1087-OR: Stencilling Accessible Chromatin Fibres Reveals Haplotype-Specific Regulation in Pancreatic Beta Cells

Introduction and Objective: The interpretation of non-coding variants that alter disease risk, such as type 2 diabetes, requires understanding both the functional and genetic context of each variant. In particular, variants must be assessed within their haplotypic context. Most existing chromatin accessibility methods rely on short read sequencing of fragmented chromatin and therefore cannot capture the genetic or functional context of individual variants. Here, we employ chromatin stencilling in a pancreatic beta-cell model, a long-read sequencing approach that phases genotype with chromatin accessibility and DNA methylation. Methods: We utilise the multiomic capabilities of Oxford Nanopore sequencing to resolve DNA modifications in EndoC-BH1 cells. An exogenous DNA methyltransferase is used to convert accessible adenines to 6mA, enabling base pair mapping of chromatin accessibility. We resolve 6mA and 5mCpG modifications to haplotypes to identify Fiber-seq Inferred Regulatory Elements (FIREs) and quantify differential regulatory activity between haplotypes. Results: We identify 968 regions with differential chromatin accessibility between EndoC-BH1 haplotypes. Of these, 575 show anticorrelated differential CpG methylation and are enriched at promoters of imprinted genes. While binding sites for common beta-cell transcription factors (PDX1, FOXA2, NKX6-1, NKX2-2) are depleted in differentially accessible regions, sites with moderate CTCF occupancy are enriched, consistent with allele-specific chromatin conformation. We also observe a modest enrichment of type 2 diabetes-associated variants (OR = 3.76, 95% CI 1.2-8.8) within differentially accessible regions, driven by multiple loci, including rs231362, which lies within a haplotype-specific NKX2-2 bound element. Conclusion: These findings demonstrate the potential of chromatin stencilling to reveal the functional basis of non-coding disease variants. Building on these results, we are now applying this approach to healthy and disease donor human pancreatic islets. Disclosure A. MacCalman: None. N. Owens: None.