The histone variant H2A.Z in yeast is almost exclusively incorporated into the +1 nucleosome in the direction of transcription

To investigate the incorporation dynamics of histone variant H2A.Z, we determined its genomic localization at single nucleosome resolution, as well as the localization of its chromatin remodelers Swr1 and Ino80. We find that Swr1 binding alone is a poor predictor of H2A.Z occupancy levels, and that normal Swr1 and Ino80 localization are actually dependent on H2A.Z. Additionally, we find that H2A.Z’s bimodal incorporation on either side of the NDR is not a general feature of TSS, but is specifically a marker for bidirectional transcription, such that the upstream flanking -1 H2A.Z-containing nucleosome is more appropriately considered as a +1 H2A.Z nucleosome for antisense transcription. MNase-ChIP-seq data was produced to determine at single nucleotide resolution the genomic localization of the histone variant H2A.Z. ChIP-seq was performed to determine the genomic localization of chromatin remodelers Ino80 and Swr1 both in the presence and absence of histone variant H2A.Z. Smore-seq was performed with both ribo depletion and poly-A selection to map transcripts across the genome.