Transcriptional regulation of vertebrate histone genes during the cell cycle is mediated by several factors interacting with a series of cis-acting elements located in the 5' regions of these genes. The arrangement of these promoter elements is different for each gene. However, most histone H4 gene promoters contain a highly conserved sequence immediately upstream of the TATA box (H4 subtype consensus sequence), and this region in the human H4 gene F0108 is involved in cell cycle control. The sequence-specific interaction of nuclear factor HiNF-D with this key proximal promoter element of the H4-FO108 gene is cell cycle regulated in normal diploid cells (J. Holthuis, T. A. Owen, A. J. van [5825][5826][5827][5828][5829][5830][5831] 1991). The H4.A gene fails to interact with factors HiNF-M and HiNF-D owing to two independent sets of specific nucleotide variants, indicating differences in protein-DNA interactions between these H4 genes. Cytosine methylation of a highly conserved CpG dinucleotide interferes with binding of HiNF-P/H4TF-2 to both the H4-FO108 and H4.A promoters, but no effect is observed for either HiNF-M or HiNF-D binding to the H4-FO108 gene. Thus, strong evolutionary conservation of the H4 consensus sequence may be related to combinatorial interactions involving overlapping and interdigitated recognition nucleotides for several proteins, whose activities are regulated independently. Our results also suggest molecular complexity in the transcriptional regulation of distinct human H4 genes.Stringent cell cycle regulation (41) of S-phase-related genes, including thymidine kinase, thymidylate synthase, dihydrofolate reductase, and histone genes, occurs at many transcriptional and posttranscriptional levels (reviewed in reference 22). Functional redundancy of these multilevel gene regulatory processes ensures a tight coupling between availability of enzymes required for DNA synthesis, histone proteins, and DNA replication in proliferating cells. The stringency with which control of gene expression is mediated is abrogated during neoplastic transformation, which may ultimately affect diverse transcriptional components regulating S-phase-related genes. For example, the interactions of nuclear factor Yi (14) with the thymidine kinase promoter and of nuclear factor HiNF-D (64) with the histone H4 promoter are regulated differently in several normal diploid and tumor cells (4, 23). HiNF-D is a proliferation-specific DNA-binding activity (64), and its nuclear abundance is cell cycle regulated in normal diploid cells (23 which is located in a histone gene cluster at chromosomal region 1q21 (1, 54). This gene is expressed in a cell cycledependent manner both as an endogenous gene in human cells (44) and when introduced as an episomal gene into murine cells (16). The 5' region of this gene mediates cell cycle-regulated transcription in cell culture (44), contributes to proliferation-specific expression in transgenic mice (58), and contains two in vivo domains of protein-DNA interactions (designated H4 site I...