Comparative analyses of longissimus muscle miRNAomes reveal microRNAs associated with differential regulation of muscle fiber development between Tongcheng and Yorkshire pigs

Abstract

Tongcheng (TC) and Yorkshire (YK) are two pig breeds with distinctive muscle morphology. Porcine microRNAome (miRNAome) of the longissimus muscle during five developmental stages (40, 55, 63, 70, and 90 days post coitum (dpc)) was explored by Solexa sequencing in the present study to find miRNAs involved in the different regulation of skeletal muscle development between the two breeds. A total of 320 known porcine miRNAs, 64 miRNAs corresponding to other mammals, and 224 potentially novel miRNAs were identified. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) suggested that the factor “pig breed” affected the miRNA expression profiles to a lesser extent than the factor “developmental stage”. Fifty-seven miRNAs were differentially expressed (DE) between the neighbor developmental stages in TC and 45 such miRNAs were found in YK, 34 in common; there were more down-regulated stage-DE miRNAs than up-regulated. And a total of 23, 30, 12, 6, and 30 breed-DE miRNAs between TC and YK were identified at 40, 55, 63, 70, and 90 dpc, respectively, which were mainly involved in cellular protein modification process, protein transport, and metabolic process. As the only highly expressed breed-DE miRNA found in no less than four developmental stages, and also a stage-DE miRNA found both in TC and YK, miR-499-5p could bind the 3’-UTR of a myofibrillogenesis regulator, destrin/actin depolymerizing factor (DSTN), as validated in dual luciferase reporter assay. The results suggested that miR-499-5p possibly play a noteworthy role in the breed-distinctive porcine muscle fiber development associated with the regulation of DSTN.

Small RNA-seq analysis of extracellular vesicles from porcine uterine flushing fluids during peri-implantation

“…This algorithm of Piano is based on the Support Vector Machine (SVM) algorithm and transposon interaction information. The miRNA expression profiles were normalized by transcript per million (TPM), as previously reported [68]. The miRNAs with expression values of >28 TPM in at least one of the 10 libraries were selected for all the following analyses.…”

“…The expression levels of small RNAs were calculated by using Transcript Per Kilobase Million (TPM) as described in a previous report [69]. Small RNAs with expression value >28 TPM in at least in one of the nine libraries were selected for subsequent data analysis [68]. Raw P-value were convert to adjusted P-value using the Benjamin-Hochberg false discovery rate [70].…”

MiR‐543 regulates myoblast proliferation and differentiation of C2C12 cells by targeting KLF6

“…Our preliminary sequencing data showed that miR-543 was differentially and highly expressed in the dorsal longest muscle at different stages during embryonic development, and the expression level was the highest at 70 days of embryo development. 14 Many studies have shown that miR-543 is involved in the regulation of various aspects of tumor cells. [15][16][17] However, less is known about the regulatory role of miR-543 in muscle development.…”

Small RNA-seq analysis of exosomes from porcine uterine luminal fluid during peri-implantation

“…The expression levels of small RNAs were calculated by using Transcript Per Kilobase Million (TPM) as described in a previous report [50]. Small RNAs with expression value >28 TPM in at least in one of the nine libraries were selected for subsequent data analysis [51]. The P-values calculated for every small RNA were adjusted to Q-values for multiple testing corrections by two alternative strategies.…”