Fifty per cent of the genome is discontinuously replicated on the lagging strand 
as Okazaki fragments. Eukaryotic Okazaki fragments remain poorly characterized 
and, because nucleosomes are rapidly deposited on nascent DNA, Okazaki fragment 
processing and nucleosome assembly potentially affect one another. Here we show 
that ligation-competent Okazaki fragments in Saccharomyces cerevisiae are sized 
according to the nucleosome repeat. Using deep sequencing, we demonstrate that 
ligation junctions preferentially occur near nucleosome midpoints rather than in 
internucleosomal linker regions. Disrupting chromatin assembly or lagging-strand 
polymerase processivity affects both the size and the distribution of Okazaki 
fragments, suggesting a role for nascent chromatin, assembled immediately after 
the passage of the replication fork, in the termination of Okazaki fragment 
synthesis. Our studies represent the first high-resolution analysis--to our 
knowledge--of eukaryotic Okazaki fragments in vivo, and reveal the 
interconnection between lagging-strand synthesis and chromatin assembly.