Epitranscriptomic regulation of the developing human pancreas | LC26

Abstract
RNA modifications are crucial regulators of gene expression in human development. They have an established role in regulating pancreatic β-cell development and function, with dysregulation resulting in diabetes. Numerous limitations have restricted the study of these modifications directly in pancreatic tissue. We utilize a cohort of human fetal pancreatic samples to determine the role of RNA modifications and transcriptome diversity to inform mechanisms relevant to disease pathogenesis. We used the Oxford Nanopore Direct RNA Sequencing Kit (dRNA-seq) on 15 human pancreas samples spanning 10–21 post-conception weeks. This enabled simultaneous detection of isoforms and eight RNA modifications (m⁶A, m⁵C, 2OmeA/T/G/C, pseudouridine [Ψ], inosine) during a critical window of endocrine cell induction. Gene-level expression reveals induction of genes reflective of the establishment of endocrine and exocrine identity. Leveraging the long-read capability of dRNA-seq revealed genes with distinct temporal isoform shifts that diverged from total expression. We identified >3,000 modifications with significant developmental dynamics. We observe a global decrease in RNA modifications across development with loss of m⁶A and 2OmeG the most predominant. We find a correlation with dynamic gene expression and dynamic modification, genes activated and repressed over the time course are associated with a gain and loss of m⁶A. Pancreas-specific genes are enriched in gains in m⁶A and Ψ, and loss of 2OmeG. We find coordinated changes in transcript isoform usage and RNA modifications. Integrating transcriptome diversity, RNA modifications, and reader localization provides insight into post-transcriptional regulation during pancreatic lineage specification. Our results provide context for interpreting genetic and epigenetic risk in pancreatic disease.

Biography
Ailsa MacCalman is a postdoctoral fellow in Nick Owens’ Gene Regulatory Defects in Disease laboratory at the University of Exeter. Ailsa received her PhD in Medical Sciences where she explored the epigenetic regulation of the developing human pancreas. Continuing this research, her work now leverages multiple Oxford Nanopore long-read sequencing techniques to understand the chromatin accessibility, transcriptomic, and epitranscriptomic regulation of the human fetal pancreas.