Chromatin structure differs between coding and upstream flanking sequences of the yeast 35S ribosomal genes

Staphylococcal nuclease (EC 3.1.4.7) and DNase I (EC 3.1.4.5) digestion analysis of the nuclear chromatin structure of the yeast 35S rDNA gene shows the presence of typical and homogeneous nucleosome patterns across the coding sequence. These nucleosomal patterns change abruptly, around the site of transcription initiation and upstream in the 5'-flanking sequences, to a unique pattern with both nucleosomal and nonnucleosomal character. The mix arises, at least partly, from heterogeneity within the population of upstream regions; some regions are nucleosomal, but the majority are nonnucleosomal. The nonnucleosomal set of upstream regions appears to be nucleoprotein associated and, in fact, may be an altered nucleosome structure rather than totally restructured. The abruptness of the transition from nucleosome to other structure suggests restricted nucleosome locations in the region around the transcription initiation site of this gene.