Histone H2A.X gene transcription is regulated differently than transcription of other replication-linked histone genes.

Abstract

Histone H2A.X is a replication-independent histone H2A isoprotein species that is encoded by a transcript alternatively processed at the 3' end to yield two mRNAs: a 0.6-kb mRNA ending with the stem-loop structure characteristic of the mRNAs for replication-linked histone species, and a second, polyadenylated 1.6-kb mRNA ending about 1 kb further downstream (C. Mannironi, W. M. Bonner, and C. L. Hatch, Nucleic Acids Res. 17:9113-9126, 1989). Of the two, the 0.6-kb H2A.X stem-loop mRNA predominates in many cell lines, indicating that the presence of two types of mRNA may not completely account for the replication independence of H2A.X protein synthesis. The ambiguity is resolved by the finding that the level of the 0.6-kb H2A.X mRNA is only weakly downregulated during the inhibition of DNA replication and only weakly upregulated during the inhibition of protein synthesis, while the levels of other replication-linked mRNAs are strongly down-or upregulated under these two conditions. Analysis of the nuclear transcription rates of specific H2A genes showed that while the rates of transcription of replication-linked H2A genes decreased substantially during the inhibition of DNA synthesis and increased substantially during the inhibition of protein synthesis, the rate of H2A.X gene transcription decreased slightly under both conditions. These differences in transcriptional regulation between the H2A.X gene and other replication-linked histone genes are sufficient to account for the differences in regulation of their respective stem-loop mRNAs.Most histone protein synthesis occurs during S phase, coordinated with the rate of DNA synthesis. The transcripts for these replication-linked histones are derived from genes without introns and are processed at a site between two conserved motifs to yield mature mRNAs which lack polyadenylate tracts and which are processed at a highly conserved stem-loop or hairpin structure (reviewed in references 18 and 26). Replication-linked histone mRNAs, among the most abundant mRNAs in proliferating cells, are accumulated and degraded rapidly in concert with changes in the rate of DNA replication during the S phase of the cell cycle (2,19,32) as well as in accordance with the rate of protein synthesis (3,11,33,39).The linkage of replication-linked histone mRNA levels to the rate of DNA replication throughout the cell cycle may involve regulation of transcription, transcript processing, and mRNA stability (15). When DNA replication is inhibited, these histone mRNA levels decrease 10-to 20-fold within 30 min, due in part to a decrease in the rates of histone gene transcription and in part to a decrease in histone mRNA stability (19,32). This latter process requires the 3'-terminal stem-loop (23,27) the cell cycle of proliferating cells (38). H3.3 is also proliferation independent, being synthesized at similar rates in proliferating and quiescent cells (40). H3.3 differs from the other H3s by a few amino acid substitutions distributed throughout the sequence; it is usually less than 10% of...

A multiprotein occupancy map of the mRNP on the 3′ end of histone mRNAs

“…SLBP levels are very low outside of S phase (Whitfield et al 2000), but the polyadenylated H2AFX mRNA is stable and some will likely be synthesized in G1 and persist into S phase when SLBP levels are high (Bonner et al 1993). RNA immunoprecipitation experiments and our α-SLBP RIP-seq data suggest that SLBP binds both isoforms, as sequencing read coverage extends downstream from the HDE into the part of the 3 ′ UTR that is present only in the long isoform (Fig.…”

“…During S phase, a short isoform (∼0.55 kb) that ends at the histone SL predominates whereas outside of S phase, a longer 1.6-kb isoformwhich is polyadenylated and replication-independent-is the predominate isoform ( Fig. 5A; Mannironi et al 1989;Bonner et al 1993). The H2A.X protein, which is encoded by the H2AFX gene comprises ∼10% of total H2A protein in mammalian cells (West and Bonner 1980); therefore, it must be synthesized in large quantities during S phase.…”

Cell cycle controlled histone H1, H3, and H4 genes share unusual arrangements of recognition motifs for HiNF‐D supporting a coordinate promoter binding mechanism

“…Thus, current transcriptional models postulate heterogeneous arrays of multi-partite proteidDNA interaction sites for individual promoters, including DNA binding activities interacting with several but not all histone genes, and factors that may interact primarily with consensus sequences present in specific histone gene subtypes (Bell et al, 1992;Breuer et al, 1993;Dalton and Wells, 1988a,b;Dailey et al, 1988;Gallinari et al, 1989;Grimes et al, 1992;Hinkley and Perry, 1992;LaBella et al, 1988LaBella et al, ,1989Lee et al, 1991;Naeve et al, 1992;Sharma et al, 1989;van Wijnen et al, 1987van Wijnen et al, , 1992bWolfe and Grimes, 1991). These models emphasize variable degrees of complexity and versatility that permit differential expression of single histone gene copies in a number of different biological contexts (e.g., Bonner et al, 1993;Collart et al, 1988Collart et al, ,1991Dalton et al, 1989;Gomez-Cuadrado et al, 1992;Graves et al, 1985;Levine et al, 1988;Winter et al, 1985). Apart from this heterogeneity in transcriptional regulation, we postulate that there also may exist a coordinating mechanism that synchronizes transcription rates of many distinct histone genes both within and across subtype-family boundaries.…”

Genome-wide analysis of mRNAs bound to the histone stem–loop binding protein

“…In addition, the replacement variant H2A family member X (H2AFX) is also present. This histone gene is unique in that it contains a stem-loop and ends in a histone 39 end when cells are in S phase but ends in a poly(A) tail outside of S phase (Bonner et al 1993). In previous work, we have shown that both forms of the H2aX mRNA are indeed bound by the SLBP in mouse cells (Whitfield 1999).…”