Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models

  • 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 are affected by DNA methylation. Overall, we find that CpG methylation decreases the likelihood of binding for the majority of 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.

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Metadaten
Author:Jan GrauORCiDGND, Florian SchmidtORCiD, Marcel Holger SchulzORCiDGND
URN:urn:nbn:de:hebis:30:3-728354
DOI:https://doi.org/10.1101/2020.10.21.348193
Parent Title (English):bioRxiv
Document Type:Preprint
Language:English
Date of Publication (online):2020/10/22
Date of first Publication:2020/10/22
Publishing Institution:Universit├Ątsbibliothek Johann Christian Senckenberg
Release Date:2023/05/02
Issue:2020.10.21.348193
Page Number:15
HeBIS-PPN:509792081
Institutes:Medizin
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Sammlungen:Universit├Ątspublikationen
Licence (German):License LogoCreative Commons - CC BY-NC - Namensnennung - Nicht kommerziell 4.0 International