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SIR2 Suppresses Replication Gaps and Genome Instability by Balancing Replication Between Repetitive and Unique Sequences

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SIR2 Suppresses Replication Gaps and Genome Instability by Balancing Replication Between Repetitive and Unique Sequences SIR2 suppresses replication gaps and genome instability by balancing replication between repetitive and unique sequences Eric J. Fossa, Uyen Laoa, Emily Dalrymplea, Robin L. Adriansea, Taylor Loea, and Antonio Bedalova,b,c,1 aDivision of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; bDepartment of Medicine, University of Washington, Seattle, WA 98195; and cDepartment of Biochemistry, University of Washington, Seattle, WA 98195 Edited by Jasper Rine, University of California, Berkeley, CA, and approved December 13, 2016 (received for review September 2, 2016) Replication gaps that persist into mitosis likely represent impor- factors, and experimentally limiting this competitive advantage tant threats to genome stability, but experimental identification of promotes replication of unique regions of the genome and ex- these gaps has proved challenging. We have developed a tech- tends lifespan (8). nique that allows us to explore the dynamics by which genome Repetitive sequences in yeast are limited to the ribosomal replication is completed before mitosis. Using this approach, we DNA (rDNA) and subtelomeric repeats. Yeast rDNA comprises demonstrate that excessive allocation of replication resources to ∼150 copies of a tandemly repeated 9.1-kilobase (kb) sequence, origins within repetitive regions, induced by SIR2 deletion, leads and represents 10% of total genomic DNA. As each repeat has to persistent replication gaps and genome instability. Conversely, its own origin of replication and there are ∼300 non-rDNA or- the weakening of replication origins in repetitive regions suppresses igins, ribosomal origins represent 1/3 of all replication origins in these gaps. Given known age- and cancer-associated changes in the yeast genome. In a cross between two genetically diverse chromatin accessibility at repetitive sequences, we suggest that rep- strains of yeast, we identified a naturally occurring single nu- lication gaps resulting from misallocation of replication resources cleotide polymorphism within the rDNA replication origin (ri- underlie age- and disease-associated genome instability. bosomal DNA Autonomously Replicating Sequence, or rARS) that both decreases origin activity and extends lifespan by 40% SIR2 | DNA replication | repetitive sequences | replication gaps | (8). By limiting replication initiation at repetitive rDNA, this ribosomal DNA polymorphism promotes replication elsewhere in the genome. Specifically, this polymorphism can (i) increase origin firing at taggered initiation of DNA replication, which is common other chromosomal origins, (ii) promote replication of plasmids Sacross eukaryotes from fungi to humans, means that, at any with weak origins, and (iii) partially suppress the temperature given time, in S phase, only a fraction of replication origins is sensitivity of a mutation in ORC2, which encodes a protein activated. In recent years, a model has emerged to explain this needed for origin “licensing”—the formation of a prereplicative pattern of DNA replication (1, 2). This model assumes that the complex at the origin. Calorie restriction, which is known to pool of initiation factors required to fire licensed origins in S extend lifespan in organisms from yeast to mammals (9), mimics phase is limited, and therefore sufficient to fire only a subset of the effect of this polymorphism by suppressing rDNA origin licensed origins at any given time. Licensed origins differ in their activity. Conversely, the absence of the histone deacetylase Sir2 ability to recruit factors required for firing, so origins with higher (silent information regulator), which decreases replicative life- affinity or accessibility fire earlier than those with lower affinity span (10), increases rDNA origin efficiency while decreasing or accessibility. After activating the initial set of origins, firing factors are released, enabling the next set of origins to fire. This Significance results in successive waves of origin activation. Genome repli- cation eventually finishes when areas with the least accessible Because the factors required to fire origins of DNA replication origins are replicated. are less abundant than the origins themselves, during S phase, In healthy human cells, the least accessible genomic regions these factors are recycled from one area of the genome to an- consist of repetitive DNA, which represents about half of the other, and, consequently, genome replication occurs in waves. genome and tends to be compacted into heterochromatin. Unique DNA sequences, which contain protein-encoding genes, However, recent studies suggest