DNA replication stress restricts ribosomal DNA copy number

Salim, Devika; Bradford, W. David; Freeland, Amy; Cady, Gillian K.; Wang, Jianmin; Pruitt, Steven C.; Gerton, Jennifer L.

doi:10.1371/journal.pgen.1007006

Cited by 92 publications

(90 citation statements)

References 51 publications

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“…While Chr XII-specific destabilization under reduced-initiation conditions has been observed previously (Ide et al, 2007; Salim et al, 2017; Sanchez et al, 2017), our observations of rDNA array instability suggest a slightly different interpretation of a similar phenomenon described by Ide et al (Ide et al, 2007). After shifting asynchronously-growing orc1-4 cells to the non-permissive temperature, Ide et al (2007) reported that instability of Chr XII preceded instability of the other chromosomes.…”

Section: Discussioncontrasting

confidence: 55%

The limiting DNA replication initiation factors Sld2 and Sld3 influence origin efficiency independent of origin firing time

Lynch

Kwan

Alvino

et al. 2018

Preprint

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36Chromosome replication in Saccharomyces cerevisiae is initiated from roughly 300 origins that 37 are regulated both by DNA sequence and by the limited abundance of four trans-acting initiation 38 proteins (Sld2, Sld3, Dpb11 and Dbf4, collectively called "SSDD"). We set out to determine how 39 the association of Sld2 or Sld3 at origins contributes to time of origin activation and/or origin 40 efficiency using auxin-induced protein degradation to further decrease their 41 abundance. Depleting cells of either factor slows growth rate, increases S-phase duration, and 42 causes viability defects, without activating the S phase checkpoint. Chr XII is uniquely unstable 43 with breakage occurring specifically within the rDNA locus. The efficiency of the rDNA origin is 44 decreased while the onset of replication initiation is unchanged. We found that origin efficiency 45 is reduced uniformly across the unique portions of the yeast genome. We conclude that the 46 abundance of Sld2 and Sld3 contribute primarily to origin efficiency. 47 93 2013; Vogelauer et al., 2002). However, the discovery that four specific replication initiation 94 factors (Sld2, Sld3, Dpb11, and Dbf4-the "SSDD" factors) are produced at concentrations 95 significantly lower than the rest of the origin/replisome components suggested that they may be 96 rate-limiting for origin initiation (Mantiero et al., 2011). When Mantiero et al. (2011 97 overexpressed all four proteins simultaneously, the temporal firing of origins was compressed, 98 and a subsequent study revealed that origin efficiency increased genome-wide (McGuffee et al.,99 2013). These findings suggest that the varying ability of different parts of the genome to 100 efficiently recruit the SSDD factors results in the pattern of origin use observed during DNA 101 replication. From their observations, Mantiero et al. (2011) developed a model whereby 102Lynch 2018 4 genome features near origins determine how well origins are able to recruit the limiting SSDD 103 factors, with the earliest and most efficient origins being the most competitive for recruiting 104 SSDD factors. Since each of these four proteins is required only for the initiation phase of DNA 105 replication (Bell and Labib, 2016; Deegan et al., 2016; Muramatsu et al., 2010; Tanaka et al., 106 2007; Zegerman and Diffley, 2007), Mantiero et al. (2011) proposed that as early and/or efficient 107 origins become active and release the limiting factors from the assembling replisome, those 108 factors are recycled to origins that are less competitive for recruiting SSDD and thereby promote 109 origin firing at later and/or more inefficient origins. 110 111 More recently, Collart et al. (2013) demonstrated that the same SSDD factors restrict origin 112 firing during early embryonic development in Xenopus laevis. At the mid-blastula transition 113 (MBT), developing embryos transition from relying on stores of maternally-derived transcripts to 114 activating embryonically-driven transcription (Farrell and O'Farrell, 2014; Langley et al....

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Section: Discussioncontrasting

confidence: 55%

The limiting DNA replication initiation factors Sld2 and Sld3 influence origin efficiency independent of origin firing time

Lynch

Kwan

Alvino

et al. 2018

Preprint

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“…Thus, reducing rDNA copy number was neither necessary nor sufficient to explain SIR -mediated suppression of cdc6-4 . Cells harboring a reduction in rDNA copy number in cdc6-4 sir2Δ populations likely arise because loss of Sir2 increases recombination frequency within the rDNA array, and rDNA copy numbers are reduced over time in many mutants compromised for replication initiation [35,41,42].…”

