DNA replication dynamics of vole genome and its epigenetic regulation

Abstract

BackgroundThe genome of some vole rodents exhibit large blocks of heterochromatin coupled to their sex chromosomes. The DNA composition and transcriptional activity of these heterochromatin blocks have been studied, but little is known about their DNA replication dynamics and epigenetic composition.ResultsHere, we show prominent epigenetic marks of the heterochromatic blocks in the giant sex chromosomes of female Microtus cabrerae cells. While the X chromosomes are hypoacetylated and cytosine hypomethylated, they are either enriched for macroH2A and H3K27me3 typical for facultative heterochromatin or for H3K9me3 and HP1 beta typical for constitutive heterochromatin. Using pulse-chase replication labeling and time-lapse microscopy, we found that the heterochromatic block enriched for macroH2A/H3K27me3 of the X chromosome is replicated during mid-S-phase, prior to the heterochromatic block enriched for H3K9me3/HP1 beta, which is replicated during late S-phase. To test whether histone acetylation level regulates its replication dynamics, we induced either global hyperacetylation by pharmacological inhibition or by targeting a histone acetyltransferase to the heterochromatic region of the X chromosomes. Our data reveal that histone acetylation level affects DNA replication dynamics of the sex chromosomes’ heterochromatin and leads to a global reduction in replication fork rate genome wide.ConclusionsIn conclusion, we mapped major epigenetic modifications controlling the structure of the sex chromosome-associated heterochromatin and demonstrated the occurrence of differences in the molecular mechanisms controlling the replication timing of the heterochromatic blocks at the sex chromosomes in female Microtus cabrerae cells. Furthermore, we highlighted a conserved role of histone acetylation level on replication dynamics across mammalian species.Electronic supplementary materialThe online version of this article (10.1186/s13072-019-0262-0) contains supplementary material, which is available to authorized users.

Developmental Changes in Genome Replication Progression in Pluripotent versus Differentiated Human Cells

“…The attributes of the replication fork, including directionality, speed, and inter-origin distances, are intricately influenced by developmental fate. To gauge fork speed, we employed total signal intensities and conducted a ratiometric analysis of nucleotide incorporation rates per active replisome, as previously described [ 30 ]. While PCNA is a component of the DNA replication machinery and is therefore indicative of the number of active replisomes, the quantity of incorporated nucleotides reflects both the number of active replisomes and the replication fork speed.…”

Perspective Article: Space-time dynamics of genome replication studied with super-resolved microscopy

“…Within a subsequent 80min chase the replication of an entire ~1Mb RD should be fully accomplished, accordingly this condition represents the post-replication status of a labeled RD. The replication of clustered replication foci in large heterochromatin blocks, constituting chromocenters of several Mb in mouse nuclei, may take longer [53,54].…”

Histone deacetylase‑2: A potential regulator and therapeutic target in liver disease (Review)

“…Studies have shown that relative levels of histone acetylation and deacetylation are of significance for the regulation of pathophysiological processes, including proliferation, cell-cycle progression, differentiation, immune evasion, inflammatory lesion, apoptosis and death ( 143 – 145 ). Pharmacological inhibition of HDAC activity or expression alters chromatin acetylation levels, subsequently confusing boundaries between transcriptionally active and quiescent chromatin ( 146 – 148 ).…”