Fig. 5
From: Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet
CentriMo [56] results for replicate 1 of OCT4 CUT&RUN in mESCs. Motifs include the top three DREME motifs with colour indicating rank: first (red); second (purple), third, where applicable (dark green). Motifs also include the top non-POU5F1 JASPAR motif (cyan), and the JASPAR POU5F1B motif (orange). Both of these motifs come from the JASPAR 2020 [62] core vertebrate set. We generated these results using \({500}\,\text {bp}\) regions centred upon the summits of MACS 2 [63] peaks generated from those CUT&RUN fragments ≤120 bp. We called peaks using IgG controls and without any spike-in calibration (Data processing). Listed p-values computed by CentriMo [56]. For consistency, we depict the JASPAR sequence logo using MEME’s relative entropy calculation and colouring. A bisulfite-converted (methylated; 2797 CUT&RUN peaks) sequences. B hmC-Seal (3974 CUT&RUN peaks) sequences. Also depicts the top MEME [64] de novo motif (blue). C Sequence logo of the POU5F1B motif (MA0792.1). D Sequence logo of the top DREME de novo motif