct(target) – Ct(sample) method. A total of 230 miRNA transcripts were expressed in at least one GI location, with 60 expressed in all 5 locations. Twenty-eight transcripts had expression restricted to a single site, 5 of which were only expressed in the pelvic flexure. Additionally, 42 transcripts have patterns of expression across a subset of anatomical locations. Notably, 10 transcripts were expressed in the VC and PF, 5 transcripts were expressed in the DC and PF, and 15 transcripts were expressed in the VC and DC but not PF. Pathway and target analysis for the miRNAs with compartment restricted expression was performed using DIANA TOOLS. Of note, miRNA transcripts expressed only in the PF were predicted to target genes in the Hippo signaling pathway, which is associated with the regulation of intestinal tissue proliferation and homeostasis. Further investigation of miRNA expression in the equine hindgut will improve our understanding of gastrointestinal homeostasis's regulatory processes.