RT Journal Article
SR Electronic
T1 SEMplMe: A tool for integrating DNA methylation effects in transcription factor binding affinity predictions
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.08.13.250118
DO 10.1101/2020.08.13.250118
A1 Nishizaki, Sierra S.
A1 Boyle, Alan P.
YR 2021
UL http://biorxiv.org/content/early/2021/02/22/2020.08.13.250118.abstract
AB Motivation Aberrant DNA methylation in transcription factor binding sites has been shown to lead to anomalous gene regulation that is strongly associated with human disease. However, the majority of methylation-sensitive positions within transcription factor binding sites remain unknown. Here we introduce SEMplMe, a computational tool to generate predictions of the effect of methylation on transcription factor binding strength in every position within a transcription factor’s motif.Results SEMplMe uses ChIP-seq and whole genome bisulfite sequencing to predict effects of methylation within binding sites. SEMplMe validates known methylation sensitive and insensitive positions within a binding motif, identifies cell type specific transcription factor binding driven by methylation, and outperforms SELEX-based predictions for CTCF. These predictions can be used to identify aberrant sites of DNA methylation contributing to human disease.Availability and Implementation SEMplMe is available from https://github.com/Boyle-Lab/SEMplMe.Contact apboyle{at}umich.eduSupplementary Information Supplementary data are available at Bioinformatics online.Competing Interest StatementThe authors have declared no competing interest.