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Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes

Nature Structural & Molecular Biology volume 24, pages 162–170 (2017)Cite this article

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Abstract

Saccharomyces cerevisiae expresses two Pif1-family helicases—Pif1 and Rrm3—which have been reported to play distinct roles in numerous nuclear processes. Here, we systematically characterized the roles of Pif1 helicases in replisome progression and lagging-strand synthesis in S. cerevisiae. We demonstrate that either Pif1 or Rrm3 redundantly stimulates strand displacement by DNA polymerase δ during lagging-strand synthesis. By analyzing replisome mobility in pif1 and rrm3 mutants, we show that Rrm3, with a partially redundant contribution from Pif1, suppresses widespread terminal arrest of the replisome at tRNA genes. Although both head-on and codirectional collisions induce replication-fork arrest at tRNA genes, head-on collisions arrest a higher proportion of replisomes. In agreement with this observation, we found that head-on collisions between tRNA transcription and replication are under-represented in the S. cerevisiae genome. We demonstrate that tRNA-mediated arrest is R-loop independent and propose that replisome arrest and DNA damage are mechanistically separable.

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Figure 1: Okazaki-fragment sequencing is a quantitative genome-wide assay detecting replisome mobility and lagging-strand biogenesis in WT and mutant cells.
Figure 2: tDNAs are sites of replication-fork arrest in rrm3Δ and rrm3Δ; pif1-m2 strains.
Figure 3: 2D gel validation of replication-fork arrest in rrm3Δ and rrm3Δ; pif1-m2 strains.
Figure 4: G quadruplexes and highly transcribed RNAP2 genes do not contribute to significant replication-fork stalling or arrest genome wide.
Figure 5: All tDNAs act as replication terminators, but head-on orientation between replication and transcription machinery increases fork arrest.
Figure 6: R loops do not mediate replication-fork arrest at tDNAs.

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Acknowledgements

We thank V. Zakian and members of the Zakian laboratory for the 2D gel protocol, for communicating data before publication, and for helpful discussions. We additionally thank S. Ercan, A. Hochwagen, H. Klein, and members of the Smith laboratory for insightful discussions and critical reading of the manuscript, D. Tranchina for help with statistical analyses, and V. Subramanian for assistance with 2D gel electrophoresis. This work was supported by NIH grant R01 GM114340, a March of Dimes Basil O'Connor Starter Scholar award (FY15-BOC-2141) and the Searle Scholars program (all to D.J.S.). J.S.O. is supported by an American Cancer Society–New York Cancer Research Fund postdoctoral fellowship (PF-16-096-01-DMB).

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  1. Jayashree Kumar

    Present address: Present address: Biological & Biomedical Sciences Program, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.,

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  1. Department of Biology, New York University, New York, New York, USA

    Joseph S Osmundson, Jayashree Kumar, Rani Yeung & Duncan J Smith

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Contributions

J.S.O., J.K., and R.Y. generated data; J.S.O., J.K., and D.J.S. analyzed data and interpreted results; J.S.O. and D.J.S. wrote the manuscript with input from J.K. and R.Y.

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Correspondence to Duncan J Smith.

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Integrated supplementary information

Supplementary Figure 1 Origin use and efficiency are similar among WT, rrm3Δ, pif1-m2, and pif1-m2; rrm3Δ strains.

A. Analysis of fork progression around confirmed and likely origins (from cerevisiae.oridb.org). The percent of forks moving from left to right was calculated by the proportion of reads mapping to the Crick strand for each 100bp bin around the annotated origin of replication averaged across all sites (n=265). The origin signal is an ascending slope in this graph (compare to Figure 2A(i) and C).

B. Scatter plot of origin usage at all confirmed and likely origins. The origin signal was calculated at each site by the difference between the percent of forks moving right to left upstream (+1-3kb) and downstream (-1-3kb) of the site, similar to the termination signal described in Figure 2, but with the opposite polarity.

Supplementary Figure 2 Further analysis of Okazaki-fragment termini in pif1 and rrm3 mutant strains.

A. Distribution of Okazaki fragment 3’ termini around consensus nucleosome dyads (Jiang & Pugh, Genome Biology 10, R109) as shown for 5’-ends in Fig 1B.

B. rrm3Δ, pif1-m2, and pif1-m2;-rrm3Δ S. cerevisiae strains generate fully ligatable, nucleosome-sized Okazaki fragments similar to those observed in wild-type cells. Genomic DNA was prepared and labeled as described in the Materials and Methods.

C. Model for Pif1 and Rrm3 activity on the lagging strand. Histones are redeposited on the nascent lagging strand through the action of Caf1 (blue) as the lagging strand is being synthesized. Either Pif1 or Rrm3 (red) is required for normal DNA Pol δ (green) processivity, with Okazaki fragment ends enriched around nucleosome dyads as shown in Figure 1B. In the absence of both Pif1 and Rrm3, mature Okazaki fragment ends are enriched upstream of the nucleosome dyads.

Supplementary Figure 3 tDNAs are the predominant sites of fork stalling genome wide.

A. Fork progression of rightward (upper) and leftward (lower) moving forks at tDNAs selected for further analysis (n=93; rightward n=51, leftward n=42; see Materials and Methods). The percent of forks moving left-to-right was calculated by the percent of reads mapping to the Crick strand.

B. Fork progression at all tDNAs with an origin in the analysis window in the WT (black) and pif1-m2;rrm3Δ (purple) mutant cells. The percent of forks moving left-to-right was calculated as described in the Materials and Methods with a correction for the slight difference in origin efficiency in the pif1-m2;rrm3Δ mutant (see Figure S1). The ascending slope in the upstream region is the origin signal (see Figure S1A).

