Thus, the controlled recruitment of DNMT1 into replication forks is an important component in the perpetuation of DNA methylation patterns and S-phase abnormalities could affect methylation patterns by altering the replication timing of sequences.
We decided to test several islands using a quantitative PCR assay [ 31, 32] to check for concordance between their replication time in fibroblasts and the replication timing ratio determined by the Woodfine group in lymphoblastoid cells [ 18, 19].
To calculate compositional skews between the leading and the lagging strands, we selected a set of 207 replication origins corresponding to clear peaks flanked on both sides by clear valleys on the replication timing profile.
The mechanism by which neocentromere formation influences the replication timing of the associated chromatin domain remains to be identified.
By contrast, six (late firing) origins inferred from the replication timing profile escaped detection by the initial slope method as their slope falls below the noise threshold (supplementary fig. S7, Supplementary Material online, and see Materials and Methods).
We selected a subset of 207 replication origins that appear as clear peaks on the replication timing profile, flanked on both sides by clear valleys that correspond to termination regions.
The reduction of these marks upon loss of ORCA leads to changes in the replication timing only of these regions as indicated by the significant decrease in late-replication patterns upon ORCA KD.
Gilbert et al. [ 22] previously reported a good correlation between open chromatin and early replication, based on the replication timing results of the 1 Mb array reported by Woodfine et al. [ 19].
DOI: http://dx.doi.org/10.7554/eLife.06496.015 Using the data set mentioned above, we examined the replication timing of the regions that showed reduction in H3K9me3 by ChIP-seq.
Using the dataset mentioned above, we examined the replication timing of the regions that showed reduction in H3K9me3 by ChIP-seq.
