Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast

Kwan, Elizabeth; Alvino, Gina M.; Lynch, Kelsey L.; Levan, Paula F; Amemiya, Haley M.; Wang, Xiaobin S; Johnson, Sarah A.; Sanchez, Joseph C.; Miller, Madison; Croy, Mackenzie; Lee, Seung‐been; Naushab, Maria; Bedalov, Antonio; Cuperus, Josh T.; Brewer, Bonita J.; Queitsch, Christine; Raghuraman, M. K.

doi:10.1016/j.celrep.2023.112161

Cited by 6 publications

(4 citation statements)

References 122 publications

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“…In the analysis above, we are assuming that the reduced rDNA size is a downstream effect of decreased rDNA origin activity. While there is ample support for this view of cause and effect (Kwan et al 2013; Salim et al 2017), rDNA shrinkage itself has been reported to increase rDNA origin activity (Kwan et al 2023). Such an effect would be expected to counteract the rDNA replication suppression conferred by FUN30 deletion, and it therefore suggests an explanation for our observation that rDNA replication timing in sir2 fun30 cells is not supressed to the level observed in WT cells.…”

Section: Resultsmentioning

confidence: 99%

“…rDNA size was measured by qPCR using DNA that was extracted by YeaStar Genomic DNA Kit (Zymo Research) using the primers listed in Supplemental Table 2. As an internal standard, qPCR was done in parallel on the DNA extracted from fob1 strains with 180 and 35 rDNA copies whose rDNA sizes had been verified by Pulsed Field Gel Electrophoresis (Kwan et al 2023).…”

Section: Methodsmentioning

confidence: 99%

“…As an internal standard, qPCR was done in parallel on the DNA extracted from fob1 strains with 180 and 35 rDNA copies whose rDNA sizes had been verified by Pulsed Field Gel Electrophoresis (Kwan et al 2023).…”

Section: Hydoxyurea Chec Time Course Experimentsmentioning

confidence: 99%

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Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy

Lichauco,

Foss,

Gatbonton-Schwager

et al. 2024

Preprint

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The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well-known, yet the specific mechanisms underlying this link remain uncertain. InSaccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA arrays (rDNA). We have previously reported that in the absence ofSIR2, a derepressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. By developing a method that can distinguish activation of closely spaced MCM complexes, here we show that the displaced MCMs at rDNA origins have increased firing propensity compared to the non-displaced MCMs. Furthermore, we found that both, activation of the repositioned MCMs and low occupancy of the adjacent nucleosomes critically depend on the chromatin remodeling activity ofFUN30. Our study elucidates the mechanism by which Sir2 delays replication timing, and it demonstrates, for the first time, that activation of a specific replication originin vivorelies on the nucleosome context shaped by a single chromatin remodeler.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy

Lichauco,

Foss,

Gatbonton-Schwager

et al. 2024

Preprint

Self Cite

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“…In all eukaryotes, the tandemly repeated and highly transcribed rDNA loci are very fragile as a result of replication stress. Distinct signaling cascades keep the duplication of select rDNA tandem repeats at specific times during the S-phase [27] under strict copy number control [27,50]. Hence, it is plausible that, in non-transformed cells, although the inhibition of SIRT1 activity does not lead to persistent excess replication in most loci, the rDNA loci manifest a distinct dependence on SIRT1 activity as a modulator of replication origin activation and suppressor of deleterious R-loops.…”

Section: Discussionmentioning

confidence: 99%

SIRT1 Prevents R-Loops during Chronological Aging by Modulating DNA Replication at rDNA Loci

Thakur,

Kusi,

Mosavarpour

et al. 2023

Cells

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In metazoans, the largest sirtuin, SIRT1, is a nuclear protein implicated in epigenetic modifications, circadian signaling, DNA recombination, replication, and repair. Our previous studies have demonstrated that SIRT1 binds replication origins and inhibits replication initiation from a group of potential initiation sites (dormant origins). We studied the effects of aging and SIRT1 activity on replication origin usage and the incidence of transcription–replication collisions (creating R-loop structures) in adult human cells obtained at different time points during chronological aging and in cancer cells. In primary, untransformed cells, SIRT1 activity declined and the prevalence of R-loops rose with chronological aging. Both the reduction in SIRT1 activity and the increased abundance of R-loops were also observed during the passage of primary cells in culture. All cells, regardless of donor age or transformation status, reacted to the short-term, acute chemical inhibition of SIRT1 with the activation of excessive replication initiation events coincident with an increased prevalence of R-loops. However, cancer cells activated dormant replication origins, genome-wide, during long-term proliferation with mutated or depleted SIRT1, whereas, in primary cells, the aging-associated SIRT1-mediated activation of dormant origins was restricted to rDNA loci. These observations suggest that chronological aging and the associated decline in SIRT1 activity relax the regulatory networks that protect cells against excess replication and that the mechanisms protecting from replication–transcription collisions at the rDNA loci manifest as differentially enhanced sensitivities to SIRT1 decline and chronological aging.

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The cell cycle revisited: DNA replication past S phase preserves genome integrity

Bournaka,

Badra-Fajardo,

Arbi

et al. 2024

Seminars in Cancer Biology

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Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast

Cited by 6 publications

References 122 publications

Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy

Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy

SIRT1 Prevents R-Loops during Chronological Aging by Modulating DNA Replication at rDNA Loci

The cell cycle revisited: DNA replication past S phase preserves genome integrity

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