Identification of the conserved long non-coding RNAs in myogenesis

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Genome regulation involves diverse mechanisms, including non-coding RNAs like long non-coding RNAs (lncRNAs).
• The functions of lncRNAs in gene regulation are not fully understood, and identifying conserved lncRNAs across species presents a significant challenge.
• Existing knowledge gaps necessitate novel approaches for lncRNA identification and functional annotation.

Purpose of the Study:

• To develop and apply a novel computational approach for identifying conserved long non-coding RNAs (lncRNAs) across species.
• To functionally annotate these conserved lncRNAs, particularly in the context of myogenesis (muscle development).
• To investigate the differential expression and genomic localization of identified lncRNAs.

Main Methods:

• Exploited existing myogenic transcriptome data from mice and humans to identify conserved lncRNAs.
• Utilized three-dimensional genome architecture to identify topologically associated domains (TADs) for lncRNAs.
• Correlated lncRNA expression within TADs with gene expression for functional annotation in myogenesis.

Main Results:

• Identified conserved lncRNAs expressed differentially during early and later stages of muscle development in mice and humans.
• Experimentally confirmed the differential expression of selected lncRNAs in cultured mouse muscle cells (C2C12).
• Functionally annotated trans-lncRNAs involved in myogenesis by integrating genomic domain information and expression data.

Conclusions:

• A novel approach successfully identified and functionally annotated conserved lncRNAs crucial for myogenesis in humans and mice.
• The study highlights a substantial number of lncRNAs involved in muscle development.
• Further research is warranted to explore the evolutionary conservation of lncRNAs despite sequence divergence and to validate their specific roles.