Figure 6

Variability in centromeric regions among cell lines persists across sequence elements and chromosomes. (a) The replication-timing bias for each centromeric sequence element type is compared across five cell lines. For each satellite sequence family, the median interquartile range across cell lines is indicated below the axis. HEK293T and A2780, which have, on average, the earliest centromeric replication timing, are earlier replicating across many different sequence elements. Compare to Fig. 4. (b, c) Inter-origin distance and RT slope are similar across cell lines. Compare to Fig. 5. (d) Average replication-timing within centromeric regions and the flanking 5 Mb on either side. For each chromosome, the entire annotated centromeric region (Fig. 3) was divided into 100 equally spaced bins. Given that centromeres differ in length among chromosomes, coordinates within the tan box represent relative position within the region. HEK293T and A2780 have the earliest average centromeric replication, while GM12878 and HCC1143 have the latest. (e) Differences in centromere replication timing among cell lines are consistent across chromosomes. Each bar represents the number of times that a given cell line had the earliest, 2nd earliest, 3rd earliest, etc. median replication timing across the entire centromeric region (analogous to the shaded region in d, but considering each chromosome independently). HEK293T and A2780 are consistently the earliest replicating, while GM12878 and HCC1143 are consistently the latest replicating, and HCC1954 is consistently intermediate.