Noble, T. D. | Search bioRxiv

bioRxiv2024

Cell Cycle-Dependent TICRR/TRESLIN and MTBP Chromatin Binding Mechanisms and Patterns

The selection of replication origins is a defining characteristic of DNA replication in eukaryotes, yet its mechanism in humans has not been well-defined. In this study, we use Cut&Run to examine genomic binding locations for TICRR/TRESLIN and MTBP, the human orthologs for the yeast DNA replication initiation factors Sld3 and Sld7. We mapped TRESLIN and MTBP binding in HCT116 colorectal cancer cells using asynchronous and G1 synchronized populations. Our data show that TRESLIN and MTBP binding patterns are more defined in a G1 synchronized population compared to asynchronously cycling cells. We also examined whether TRESLIN and MTBP are dependent on one another for binding. Our data suggest MTBP is dependent on TRESLIN for proper association with chromatin during G1 but not S phase. Finally, we asked whether TRESLIN and MTBP binding to chromatin requires licensed origins. Using cell lines with a non-degradable inducible Geminin to inhibit licensing, we show TRESLIN and MTBP binding does not require loaded MCMs. Altogether, our Cut&Run data provides evidence for a chromatin binding mechanism of TRESLIN-MTBP during G1 that is dependent on TRESLIN and does not require interactions with licensed origins.

genomics↗

bioRxiv2022

Zebrafish Rif1 Impacts Zygotic Genome Activation, Replication Timing, and Sex Determination

Deregulated DNA replication causes human developmental disorders and cancer, but we know little about how DNA replication is coordinated with changes in transcription and chromatin structure. The initiation of replication forks follows a spatiotemporal pattern called the replication timing program. We have developed the zebrafish into a model system to study the mechanisms by which the replication timing program changes during the extensive changes in the cell cycle, transcription, chromatin organization, and nuclear structure that occur during development. Our previous studies identified changes in DNA replication timing patterns occurring from the onset of zygotic transcription through gastrulation in zebrafish embryos. Rif1 is required for DNA replication timing in a wide range of eukaryotes. The broader role of Rif1 in establishing the replication timing program and chromatin structure during early vertebrate development remains unknown. We have generated Rif1 mutant zebrafish and have performed RNA sequencing and whole-genome replication timing analyses on multiple developmental stages. Rif1 mutants were viable but had a defect in female sex determination. Surprisingly, Rif1 loss predominantly affected DNA replication timing after gastrulation, while its impacts on transcription were more substantial during zygotic genome activation. Our results indicate that Rif1 has distinct roles in DNA replication and transcription control that manifest at different stages of development.

cell biology↗