Sequencing DNA methylation and hydroxymethylation at co-occurring chromatin features

TL;DR

A new method called 6-base-CUT&Tag allows researchers to study DNA modifications and chromatin features together, revealing how they work together in mouse embryonic stem cells.

Contribution

The development of 6-base-CUT&Tag enables simultaneous profiling of DNA methylation and chromatin features at single DNA fragments.

Findings

5mC and 5hmC signatures are feature-dependent and previously unresolvable.

DNA methylation and hydroxymethylation are coupled with H3K4me1 in mESC enhancers.

H3K4me1-derived signatures distinguish different enhancer functional states.

Abstract

Epigenetic modifications govern chromatin dynamics and cell state. However, current methods cannot simultaneously resolve the presence of multiple DNA modifications at co-occurring chromatin-associated features. It is thus not clear how these features are physically coupled and how their combinations regulate genome function. To address this key question, we report 6-base-CUT&Tag, a method for simultaneous 6-base DNA sequencing at target chromatin features. Using 6-base-CUT&Tag to profile 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) at co-occurring histone modifications in mouse embryonic stem cells (mESCs), we identify feature-dependent 5mC/5hmC signatures previously unresolvable with untargeted or bisulfite-based workflows. We show that DNA methylation and hydroxymethylation are specifically coupled with the H3K4me1 mark in mESC enhancers and that H3K4me1-derived signatures robustly distinguish different enhancer functional states.

Chemical modifications on DNA are key regulators of epigenetic function. Here, the authors develop 6-base-CUT&Tag to simultaneously profile multiple DNA and chromatin features on the same DNA fragment. This work reveals how specific DNA and histone marks colocalise at different enhancer regions.

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