Regulation of DNA Replication through Natural  Impediments in the Eukaryotic Genome

Gadaleta, Mariana C.; Noguchi, Eishi

doi:10.3390/genes8030098

Cited by 48 publications

(57 citation statements)

References 238 publications

(318 reference statements)

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“…Rapidly growing cells may experience elevated levels of transcription as well as DNA replication in order to support cell growth. As transcription and replication use the same template DNA, collisions between the two machineries are inevitable (Gadaleta & Noguchi, ). Such collisions may promote genomic instability due to replication fork stalling or damage at highly transcribed genes such as tRNAs (Dutta, Shatalin, Epshtein, Gottesman, & Nudler, ).…”

Section: Discussionmentioning

confidence: 99%

Maf1‐dependent transcriptional regulation of tRNAs prevents genomic instability and is associated with extended lifespan

et al. 2019

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Maf1 is the master repressor of RNA polymerase III responsible for transcription of tRNAs and 5S rRNAs. Maf1 is negatively regulated via phosphorylation by the mTOR pathway, which governs protein synthesis, growth control, and lifespan regulation in response to nutrient availability. Inhibiting the mTOR pathway extends lifespan in various organisms. However, the downstream effectors for the regulation of cell homeostasis that are critical to lifespan extension remain elusive. Here we show that fission yeast Maf1 is required for lifespan extension. Maf1's function in tRNA repression is inhibited by mTOR-dependent phosphorylation, whereas Maf1 is activated via dephosphorylation by protein phosphatase complexes, PP4 and PP2A. Mutational analysis reveals that Maf1 phosphorylation status influences lifespan, which is correlated with elevated tRNA and protein synthesis levels in maf1∆ cells. However, mTOR downregulation, which negates protein synthesis, fails to rescue the short lifespan of maf1∆ cells, suggesting that elevated protein synthesis is not a cause of lifespan shortening in maf1∆ cells. Interestingly, maf1∆ cells accumulate DNA damage represented by formation of Rad52 DNA damage foci and Rad52 recruitment at tRNA genes. Loss of the Rad52 DNA repair protein further exacerbates the shortened lifespan of maf1∆ cells. Strikingly, PP4 deletion alleviates DNA damage and rescues the short lifespan of maf1∆ cells even though tRNA synthesis is increased in this condition, suggesting that elevated DNA damage is the major cause of lifespan shortening in maf1∆ cells. We propose that Maf1-dependent inhibition of tRNA synthesis controls fission yeast lifespan by preventing genomic instability that arises at tRNA genes.

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Section: Discussionmentioning

confidence: 99%

Maf1‐dependent transcriptional regulation of tRNAs prevents genomic instability and is associated with extended lifespan

et al. 2019

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“…These include alternate DNA structures, protein: DNA adducts, DNA covalent modifications introduced by endogenous or endogenous reactants, depleted nucleotide precursor pools, etc. Replication stress activates the ATR (ATM- and Rad3-related) kinase, with hundreds of substrates, including MCM proteins 16–18 , and stimulates the recruitment of numerous factors to stalled replication forks 19–22 . These function in a variety of pathways to relieve obstacles, reconstruct broken forks, and restart replication.…”

Section: Introductionmentioning

confidence: 99%

DONSON and FANCM associate with different replisomes distinguished by replication timing and chromatin domain

