Biology subjects

Marheineke, K.

Publications and source records attributed to Marheineke, K..

4 recordsLinked to original sources

bioRxiv2026

Ploidy-dependent modulation of DNA replication kinetics in Xenopus

DNA replication in multicellular organisms follows a tightly regulated spatio-temporal program. Although the mechanisms underlying this replication program remain only partially understood, studies in model systems such as Xenopus laevis have highlighted the importance of titrating low-abundance replication factors. Whole-genome duplications as a consequence of polyploidization introduce additional layers of complexity, yet comparative analyses of replication programs across closely related polyploid species are scarce. Here, we developed an interspecies in vitro replication system using X. laevis egg extracts and sperm nuclei from three Xenopus species with varying ploidy: diploid (X. tropicalis), tetraploid (X. laevis), and dodecaploid (X. eysoole). Replication in diploid X. tropicalis was faster than in tetraploid X. laevis nuclei, due to higher fork density and speed. Surprisingly, dodecaploid X. eysoole replication was also accelerated compared to tetraploid nuclei, suggesting that higher ploidy does not necessarily extend S phase. Since replication genes are highly conserved between these species, these results imply dynamic tuning of replication programs across polyploid species and shed light on the evolutionary adaptability of DNA replication in response to genome duplication.

molecular biology↗

bioRxiv2024

Dual DNA Replication Modes: Varying Fork Speeds and Initiation Rates within the spatial replication program in Xenopus

Large vertebrate genomes duplicate by activating tens of thousands of DNA replication origins, irregularly spaced along the genome. The spatial and temporal regulation of the replication process is not yet fully understood. To investigate the DNA replication dynamics, we developed a methodology called RepliCorr, which uses the spatial correlation between replication patterns observed on stretched single-molecule DNA obtained by either DNA combing or high-throughput optical mapping. The analysis revealed two independent spatiotemporal processes that regulate the replication dynamics in the Xenopus model system. These mechanisms are referred to as a fast and a slow replication mode, differing by their opposite replication fork speed and rate of origin firing. We found that Polo-like kinase 1 (Plk1) depletion abolished the spatial separation of these two replication modes. In contrast, neither replication checkpoint inhibition nor Rif1 depletion affected the distribution of these replication patterns. These results suggest that Plk1 plays an essential role in the local coordination of the spatial replication program and the initiation-elongation coupling along the chromosomes in Xenopus, ensuring the timely completion of the S phase.

bioinformatics↗

bioRxiv2021

A non-transcriptional function of Yap orchestrates the DNA replication program

In multicellular eukaryotic organisms, the initiation of DNA replication occurs asynchronously throughout S-phase according to a regulated replication timing program. Here, using Xenopus egg extracts, we showed that Yap (Yes-associated protein 1), a downstream effector of the Hippo signaling pathway, is required for the control of DNA replication dynamics. We found that Yap is recruited to chromatin at the start of DNA replication and that Yap depletion accelerates DNA replication dynamics by increasing the number of activated replication origins. Furthermore, we identified Rif1, a major regulator of the DNA replication timing program, as a novel Yap binding protein. In Xenopus embryos, using a Trim-Away approach during cleavage stages devoid of transcription, we found that both Yap and Rif1 depletion trigger an acceleration of cell divisions, suggesting a shorter S-phase by alterations of the replication program. Finally, our data show that Rif1 knockdown leads to defects in the partitioning of early versus late replication foci in retinal stem cells, as we previously showed for Yap. Altogether, our findings unveil a non-transcriptional role for Yap in regulating replication dynamics. We propose that Yap and Rif1 function as breaks to control the DNA replication program in early embryos and post-embryonic stem cells. HighlightsO_LIYap is recruited to chromatin during DNA replication dependent on pre-replicative complex assembly. C_LIO_LIYap controls DNA replication dynamics by limiting origin firing. C_LIO_LIThe replication timing regulatory factor 1, Rif1, is a novel Yap binding-partner. C_LIO_LIBoth Yap and Rif1 regulate the length of the first embryonic cell cycles. C_LIO_LILike Yap, Rif1 controls retinal stem cell DNA replication timing. C_LI

developmental biology↗

bioRxiv2020

Organization of DNA replication origin firing in Xenopus egg extracts : the role of intra-S checkpoint

During cell division, the duplication of the genome starts at multiple positions called replication origins. Origin firing requires the interaction of rate-limiting factors with potential origins during the S(ynthesis)-phase of the cell cycle. Origins fire as synchronous clusters which is proposed to be regulated by the intra-S checkpoint. By modelling the unchallenged, the checkpoint-inhibited and the checkpoint protein Chk1 over-expressed replication pattern of single DNA molecules from Xenopus sperm chromatin replicated in egg extracts, we demonstrate that the quantitative modelling of data requires: 1) a segmentation of the genome into regions of low and high probability of origin firing; 2) that regions with high probability of origin firing escape intra-S checkpoint regulation and 3) the variability of the rate of DNA synthesis close to replication forks is a necessary ingredient that should be taken in to account in order to describe the dynamic of replication origin firing. This model implies that the observed origin clustering emerges from the apparent synchrony of origin firing in regions with high probability of origin firing and challenge the assumption that the intra-S checkpoint is the main regulator of origin clustering. Author summaryDNA replication is one of the fundamental cell functions. The genome of eukaryotic organisms is duplicated from multiple positions named replication origins. Single molecule experiments allow to visualise the dynamics of spatio-temporal patterns created during replication process. The dynamic of replication process is regulated by checkpoints. However, the influence and the role of checkpoint regulation in the dynamics of spatio-temporal patterns of DNA replication is not understood. In this work we build a minimal, process-based and data rooted numerical model that allows to decipher the impact of checkpoint regulation on the dynamics of spatio-temporal pattern of DNA replication.

cell biology↗