Please use this identifier to cite or link to this item: http://dx.doi.org/10.25673/111388
Title: Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models
Author(s): Grau, JanLook up in the Integrated Authority File of the German National Library
Schmidt, Florian
Schulz, Marcel HolgerLook up in the Integrated Authority File of the German National Library
Issue Date: 2023
Type: Article
Language: English
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.
URI: https://opendata.uni-halle.de//handle/1981185920/113342
http://dx.doi.org/10.25673/111388
Open Access: Open access publication
License: (CC BY-NC 4.0) Creative Commons Attribution NonCommercial 4.0(CC BY-NC 4.0) Creative Commons Attribution NonCommercial 4.0
Journal Title: Nucleic acids research
Publisher: Oxford Univ. Press
Publisher Place: Oxford
Volume: 51
Issue: 18
Original Publication: 10.1093/nar/gkad693
Page Start: 1
Page End: 20
Appears in Collections:Open Access Publikationen der MLU

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