Protected region upstream and limited nucleosomal positioning downstream of the transcription initiation region of yeast 35S ribosomal gene

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Abstract
To locate nucleosome positions around the transcription initiation site of 35S r[ribosomal]DNA in yeast, single and double cleavage site data for staphylococcal nuclease and single cleavage site data for DNase I were obtained by methods involving some modifications of the usual indirect end-labeling procedure. Immediately upstream of the initiation site there is an .apprx. 225 base pair (bp) stretch of chromatin which is quite resistant to nuclease digestion. The nucleosomal domain begins on the coding sequences, at the downstream end of the resistant region, with the major locus 30 bp and a minor locus 5 bp downstream of the initiation site in growing cells. The location of the major locus is corroborated by analysis within the coding sequences, although results within the gene are less convincing because of a strong similarity of chromatin and naked DNA digestion profiles. The staphylococcal nuclease cleavage maps were tested by their ability to reproduce chromatin digest profiles and to explain the presence or absence, depending on which parts of the region were used as probes, of specific bands within the pattern. The site of the major upstream locus of the nucleosomal domain differs in growing and stationary cells. This shift changes the accessibility of .apprx. 25 bp of DNA and may be associated with the expression of these genes.