By use of synchronized human HeLa S3 cells, a site sensitive to both DNase I and nuclease S1 was identified 50-150 base pairs upstream of the ATG codon of a cell cycle-dependent histone H4 gene. This site expanded to include a broad region of -30O base pairs sensitive to DNase I throughout S phase and then narrowed again to the original site after the completion of DNA replication. The level of nuclease S1 sensitivity was greatest during early S phase, when the gene is replicated and its transcription rate is maximal. The chromatin structure of the human fglobin gene, which is not expressed in HeLa cells, was also analyzed throughout the cell cycle, and in no case was a sub-band seen as a result of DNase I or nuclease S1 digestion, nor were there any changes in nuclease sensitivity correlated with its replication. Thus the cell cycle-dependent chromatin alterations in this histone H4 gene appear to be due to the coupled replication and expression of this gene rather than simply its replication. These results suggest that histone genes, as compared with developmentally regulated genes, exhibit an "intermediate" level of regulation whereby the gene is never in a completely inactive conformation, but changes in chromatin structure occur as a function of the cell cycle and expression.Changes in the structural organization of chromatin play an important role in determining the transcriptional state of eukaryotic genes (1-6). Active chromatin characteristically exhibits increased susceptibility to nucleases (7-9), and short regions hypersensitive to DNase I and/or nuclease S1 commonly occur near the 5' end of active or potentially active genes (1, 10-13), suggesting a role for these sites in the regulation of gene expression. The correlation between changes in chromatin structure and the activation or inactivation of eukaryotic genes has been reported for developmentally controlled genes (9, 14-16) or genes under hormonal control (17-21). Here we present evidence that a cell cycleregulated human histone H4 gene undergoes chromatin alterations during the cell cycle that reflect its expression.The histone genes offer an excellent opportunity to examine the potential chromatin reconfigurations of cell cycledependent genes. In most eukaryotic cells, there is a temporal relationship between histone protein synthesis, histone mRNA synthesis, and DNA replication (22-30). The accumulation of histone mRNA parallels DNA synthesis, while histone transcription rates peak in early S phase (30-32). Additionally, following the inhibition of DNA synthesis and, consequently, of histone gene expression, recovery involves the "remembering" of the specific position of the cell in S phase (29,33,34).The histone H4 gene used in these studies (designated pFO108A) has been well characterized and has been shown to be expressed in a cell cycle-dependent manner (30,33,35). We have identified a site sensitive to both DNase I and nuclease S1 in the 5' flanking region of this gene, using HeLa S3 cells synchronized by a double thymidine blo...