Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes

Objective: Although glucagon-secreting a-cells and insulin-secreting beta-cells have opposing functions in regulating plasma glucose levels, the two cell types share a common developmental origin and exhibit overlapping transcriptomes and epigenomes. Notably, destruction of beta-cells can stimulate repopulation via transdifferentiation of alpha-cells, at least in mice, suggesting plasticity between these cell fates. Furthermore, dysfunction of both alpha- and 3 -cells contributes to the pathophysiology of type 1 and type 2 diabetes, and beta-cell de-differentiation has been proposed to contribute to type 2 diabetes. Our objective was to delineate the molecular properties that maintain islet cell type specification yet allow for cellular plasticity. We hypothesized that correlating cell type-specific transcriptomes with an atlas of open chromatin will identify novel genes and transcriptional regulatory elements such as enhancers involved in alpha- and beta-cell specification and plasticity. Methods: We sorted human a-and beta-cells and performed the Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) and mRNA-seq, followed by integrative analysis to identify cell type-selective gene regulatory regions. Results: We identified numerous transcripts with either alpha-cell-or beta-cell-selective expression and discovered the cell type-selective open chromatin regions that correlate with these gene activation patterns. We confirmed cell type-selective expression on the protein level for two of the top hits from our screen. The group specific protein (GC; or vitamin D binding protein) was restricted to alpha-cells, while CHODL (chondrolectin) immunoreactivity was only present in beta-cells. Furthermore, a -cell-and 13-cell-selective ATAC-seq peaks were identified to overlap with known binding sites for islet transcription factors, as well as with single nucleotide polymorphisms (SNPs) previously identified as risk loci for type 2 diabetes. Conclusions: We have determined the genetic landscape of human a-and 3 -cells based on chromatin accessibility and transcript levels, which allowed for detection of novel a-and beta-cell signature genes not previously known to be expressed in islets. Using fine-mapping of open chromatin, we have identified thousands of potential cis-regulatory elements that operate in an endocrine cell type-specific fashion.