Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae

Abstract

BackgroundEukaryotic genomes are replicated during S phase according to a temporal program. Several determinants control the timing of origin firing, including the chromatin environment and epigenetic modifications. However, how chromatin structure influences the timing of the activation of specific origins is still poorly understood.ResultsBy performing high-resolution analysis of genome-wide nucleosome positioning we have identified different chromatin architectures at early and late replication origins. These different patterns are already established in G1 and are tightly correlated with the organization of adjacent transcription units. Moreover, specific early and late nucleosomal patterns are fixed robustly, even in rpd3 mutants in which histone acetylation and origin timing have been significantly altered. Nevertheless, higher histone acetylation levels correlate with the local modulation of chromatin structure, leading to increased origin accessibility. In addition, we conducted parallel analyses of replication and nucleosome dynamics that revealed that chromatin structure at origins is modulated during origin activation.ConclusionsOur results show that early and late replication origins present distinctive nucleosomal configurations, which are preferentially associated to different genomic regions. Our data also reveal that origin structure is dynamic and can be locally modulated by histone deacetylation, as well as by origin activation. These data offer novel insight into the contribution of chromatin structure to origin selection and firing in budding yeast.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-791) contains supplementary material, which is available to authorized users.

A Novel Rrm3 Function in Restricting DNA Replication via an Orc5-Binding Domain Is Genetically Separable from Rrm3 Function as an ATPase/Helicase in Facilitating Fork Progression

“…Instead of a global role in controlling origin activity, the wildtype level of HU sensitivity of rrm3Δ cells, the less pronounced S phase progression in HU than that of the rad53 Δ mutant, and the importance of Rrm3 for replicating through certain nonhistone-protein-bound regions suggest that Rrm3 may play a role at origins in specific loci, such as those in highly transcribed regions and regions with converging transcription, which are often late-firing [57], rRNA and tRNA coding loci, or highly transcribed metabolic genes, where ORC has been found to be bound to the open reading frames, possibly to coordinate the timing of replication with transcription [58]. Indeed, our analysis so far has revealed that Rrm3 appears to associate only with a subset of replication origins.…”

A basic domain in the histone H2B N-terminal tail is important for nucleosome assembly by FACT

“…Analysis of histone occupancy near early and late replication origins was performed similarly. Replication origin coordinates were from a published data set (30). …”

How and why multiple MCMs are loaded at origins of DNA replication

“…2C). Early origins tend to have both larger NFRs and higher rates of nucleosome exchange [30,34], both of which could lead to increased MCM loading. Finally, a number of trans-acting factors, such as Rif1, Rpd3, and Fkh1, have been shown to regulate origin timing [35][36][37][38] (Fig.…”