RNA-Seq Reveals miRNA Role Shifts in Seven Stages of Skeletal Muscles in Goat Fetuses and Kids

Abstract

MicroRNAs (miRNAs) are indispensable for the regulation of skeletal muscle. We performed RNA sequencing (RNA-seq) to establish a comprehensive miRNA profiling of goats in seven stages, namely, 45-(F45), 65-(F65), 90-(F90), 120-(F120), and 135-day (F135) fetuses, newborn (B1), and 90-day-old (B90) kids. In total, 421 known miRNAs and 228 goat novel miRNAs were identified in the data, and the average abundance of 19 miRNAs in seven stages exceeds 10,000 reads per million. Furthermore, 420 differentially expressed miRNAs (DEmiRNAs) were identified in all comparison group at seven stages, 80 of which were uniquely differentially expressed in the B1 and B90 comparison groups. Pathway analysis indicated that this group was associated with the release of muscle hypertrophy and regulation of myoblast proliferation. Besides, 305 DEmiRNAs were clustered into three significantly enriched profiles (profiles 11, 16, and 19). Function analysis revealed that profile 16 was related to muscle hypertrophy and differentiation. Profile 11 was involved in multiple enzyme activities and metabolic processes in muscle cells. And profile 19 was involved in material transport and structural stability. Two highly expressed miRNAs and three key miRNAs (chi-miR-328-3p, chi-miR-767, and chi-miR-150) of these profiles were verified to be consistent with the data by quantitative real-time PCR. These results provided a catalog of goat muscleassociated miRNAs, allowing us to better understand the transformation of miRNA roles during mammalian muscle development.

Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

“…Muscles have an incredible ability to change their functional characteristics in order to adapt and function optimally in response to the physiological state of the animal (e.g., growing, maintaining, or senescing). The regulatory non-coding RNAs at different stages of muscle development in multiple species are gradually being revealed, such as duck [ 14 ], sheep [ 15 ], pig [ 16 ] and goat [ 17 ]. For example, 1,498 circRNAs were identified in the skeletal muscles of pigs at three stages after birth.…”

“…Among them, the continuous stage and unique expression differential circRNAs and their potential functions have also been explored [ 16 ]. In addition, the dynamic expressions of miRNAs and lncRNAs in 7 stages of goat was revealed, which have the potential to affect skeletal muscle development [ 17 , 18 ]. Therefore, exploring the regulatory molecules of muscle physiological changes at different stages is equally essential for the breeding of meat rabbits.…”

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

“…For example, Wang et al identified 336 differentially expressed miRNAs in skeletal muscle of Huanghuai goats between fetal stage and 6-month-old stage, of which miR-424-5p, miR-29a, miR-129-3p, miR-181b, and miR-181d were involved in multiple important pathways related to muscle development ( 18 ). Guo et al and Ling et al also found some important differentially expressed miRNAs in skeletal muscle from prenatal stages to neonatal stage in Jianzhou Da′er goats and Anhui white goats ( 19 , 20 ). However, little is known about the miRNA profiles of muscle tissues in other goat breeds, or between different goat breeds.…”

Expression of microRNAs in the hypothalamus of pregnant and non-pregnant goats

“…An aliquot of 3 μg of total RNA per sample was used as input material for generation of a small RNA library. Sequencing libraries were generated using a NEBNext ® Multiplex Small RNA Library Prep Set for Illumina ® (NEB, Ipswich, MA, USA) following the manufacturer's recommendations, and the index codes were added to attribute sequences to each sample (Ling et al 2020). The library quality was assessed by an Agilent 2100 Bioanalyzer System (Thermo Fisher Scientific, Waltham, MA, USA) using a high-sensitivity DNA chip.…”