Fig. 7

Genes sorted by average size of the long fragments from H4Q85C cleavage data. a Genes aligned at the +1 nucleosome and sorted according to the average size of the long fragments (135–175 bp) that were produced by H3Q85C cleavage. The transcription levels, as measured by the levels of nascent transcripts obtained from NET-seq data [73], indicate that the more transcribed genes have more compact nucleosome arrays. b Average nucleosome dyad density for the yeast genes separated into five quintiles: quintile 1, the top fifth from a, through quintile 5, the bottom fifth from a. The decrease in nucleosome spacing correlates with a widening of the NDR, which is characteristic for the highly transcribed genes. c The distribution of linker histone H1 (Hho1 data from [80]) is also correlated with nucleosome spacing: the longer the nucleosome spacing, the more H1 is bound to the corresponding nucleosomes. The H2A.Z variant is enriched in the +1 nucleosomes (data from [61]); the less active genes appear to have more H2A.Z histones incorporated into their +1 nucleosomes. The more active genes contain more H3K4me3 marks on their bodies (data from [81]) and more TBP bound to their promoters (data from [62]). d Average properties for the five quintiles