Extended Data Fig. 11 |. Localized SSB repair in neurons correlates with sites of oxidized 5-methylcytosine.

a, Genome browser screenshot of chromosome 7 showing SAR-seq profiles from two biological replicates and input DNA in i³Neurons without MMS treatment (NT, n = 2) or after treatment with 0.1 mg ml⁻¹ MMS (n = 2) for the final 15 min of an 18-h incubation with EdU. After streptavidin pull-down and PCR amplification, total DNA was quantified (NT rep 1: 0.95 μg; NT rep 2: 1.7 μg; MMS rep 1: 3.8 μg; MMS rep 2: 4.5 μg). Stochastic DNA damage results in loss of DNA synthesis at recurrent sites. b, Quantitative RT–PCR analysis showing PNKP mRNA transcript level in i³Neurons after CRISPRi knockdown, cultured in parallel with samples used for SAR-seq. P = 0.00015 by unpaired two-tailed Student’s t-test; ***P < 0.0001 (n = 3). c, Bottom, heat maps of SAR-seq intensities for 1 kb on either side of SAR-seq peak summits for i³Neurons expressing sgControl (n = 2) or sgPNKP (n = 2). Top, aggregate plots of SAR-seq intensity. d, Bottom, heat map of SAR-seq intensity for 1 kb on either side of the transcription start site in i³Neurons, ordered by SAR-seq intensity. i³Neurons expressing sgControl or sgPNKP were either not treated (NT, n = 2) or treated with 25 μM camptothecin (CPT, n = 2) during incubation with EdU. Top, aggregate plots of SAR-seq intensity. e, Scatter plots showing correlations of intensities (RPKM) between SSBs (ddN S1 END-seq) and 5fC or 5hmC, respectively, for 1 kb on either side of SAR-seq peak summits for i³Neurons. Spearman correlation coefficients and P values are indicated. f, Scatter plots showing correlations of intensities (RPKM) between SAR-seq for i³Neurons expressing sgPOLB and ddN S1 END-seq, 5fC, or 5hmC for 1 kb on either side of SAR-seq peak summits. Spearman correlation coefficients and P values are indicated.