ArticleCommunications biology2024
Identifying the "stripe" transcription factors and cooperative binding related to DNA methylation.
Article in Communications biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
3 citing papers in PubMed.
- MeDReaders 2.0: an updated database for modified DNA readers.BMC genomics · 2026Article
- Bioinformatics insights into plant genomic imprinting: approaches, challenges, and future perspectives.Briefings in functional genomics · 2026Review
- cfMethylPre: deep transfer learning enhances cancer detection based on circulating cell-free DNA methylation profiling.Briefings in bioinformatics · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
DNA methylation plays a critical role in gene regulation by modulating the DNA binding of transcription factors (TFs). This study integrates TFs' ChIP-seq profiles with WGBS profiles to investigate how DNA methylation affects protein interactions. Statistical methods and a 5-letter DNA motif calling model have been developed to characterize DNA sequences bound by proteins, while considering the effects of DNA modifications. By employing these methods, 79 significant universal "stripe" TFs and cofactors (USFs), 2360 co-binding protein pairs, and distinct protein modules associated with various DNA methylation states have been identified. The USFs hint a regulatory hierarchy within these protein interactions. Proteins preferentially bind to non-CpG sites in methylated regions, indicating binding affinity is not solely CpG-dependent. Proteins involved in methylation-specific USFs and cobinding pairs play essential roles in promoting and sustaining DNA methylation through interacting with DNMTs or inhibiting TET binding. These findings underscore the interplay between protein binding and methylation, offering insights into epigenetic regulation in cellular biology.
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Registered trials
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