Extended Data Fig. 6: Chromatin accessibility, Transcription Factor binding and Epigenetic modifications at the HK1 locus over pancreatic differentiation.

a) snATAC-seq data in human islets showing mean chromatin accessibility over nuclei assigned to alpha, beta and delta-cell clusters in hormone high and hormone low conditions (GSE160472)¹⁷. Critical region containing variants encompassed within grey box. Alpha, beta and delta-cells each show accessibility in hormone high state, whereas only beta-cells retain accessibility in hormone low cells. Hormone high and low states characterised by level of accessibility over endocrine cell secreted hormone promoter, alpha – GCG, beta – INS, delta – SST. Data show in reads per million (RPM). b) Chromatin accessibility of pancreatic differentiation assessed by ATAC-seq (GSE149148)²¹, wider locus view of same data shown in Fig. 3c. Critical region containing variants encompassed within grey box. Stages: ES–embryonic stem cell, DE–definitive endoderm, Early/Late PP–pancreatic progenitor. c) Transcription factor binding in pancreatic progenitors (GSE149148)²¹ and in Carnegie Stage 16–18 liver bud for FOXA2 (E-MTAB-3061)²², data shown as a) and b). Liver bud data reveals that whilst FOXA2 binds critical region in pancreatic progenitors and human islets (Fig. 3b), it does not bind in liver bud, suggesting that critical region encodes pancreas specific regulation of HK1. d) Epigenetic modifications over HK1 locus, shown are active marks H3K27ac and H3K4me1 and repressive mark H3K27me3 over in vitro pancreatic cell differentiation (GSE149148)²¹ stages as in b) in vitro beta-cell line EndoC-BH1 (GSE118588)²⁵ and human islets H3K27ac and H3K4me1 (E-MTAB-1919)¹⁶ and H3K27me3 (E087 – roadmap epienomics²³); cell-sorted pancreatic alpha, beta and exocrine cells (GSE50386)²⁴. Grey box encompasses critical region containing variants. Data reveals that H3K27ac broadly marks short isoform promoter (Extended Data Fig. 3) at ES cells stage is reduced by DE stage, whilst focal mark over regulatory region is present in EndoC-BH1 and human islets. Similarly, H3K4me1 shows string focal enrichment over regulatory region in EndoC-BH1 and islets. Finally, repressive mark H3K27me3 is absent over the course of pancreatic cell differentiation and is present in a broad domain in adult islets, EndoC-BH1’s, beta-cells and to reduced extent in exocrine cells.