Abstract
The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements. However, unlike their yeast counterparts, both plant and metazoan origins are G/C-rich and are associated with transcription start sites. Here we show that an industrially important methylotrophic budding yeast, Pichia pastoris, simultaneously employs at least two types of replication origins—a G/C-rich type associated with transcription start sites and an A/T-rich type more reminiscent of typical budding and fission yeast origins. We used a suite of massively parallel sequencing tools to map and dissect P. pastoris origins comprehensively, to measure their replication dynamics, and to assay the global positioning of nucleosomes across the genome. Our results suggest that some functional overlap exists between promoter sequences and G/C-rich replication origins in P. pastoris and imply an evolutionary bifurcation of the modes of replication initiation.
Highlights
Eukaryotic DNA replication initiates at multiple genomic loci termed replication origins
An early study identified two regions of the P. pastoris genome that have autonomously replicating sequences (ARSs) function, but do not have ARS Consensus Sequence (ACS) elements seen in S. cerevisiae ARSs [37]
The extensively studied yeasts S. cerevisiae and S. pombe have yielded great insights into origin function, but lack several properties exhibited by metazoan origins
Summary
Eukaryotic DNA replication initiates at multiple genomic loci termed replication origins. While the initiation of DNA replication at origins is a key regulatory feature of genome replication in all organisms studied, the structural components of these cis-acting elements are remarkably diverse [1]. Yeast origins are generally short, intergenic, A/T-rich DNA elements. Metazoan and plant origins are large, poorly-defined zones enriched for genes and G/C-rich DNA [2,3,4,5,6]. While metazoan origin activity correlates with expression of adjacent genes [2,3,7], no such correlation is seen in yeast. Though much has been learned about DNA replication using the highly tractable yeast models, these differences have limited the usefulness of yeast for the study of some aspects of mammalian DNA replication
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