Skip to main content
Fig. 2 | Genome Biology

Fig. 2

From: Toward a base-resolution panorama of the in vivo impact of cytosine methylation on transcription factor binding

Fig. 2

CpG methylation preference of CTCF in HEK293 cells. A Motif logo and dot plot representations of the sequence/methylation preference of CTCF. The logo (top) shows methylation coefficients as arrows, with the arrow length proportional to the mean estimate of methylation effect. The dot plot (bottom) shows the magnitude of the preference for each nucleotide at each position using the size of the dots, with red and blue representing positive and negative coefficients, respectively. The dumbbell-like shapes demarcate the CpG dinucleotides with significant methylation effects (at FDR < 1 × 10−5). The color of the dumbbell shows the signed logarithm of P-value of the methylation coefficient, with red and blue corresponding to increased or decreased binding to methylated C, respectively. B Heatmap representation of the sequence (left), accessibility (middle), and CpG methylation (right), for a subset of CTCF peaks that have high DNA accessibility, a close sequence match to the initial CTCF motif, and CpGs at dinucleotide positions 2/3 and 12/13. Peaks (rows) are sorted by the residual of a reduced JAMS model that does not use the methylation level of C2pG3 and C12pG13 for predicting the CTCF binding signal. Note that in the methylation heatmap (right), the methylation level of a CpG dinucleotide is shown in the column that corresponds to the position of the C nucleotide. For example, values in column 2 correspond to the methylation level of the C2pG3 dinucleotide

Back to article page