Fig. 1

Global H3.3 and H3.1 genome-wide occupancy relative to replication timing and transcriptional activity. a H3.3 and H3.1 genomic coverage normalized to input (chromosome 3 centromeric band±15 Mb, x-axis). The y-axis shows the log₂ ratio between the mean per-base number of reads from H3.3 (green) and H3.1 (purple) and their respective input, at consecutive 10 kb bins (smoothed over 5 non-zero bins). Enriched regions (i.e., log₂ ratio ≥ 0) are highlighted in darker colors. b H3.3 and H3.1 occupancy by replication timing: the panels show the histogram and Gaussian kernel density corresponding to the log₂ ratio to input for H3.3 (green) and H3.1 (purple) at 10 kb regions ranked by replication timing from early to late (S-phase fraction with the highest mean coverage in Repli-Seq data from Dellino et al.³⁸). c Mean values corresponding to b. d H3.3 and H3.1 occupancy by replication timing at increasing levels of nascent transcription: the mean log₂ ratio to input for H3.3 (green, left) and H3.1 (purple, right) at 10 kb regions ranked by replication timing (as in b) and transcription percentile (based on nascent RNA-Seq data from Liang et al.⁵³). The color gradient represents increasing levels of nascent transcription computed from the log₂-transformed mean coverage: absence of measurable transcription (none), lower 10th percentile (low), 10th to 90th percentile (mid) or upper 10th percentile (high). e H3.3 and H3.1 correlation with early DNA synthesis at increasing transcription levels. H3.3 (top) and H3.1 (bottom) log₂ ratio to input (x-axis) against S₁ coverage normalized to the average over all fractions (log₂ ratio, z-axis) at 10 kb regions ranked by transcriptional status (y-axis). The rank reflects the level of nascent transcription as described above