美国约翰霍普金斯大学Winston Timp课题组利用纳米孔测序实现对人类细胞系染色质可及性和甲基化的同时检测。相关论文于2020年11月23日在线发表在《自然—方法学》杂志上。

通过应用GpC甲基转移酶外源性标记开放染色质，研究人员使用纳米孔测序来同时评估了长链DNA上的CpG甲基化和染色质可及性。研究人员对四种人类细胞系（GM12878、MCF-10A、MCF-7和MDA-MB-231）进行了核小体占有率和甲基化组（nanoNOMe）的纳米孔测序。单分子拆分可实现蛋白质和核小体结合的印迹，并确定了单个分子上的组合启动子表观遗传学特征。

长读测序使将读段稳固地分配给单倍型成为可能，从而能够生成完全分阶段的人类表观基因组，这由染色体水平的等位基因特异性CpG甲基化和染色质可及性组成。研究人员进一步将其应用于乳腺癌模型，从而评估了差异性甲基化和癌细胞之间的可及性。

据了解，在DNA上探测表观遗传学特征具有巨大的潜力，可以增进人们对分阶段表观基因组的了解。

附：英文原文

Title: Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

Author: Isac Lee, Roham Razaghi, Timothy Gilpatrick, Michael Molnar, Ariel Gershman, Norah Sadowski, Fritz J. Sedlazeck, Kasper D. Hansen, Jared T. Simpson, Winston Timp

Issue&Volume: 2020-11-23

Abstract: 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.

DOI: 10.1038/s41592-020-01000-7

Source: https://www.nature.com/articles/s41592-020-01000-7