Pokrovsky, D. | bioRxiv Science

bioRxiv2020

Mitotic activity shapes stage-specific histone modification profiles during Xenopus embryogenesis

Forming an embryo from a zygote poses an apparent conflict for epigenetic regulation. On one hand, the de novo induction of cell fate identities requires the establishment and subsequent maintenance of epigenetic information to harnish developmental gene expression. On the other hand, the embryo depends on cell proliferation, and every round of DNA replication dilutes preexisting histone modifications by incorporation of new unmodified histones into chromatin. Here we investigated the possible relationship between the propagation of epigenetic information and the developmental cell proliferation during Xenopus embryogenesis. We systemically inhibited cell proliferation during the G1/S-transition in gastrula embryos and followed their development until the tadpole stage. Comparing wild-type and cell cycle-arrested embryos, we show that the inhibition of cell proliferation is principally compatible with embryo survival and cellular differentiation. In parallel, we quantified by mass spectrometry the abundance of a large set of histone modification states, which reflects the developmental maturation of the embryonic epigenome. The arrested embryos developed abnormal stage-specific histone modification profiles, in which transcriptionally repressive histone marks were overrepresented. Embryos released from the cell cycle block during neurulation reverted back towards normality on morphological, molecular and epigenetic levels. These results indicate that replicational dilution of histone marks has a strong impact on developmental chromatin maturation. We propose that this influence is strong enough to control developmental decisions, specifically in cell populations that switch between resting and proliferating states such as stem cells.

molecular biology↗

bioRxiv2020

Computational modeling reveals cell-cycle dependent kinetics of H4K20 methylation states during Xenopus embryogenesis

Histone modifications regulate chromatin architecture and thereby control gene expression. Rapid cell divisions and DNA replication however lead to a dilution of histone modifications and can thus affect chromatin mediated gene regulation So how does the cell-cycle shape the histone modification landscape, in particular during embryogenesis when a fast and precise control of cell-specific gene expression is required? We addressed this question in vivo by manipulating the cell-cycle during early Xenopus laevis embryogenesis. The global distribution of un-, mono- di- and tri-methylated histone H4K20 was measured by mass spectrometry in normal and cell-cycle arrested embryos over time. Using multi-start maximum likelihood optimization and quantitative model selection, we found that three specific methylation rate constants were required to explain the measured H4K20 methylation state kinetics. Interestingly, demethylation was found to be redundant in the cycling embryos but essential in the cell-cycle arrested embryos. Together, we present the first quantitative analysis of in vivo histone H4K20 methylation kinetics. Our computational model shows that demethylation is only essential for regulating H4K20 methylation kinetics in non-cycling cells. In rapidly dividing cells of early embryos, we predict that demethylation is dispensable, suggesting that cell-cycle mediated dilution of chromatin marks is an essential regulatory component for shaping the epigenetic landscape during early embryonic development.

bioinformatics↗