Finding De novo methylated DNA motifs

BioRxiv : the Preprint Server for Biology
Vu Ngo, Mengchi Wang


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.

Related Concepts

Protein Methylation
Post-Translational Protein Processing
DNA Methylation
PTMS gene
Chromatin Immunoprecipitation
Protein Domain
Transcription Factor

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