Replication forks face multiple obstacles that slow their progression. By 
two-dimensional gel analysis, yeast forks pause at stable DNA protein complexes, 
and this pausing is greatly increased in the absence of the Rrm3 helicase. We 
used a genome-wide approach to identify 96 sites of very high DNA polymerase 
binding in wild-type cells. Most of these binding sites were not previously 
identified pause sites. Rather, the most highly represented genomic category 
among high DNA polymerase binding sites was the open reading frames (ORFs) of 
highly transcribed RNA polymerase II genes. Twice as many pause sites were 
identified in rrm3 compared with wild-type cells, as pausing in this strain 
occurred at both highly transcribed RNA polymerase II genes and the previously 
identified protein DNA complexes. ORFs of highly transcribed RNA polymerase II 
genes are a class of natural pause sites that are not exacerbated in rrm3 cells.