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...