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

Area of Science:

• Molecular Biology
• Genomics
• Developmental Biology

Background:

• Muscle tissue is crucial for organismal viability and locomotion.
• Despite extensive research, a complete understanding of the muscle transcriptome and its role in development and function remains elusive.

Purpose of the Study:

• To comprehensively characterize the muscle transcriptome in Caenorhabditis elegans.
• To identify novel genes, transcription factors, RNA-binding proteins, and microRNAs involved in muscle function.
• To explore the regulatory networks and cis-acting elements governing muscle gene expression.

Main Methods:

• Updated nuclear Fluorescence-Activated Cell Sorting (FACS) methodology for isolating muscle tissue.
• High-throughput sequencing to generate a high-quality muscle transcriptome.
• Bioinformatic analyses including interaction network, promoter analysis, and miRNA interactome construction.
• In vivo functional studies of muscle-specific microRNAs using fluorochrome-based assays.

Main Results:

• Identified 2848 muscle-specific protein-coding genes, including 78 transcription factors and 206 RNA-binding domain-containing proteins.
• Discovered novel muscle-specific cis-acting elements through detailed promoter analysis.
• Identified 16 high-quality muscle-specific microRNAs and characterized their in vivo function.
• Developed a comprehensive C. elegans miRNA interactome integrating multiple muscle-specific datasets.

Conclusions:

• This study provides an expanded view of muscle tissue function in C. elegans at the transcriptomic level.
• The identified genes and regulatory elements offer insights into muscle development and function.
• Findings have potential implications for understanding and treating human muscular diseases.