MEME-ChIP motif analysis

The 500 bp Sequences around the peak summits from the Promoter Region were extracted. We imported the sequences into the MEME-ChIP motif discovery tool (v5.3.3). ⁶⁰ Motif Discovery was performed in the Discriminative Mode by using Sequences obtained from treated samples as Primary Sequence and Sequences from Control Sample as Control sequences in the MEME-ChIP Program. Default Parameters were used for the discovery of motifs. HOCOMOCO Human (v11)^60,61 was used as a Known Motif Database. Motifs discovered for H3K4me3-6h and H3K4me3-24h through the MEME-ChIP tool were compared against the HOCOMOCO Human(v11) motifs database using Tomtom-a Motif Comparison tool-using default settings. ⁶²