Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition

Abstract

The identification of the molecular mechanisms regulating pathways associated with the potential for fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of fat traits. Interactions of microRNAs (miRNAs) with target RNAs regulate gene expression and modulate pathway activation in cells and tissues. In pigs, miRNA discovery is far from saturation, and the knowledge of miRNA expression in backfat tissue and particularly of the impact of miRNA variations is still fragmentary. Using RNA-seq, we characterized the small RNA (sRNA) expression profiles in Italian Large White pig backfat tissue. Comparing two groups of pigs divergent for backfat deposition, we detected 31 significant differentially expressed (DE) sRNAs: 14 up-regulated (including ssc-miR-132, ssc-miR-146b, ssc-miR-221-5p, ssc-miR-365-5p and the moRNA ssc-moR-21-5p) and 17 down-regulated (including ssc-miR-136, ssc-miR-195, ssc-miR-199a-5p and ssc-miR-335). To understand the biological impact of the observed miRNA expression variations, we used the expression correlation of DE miRNA target transcripts expressed in the same samples to define a regulatory network of 193 interactions between DE miRNAs and 40 DE target transcripts showing opposite expression profiles and being involved in specific pathways. Several miRNAs and mRNAs in the network were found to be expressed from backfat-related pig QTL. These results are informative for the complex mechanisms influencing fat traits, shed light on a new aspect of the genetic regulation of fat deposition in pigs and facilitate the prospective implementation of innovative strategies of pig genetic improvement based on genomic markers.

LncRNA IMFlnc1 promotes porcine intramuscular adipocyte differentiation by sponging miR-199a-5p to up-regulate CAV-1

“…showed a lower expressional level in the backfat of the lean groups than that in the fat group [54]. Its expressional level was also higher in undifferentiated 3T3-L1 adipocytes, and rapidly reduced during differentiation [55].…”

MiR&moRe2: A Bioinformatics Tool to Characterize microRNAs and microRNA-Offset RNAs from Small RNA-Seq Data

“…In this work, we presented miR&moRe2, a novel bioinformatics tool for detection and quantification of miRNAs, moRNAs, and their isoforms, from sRNA-seq data. The former implementation of miR&moRe [6] was proven successful in applicative studies [8,13,15,17,19] but was developed as an in-house method and considered only human data. Since then, the miR&moRe pipeline has been considerably improved by adding new features.…”

“…As performed in our earlier studies [15,17,19], the sRNA characterization performed by miR&moRe2 allowed a comprehensive evaluation of miRNA and moRNA differential expression. Interestingly, moRNAs with significantly varied expression levels among cell populations were identified.…”

“…demonstrated to be functional RNAs [14], potentially having an miRNA-like regulative effect [5]. Moreover, it has been shown that moRNA expression can vary between different phenotypes in mammals [19] and is deregulated in human disease [15,17]. Although moRNA biogenesis has not yet been fully elucidated, it has been hypothesized that moRNAs may originate by alternative Drosha/DGCR8-mediated processing of the pre-miRNA hairpins [15,20].…”

LncRNA IMFlnc1 Promotes Porcine Intramuscular Adipocyte Adipogenesis by Sponging Mir-199a-5p to Up-regulate CAV-1

“…In diabetic individuals, miR-199a-5p may be involved in skeletal muscle insulin resistance by inhibiting glucose transporter 4 (GLUT4) and hexokinase 2 (HK2) [38]. MiR-199a-5p also participates in lipid metabolism,in Italian Large White pigs, miR-199a-5p showed a higher expressional level in the backfat of the lean groups than that in the fat group [39]. Its expressional level was also higher in undifferentiated 3T3-L1 adipocytes, and rapidly reduced during differentiation [40].…”