ArticleNucleic acids research2023
Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Single-cell profiling of DNA methylation in autism spectrum disorder prefrontal cortex reveals distinct regulatory and aging signatures.Cell genomics · 2026Article
- The Landscape of BRCA1-Associated Post-Translational Modifications.Cell biology international · 2026Review
- BayesPI-FLY: a Bayesian neural network approach for inferring feature weighted TF-DNA interaction.Briefings in bioinformatics · 2026Article
- Identification and functional analysis of Rattus norvegicus Mammary carcinoma susceptibility 1b (Mcs1b) nominated variants.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- The specificity landscape of WRKY transcription factors reveals the bidirectional influence of non-CG methylation.Nucleic acids research · 2025Article
- Article
- The amniote-conserved DNA-binding domain of CGGBP1 restricts cytosine methylation of transcription factor binding sites in proximal promoters to regulate gene expression.BMC genomic data · 2024Article
- Developmentally dynamic changes in DNA methylation in the human pancreas.BMC genomics · 2024Article
- Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet.Genome biology · 2024Article
- JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles.Nucleic acids research · 2024Article
- Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation.Nature genetics · 2022Article
- Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding.Genome biology · 2022Article
- Next-generation DNA methylation sequencing: loci and regions differentially methylated in adolescents with chronic postsurgical pain.Neurobiology of pain (Cambridge, Mass.)Article
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Authors and funding
3 authors.
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Abstract
Several studies suggested that transcription factor (TF) binding to DNA may be impaired or enhanced by DNA methylation. We present MeDeMo, a toolbox for TF motif analysis that combines information about DNA methylation with models capturing intra-motif dependencies. In a large-scale study using ChIP-seq data for 335 TFs, we identify novel TFs that show a binding behaviour associated with DNA methylation. Overall, we find that the presence of CpG methylation decreases the likelihood of binding for the majority of methylation-associated TFs. For a considerable subset of TFs, we show that intra-motif dependencies are pivotal for accurately modelling the impact of DNA methylation on TF binding. We illustrate that the novel methylation-aware TF binding models allow to predict differential ChIP-seq peaks and improve the genome-wide analysis of TF binding. Our work indicates that simplistic models that neglect the effect of DNA methylation on DNA binding may lead to systematic underperformance for methylation-associated TFs.
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