The role of local transcription and chromatin structure in establishing DNA replication origins

Abstract

In order to duplicate the genome within S‐phase, DNA replication must initiate at multiple start sites. We are using genomic approaches in the model organism Drosophila to elucidate how origins of replication are selected and regulated to maintain genomic stability. As part of the model organism ENCODE consortium we have characterized the average time of replication for all unique sequences, mapped early origins of replication and identified sites of preRC localization in multiple cell lines. We have found that ORC preferentially localizes to open chromatin near the transcription start site of active genes. ORC binding sites are enriched for the histone variant H3.3 which marks open and dynamic chromatin. The large number of ORC binding sites has provided us the opportunity to use machine learning algorithms to identify complex sequence elements that direct ORC localization. We have also found that the single X chromosome of male cell lines replicates significantly earlier than the autosomes, suggesting a link between DNA replication and dosage compensation. Funding from NIH grant HG004279.