Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle

Abstract

The sheep is an economically important animal, and there is currently a major focus on improving its meat quality through breeding. There are variations in the growth regulation mechanisms of different sheep breeds, making fundamental research on skeletal muscle growth essential in understanding the regulation of (thus far) unknown genes. Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In this study, we used deep sequencing data from sheep longissimus dorsi (LD) muscles sampled at day 60, 90, and 120 of gestation, as well as at day 0 and 360 following birth, to identify and examine the lncRNA and miRNA temporal expression profiles that regulate sheep skeletal myogenesis. We stained LD muscles using histological sections to analyse the area and circumference of muscle fibers from the embryonic to postnatal development stages. Our results showed that embryonic skeletal muscle growth can be characterized by time. We obtained a total of 694 different lncRNAs and compared the differential expression between the E60 vs. E90, E90 vs. E120, E120 vs. D0, and D0 vs. D360 lncRNA and gene samples. Of the total 701 known sheep miRNAs we detected, the following showed a wide range of expression during the embryonic stage: miR-2387, miR-105, miR-767, miR-432, and miR-433. We propose that the detected lncRNA expression was time-specific during the gestational and postnatal stages. GO and KEGG analyses of the genes targeted by different miRNAs and lncRNAs revealed that these significantly enriched processes and pathways were consistent with skeletal muscle development over time across all sampled stages. We found four visual lncRNA–gene regulatory networks that can be used to explore the function of lncRNAs in sheep and may be valuable in helping improve muscle growth. This study also describes the function of several lncRNAs that interact with miRNAs to regulate myogenic differentiation.

Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues

“…In addition, Chao et al sequenced the longissimus dorsi muscles of sheep from the 60, 90, and 120th days of pregnancy and the 0 and 360th days after birth and identified the differentially expressed miR-433. These findings suggest that miR-433 might affect sheep skeletal muscle development by regulating myogenic differentiation ( 39 ). Qin et al found that the overexpression of miR-22-5p in rat cardiomyocytes can affect the RAP1/ERK pathway and cardiomyocyte apoptosis ( 40 ).…”

MiR-22-3p Inhibits Proliferation and Promotes Differentiation of Skeletal Muscle Cells by Targeting IGFBP3 in Hu Sheep

“…Since the number of myotubes is constant before birth, we focus on miRNAs with low expression before birth and high expression after birth. MiR-22-3p has been detected in the longissimus dorsi muscle of sheep and the expression of miR-22-3p is the lowest at 60 days of pregnancy and the highest at 360 days after birth [ 10 ]. Cancer literatures proved that miR-22-3p targets SP1 , inhibits the expression of downstream genes CCND1 and BCL2 , thereby inhibiting the growth of liver cancer cells, and the low expression of miR-22-3p is associated with metastatic liver cancer [ 27 , 28 ].…”

“…MiR-22-3p has been found as one of the differentially expressed miRNAs during Hu sheep muscle development [ 10 ]. A recent study showed that miR-22-3p treats fibrous cataract by targeting HDAC6 [ 11 ].…”

Deep Small RNA Sequencing Reveals Important miRNAs Related to Muscle Development and Intramuscular Fat Deposition in Longissimus dorsi Muscle From Different Goat Breeds

“…Up to now, research into expression profiles of miRNAs in the skeletal muscle tissue of domestic animals have mainly been focused on pigs ( 6 – 9 ), cattle ( 10 – 13 ), and sheep ( 14 – 17 ). It was found from these studies described above that miRNAs were differentially expressed in skeletal muscle at different developmental periods, or between different breeds.…”