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Fig. 2 | BMC Research Notes

Fig. 2

From: Dynamic bimodal changes in CpG and non-CpG methylation genome-wide upon CGGBP1 loss-of-function

Fig. 2

Genomic regions dependent on CGGBP1 for stability of cytosine methylation have inter-strand G/C asymmetry. a A frequency plot of GC-skew calculated as {(G−C)/(G+C)} for all GoM (red solid line) and all LoM (blue solid line) regions showed a clear clustering of GoM and LoM regions into two groups; one peaking near − 0.5 and other around + 0.5. The distribution of the data could not be fitted with a single Gaussian curve, but with a sum of two Gaussian curves with very high confidence (Additional file 1: Table S10). When these datasets were split into L1-LINEs (nearly 20% of the GoM and LoM sets; dashed broken lines) and non-L1 regions (dotted lines), we observed a clear difference between the L1 sequences versus the rest with the GoM-L1 and LoM-L1 sequences exhibiting lesser GC-skew than the non-L1 GoM and LoM sequences. However, all of these could be fitted only with a sum of two Gaussian curves. b The GC-skew observed with the GoM-L1 and LoM-L1 sequences was unexpected as the L1 sequences from Repbase and NCBI L1 consensus showed an absolutely Gaussian distribution of GC-skew centred near zero. c, d The RoM and RuN regions did not display the GC-skew as seen for GoM and LoM regions. The GC-skew frequency for RoM and RuN was centred around zero in a binomial fashion. eh GC-skew regions genome-wide are prone to methylation gain upon CGGBP1 depletion. The distribution of methylated cytosines centred at the middle of GC-skew regions displayed a binomial increase in methylation on both the strands in the absence of CGGBP1 function. This increase in methylation is highly specific and restricted to less than 1 kb flanks of the GC-skew regions genome-wide [6] with mean length of 747 ± 482 bp. e Negative GC-skew, methylation on bottom strand. f Negative GC-skew, methylation on top strand. G: Positive GC-skew, methylation on bottom strand. h Positive GC-skew, methylation on top strand. Red line = S2, blue line = S1. X axis represents genomic location from the centre of GC-skew regions. Y axis represents methylated cytosine counts in bins with sizes as indicated. Plots were generated using deepTools [8]

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