DNA Methylation Concurrence, Independent of DNA Methylation Ratios, Is Associated with Chromatin Accessibility and 3D Genome Architecture.

Guian Zhang, Yixian Yang, Dan Cui, Jia Li

Abstract read

In one paragraph

Article in International journal of molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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1 · What the graph read from it

What it found

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

4 authors.

Guian ZhangState Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou 510120, China.

Yixian YangState Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou 510120, China.

Dan CuiGuangzhou National Laboratory, Guangzhou 510005, China.

Jia LiState Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou 510120, China.

Funding

Guangzhou Municipal Science and Technology Bureau, Guangzhou Key Research and Development Program 2024B03J0046National Natural Science Foundation of China 82370148R&D Program of Guangzhou Laboratory GZNL2023A02003R&D Program of Guangzhou Laboratory GZNL2023A02011Supported by the grant of State Key Laboratory of Respiratory Disease SKLRD-Z-202307

6 · The paper itself

Abstract

Multiple metrics for read-level DNA methylation pattern analysis have provided new insights into DNA methylation modifications. However, the performance of these metrics and their relationship with DNA methylation ratios in identifying biologically meaningful regions have remained unclear. Here, we systematically benchmarked five read-level DNA methylation metrics using whole-genome bisulfite sequencing data from 59 individuals across six healthy tissue types and six tumor types. We found that DNA methylation concurrence (MCR) effectively captured tissue-specific features independent of the DNA methylation ratios. Regions that exhibited decreased MCR (MCDRs) in tumors were significantly enriched in promoter and intergenic regions and strongly overlapped with tumor-gained chromatin accessibility sites. The further analysis of histone modifications, including H3K4me3, H3K27ac, and H3K9ac, confirmed that MCDRs marked active gene regulatory elements. Motif enrichment analysis revealed a strong preference for CTCF binding within MCDRs. Additionally, 3D genome analysis supported a model in which MCDRs, independent of DNA methylation ratios, contribute to active gene regulation by facilitating CTCF binding and long-range chromatin interactions.

Indexed as

ChromatinDNA MethylationGenome, HumanCCCTC-Binding FactorHistonesHumansNeoplasmsPromoter Regions, GeneticCCCTC-Binding FactorChromatinHistonesCTCFepigenomicshistone modificationpan cancerread-level DNA methylation patternscATAC-seq

Identifiers

PMID40806343

DOI10.3390/ijms26157199

PMCPMC12346627

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.