The replication checkpoint protects fork stability by releasing transcribed genes from nuclear pores

Abstract

Transcription hinders replication fork progression and stability, and the Mec1/ATR checkpoint protects fork integrity. Examining checkpoint-dependent mechanisms controlling fork stability, we find that fork reversal and dormant origin firing due to checkpoint defects are rescued in checkpoint mutants lacking THO, TREX-2, or inner-basket nucleoporins. Gene gating tethers transcribed genes to the nuclear periphery and is counteracted by checkpoint kinases through phosphorylation of nucleoporins such as Mlp1. Checkpoint mutants fail to detach transcribed genes from nuclear pores, thus generating topological impediments for incoming forks. Releasing this topological complexity by introducing a double-strand break between a fork and a transcribed unit prevents fork collapse. Mlp1 mutants mimicking constitutive checkpoint-dependent phosphorylation also alleviate checkpoint defects. We propose that the checkpoint assists fork progression and stability at transcribed genes by phosphorylating key nucleoporins and counteracting gene gating, thus neutralizing the topological tension generated at nuclear pore gated genes.

Graphical abstract

Figure 1

TREX-2 and THO Ablations Rescue rad53 HU Sensitivity (A) GAL-rad53-D339A SGA YP galactose or YP glucose plates containing 10 mM HU. White boxes mark suppressors of rad53-D339A HU sensitivity. (B) WT, sac3Δ, rad53-K227A, rad53-K227A sac3Δ, thp1Δ, rad53-K227A thp1Δ, sus1Δ, and rad53-K227A sus1Δ cells plated without (YPDA) or with 5 mM HU. (C) Summary of THO/TREX, TREX-2, and NPC genes and their genetic interactions with rad53-K227A. Human orthologs are indicated. Null, gene deletion phenotype; rad53 rescue, suppression of rad53-K227A lethality at 5–10 mM HU; ss with rad53, synthetic sickness in combination with rad53-K227A; HU sensitivity, growth defects at 100–200 mM HU; phosphosites, the residues targeted by the checkpoint kinases (in parentheses) are shown. For schematic summary, see Figure S1.

Figure 2

RNase H Overexpression Does Not Influence rad53 or rad53 sac3 Cells' HU Sensitivity (A) WT, sac3Δ, rad53-K227A, and rad53-K227A sac3Δ cells carrying either the vector (pYES) or pGW-RNH1, expressing RNH1 under the GAL1 promoter (GAL RNH1), were plated in glucose (GLU)- or galactose (GAL)-containing media without (−) or with 5 mM HU. (B) WT, rnh1Δ, rad53-K227A, rad53-K227A rnh1Δ, rnh201Δ, rad53-K227A rnh201Δ, rnh202Δ, and rad53-K227A rnh202Δ cells were plated without (YPDA) or with 2.5 or 5 mM HU.

Figure 3

SAC3 Deletion Suppresses rad53 Cells' Fork Defects (A) BrdU-IP-Chip analysis of replicon dynamics of WT, sac3Δ, rad53-K227A, and rad53-K227A sac3Δ cells 60 min after release from G1 into S phase in 25 mM HU. Orange (BrdU-IP) histogram bars in the y axis show the average signal ratio in log2 scale of loci along the reported region on chromosome III. The x axis shows chromosomal coordinates. Positions of early and late/dormant ARS elements are in red and gray, respectively. Blue and red horizontal bars mark the BrdU incorporation tracks corresponding to forks emanated from early replication origins in WT, sac3Δ, and rad53-K227A sac3Δ cells or rad53-K227A mutants, respectively. Red triangles mark additional BrdU tracks generated by unscheduled dormant origin firing in rad53-K227A cells. (B) 2D gel analysis of replication intermediates in WT (SAC3 RAD53), sac3Δ (sac3 RAD53), rad53-K227A (SAC3 rad53), and rad53-K227A sac3Δ (sac3 rad53) cells at the indicated times after release from G1 into S phase in 25 mM HU. A schematic representation of the 2D gel profiles observed in RAD53 and rad53 cells is shown. Histogram plots of the ratio between quantified “Spike” and “Large Y” intermediates signals are shown.

Figure 4

The Replication Checkpoint Negatively Regulates Gene Gating (A) WT, sac3Δ, rad53-K227A, and rad53-K227A sac3Δ cells carrying pGAL-LACZ-IN (IN) were grown in synthetic complete −Ura plates containing glucose (SC –Ura) or galactose (SGal –Ura). (B) Representative images of Nup49-GFP, TETR-GFP, TETO::GAL1/10/7, Nop1-Cherry glucose-grown cells and percentage of cells showing central or NPC-tethered (peripheral) GAL loci in WT or mlp1Δ cells grown in the presence of glucose (GLU) or galactose (GAL). (C) WT and rad53-K227A cells were grown overnight in the presence of galactose (GAL) and treated with 0.2 M HU for the indicated times. The mean percentages of cells showing peripheral GAL loci and standard deviations (histogram error bars) from three independent experiments are shown. (D) Serial dilutions of WT, sac3ΔCID, rad53-K227A, and rad53-K227A sac3ΔCID cells plated in the absence (YPDA) or presence of 5 mM HU.

