BRCA1 promotes unloading of the CMG helicase from a stalled DNA replication fork

Abstract

The tumor suppressor protein BRCA1 promotes homologous recombination (HR), a high-fidelity mechanism to repair DNA double-strand breaks (DSBs) that arise during normal replication and in response to DNA-damaging agents. Recent genetic experiments indicate that BRCA1 also performs an HR-independent function during the repair of DNA interstrand crosslinks (ICLs). Here we show that BRCA1 is required to unload the CMG helicase complex from chromatin after replication forks collide with an ICL. Eviction of the stalled helicase allows leading strands to be extended toward the ICL, followed by endonucleolytic processing of the crosslink, lesion bypass, and DSB repair. Our results identify BRCA1-dependent helicase unloading as a critical, early event in ICL repair.

Figure 1. ICL repair in Xenopus egg extract

(A) pICL schematic. ICL and cross-linked nucleotides are shown in blue. ChIP primer pairs are shown for “ICL” (25-132 bp from ICL) and “FAR” (2523-2622 bp from ICL) loci. (B) Model of ICL repair (Fu et al., 2011; Knipscheer et al., 2009; Long et al., 2011; Raschle et al., 2008). Parental DNA strands are black, and nascent strands are gray, or red for emphasis. CMG (replicative helicase complex comprised of Cdc45, MCM7, and Sld5), Ub (ubiquitin). See Figure S7 for revised model.

Figure 2. Ubiquitin signaling is required for replicative helicase unloading

pICL was replicated in egg extract supplemented with buffer (+Buffer), 14 μM UbVS (+UbVS), or 14 μM UbVS and 50 μM ubiquitin (+UbVS+Ub). Samples were analyzed by agarose gel electrophoresis to determine the efficiency of (A) replication and (B) ICL repair (described in Methods). (C-E) Protein recruitment to the ICL was analyzed by ChIP with the indicated antibodies. (F) Schematic of leading strand intermediates from the rightward moving fork as it bypasses the ICL. (G) Nascent strand products were analyzed by denaturing polyacrylamide gel electrophoresis. (H-J) ICL recruitment was analyzed by ChIP with the indicated antibodies. Note that the MCM7 ChIP signal starts high because MCM2-7 has already been loaded onto DNA at the 0 minute time point as a result of licensing in HSS extract (see Methods). All data shown was analyzed from a single experiment. See Figure S1 for primary gel data, ChIP recovery at the FAR locus, quantification of nascent strand products, and experimental replicates.

Figure 3. BRCA1 has an early role at ICL-stalled forks

(A-C) pICL was replicated in egg extract and ICL recruitment of various proteins was analyzed by ChIP. Samples were also analyzed for accumulation of ICL-stalled forks (Converged Forks) by agarose gel electrophoresis. Relative recovery shown with data normalized to peak accumulation. All data shown was analyzed from a single experiment with Converged Forks duplicated in A and B, and BRCA1-ChIP duplicated in B and C. pICL was replicated in mock-depleted (Mock) or BRCA1-depleted (ΔBRCA1) extract. Samples from the same reaction were analyzed by: Western blot with the indicated antibodies (D), agarose gel electrophoresis to determine the efficiency of replication (E) and ICL repair (F), ChIP with the indicated antibodies (G-J), and two-dimensional agarose gel electrophoresis (2DGE) (K) to analyze accumulation of converged forks (open arrowhead, see schematic and Figure 1B, i), which is quantified in (L). See Figure S2 for primary gel data, replicates of ICL repair data, and ChIP recovery at the FAR locus.

Figure 4. Analysis of strand resection during ICL repair

Mock-depleted and BRCA1-depleted samples from Figure 3D-L were used to analyze: (A) RPA recruitment by ChIP, and (B) the presence of ssDNA by quantitative PCR (described in Methods). The table indicates the distance in base pairs from the 3’ end of the Test primer to the ICL (“0”). The same information is also graphically indicated in (C). (D) Stalled fork schematic showing the 118 ssDNA Test primer (wavy orange line), which is extended (dashed orange line) after annealing to ssDNA. Amplification of the extended Test primer with Left and Right primers (red arrows) produces a 146 base pair product that is analyzed by quantitative PCR.

Figure 5. BRCA1 depletion inhibits leading strand Approach and helicase unloading

Mock-depleted or BRCA1-depleted samples from Figure 3 were analyzed by denaturing polyacrylamide gel electrophoresis (A) and by ChIP with the indicated antibodies (B-D). See Figure S3 for quantification of nascent strand products, ChIP recovery at the FAR locus, and experimental replicates.

Figure 6. The BRCA1-BARD1 complex is required to promote leading strand Approach and helicase unloading

pICL was replicated in extracts that were partially depleted of BRCA1 (Figure S4A), then supplemented with buffer (+Buffer), wild-type RING peptide (+RING^WT), or RING peptide containing two alanine insertions (+RING^AA). Samples from the same reaction were analyzed by denaturing polyacrylamide gel electrophoresis (A) and by ChIP with the indicated antibodies (B-C). See Figure S4 for quantification of nascent strand products, ChIP recovery at the FAR locus, and experimental replicates.

Figure 7. BRCA1 and DNA polymerase independently promote helicase unloading

pICL was replicated in egg extract for 12 minutes. The reaction was then split and supplemented with buffer (+Buffer) or 50 μM aphidicolin (+Aphidicolin) to block polymerase activity. Samples from the same reaction were analyzed by: (A) denaturing polyacrylamide gel electrophoresis, (B) agarose gel electrophoresis to determine the efficiency of replication, (C-E) ChIP with the indicated antibodies, (F) 2DGE to visualize the accumulation of converged forks, and (G) agarose gel electrophoresis to determine the efficiency of ICL repair. See Figure S5 for primary gel data, quantification of nascent strand products, and ChIP recovery at the FAR locus. (H-J) pICL was replicated in mock-depleted (Mock) or BRCA1-depleted (ΔB1) extract for 30 minutes. Each reaction was then split and supplemented with buffer or aphidicolin (+Aph) to block polymerase extension. Protein recruitment to the ICL was analyzed by ChIP with the indicated antibodies. See Figure S6 for primary experimental data.