Sequence-directed nucleosome positions on the yeast SNR6 gene. Numbers denote the positions of the promoter elements and MNase cuts in the genomic DNA in base pairs while ovals represent individual nucleosomes. (A) Schematic representation of reported nucleosome positions in vivo on the gene and its flanking regions. Arrow marks the transcription initiation site. (B) and (C) Indirect end-labeling analysis of the chromatin structure reconstituted on the SNR6 gene in the plasmids in vitro. Naked DNA (lanes 1, 2) and chromatin (lanes 3,4) were digested with MNase and probed with a primer away from the gene region. Positions of the boxes A and B are marked, M denotes molecular size marker and the vertical bar marks the genomic DNA region in the plasmid. (B) Primer hybridizes 1281 bp upstream of the SNR6 TATA box. Bands at -545, -656 and +830 bp map in the vector DNA. As compared with -241 and -453, bands at -368 and -545 are faint (black dots, lanes 3 and 4) and may not be the chromatin-specific cuts (cf. naked DNA cuts at -349 and -517, lanes 1 and 2). Two alternate registers are shown on two sides of lanes 3 and 4. (C) Primer hybridizes 894 bp upstream of the TATA box. Positions -264 and +558 fall in the vector DNA.