Probing epigenetic features on DNA has tremendous potential to advance our understanding of the phased epigenome. In this study, we use nanopore sequencing to evaluate CpG methylation and chromatin accessibility simultaneously on long strands of DNA by applying GpC methyltransferase to exogenously label open chromatin. We performed nanopore sequencing of nucleosome occupancy and methylome (nanoNOMe) on four human cell lines (GM12878, MCF-10A, MCF-7 and MDA-MB-231). The single-molecule resolution allows footprinting of protein and nucleosome binding, and determination of the combinatorial promoter epigenetic signature on individual molecules. Long-read sequencing makes it possible to robustly assign reads to haplotypes, allowing us to generate a fully phased human epigenome, consisting of chromosome-level allele-specific profiles of CpG methylation and chromatin accessibility. We further apply this to a breast cancer model to evaluate differential methylation and accessibility between cancerous and noncancerous cells.

探索 DNA 上的表观遗传特征对于促进我们对阶段表观基因组的理解具有巨大的潜力。在本研究中，我们使用纳米孔测序通过应用 GpC 甲基转移酶外源标记开放染色质来同时评估长链 DNA 上的 CpG 甲基化和染色质可及性。我们对四种人类细胞系（GM12878、MCF-10A、MCF-7 和 MDA-MB-231）进行了核小体占据和甲基化组 (nanoNOMe) 的纳米孔测序。单分子分辨率允许对蛋白质和核小体结合进行足迹分析，并确定单个分子上的组合启动子表观遗传特征。长读长测序可以将读长可靠地分配给单倍型，使我们能够生成一个全阶段的人类表观基因组，由 CpG 甲基化和染色质可及性的染色体水平等位基因特异性谱组成。我们进一步将其应用于乳腺癌模型，以评估癌细胞和非癌细胞之间的差异甲基化和可及性。