Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding.

ABSTRACT:

Background

While methylation of CpG dinucleotides is traditionally considered antagonistic to the DNA-binding activity of most transcription factors (TFs), recent in vitro studies have revealed a more complex picture, suggesting that over a third of TFs may preferentially bind to methylated sequences. Expanding these in vitro observations to in vivo TF binding preferences is challenging since the effect of methylation of individual CpG sites cannot be easily isolated from the confounding effects of DNA accessibility and regional DNA methylation. Thus, in vivo methylation preferences of most TFs remain uncharacterized.

Results

We introduce joint accessibility-methylation-sequence (JAMS) models, which connect the strength of the binding signal observed in ChIP-seq to the DNA a

SUBMITTER: Hernandez-Corchado A 

PROVIDER: S-EPMC9264634 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature