Dataset Information

Identification of novel mRNA splicing isoforms in human myogenesis

ABSTRACT: Myogenesis, the process of muscle formation and regeneration, requires significant changes in gene expression program. However, alternative splicing during human myogenesis has not been systematically studied. Here, we examined mRNA splicing changes during myogenesis in two human myoblast cell lines using hybrid transcriptomic approaches by combining short-read (Illumina) and long-read (Nanopore) RNA-seq analyses. We identified 13,853 new significant splicing isoforms (60,582 in total), with RNAs increasing and decreasing in abundance between days 0 and 3 (3,771 and 3,649, respectively), and between days 3 and 5 (1,302 and 1,109, respectively). We identified 1,937 significant differential transcript usage events (DTU), which pathways were involved in muscle regulation. Findings were validated using RT-qPCR and across mouse and human models, including clinical samples from peripheral artery disease patients. Artificial Intelligence algorithms predicted 595 myogenesis-associated high-confidence novel protein-coding splicing isoforms. Our findings underscore the importance of mRNA splicing isoforms in muscle biology.

ORGANISM(S): Homo sapiens

PROVIDER: GSE287954 | GEO | 2025/11/18

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Dynamin-related protein 1 (Drp1, encoded by DNM1L) is a key regulator of mitochondrial fission, yet its functional role remains controversial, likely due to isoform-specific effects arising from alternative splicing. Conventional short-read RNA sequencing complicates the characterization of full-length isoforms, limiting our understanding of their biological significance. To resolve this, we applied a targeted long-read sequencing approach to capture full-length DNM1L transcripts in primary human left ventricle and iPSC-derived cardiomyocytes. We recovered the complete spectrum of annotated isoforms and found broadly conserved expression patterns, with isoforms 1-4 expressed most abundantly. Recombinant protein assays further revealed that isoform abundance does not directly predict enzymatic activity, emphasizing the need for combined expression and functional analyses. Extending this framework to mouse, we profiled Dnm1l isoforms across six tissues (brain, heart, skeletal muscle, lung, kidney, and spleen) using the same long-read pipeline. All annotated isoforms were recovered, with distinct tissue-enriched expression patterns. Notably, several isoforms displayed strong tissue specificity, with subsets preferentially expressed in brain, heart, or skeletal muscle, suggesting specialized regulatory roles in mitochondrial dynamics. Functional rescue experiments in Drp1-knockout mouse embryonic fibroblasts revealed isoform-dependent differences in mitochondrial fission activity. Isoforms lacking the A-insert within the GTPase domain (e.g., isoforms b and d) robustly restored mitochondrial fragmentation, whereas the canonical brain-enriched isoform (isoform e) and a muscle-enriched isoform (isoform o) exhibited only partial rescue. These results indicate that inclusion of exons 2 and 3 may negatively regulate Drp1 fission activity. Together, our work establishes a cross-species atlas of DNM1L/Dnm1l isoforms, integrating long-read transcriptomics with functional assays. We demonstrate that Drp1 isoform diversity is tightly linked to tissue identity and that structural differences among isoforms critically shape mitochondrial fission activity, offering new insights into the pathophysiology of Drp1 in human health and disease.

Dataset Information

Identification of novel mRNA splicing isoforms in human myogenesis

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets