Extended Data Fig. 1: Supporting Data for Fig. 1.

a) Sequence logo showing the sequence context preference for DddA11 on naked DNA. b) Aggregate profile of cytidine deamination fractions (y axis) around DNase I hypersensitive sites (DHSs) from whole-genome sequencing (WGS) of DddA11-treated K562 cells. c) Bar plots comparing modified cytosine profiles between DddA11-WGS and NOMe-seq²³. Left: Number of modified cytosines in open chromatin. Middle: Total number of modified cytosines detected genome-wide. Right: Fraction of modified cytosines overlapping CREs.d) Bar plot showing C•G-to-T•A editing rates at unmethylated, methylated, or untreated cytidines in CpG sites of varying sequence contexts in the chr7:27158522–27163197 region. e) Histogram showing the number of C•G-to-T•A mutations per read at the HS2 locus (chr11:5279265-5282582) in DddA11-free and DddA11-treated samples. The dashed line represents a 2% threshold of all candidate cytosines. f) Histogram of edit differences between randomly sampled read pairs at the HS2 locus in DddA11-free and DddA11-treated samples. The dashed line represents a 2% threshold of all candidate cytosines. g) Genome tracks displaying ATAC-seq, TDAC-seq, and DADs across indicated genomic regions. TDAC-seq signal represents the average number of DddA11 edits in a 50-bp window. h) TDAC-seq at the HS2 locus under varying DddA11 concentrations and reaction times, compared with ATAC-seq. TDAC-seq signal represents the average number of DddA11 edits in a 50-bp window. i) Schematic of hidden Markov model used to call DADs. j) Scatter plot showing the percentage of bases covered by both DAD signal and ATAC-seq peaks (x-axis) versus bases covered only by DAD signal (y-axis). The dashed diagonal line represents equal coverage. Each point represents TDAC-seq from a different locus. k) Top: genome tracks showing chromatin profiles, TDAC-seq, and DADs at the ZBTB38 locus. Bottom: heatmap showing DAD co-accessibility, shown as observed minus expected, calculated as the product of individual accessibility fractions. Data in b,g,j, and k are representative examples of n = 2 replicates. Correlation between TDAC-seq replicates is presented in Supplementary Fig. 1.