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Fig. 5 | BMC Genetics

Fig. 5

From: CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity

Fig. 5

Stochastic allelic imbalances in cytosine methylation are exacerbated by CGGBP1 depletion

a Allelic imbalances in HEK293T MeDIP are strongly different from the allelic ratios expected in the input with negligible differences between CT and KD. b and c The poor correlation between allelic imbalances in the input and CT (b) or KD (c) is evident in the heat scatters. d The stochastic allelic choices for methylation give rise to a random distribution of allelic representations in HEK293T CT and KD MeDIP (r2 = 0.361). e The allelic imbalances between GM02639 CT and KD were however highly anticorrelated as expected due to less stochasticity in these samples (r2 = 0.013). f and g Parent-of-origin specific allelic imbalance scatter plot between GM02639 CT and KD (f) shows that CGGBP1 depletion enhances a random monoallelic bias with no preference for the maternal or the paternal alleles. For all locations where the CT and KD are expected to be heterozygous ([(Pat-Mat)/(Pat+Mat)] values = 0 ± 0.5), the observed heterozygosity was very low (green shade; see text for details). Instead the unbiased monoallelic methylation with no difference between CT and KD ([(Pat-Mat)/(Pat+Mat)] values < − 0.5 or > 0.5) were observed for the majority of loci (red shades). A skewed allelic imbalance only in CT (aqua shade) or KD (pink shade). For a proportionate subset of loci, the parent-of-origin identities of the methylated alleles were reversed between CT and KD (yellow shades). g A frequency plot of the differences between percent of maternal and paternal allele contributions to the MeDIP DNA shows that CGGBP1 depletion minimizes allelic equivalence (X-axis = 0, Y-axis = − 1) and enhances exclusive maternal or paternal methylation (positive Y-axis values for X-axis = − 1 or + 1). Mat and Pat stand for Maternal and Paternal alleles respectively.

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