Nucleosome positioning maps of several organisms have shown that Transcription 
Start Sites (TSSs) are marked by nucleosome depleted regions flanked by strongly 
positioned nucleosomes. Using genome-wide nucleosome maps and histone variant 
occupancy in the mouse liver, we show that the majority of genes were associated 
with a single prominent H2A.Z containing nucleosome in their promoter region. We 
classified genes into clusters depending on the proximity of H2A.Z to the TSS. 
The genes with no detectable H2A.Z showed lowest expression level, whereas H2A.Z 
was positioned closer to the TSS of genes with higher expression levels. We 
confirmed this relation between the proximity of H2A.Z and expression level in 
the brain. The proximity of histone variant H2A.Z, but not H3.3 to the TSS, over 
seven consecutive nucleosomes, was correlated with expression. Further, a 
nucleosome was positioned over the TSS of silenced genes while it was displaced 
to expose the TSS in highly expressed genes. Our results suggest that gene 
expression levels in vivo are determined by accessibility of the TSS and 
proximity of H2A.Z.