Multi-Transcript Level Profiling Revealed Distinct mRNA, miRNA, and tRNA-Derived Fragment Bio-Signatures for Coping Behavior Linked Haplotypes in HPA Axis and Limbic System

Abstract

The molecular basis of porcine coping behavior (CB) relies on a sophisticated interplay of genetic and epigenetic features. Deep sequencing technologies allowed the identification of a plethora of new regulatory small non-coding RNA (sncRNA). We characterized mRNA and sncRNA profiles of central parts of the physiological stress response system including amygdala, hippocampus, hypothalamus and adrenal gland using systems biology for integration. Therefore, ten each of high- (HR) and low- (LR) reactive pigs (n = 20) carrying a CB associated haplotype in a prominent QTL-region on SSC12 were selected for mRNA and sncRNA expression profiling. The molecular markers related to the LR group included ATP1B2, MPDU1, miR-19b-5p, let-7g-5p, and 5′-tiRNALeu in the adrenal gland, miR-194a-5p, miR-125a-5p, miR-7-1-5p, and miR-107-5p in the hippocampus and CBL and PVRL1 in the hypothalamus. Interestingly, amygdalae of the LR group showed 5′-tiRNA and 5′-tRF (5′-tRFLys, 5′-tiRNALys, 5′-tiRNACys, and 5′-tiRNAGln) enrichment. Contrarily, molecular markers associated with the HR group encompassed miR-26b-5p, tRNAArg, tRNAGlyiF in the adrenal gland, IGF1 and APOD in the amygdala and PBX1, TOB1, and C18orf1 in the hippocampus and miR-24 in the hypothalamus. In addition, hypothalami of the HR group were characterized by 3′-tiRNA enrichment (3′-tiRNAGln, 3′-tiRNAAsn, 3′-tiRNAVal, 3′-tRFPro, 3′-tiRNACys, and 3′-tiRNAAla) and 3′-tRFs enrichment (3′-tRFAsn, 3′-tRFGlu, and 3′-tRFVal). These evidence suggest that tRNA-derived fragments and their cleavage activity are a specific marker for coping behavior. Data integration revealed new bio-signatures of important molecular interactions on a multi-transcript level in HPA axis and limbic system of pigs carrying a CB-associated haplotype.

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tiRNAs: Insights into Their Biogenesis, Functions, and Future Applications in Livestock Research

“…Whereas the hypothalamus from the high-reactive haplogroup evidenced an enrichment of 3 -tiRNAs, including 3 -tiRNA Gln , 3 -tiRNA Asn , 3 -tiRNA Val , 3 -tiRNA Cys , and 3 -tiRNA Ile . The same study suggests that 5 -tiRNA Leu , together with other miRNAs and mRNAs molecules, may have a specific function as a gene regulator and signalling molecules across coping behaviour haplogroups [116]. Comparative transcriptomic studies between primates and other mammals also revealed different expression profiles across species, suggesting that 5 -tiRNAs are more expressed in the hippocampus in primates, pigs, rats, and mice.…”

“…have a specific function as a gene regulator and signalling molecules across coping behaviour haplogroups [116]. Comparative transcriptomic studies between primates and other mammals also revealed different expression profiles across species, suggesting that 5′-tiRNAs are more expressed in the hippocampus in primates, pigs, rats, and mice.…”

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