Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet

As part of our larger study, we validated our predicted methylated and hydroxymethylated binding preferences of OCT4. This represents the first conjoint CUT&RUN experiment across conventional, methylation-, and hydroxymethylation-enriched sequences. Overall design: We employed cleavage under targets and release using nuclease (CUT&RUN), across an aggregated OCT4 sample, with two replicates, which was then sequenced via 3 different strategies. We also included a single IgG control.