Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots

Abstract

Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize ( Zea mays ) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed.

Delayed DNA replication in haploid human embryonic stem cells

“…Disruption of the replication initiation factors ORC2 or GINS2 has also been shown to induce polyploidization in human cells ( Rantala et al 2010 ; Huang et al 2016 ). Similarly, it was recently shown that ∼2% of the maize genome is delayed in its replication in endocycles compared to normal mitotic cycles ( Wear et al 2020 ). Polyploidization is also very common in cancer ( Bielski et al 2018 ), and so is replication stress; it is intriguing to consider whether these two phenomena are related to each other.…”

Delayed DNA replication in haploid human embryonic stem cells

“…Disruption of the replication initiation factors ORC2 or GINS2 has also been shown to induce polyploidization in human cells (Huang et al, 2016; Rantala et al, 2010). Similarly, it was recently shown that ~2% of the maize genome is delayed in its replication in endocycles compared to normal mitotic cycles (Wear et al, 2020). Polyploidization is also very common in cancer (Bielski et al, 2018), and so is replication stress; it is intriguing to consider whether these two phenomena are related to each other.…”

The structure, function, and evolution of plant centromeres

“…Together with dense DNA methylation, centromeres typically share other features of classical heterochromatin, including cytological condensation and late DNA replication ( Schubert et al 2020 ; Wear et al 2020 ). It should also be noted that many eukaryotes, including budding yeast, fission yeast, D. melanogaster , and C. elegans lack detectable DNA cytosine methylation, although other chromatin marks, including H3K9me3, can function to suppress transposons in its place ( Gutbrod and Martienssen 2020 ).…”