Figure 6. CENP-A-directed methylation within chromosome X centromeric higher order repeats.

a, Schematic of DiMeLo-seq with AlphaHOR-RES centromere enrichment. b, Genome browser plot on HG002 chromosome X of read coverage from DiMeLo-seq libraries with centromere enrichment (top) or without (middle). Bottom track depicts the region of the alpha satellite array. c, Barplot of percentage mA/A (using a stringent Guppy probability threshold of 0.95) for reads from each library that contain or do not contain CENP-A enriched k-mers. Fold enrichment of methylation percentage on CENP-A reads over Non-CENP-A reads reported on top. Error bars represent 95% confidence intervals. d, View of a 250 kb region spanning the CDR within the active chrX HOR array. (top) Single-molecule view, with individual reads as gray lines and mCpG positions as orange dots shaded by Guppy’s methylation probability. (bottom) CpG methylation frequency from nanopore sequencing reported in ³⁵. e, Single-molecule view of reads in (d). mA positions are depicted as blue dots shaded by Guppy’s methylation probability. f, Aggregate view of mA. mA/A plot indicates the fraction of reads with a Guppy methylation probability above 0.6 at each adenine position (averaged over a 250 bp rolling window for visualization). Marker deserts (regions of at least 10 kb without unique 51 bp k-mers) are shown in orange to illustrate difficult-to-map locations for short-read sequencing. g, For CENP-A or IgG control DiMeLo-seq, read coverage (top plots) and average fraction of nucleosomes detected as CENP-A (bottom plot) per read in sliding 5 kb windows (step size 1 bp), providing a measure of the density of CENP-A nucleosomes within single DNA molecules across the region. Thick lines indicate a 25 kb rolling average. Cartoon below shows representations of detected CENP-A nucleosomes within a 5 kb region corresponding to the CDR or CDR-adjacent region.