Whole-transcriptome analysis reveals key transcriptional and noncoding RNA regulators of skeletal muscle satellite cell differentiation in quail

Abstract

Skeletal muscle growth in poultry depends on the proliferation and differentiation of skeletal muscle satellite cells (SMSCs), yet the regulatory landscape governing these processes in quail remains poorly defined. In this study, primary SMSCs were isolated from embryonic day 15 quail pectoral muscle and validated by PAX7 immunostaining and MYHC immunostaining following induction of differentiation. rRNA–depleted RNA-seq was performed at three developmental stages: satellite cells after differential adhesion (DA), proliferating myoblasts (GM), and differentiated myotubes after 4 d (DM4). Transcriptome profiling identified 9,728 common genes expressed in three group, with 1,254 genes differentially expressed across all pairwise comparisons. Functional enrichment analyses indicated a coordinated shift from cell cycle progression in proliferating cells to muscle contraction, oxidative phosphorylation, and calcium signaling during differentiation. Short time-series expression miner (STEM) analysis revealed distinct temporal expression patterns, highlighting proliferation-associated regulators (e.g., KDR, PIK3R1, MYF5, MYF6, NOTCH1, and WNT2) and myotube-related genes (e.g., ALDH18A1, HOXC8, TBX5, and EN1) as central nodes within stage-specific networks. In addition, 935 lncRNAs and 13,588 circRNAs were detected, many displaying stage-specific expression patterns. Predicted lncRNA–mRNA interactions and circRNA host gene enrichment implicated these noncoding RNAs in muscle development and metabolic remodeling. A competing endogenous RNA network highlighted miR-466-x and novel-m0255-5p as potential post-transcriptional regulators of muscle-related genes, including VEGFA, HDAC4, MYLK4, and NOX4. These findings provide a comprehensive transcriptomic resource for quail myogenesis and identify candidate coding and noncoding regulators relevant to muscle growth in poultry.