Figure 5

Nucleoporin Mutations Abolishing Gene Gating Suppress rad53 Phenotypes (A) rad53-K227A and rad53-K227A mlp1Δ cells were grown overnight with galactose (GAL) and treated with 0.2 M HU. The mean percentages of cells showing peripheral GAL loci and standard deviations (histogram error bars) from three independent experiments are shown. (B) Serial dilutions of WT, nup1Δ, rad53-K227A, rad53-K227A nup1Δ, mlp1Δ, and rad53-K227A mlp1Δ cells plated in the absence (YPDA) or presence of 5 mM HU. (C) Evolutionary comparison of a portion of the Mlp1 globular domain containing residues phosphorylated by checkpoint kinases. Conserved residues are labeled in green. (D) Percentage of cells showing central or NPC-tethered (peripheral) GAL loci in WT, mlp1S1710A, mlp1S1710D, and mlp1Δ cells grown in the presence of glucose (GLU) or galactose (GAL). (E) Serial dilutions of WT, mlp1S1710D, rad53-K227A, and rad53-K227A mlp1S1710D cells plated in the absence (YPDA) or presence of 5 mM HU. For related data, see Figure S2.

Figure 6

DSB Induction Counteracts Fork Reversal in rad53 Mutants Replication intermediates in WT HO-inc, WT HO, rad53-K227A HO-inc, and rad53-K227A HO cells following α factor-induced G1 arrest, DSB formation by galactose addition, and release in 25 mM HU. Schematic representations of the 2D gel digestion strategies used are shown. Histograms indicate the ratio between reversed fork signal intensities at ARS305 and ARS202 for rad53 cells at each time point. For related data, see Figure S4.

Figure 7

Hypothetical Transitions at Forks Encountering Nuclear Pore Gated Genes (A) Hypothetical schematic representation of the topological architecture of forks encountering nuclear pore-gated transcribed genes. Small red circles represent phosphorylation events mediated by the checkpoint. Yellow ovals surrounded by blue indicate those proteins whose gene deletions rescue rad53. The red line indicates mRNA. We speculate that Mec1 senses vibrations resulting from the clash between forks and gated genes. Rad53 is then activated and phosphorylates nucleoporins in the inner basket. Some of these phosphorylation events might also regulate tRNA metabolism and/or dNTP pools. See text for details. (B) The “R” indicates replisome; “P,” RNA polymerase II. In WT cells, forks pause in front of the transcribed region (Azvolinsky et al., 2009) and activate the checkpoint (DDR). Checkpoint activation then releases the tethering between the transcribed gene and the nuclear pore. Consequently, the architectural domain of the transcribed region (Bermejo et al., 2009) is simplified, thus enabling fork restart. In rad53 mutants, the clash between the fork and the transcribed region is not assisted by the checkpoint, and consequently, the fork collapses, leading to replisome dissociation and fork reversal owing to the unsolved topological stress. For related information, see Figure S3.

Figure S1

THO and TREX-2 Factors Coordinating Gene Transcription, mRNP Maturation, mRNP Export, and Gene Gating Are Targeted by DNA Damage Checkpoint Kinases, Related to Figure 1 Schematic representation of the physical interaction of THO/TREX, TREX-2 and Nuclear Pore Complex (NPC) factors linking gene transcription with mRNA export. Factors whose ablation suppresses rad53 cells HU sensitivity are represented in blue. Factors whose ablation does not alter rad53 cells HU sensitivity are represented in light gray. Orange, yellow and purple stars mark factors phosphorylated in a Mec1/Tel1, Rad53 or Dun1 dependent manner respectively (see Chen et al., 2010; Smolka et al., 2007) for details).

Figure S2

Effect of NUP2 or NUP60 Ablation on rad53 Cells' Sensitivity to HU, Related to Figure 5 Serial Dilutions of WT, nup2Δ, nup60Δ, rad53-K227A, nup2Δ rad53-K227A, and nup60Δ rad53-K227A Cells Plated in the Absence or Presence of 5 mM HU, Related to Figure 5.

Figure S3

Rad53 Interactome and DNA Replication—NPC Connections, Related to Figure 7 Interaction networks generated using Osprey (http://biodata.mshri.on.ca/osprey/servlet/Index). (A) Rad53 interacting factors are involved in the regulation of dNTP pools, nuclear pore architecture, mRNA biogenesis and export and tRNA biogenesis and export. (B) Nuclear Pore Complex (NPC) associated proteins interact with factors mediating DNA replication pre-initiation, initiation and elongation steps.

Figure S4

X-Shaped Molecules Resembling Reversed Forks Accumulate upon Concomitant Top1 and Top2 Inactivation, Related to Figure 6 (A) top1Δ top2-1 and top1Δ top2-1 rad53K227A cells were released from an α-factor induced G1 block into S-phase at 25°C (permissive temperature for the top2-1 allele). After 30 minutes cells were transferred to fresh medium pre-warmed to 37°C, in order to inactivate Top2, and samples were collected at the indicated time points for psoralen cross-linking and 2D gel analysis. White arrowheads indicate the position of cruciform molecules migrating as spike signals. Quantification of the spike signal intensities in the different time points is shown.