Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts

Abstract

During S phase, the entire genome must be precisely duplicated, with no sections of DNA left unreplicated. Here, we develop a simple mathematical model to describe the probability of replication failing due to the irreversible stalling of replication forks. We show that the probability of complete genome replication is maximized if replication origins are evenly spaced, the largest inter-origin distances are minimized, and the end-most origins are positioned close to chromosome ends. We show that origin positions in the yeast Saccharomyces cerevisiae genome conform to all three predictions thereby maximizing the probability of complete replication if replication forks stall. Origin positions in four other yeasts—Kluyveromyces lactis, Lachancea kluyveri, Lachancea waltii and Schizosaccharomyces pombe—also conform to these predictions. Equating failure rates at chromosome ends with those in chromosome interiors gives a mean per nucleotide fork stall rate of ∼5 × 10−8, which is consistent with experimental estimates. Using this value in our theoretical predictions gives replication failure rates that are consistent with data from replication origin knockout experiments. Our theory also predicts that significantly larger genomes, such as those of mammals, will experience a much greater probability of replication failure genome-wide, and therefore will likely require additional compensatory mechanisms.

Large transcription units unify copy number variants and common fragile sites arising under replication stress

“…Here we draw on models of CNV formation in which Fork Stalling and Template Switching (FoSTeS) and Microhomology-Mediated Break-Induced Replication (MMBIR) create de novo junctions at stalled replication forks by invasion of nascent DNA strands into ectopic locations (Lee et al 2007;Hastings et al 2009). We also draw on mathematical modeling in which the probability of fork failure at a locus is a function of the distance that a fork must travel (N) divided by the median distance that forks travel prior to stalling (N s ) (Newman et al 2013). In this framework, inhibiting replication decreases N s and leads to increased fork failures and FoSTeS and MMBIR events and thus sporadic CNV formation genome-wide.…”

Behavior of replication origins in Eukaryota – spatio-temporal dynamics of licensing and firing

“…For finite strands R < 1 and this factor reflects some degree of randomness. 32 All of the 16 yeast chromosomes have an R lower than that given by random distribution which indicates that their origin spatial distribution is below randomness. Similar conclusions were arrived at after comparison of 3 other yeast species -Kluyveromyces lactis, Lachancea kluyveri and Kluyveromyces waltii (recently named Lachancea waltii).…”

“…Another algorithmical theory takes into account the probability of fork stalling and replication failure and may be applied for cells without restrictions of the duration of replication. 32 If we consider a region of the genome between 2 neighboring ROs (denoted by a symbol 'D' after Newman et al 32 ), there is a small probability of a fork stalling at each one of the base pairs within this area. To maintain unreplicated DNA within 'D' after firing or inactivating (after passive replication) all of the origins, both of the forks shall enter 'D' from left and right side and both shall stall before meeting (double fork stall; see also Fig.…”

“…Examination of S. cerevisiae origins clearly reveals that in vivo they are distributed uniformly with only some minor deviations, which meets all of the above calculations. [30][31][32] Theoretically, for an infinite chromosome with randomly-placed origins, the calculated ratio of the standard deviation of origin separation divided by the mean (R) equals 1. For finite strands R < 1 and this factor reflects some degree of randomness.…”

SIR2 suppresses replication gaps and genome instability by balancing replication between repetitive and unique sequences

“…Given the limited pool of initiation factors, we propose that an increase in density of active origins within repetitive regions could result in a decreased density of such origins in unique regions of the genome, which, when combined with the stochastic nature of origin firing, may occasionally result in replication gaps, i.e., unique regions of the genome that are unable to complete replication before mitosis. This so-called "Random Replication Gap Problem" (RRGP) is the subject of long-standing speculation, but such gaps have never been experimentally demonstrated (6,7). We have identified a situation in yeast in which repetitive sequences more effectively compete for replication initiation factors, and experimentally limiting this competitive advantage promotes replication of unique regions of the genome and extends lifespan (8).…”