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These results suggest that nucleosome occupancy around origins is reset after S phase, then reestablished in every cell cycle for DNA replication. It should be noted that nucleosome occupancy measured by H3 ChIP-seq reflects the fraction of cells within a population having nucleosomes at any given locus.
This nature of nucleosome occupancy is therefore consistent with findings from single-cell analyses that origin firing is stochastic and that origin properties define the probability of origin activation Czajkowsky et al.
Our results suggest that there are multiple factors that affect origin properties, and nucleosome occupancy is one of these factors.
For example, Fkh1 and Fkh2 Knott et al. Hoggard et al.
It is not unexpected that origins are regulated by multiple factors, given that strict regulation of origin activation is necessary for proper DNA replication. However, the fact that most early firing origins lose activities whereas many late firing origins gain activities in the orc mutant supports our conclusion that nucleosome occupancy around origins play critical roles in origin usage profiles genome-wide.
Our results are consistent with this model and provide evidence that nucleosome occupancy is likely one of the key features that dictate which origins are targeted by limiting replication factors.
Histone-DNA interactions within nucleosomes are very stable, and active mechanisms are usually used to slide, evict, or replace histones at gene promoters for transcriptional regulation Li et al.
One possibility is that the pre-RC recruits chromatin regulators to facilitate the removal of nucleosomes around origins.
The histone chaperone facilitates chromatin transcription FACT was shown to bind histones together with Mcm and maintain proper levels of nucleosome occupancy at subtelomeric regions Foltman et al. Although this result does not exclude the possibility that the MCM complex collaborates with unidentified factors, it does suggest that the histone binding activity of Mcm2 alone is not sufficient for regulating levels of nucleosome occupancy at origins.
Another possibility is that chromatin regulators could affect pre-RC binding, which in turn can alter nucleosome occupancy at origins. Indeed, nucleosome positions were found to be important for loading Mcm onto origins in a specific manner Belsky et al.
We preliminarily screened for potential chromatin regulators using H3 ChIP-seq, but thus far have not found any factor responsible for the reduction in nucleosome occupancy around origins at G1.
Although we cannot exclude the possibility that pre-RC formation alone can reduce nucleosome occupancy, this seems highly unlikely because the affinity of ORC to origins alone Hoggard et al.
Furthermore, Mcm ChIP-seq revealed that Mcm localizes to origins to a similar extent in both mid and high H3 classes of origins, supporting the idea that the change in nucleosome occupancy is a regulated process and not a simple consequence of pre-RC binding.
Given that genetic screens for mutants that alter origin properties are likely difficult to establish, biochemical screens for such factors may be more fruitful.
Recently established in vitro DNA replication systems Heller et al. Thus far, understanding mechanisms of origin control through chromatin regulation has proven to be difficult because of the contribution of multiple factors.
Origin initiation must be strictly controlled but also able to adapt to diverse cellular environments. We propose nucleosome occupancy is an important factor in origin regulation and believe further work will help elucidate how nucleosome occupancy functions, together with other determinants of origin activation, in the regulation of origin activities.
All yeast strains are MATa and congenic to Wa with a correction for the weak rad5 allele in the original W Thomas and Rothstein All the experiments using orc allele were performed at a permissive temperature room temperature.
Chromatin preparation and ChIP Cells were harvested and chromatin was prepared as previously described Rodriguez et al.
Bead conjugation and the ChIP were performed as previously described Rodriguez et al. BrdU profiling G1 arrested cells were filtered on a 0. G1 and S phase cells were harvested by adding a 0. Libraries were deep sequenced, aligned, and normalized as previously described McKnight and Tsukiyama ; McKnight et al.
Analysis and ranking of nucleosome occupancy Z-score normalization was performed as described previously using nucleosome occupancy from 1 kb upstream of and downstream from transcription start sites TSSs Nagalakshmi et al. As a control locus, H3 occupancy was averaged at transcription termination sites TTSs Nagalakshmi et al. H3 occupancy was determined for total origins from OriDB Nieduszynski et al. H3 occupancy was ranked as low, mid, and high based on averaged H3 signal bp upstream of and downstream from the midpoint of the ACS for ORC-bound origins, excluding four origins that were too close to the ends of chromosomes or poorly annotated regions.
Analysis of origin properties and pre-RC binding Origin timing data was obtained from hydroxyurea HU experiments Belsky et al. Retrieved from " https: Hidden category: Uses Book template.
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