Section: Resultsmentioning

confidence: 99%

Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins

Hoggard

Chang

Perry

et al. 2018

Preprint

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25Most active DNA replication origins are found within euchromatin, while origins within 26 heterochromatin are often inactive or inhibited. In yeast, origin activity within 27 heterochromatin is negatively controlled by the histone H4K16 deacetylase, Sir2, and at 28 some heterochromatic loci also by the nucleosome binding protein, Sir3. The prevailing 29 view has been that direct functions of Sir2 and Sir3 are confined to heterochromatin. 30However, growth defects in yeast mutants compromised for loading the MCM helicase, 31 such as cdc6-4, are robustly suppressed by deletion of either SIR2 or SIR3. While this 32 and other observations indicate that SIR2,3 can have a negative impact on at least some 33 euchromatic origins, the genomic scale of this effect was unknown. It was also unknown 34 whether this suppression resulted from direct functions of Sir2,3 within euchromatin, or 35 was an indirect effect of their previously established roles within heterochromatin. Using 36 both MCM ChIP-Seq and MNase-H4K16ac ChIP-Seq data, we show that a SIR2 37 deletion rescues MCM complex loading at ~80% of euchromatic origins in cdc6-4 cells. 38Therefore, Sir2 exhibits a pervasive effect at the majority of euchromatic origins. 39Importantly, in wild type (i.e. CDC6) cells, origin-adjacent nucleosomes were depleted 40 for H4K16 acetylation in a SIR2-dependent manner. In addition, both Sir2 and Sir3 41 directly bound to nucleosomes adjacent to euchromatic origins. The relative levels of 42 each of these molecular hallmarks of yeast heterochromatin -SIR2-dependent H4K16 43 hypoacetylation, Sir2, and Sir3 -correlated with how strongly a SIR2 deletion 44 suppressed the MCM loading defect in cdc6-4 cells. Finally, a screen for histone H3 and 45 H4 mutants that could suppress the cdc6-4 growth defect identified amino acids that 46 map to a surface of the nucleosome important for Sir3 binding. We conclude that 47 heterochromatin proteins directly bind euchromatic DNA replication origins and modify 48 their local chromatin environment. 49 50 3 AUTHOR SUMMARY 51When a cell divides, it must copy or "replicate" its DNA. DNA replication starts at 52 chromosomal regions called origins when a collection of replication proteins gains local 53 access to unwind the two strands. Chromosomal DNA is packaged into a protein-DNA 54 complex called chromatin and there are two major structurally and functionally distinct 55 types. Euchromatin allows DNA replication proteins to access origin DNA, while 56 heterochromatin inhibits their access. The prevalent view has been that the 57 heterochromatin proteins required to inhibit origins are confined to heterochromatin. In 58 this study, the conserved heterochromatin proteins, Sir2 and Sir3, are shown to both 59 physically and functionally associate with the majority of origins in euchromatin. This 60 raises important new questions about the chromosomal targets of heterochromatin 61 proteins, and how and why the majority of origins exist within a potentially repressive 62 chromatin structure. 63 64 replic...

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“…Copy number is a rapidly evolving trait, and mechanisms for both rDNA copy number expansion and contraction have been described (Szostak & Wu, ). The consequences of rDNA CNV have received considerable attention in the context of DNA damage response (Ide, Miyazaki, Maki, & Kobayashi, ), DNA replication stress (Salim et al, ) and the expression of nonribosomal genes (Paredes, Branco, Hartl, Maggert, & Lemos, ). Similarly, the ecological importance of rDNA CNV has also been well characterized, with rDNA copy number being linked to ecosystem stoichiometry (Elser et al, ), growth rate and competitive ability (Klappenbach, Dunbar, & Schmidt, ; Nemergut et al, ) as well as bias in estimates of organismal abundance in high‐throughput amplicon sequencing (Kembel et al, , Perisin, Vetter, Gilbert, & Bergelson, ).…”

Section: Introductionmentioning

confidence: 99%

Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

et al. 2019

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Ribosomal DNA (rDNA) copy number variation (CNV) has major physiological implications for all organisms, but how it varies for fungi, an ecologically ubiquitous and important group of microorganisms, has yet to be systemically investigated. Here, we examine rDNA CNV using an in silico read depth approach for 91 fungal taxa with sequenced genomes and assess copy number conservation across phylogenetic scales and ecological lifestyles. rDNA copy number varied considerably across fungi, ranging from an estimated 14 to 1,442 copies (mean = 113, median = 82), and copy number similarity was inversely correlated with phylogenetic distance. No correlations were found between rDNA CNV and fungal trophic mode, ecological guild or genome size. Taken together, these results show that like other microorganisms, fungi exhibit substantial variation in rDNA copy number, which is linked to their phylogeny in a scale‐dependent manner.

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DNA replication stress restricts ribosomal DNA copy number

Cited by 92 publications

References 51 publications

The limiting DNA replication initiation factors Sld2 and Sld3 influence origin efficiency independent of origin firing time

The limiting DNA replication initiation factors Sld2 and Sld3 influence origin efficiency independent of origin firing time

Yeast heterochromatin regulators Sir2 and Sir3 act directly at euchromatic DNA replication origins

Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

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