RT Journal Article SR Electronic T1 Finding De novo methylated DNA motifs JF bioRxiv FD Cold Spring Harbor Laboratory SP 043810 DO 10.1101/043810 A1 Vu Ngo A1 Wei Wang YR 2016 UL http://biorxiv.org/content/early/2016/03/15/043810.abstract AB 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.