Zhang

Bellani

James

et al. 2020

Preprint

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25Duplication of mammalian genomes requires replisomes to overcome numerous impediments 26 during passage through open (eu) and condensed (hetero) chromatin. Typically, studies of 27 replication stress characterize mixed populations of challenged and unchallenged replication forks, 28 averaged across S phase, and model a single species of "stressed" replisome. However, in cells 29 containing potent obstacles to replication, we find two different lesion proximal replisomes. One 30 is bound by the DONSON protein and is more frequent in early S phase, in regions marked by 31 euchromatin. The other interacts with the FANCM DNA translocase, is more prominent in late S 32 phase, and favors heterochromatin. The two forms can also be detected in unstressed cells. CHIP-33 seq of DNA associated with DONSON or FANCM confirms the bias of the former towards regions 34 that replicate early and the skew of the latter towards regions that replicate late. 35Introduction 36 Eukaryotic replisomes are multiprotein complexes consisting, minimally, of the CMG 37 helicase [MCM2-7 (M), CDC45 (C), and GINS (go, ichi, ni, san) proteins (G)] which forms a ring 38 around the leading strand template. Other components include the pol α, ε, and δ polymerases, 39 MCM10, and a few accessory factors [1][2][3][4][5][6][7] . The identification and characterization of the minimal 40 components of biochemically active replisomes, the result of decades of extraordinary work from 41 multiple laboratories, necessarily reflects studies with deproteinized model DNA substrates under 42 carefully controlled conditions. However, in vivo there are hundreds of replisome associated 43 proteins 8-12 . Presumably this reflects the multiple layers of complexity that characterize replication 44 of the genome in living cells. For example, three dimensional analyses of chromosome structure 45 demonstrate two major domains. The A compartment contains euchromatin, which is accessible, 46 transcriptionally active, and marked by specific histone modifications, such as H3K4me3. The B 47 compartment, which is more condensed, contains inactive genes, many repeated elements, and is 48 associated with different histone modifications, including H3K9me3 13 . In addition to the structural 49 distinctions, regions of the genome are also subject to temporal control of replication during S 50 phase. Sequences in Compartment A tend to replicate early in S phase, while those in B are 51 duplicated in late S phase 14,15 . 52 Other influential effectors of replisome composition are the frequent encounters with 53 impediments, that stall or block either the progress of the CMG helicase or DNA synthesis. These 54 3 include alternate DNA structures, protein: DNA adducts, DNA covalent modifications introduced 55 by endogenous or endogenous reactants, depleted nucleotide precursor pools, etc. Replication 56 stress activates the ATR (ATM-and Rad3-related) kinase, with hundreds of substrates, including 57 MCM proteins [16][17][18] , and stimulates the recruitment of numerous facto...

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“…However, in vivo the speed of the replisome is not uniform, as it 39 temporarily or terminally slows/pauses/arrests/stalls at certain locations, called replication fork barriers 40 (RFBs). RFBs are comprised by 'unconventional' DNA structures (inverted repeats, trinucleotide repeats, G4 41 quadruplexes), RNA/DNA hybrids (R-loops), and tight protein/DNA complexes (Gadaleta and Noguchi 2017). 42…”

Section: Introduction 32mentioning

confidence: 99%

“…Examples in yeast of the latter type of RFB are found at the rDNA repeat array, tRNA genes (tDNA), 43 telomeres, centromeres, silent mating type loci (HML/HMR) silencer elements, and dormant origins of 44 replication (Gadaleta and Noguchi 2017). 45…”

Section: Introduction 32mentioning

confidence: 99%

Fork Pausing Complex Engages Topoisomerases at the Replisome

Shyian

Albert

Zupan

et al. 2019

Preprint

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17Replication forks temporarily or terminally pause at hundreds of hard-to-replicate regions around the 18 genome. A conserved pair of budding yeast replisome components Tof1-Csm3 (fission yeast Swi1-Swi3 and 19 human TIMELESS-TIPIN) acts as a 'molecular brake' and promotes fork slowdown at proteinaceous 20 replication fork barriers (RFBs), while the accessory helicase Rrm3 assists the replisome in removing protein 21 obstacles. Here we show that Tof1-Csm3 complex promotes fork pausing independently of Rrm3 helicase by 22 recruiting topoisomerase I (Top1) to the replisome. Topoisomerase II (Top2) partially compensates for the 23 pausing decrease in cells when Top1 is lost from the replisome. The C-terminus of Tof1 is specifically 24 required for Top1 recruitment to the replisome and fork pausing but not for DNA replication checkpoint 25 (DRC) activation. We propose that forks pause at proteinaceous RFBs through a 'sTOP' mechanism ('slowing 26 down with TOPoisomerases I-II'), which we show also contributes to protecting cells from topoisomerase-27 blocking agents. 28 29

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Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome

Cited by 48 publications

References 238 publications

Maf1‐dependent transcriptional regulation of tRNAs prevents genomic instability and is associated with extended lifespan

Maf1‐dependent transcriptional regulation of tRNAs prevents genomic instability and is associated with extended lifespan

DONSON and FANCM associate with different replisomes distinguished by replication timing and chromatin domain

Fork Pausing Complex Engages Topoisomerases at the Replisome

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