A distinct H2A.X isoform is enriched in Xenopus laevis eggs and early embryos and is phosphorylated in the absence of a checkpoint

Histone H2A.X is an H2A variant present in multicellular organisms that is specifically phosphorylated on the serine in the C-terminal consensus sequence, canonically "SQEY," in response to DNA damage. We have recently shown the significance of phosphorylation of the penultimate tyrosine for maintenance and processing of the DNA damage response in mammalian cells. Here, we report the identification of distinct H2A.X variants in the eggs and early embryos of the frog Xenopus laevis that contain a C-terminal SQEF, among other changes; we have denoted these proteins as "H2A.XF." H2A.X-F is present only in late-staged oocytes, eggs, and premidblastula transition embryos and is not present in somatic cells. Similar unannotated isoforms were identified in other rapidly developing aquatic species, such as Xenopus tropicalis, goldfish, and zebrafish, and in Arabidopsis and chickpea. Furthermore, we demonstrate by mass spectrometry and phospho-specific antibodies that H2A.X-F is phosphorylated in the absence of exogenous DNA damage, in both actively dividing, unperturbed embryos and cell-free egg extract in the absence and presence of DNA damage and S-phase checkpoint conditions. We propose that this isoform may be involved in modulating the cellular response to the rapid early cell cycles in externally developing species.