C. Fork progression at all tDNAs without an origin within the analysis window as shown in part B.

D. Fork progression at tDNAs without an origin in the analysis window and without an origin-proximal tDNA plotted as in part B, and corrected for the slight difference in origin efficiency.

E-G. Random sites with an origin within the analysis window (E), without an origin in the analysis window (F), and without an tDNA in the analysis window or proximal to the nearest upstream origin of replication (G) plotted as in part B with a correction for the slight difference in origin efficiency.

H. Grand mean ± SD from three independent experiments of the change in replication direction, interpreted as indicative of replisome stalling, at random sites (n=381), random sites that exclude tDNAs in the window of analysis (n=292), and tDNAs (n=93) for the indicated strains. Significance was determined by Monte Carlo resampling; *** indicates a p<0.0001; n/s indicates p>0.05.

Supplementary Figure 4 Fork arrest is a feature common to tDNAs.

A. Heatmap showing the difference in percent forks moving left to right (calculated by the percent reads mapping to the Crick strand) between the WT and the pif1- m2 rrm3Δ double mutant. tDNAs were sorted by their average fork direction (see Materials and Methods), and data were binned to 100bp. Negative values (i.e. pif1- m2 rrm3Δ forks more leftward moving than wild type) were visualized in yellow while positive values (i.e. pif1- m2; rrm3Δ forks more rightward moving than wild type) were visualized in blue. Heatmap was constructed with Gitools.

B. Scatter plot of all 93 tDNAs without a nearby origin or sequence gap. The change in replication direction was calculated for the same site in the WT and pif1- m2; rrm3Δ strains. Black dots are the WT plotted against the WT data and therefore give a line with the slope of 1. The pif1- m2; rrm3Δ change in replication direction divided by the change in the WT strain is plotted in purple.

C. Reproducibility of tDNA arrest signal from biological replicate 1 to biological replicate 2. The change in replication direction from dataset 1 and dataset 2 at the 93 tDNAs included in our analysis. Each site was plotted four times, once for each strain, and the data were colored by strain. R2-values for the correlation between datasets for each strain were calculated using Graphpad Prism.

Supplementary Figure 5 Lack of robust stalling or arrest signal at RNA Pol II genes and G-quadruplex-forming sequences

A. Grand mean ± SD for three independent experiments of the change in replication direction, interpreted as indicative of replisome arrest, at random sites (n=381), G-quadruplex forming sequences (Capra, J. A. et al. PLoS Comput Biol 6, e1000861 (2010)) (n=180), Highly transcribed RNA Pol II genes (Pelechano, V., Wei, W. & Steinmetz, L. M. Nature 497, 127-131 (2013)) (n=207), ribosomal protein genes (n=56), and tDNAs (n=93) as calculated in Figure 2E. In this analysis, random sites, G-quadruplex sequences, and RNA pol II genes with a tDNA in the analysis window were not removed (compare to Figure 4A). Significance was determined by Monte Carlo resampling; *** indicates a p<0.0001; * indicates 0.0001 < p < 0.05. n/s indicates p>0.05.

B. Scatter plot of the change in replication direction at individual sites for all G-quadruplex forming sequences (n=180), highly transcribed RNA pol II genes (n=207), and tDNAs (n=93) for the WT (gray) and pif1-m2;rrm3Δ strain (purple). Sites are as defined in part A. Individual termination signals were calculated at each site as described in Figure 2 and the sites used were described in part A. The mean of each dataset is depicted as a black bar.

C. Grand mean ± SD of the change in replication direction from three independent experiments at different subsets of G-quadruplex sites previously shown to stall the fork or bind to Pif1(Paeschke, K., Capra, J. A. & Zakian, V. A. Cell 145, 678-691 (2011); Paeschke, K. et al. Nature 497, 458-462 (2013)) (Pol2-pause n=53; Pol2-pause without tDNA in window n=43; Pif1-binding peak n=19; Pif1-binding peak no tDNA in window n=14). Significance was determined by Monte Carlo resampling; *** indicates a p<0.0001; * indicates 0.0001 < p < 0.05. n/s indicates p>0.05.

D. Addition of Hydroxyurea (HU, 25mM) to the growth media, which slows replication forks by depleting the dNTP pool, did not increase specific stalling at G-quadruplex forming structures or tDNA sites. Grand mean ± SD of three independent experiments for replisome arrest was plotted for G-quadruplex forming sites (n=180) and tDNAs (n=93) as in part A. Significance was determined by Monte Carlo resampling; *** indicates a p<0.0001. n/s indicates p>0.05.

E. Selection of a subset of G-quadruplexes and random sites with a significant stalling in the pif1-m2;rrm3Δ double mutant. For both the G-quadruplex forming sequences (n=46, p<0.0001) and the random sites (n=43, p<0.0001), we were able to select a subset of the sites that shows significant stalling. Significance was determined by Monte Carlo resampling; *** indicates a p<0.0001; * indicates 0.0001 < p < 0.05. n/s indicates p>0.05.

Supplementary Figure 6 Direction of transcription at RNA Pol II genes and the strand of the G-quadruplex structure do not affect fork stalling or arrest at these sites.

A. Grand mean ± SD from three independent experiments of the change in replication direction, interpreted as indicative of replisome arrest, at RNA Pol II genes and G-quadruplex sequences binned by direction of replication (see Materials and Methods). Significance was determined by Monte Carlo resampling; n/s indicates p>0.05.

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Osmundson, J., Kumar, J., Yeung, R. et al. Pif1-family helicases cooperatively suppress widespread replication-fork arrest at tRNA genes. Nat Struct Mol Biol 24, 162–170 (2017). https://doi.org/10.1038/nsmb.3342

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