Fig. 4

Nucleosome phasing patterns are characteristic of 5’ but not 3’ gene ends. a Nucleosome dyads from combined H4S47C- and H3Q85C-anchored cleavage data. Gene promoters aligned at +1 nucleosomes. Divergent (top) and tandem (bottom) genes are separated and sorted according to the distance between the +1 nucleosome and the NDR of the upstream gene. The vertical red stripes from the gene bodies indicate strong nucleosome phasing relative to the NDR. The nucleosome distribution in the region between neighboring NDRs is characterized by an interference pattern generated by phasing signals originating from both flanking NDRs. b Nucleosome distribution at the 3’ gene ends aligned at the transcription termination site (TTS). Convergent (top) and tandem (bottom) genes are separated and sorted according to the distance between the TTS and the NDR of the downstream gene. The absence of vertical red stripes at the TTS of convergent genes indicates that the TTS is not a nucleosome phasing element, unless it overlaps with the TSS of the downstream gene, as in the case of some of the tandem genes. Even in the case of tandem genes, it is evident that nucleosomes are not phased relative to the TTS but relative to the position of the nearby TSSs, as the red stripes are not vertical but bent according to the positions of the downstream genes. c, d Organization of in vitro reconstituted nucleosomes (data from [13]) near gene ends shows that DNA sequence is not sufficient to dictate nucleosome phasing patterns. In vitro, NDRs are formed on the regions of high A/T content, suggesting that they may be artifacts of MNase-seq, introduced by the MNase sensitivity of the nucleosomes located on A/T-rich sequences [68, 69], which are easily overdigested. e, f A/T content (ratio of nucleotides A or T) near gene ends shows that TTSs are among the most A/T-rich regions in the yeast genome. In vitro, NDRs near TTSs form at A/T-rich regions and not at the positions where they are observed in live cells