Identification of microRNA-dependent gene regulatory networks driving human pancreatic endocrine cell differentiation [ATAC-seq]

MicroRNAs (miRNAs) are small non-coding RNA molecules that have the ability to drive cell lineage decisions by regulating the expression of hundreds of genes. Although evidence indicates that miRNAs have roles in pancreas development and endocrine cell function, the role of miRNAs in pancreatic endocrine cell differentiation has not been systematically explored. To address this, we performed genome-wide small RNA sequencing analysis in pancreatic progenitor cells differentiated in vitro from human embryonic stem cells and endocrine cells isolated from whole human islets. This analysis revealed miRNAs that increase in expression during endocrine cell differentiation. Employing gain-of-function experiments, we identified four miRNAs that can repress a large number of genes that are normally down-regulated during endocrine cell differentiation, including genes encoding transcription factors known to regulate endocrine cell development as well as cell cycle regulators. This knowledge about miRNA target genes in conjunction with HITS-CLIP data allowed us to construct an integrated miRNA-gene regulatory network of endocrine cell differentiation. Our integrated analysis indicates a key role for the identified miRNAs in establishing a transcriptional landscape that promotes the differentiation of pancreatic progenitor cells into endocrine cells.  This study not only sheds light on the mechanisms that underlie human endocrine cell differentiation, but also has important implications for devising improved protocols for producing replacement beta cells for diabetes cell therapy. ATAC-seq analysis of CyT49 cells differentiated pancreatic progenitor stage cells.