Chromatin structure and transcriptional activity around the replication forks arrested at the 3' end of the yeast rRNA genes.

Replication intermediates containing forks arrested at the replication fork barrier near the 3' end of the yeast rRNA genes were analyzed at the chromatin level by using in vivo psoralen cross-linking as a probe for chromatin structure. These specific intermediates were purified from preparative two-dimensional agarose gels, and the extent of cross-linking in the different portions of the branched molecules was examined by electron microscopy and by using a psoralen gel retardation assay. The unreplicated section corresponding to the rRNA coding region upstream of the arrested forks appeared mostly heavily cross-linked, characteristic of transcriptionally active rRNA genes devoid of nucleosomes, whereas the replicated daughter strands representing newly synthesized spacer sequences showed a nucleosomal organization typical for bulk chromatin. The failure to detect replication forks arrested at the 3' end of inactive rRNA gene copies and the fact that most DNA encoding rRNA (rDNA) is replicated in the same direction as transcription suggest that replication forks seldom originate from origins of replication located immediately downstream of inactive genes.