widespread opening of hetro- replicate before repetitive “junk” sequences. By modulating – chromatin during carcinogenesis and aging (3 5). Such re- competition for replication resources between these types of organization of chromatin would expose a new suite of origins sequences, we demonstrate that increased allocation of resources within repetitive DNA that could potentially compete initiation to repetitive sequences, which we previously showed to be as- factors away from unique portions of the genome, thereby dis- sociated with reduced lifespan, prevents completion of replica- rupting the normal genome-wide hierarchy of replication timing. tion in unique portions of the genome. We suggest that, as cells Increased origin activity within repetitive DNA could thus age, repetitive sequences compete more effectively for replica- compromise replication elsewhere in the genome. Given the tion initiation factors and that the resulting replication gaps form limited pool of initiation factors, we propose that an increase in the basis of replicative senescence. density of active origins within repetitive regions could result in a decreased density of such origins in unique regions of the ge- Author contributions: E.J.F. and A.B. designed research; E.J.F., U.L., E.D., R.L.A., and T.L. nome, which, when combined with the stochastic nature of origin performed research; E.J.F. analyzed data; and E.J.F. and A.B. wrote the paper. firing, may occasionally result in replication gaps, i.e., unique The authors declare no conflict of interest. regions of the genome that are unable to complete replication This article is a PNAS Direct Submission. “ before mitosis. This so-called Random Replication Gap Prob- Data deposition: The sequence reported in this paper has been deposited in the Gene lem” (RRGP) is the subject of long-standing speculation, but Expression Omnibus (GEO) database (accession no. GSE90151). such gaps have never been experimentally demonstrated (6, 7). 1To whom correspondence should be addressed. Email: [email protected]. We have identified a situation in yeast in which repetitive This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. sequences more effectively compete for replication initiation 1073/pnas.1614781114/-/DCSupplemental. 552–557 | PNAS | January 17, 2017 | vol. 114 | no. 3 www.pnas.org/cgi/doi/10.1073/pnas.1614781114 Downloaded by guest on September 27, 2021 origin efficiency at other loci (11, 12). Overall, these observations cells to identify early origins, as has been done previously (Fig. suggest that increased replication of repetitive regions of the 1A) (13, 14). All read depths were normalized to those in G1. genome can lead to replication gaps elsewhere, and that the We tested our method, which we refer to as G2-seq, using a presence of such gaps may constitute the proximal cause of death strain of yeast containing an artificial chromosome. Although the in cellular aging. native chromosomes replicate in a timely manner, the artificial To directly determine whether competition between repetitive chromosome completes replication only very late in the cell cy- and unique regions of the genome leads to random replication cle. This yeast artificial chromosome (YAC) contains a 240-kb gaps (RRGs), we developed a technique that both identifies and fragment of the human TCR-β (T-cell receptor, beta chain) re- quantifies such gaps. Combining this technique with our ability to gion deleted for sequences that fortuitously behave as DNA experimentally manipulate the balance of origin activity in re- replication origins in yeast (15–17). The replication of this YAC, petitive versus unique regions, we demonstrate here that in- which now depends on a strong yeast origin (ARS1) at the tip of creased origin firing at repetitive sequences promotes the the left arm, is markedly delayed, making the YAC genetically formation of replication gaps elsewhere. unstable and prone to large deletions due to incomplete repli- cation (16, 17). We analyzed G2-seq data from a strain con- Results taining this YAC using two complementary methods: (i)by To identify genomic regions potentially vulnerable to the RRGP, comparing completion of replication along native chromosomes we needed a method to monitor the final stages of genome (e.g., chromosome XV, Fig. 1B, Left) with that along the YAC replication. Deep sequencing has been used effectively to dissect (Fig. 1B, Right) and (ii) by comparing global replication of in- the early stages of DNA replication, as read depths change from dividual chromosomes with the global replication of the YAC 1× to 2× over the course of S phase (13, 14). Because this (Fig. 1C). Patterns of origin firing at native chromosomes transition begins at active replication origins, comparing read revealed by S-phase read depths (Fig. 1B, in red) coincided with depths for S-phase-sorted cells with cells in G1 or G2
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