Abstract
There is increasing evidence that posttranslational modifications (PTMs) such as methylation and hydroxymethylation on cytosine would greatly impact the binding of transcription factors (TFs). We modified a motif finding method Epigram to discover methylated motifs and other motifs containing other PTMs. When applied to TF ChIP-seq and DNA methylome data in H1 and GM12878, our method successfully identified novel methylated motifs that can be recognized by the TFs or their co-factors. We also observed spacing constraint between the canonical motif of the TF of interest and the newly discovered methylated motifs, which suggests operative recognition of these cis-elements by collaborative proteins.
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