One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci.

Publisher: Cell Press Country of Publication: United States NLM ID: 101676030 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2451-9448 (Electronic) Linking ISSN: 24519448 NLM ISO Abbreviation: Cell Chem Biol Subsets: MEDLINE

Original Publication: Cambridge, MA : Cell Press, 2016-

Chromatin*/genetics ; DNA Methylation*; Cytosine ; Gene Expression Regulation ; DNA/metabolism ; 5-Methylcytosine

We present a method, named Mx-TOP, for profiling of three epigenetic regulatory layers-chromatin accessibility, general DNA modification, and DNA hydroxymethylation-from a single library. The approach is based on chemo-enzymatic covalent tagging of unmodified CG sites and hydroxymethylated cytosine (5hmC) along with GC sites in chromatin, which are then mapped using tag-selective base-resolution TOP-seq sequencing. Our in-depth validation of the approach revealed its sensitivity and informativity in evaluating chromatin accessibility and DNA modification interactions that drive transcriptional regulation. We employed the technology in a study of chromatin and DNA demethylation dynamics during in vitro neuronal differentiation. The study highlighted the involvement of gene body 5hmC in modulating an extensive decoupling between promoter accessibility and transcription. The importance of 5hmC in chromatin remodeling was further demonstrated by the observed resistance of the developmentally acquired open loci to the global 5hmC erasure in neuronal progenitors.
Competing Interests: Declaration of interests S.K. and E.K. are inventors on patents related to TOP-seq analysis: EP2776575B1, US9347093B2, and US9988673B2.
(Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

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Keywords: 5hmC; DNA hydroxymethylation; DNA modification; TOP-seq; chromatin accessibility; covalent DNA labeling; methyltransferases; synthetic AdoMet cofactors; uCG

0 (Chromatin)
8J337D1HZY (Cytosine)
9007-49-2 (DNA)
6R795CQT4H (5-Methylcytosine)

Date Created: 20231228 Date Completed: 20240325 Latest Revision: 20240327

20240327

PMC10962225

10.1016/j.chembiol.2023.12.003

38154461