The Saccharomyces cerevisiae RRM3 gene encodes a 5' to 3' DNA helicase. While 
replication of most of the yeast genome was not dependent upon Rrm3p, in its 
absence, replication forks paused and often broke at an estimated 1400 discrete 
sites, including tRNA genes, centromeres, inactive replication origins, and 
transcriptional silencers. These replication defects were associated with 
activation of the intra-S phase checkpoint. Activation of the checkpoint was 
critical for viability of rrm3Delta cells, especially at low temperatures. Each 
site whose replication was affected by Rrm3p is assembled into a nonnucleosomal 
protein-DNA complex. At tRNA genes and the silent mating type loci, disruption 
of these complexes eliminated dependence upon Rrm3p. These data indicate that 
the Rrm3p DNA helicase helps replication forks traverse protein-DNA complexes, 
naturally occurring impediments that are encountered in each S phase.