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Fig. 6 | Genome Biology

Fig. 6

From: Strand asymmetry influences mismatch resolution during single-strand annealing

Fig. 6

Using CG>TG transitions during UMI-LA to infer methylation status. a Calibrating the deamination assay with a positive control. UMI-LA is performed on barcoded methylated oligonucleotides. Methylated cytosine can spontaneously deaminate at high temperature and be converted into thymine, thus producing conflicting UMIs. b Frequency of alterations during UMI-LA. The bar graph shows the percentage of barcodes with associated alterations found among their UMIs. c Principle of the assay. Uncut reporters in control experiments contain 19 CpGs that can be assayed as in a. d Dot plot showing the ratio of CG>TG transitions inside vs outside the CpGs of the F segments for four replicates. The average around 10 matches the 10-fold increase observed for methylated CpG in panel b. e Proportion of pristine reporters with CG>TG transitions in different chromatin contexts. Histone marks present at the insertion site are indicated on the x-axis. Dots indicate the local mean and vertical bars show the limits of a 99% confidence interval for this mean. The horizontal bar shows the global average of reporters with CG>TG transitions (the value around 20% is consistent with the baseline of Fig. 6b, taking into accounts that there are 19 CpG and 4 pooled replicates). P-values below 0.01 are indicated on the graph (two-tailed Student’s t test to compare proportions, n = 2182). Significant reductions of CG>TG transitions are observed in H3K27me3, H3K4me2, H3K4me3, and H3K9ac, all associated with active promoters in mouse ES cells

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