The role of DNA replication timing in the establishment of gene expression and chromatin organisation patterns

Eukaryotic DNA is duplicated according to an evolutionary conserved temporal pattern, meaning that different genomic regions are replicated at different times during S-phase. This temporal pattern of DNA replication is altered during development and differentiation and can be dysregulated in cancers. While temporal changes in genome duplication are associated with altered transcription and chromatin organisation, it is still unknown whether DNA replication timing is a cause or consequence of cellular fate changes.

We are using budding yeast to conditionally perturb DNA replication timing genome-wide, combined with genome-wide and targeted molecular and genetic approaches, to address what is the effect of this perturbation in gene expression and chromatin conformation.

Using this approach we have identified many differentially expressed (DE) genes and genes with alterations in their chromatin landscape. Among these are meiotic genes, which shouldn't be expressed as our experiments were performed in haploid cells and the diploid stage of the yeast life cycle is the only one that can undergo meiosis. This observation supports the hypothesis that replication timing is important to regulate cellular differentiation. Moreover, by analysing published ChIP datasets we identified an enrichment for the binding of Ume6, a regulator of meiotic genes, among our DE genes. These results suggest that perturbations in the temporal order of DNA replication perturb transcription-factor binding dynamics. Therefore, we are currently analysing transcription-factor binding dynamics genome-wide using our conditional system.

Our results show that global changes in replication timing have a genome-wide effect in transcription and chromatin organisation. We are currently exploring the mechanism behind these changes, and hope to increase our understanding of replication timing control of gene expression. A comprehensive analysis of alterations in the genome during cellular division will be of major importance for understanding the mechanisms regulating cell fate changes during differentiation and development.