Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

Abstract

Background Skeletal muscle development is a multistep process whose understanding is central in a broad range of fields and applications, from the potential medical value to human society, to its economic value associated with improvement of agricultural animals. Skeletal muscle initiates in the somites, with muscle precursor cells generated in the dermomyotome and dermomyotome-derived myotome before muscle differentiation ensues, a developmentally regulated process that is well characterized in model organisms. However, the regulation of skeletal muscle ontogeny during embryonic development remains poorly defined in farm animals, for instance in pig. Here, we profiled gene expression and chromatin accessibility in developing pig somites and myotomes at single-cell resolution. Results We identified myogenic cells and other cell types and constructed a differentiation trajectory of pig skeletal muscle ontogeny. Along this trajectory, the dynamic changes in gene expression and chromatin accessibility coincided with the activities of distinct cell type-specific transcription factors. Some novel genes upregulated along the differentiation trajectory showed higher expression levels in muscular dystrophy mice than that in healthy mice, suggesting their involvement in myogenesis. Integrative analysis of chromatin accessibility, gene expression data, and in vitro experiments identified EGR1 and RHOB as critical regulators of pig embryonic myogenesis. Conclusions Collectively, our results enhance our understanding of the molecular and cellular dynamics in pig embryonic myogenesis and offer a high-quality resource for the further study of pig skeletal muscle development and human muscle disease.

Comparative analyses of dynamic transcriptome profiles highlight key response genes and dominant isoforms for muscle development and growth in chicken

“…Functionally similar genes tend to exhibit co-expression patterns [ 46 ]. In this study, the genes related to skeletal muscle development, including 10 TF genes essential for myogenesis, such as MYOG, HEY1, and SOX8 [ 47 , 48 ], had similar expression patterns in the breast muscle of both breeds. However, this approach did not identify muscle-related genes which exhibited different transcriptional characteristics between the two breeds.…”

Single-cell sequencing reveals the evolution of immune molecules across multiple vertebrate species

“…RNA-seq at single cell level allows for comprehensive identification of cell types, states and gene expression profiles [13] , and compared to single-nucleus RNA sequencing (snRNA-seq), scRNA-seq is more preferable for immune cell analysis [14] , [15] . Here, we utilized scRNA-seq to dissect the transcriptome of immune cell populations and subpopulations in the spleen across 7 vertebrate species with complete genomic information accessible including Fish (Zebrafish), Frog (Xenopus tropicalis), Mouse (C57BL/6J), Rat (Sprague Dawley), Pig (Bama miniature pig), Monkey (Rhesus macaque) and Human being.…”

Single-Cell RNA Sequencing Reveals the Cellular Landscape of Longissimus Dorsi in a Newborn Suhuai Pig

“…The longissimus dorsi (LD) plays a crucial role in determining pork quality, and has been utilized to assess various meat quality traits, including meat color [1], flavor [2], tenderness [3], and others. The inherent cellular composition and physiological functions of meat endow its characteristics [4,5]. As a representative muscle model for assessing lean meat production and evaluating meat quality in pig breeding, the LD has been the focus of numerous studies, encompassing relevant data such as histological, genetic, transcriptomic, and epigenetic information [6,7].…”