An updated C. elegans nuclear body muscle transcriptome for studies in muscle formation and function

The body muscle is an important tissue used in organisms for proper viability and locomotion. Although this tissue is generally well studied and characterized, and many pathways have been elucidated throughout the years, we still lack a comprehensive understanding of its transcriptome and how it controls muscle development and function. Here, we have updated a nuclear FACS sorting-based methodology to isolate and sequence a high-quality muscle transcriptome from Caenorhabditis elegans mixed-stage animals. We have identified 2848 muscle-specific protein-coding genes, including 78 transcription factors and 206 protein-coding genes containing an RNA binding domain. We studied their interaction network, performed a detailed promoter analysis, and identified novel muscle-specific cis-acting elements. We have also identified 16 high-quality muscle-specific miRNAs, studied their function in vivo using fluorochrome-based analyses, and developed a high-quality C. elegans miRNA interactome incorporating other muscle-specific datasets produced by our lab and others. Our study expands our understanding of how muscle tissue functions in C. elegans and in turn provides results that can in the future be applied to humans to study muscular-related diseases. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13395-023-00314-2.