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Pivotal Role of the NuRD Complex in Remodeling Chromatin Environment and Maintaining Genome Architecture at CTCF Sites [Hi-C]

ABSTRACT: Interactions between nuclear proteins and chromatin are critical in transcriptional regulation. The state-of-the-art approaches provide merely snapshot information on their interactions, which impedes our understanding of the causality in the dynamic regulatory processes. Here, we developed a novel method termed G-MAT that profiles the footprints of a nuclear protein on chromatin and DNA methylome simultaneously in living mammalian cells. Utilizing G-MAT to transcription factor CTCF, we inferred that CTCF searches its binding sites in the genome through stochastic collision to the chromatin. Together with eBioID, which is an enhanced BioID method facilitated by the Suntag system, we found hundreds of proteins with distinct functions co-occupying CTCF binding sites on chromatin, including RNA splicing and chromatin remodeling. Intriguingly, two methyl-CpG binding domain (MBD) proteins were found as interacting partners of CTCF, largely leading CTCF to preferentially bound to methylated DNA segments, consistent with the co-occurrence of CTCF footprints and DNA hyper-methylation when analyzing the G-MAT data at the single-molecule resolution. MBD2, one of the MBD proteins shown to be associated with demethylases, could likely erase DNA methylation near CTCF binding sites, resulting in seemingly anti-correlations between CTCF binding and DNA methylation. Altogether, G-MAT has enabled us to investigate the causal relationship between CTCF target searching and DNA methylation at the single-molecule level, providing an important data resource and novel insights for advanced understanding of transcriptional regulation dynamics.

ORGANISM(S): Homo sapiens

PROVIDER: GSE178813 | GEO | 2026/05/04

REPOSITORIES: GEO

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