Coordinate Control and Selective Expression of the Full Complement of Replication-dependent Histone H4 Genes in Normal and Cancer Cells

Abstract

The replication of eukaryotic genomes necessitates the coordination of histone biosynthesis with DNA replication at the onset of S phase. The multiple histone H4 genes encode identical proteins, but their regulatory sequences differ. The contributions of these individual genes to histone H4 mRNA expression have not been described. We have determined, by real-time quantitative PCR and RNase protection, that the human histone H4 genes are not equally expressed and that a subset contributes disproportionately to the total pool of H4 mRNA. Differences in histone H4 gene expression can be attributed to observed unequal activities of the H4 gene promoters, which exhibit variations in gene regulatory elements. The overall expression pattern of the histone H4 gene complement is similar in normal and cancer cells. However, H4 genes that are moderately expressed in normal cells are sporadically silenced in tumor cells with compensation of expression by other H4 gene copies. Chromatin immunoprecipitation analyses and in vitro DNA binding assays indicated that 11 of the 15 histone H4 genes interact with the cell cycle regulatory histone nuclear factor P, which forms a complex with the cyclin E/CDK2-responsive co-regulator p220 NPAT . These 11 H4 genes account for 95% of the histone H4 mRNA pool. We conclude that the cyclin E/CDK2/p220 NPAT /histone nuclear factor P signaling pathway is the principal regulator of histone H4 biosynthesis.Histones have crucial roles in replication, transcription, repair, and recombination (1-3). There is a fundamental requirement for coordinated de novo synthesis of the core histone proteins H2A, H2B, H3, and H4 as well as the linker H1 protein during S phase to package nascent genomic DNA (1, 2). Replication of a complete mammalian genome requires 10 8 of each of the individual histone proteins. Efficient production of this vast quantity of proteins necessitates that transcription of multiple histone genes at multiple loci be coordinately regulated with the onset and progression of genome replication during the cell cycle (4).Histone biosynthesis is a unique process involving transcription initiation from compact promoters to form primary transcripts that lack introns and that contain a highly conserved stem-loop structure that forms the 3Ј-end of the mature non-polyadenylated mRNA (4, 5). Histone genes are organized into clusters, and this organization has persisted throughout the course of evolution from yeast to human (2, 4). The majority of the 74 known and characterized human histone genes is located in two major clusters at chromosomes 6p21 and 1q21, respectively (TABLE ONE) (1, 6 -8). It is now known that the human genome contains 15 histone H4 genes that encode identical proteins. H4 genes in lower eukaryotes (e.g. sea urchin and Drosophila) are organized with the other histone gene types (i.e. H2A, H2B, H3, and H1) into units that are tandemly repeated, and all H4 genes in these organisms have virtually identical promoters and coding regions. Although the coding regions of the human...

The histone gene activator HINFP is a nonredundant cyclin E/CDK2 effector during early embryonic cell cycles

“…Because HINFP controls expression of multiple histone H4 genes in cultured cells (13,34), we assessed whether the Hinfp gene is transcriptionally active in blastocysts. Clear ␤-galactosidase staining was only observed in Hinfp LacZ/ϩ embryos ( Fig.…”

“…The human histone gene transcription factor HINFP is the final and essential link in the cyclin E/CDK2/p220 NPAT /HINFP pathway that is required for cell cycle-dependent activation of histone H4 genes at the G1/S phase transition (11)(12)(13). This pathway is activated at the restriction point (R-point) by cyclin E/CDK2, in parallel with the E2F/pRB pathway that controls transcription of genes involved in nucleotide metabolism and DNA synthesis (14).…”

“…HINFP interacts with Site II and integrates signals emanating from the cyclin E/CDK2 kinase cascade (11-13, 15, 18). HINFP recruits p220 NPAT to multiple human histone H4 genes in the human diploid genome (13). p220…”

Cell cycle dependent phosphorylation and subnuclear organization of the histone gene regulator p220NPAT in human embryonic stem cells

“…Seminal studies by Pardee and colleagues have defined the restriction (R) point in the G1 phase of somatic cells that represents the stage when commitment towards initiation of DNA synthesis at the G1/S phase transition becomes growth factor independent (Pardee, 1974(Pardee, , 1989. Studies in our laboratory have examined the functional coupling between the R point and signaling pathways that control the activation of histone gene expression ('S point') which is essential for the packaging of newly replicated DNA (Stein et al, 1992(Stein et al, , 1996Luong et al, 2002;Mitra et al, 2003;Braastad et al, 2004;Holmes et al, 2005;Miele et al, 2005;Becker et al, 2006;Becker et al, 2007). One essential difference between human ES and somatic cells is the length of G1 phase during which cells commit to S phase entry.…”

Staged assembly of histone gene expression machinery at subnuclear foci in the abbreviated cell cycle of human embryonic stem cells

“…However, hES cells lack a classical R point and have the capacity for continuous cell division. A principal mechanism that is required for the initiation of S phase in hES cells is the induction of histone gene expression, which is essential for the packaging of newly replicated DNA into chromatin by specific transcription factors (1,2,(5)(6)(7)(8)(9)(10)(11)(12).…”