Identifying the link between non-coding regulatory RNAs and phenotypic severity in a zebrafish model of gmppb dystroglycanopathy
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Muscular Dystrophy (MD) is characterized by varying severity and time-of-onset by individuals afflicted with the same forms of MD, a phenomenon that is not well understood. Mutations in gmppb, an enzyme that glycosylated dystroglycan, cause dystroglycanopathic MD1. Like human patients, gmppb mutant zebrafish present both mild and severe phenotypes. In order to understand the molecular mechanisms involved, we performed high-throughput RNA Sequencing (RNA-Seq) and small RNA Sequencing at 4 and 7 days-post-fertilization (dpf) in mild and severe gmppb mutants and controls. We hypothesize that variable phenotypes in gmppb mutants are due to differences in gene regulation; therefore, we identified differentially expressed (DE) long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) - both potent genetic regulators. In the 4dpf severe mutants, we identified DE “MD-relevant” Ensembl-annotated genes that were predicted targets of DE miRNAs – identifying 55 of these interactions. We utilized a novel method of visualizing gene expression networks by generating co-expression miRNA networks and subsequently removing miRNA nodes to identify miRNAs that maintain network stability. We identified 95 potential lncRNAs for further analysis. By integrating analyses of both coding and non-coding genes, we hope to better understand the molecular mechanisms of dystroglycanopathy, highlighting potential phenotypic modulators.