Nap1 is a nucleosome assembly protein which is necessary to keep proper nucleosome structures in transcription and replication in vitro. In Saccharomyces cerevisiae, additional functions have been ascribed to Nap1, as it has been shown to interact with Clb2 (B type cyclin) and Gin4 (septum formation). In this study, we investigate genome-wide expression in the Deltanap1 cells using DNA microarrays. About 10% of all yeast open reading frames changed the transcription level more than 2-fold in the Deltanap1 strain, compared with wild-type strain, in one experiment. Interestingly, these genes, whose expressions are up- or down-regulated in the Deltanap1 cells, are clustered. This result suggests that yeast NAP1 is required for the maintenance of cumulative nucleosome formation in vivo and the loss of Nap1 leads to a change in the gene expression level in a cluster.