Stencilling accessible chromatin fibres reveals haplotype-specific regulation | LC 25

Biography

Nick Owens leads an interdisciplinary research group studying gene regulatory defects in disease. He has an undergraduate and PhD in computer science and machine learning, and postdoctoral training studying gene regulation in stem cells and development. His research group uses laboratory and computational methods to understand how regulatory sequences of the genome control gene expression, and how changes in these sequences lead to diseases such as diabetes. The group uses Oxford Nanopore sequencing to measure base-pair resolution chromatin accessibility.

Abstract

Understanding how genetic variants in the non-protein-coding genome impact function remains a fundamental challenge in the genetic study of disease. These variants can influence the binding of transcription factors, which may lead to large-scale changes in chromatin state and conformation. Each variant resides within a haplotype and interpretation of variant function requires an understanding of the sequence context of the haplotype and its associated regulatory activity. We therefore require a technology that can identify the simultaneous binding of multiple transcription factors and chromatin features resolved to each haplotype. Here, we utilise the multiomic capabilities of Oxford Nanopore sequencing to resolve genotype with phased DNA methylation and open chromatin simultaneously. We employ an exogenous DNA methyltransferase to convert accessible adenines (As) to 6mA, to map chromatin accessibility at base-pair resolution. We use nanopore sequencing to resolve 6mA and 5mCG modifications to a haplotype to identify Fiber-seq inferred regulatory elements (FIREs) and calculate differential regulatory activity between haplotypes. We report on our progress studying genetic defects associated with diabetes using stem cell derived pancreatic islets. For example, in human embryonic stem cells, we identify haplotype-specific regulatory regions bound by factors associated with chromatin conformation (CTCF and RAD21) and pluripotency (OCT4, SOX2, and NANOG), together with an enrichment of gene promoters subject to epigenetic repression. Our findings highlight the potential of Oxford Nanopore sequencing for understanding haplotype-specific chromatin organisation to gain insights in regulatory variants in disease.