CtIP maintains stability at common fragile sites and inverted repeats by end resection-independent endonuclease activity

Abstract

Chromosomal rearrangements often occur at genomic loci with DNA secondary structures, such as common fragile sites (CFSs) and palindromic repeats. We developed assays in mammalian cells that revealed CFS-derived AT-rich sequences and inverted Alu repeats (Alu-IRs) are mitotic recombination hotspots, requiring the repair functions of carboxy-terminal binding protein (CtBP)-interacting protein (CtIP) and the Mre11/Rad50/Nbs1 complex (MRN). We also identified an endonuclease activity of CtIP that is dispensable for end resection and homologous recombination (HR) at I-SceI-generated "clean" double-strand breaks (DSBs) but is required for repair of DSBs occurring at CFS-derived AT-rich sequences. In addition, CtIP nuclease-defective mutants are impaired in Alu-IRs-induced mitotic recombination. These studies suggest that an end resection-independent CtIP function is important for processing DSB ends with secondary structures to promote HR. Furthermore, our studies uncover an important role of MRN, CtIP, and their associated nuclease activities in protecting CFSs in mammalian cells.

Figure 1. The AT-rich Flex1 sequences derived from CFS FRA16D are mitotically unstable

A. The HR-Flex and HR-Luc substrates with I-SceI cleavage site at one side (top, D-EGFP: donor EGFP fragment). Three U2OS clones with single-integration of HR-Flex or HR-Luc were mock treated (No), treated with 2 mM hydroxyurea (HU) for 24 hr, or subjected to double-thymidine block then HU-treated for 24 hr (Thy + HU), and assayed for EGFP-positive events 72 hr after HU treatment (bottom). B. U2OS clones carrying HR-Flex or HR-Luc were sorted for EGFP-negative cells, cultured for 2 or 3 weeks, and assayed for spontaneous mitotic recombination. C. A model for DSB formation on stalled replication forks induced by the Flex1 sequence close to an EBV origin (top left). Plasmid instability assay of U2OS cells carrying pCEP4-Flex1(AT)34 or pCEP4-Luc after culturing without hygromycin for 1 week (top right), or in cell lines expressing shRNAs against Mre11, CtIP or control MKO (bottom left), or expressing Mre11 (WT or H129N) or CtIP (WT or N181A/R185A), with endogenous Mre11 or CtIP silenced by shRNAs. D–F. U2OS cells carrying HR-Flex or HR-Luc, expressing indicated shRNAs or control MKO, or in F, expressing Myc-Mre11 (WT or H129N) or vector, with endogenous Mre11 silenced, were induced with HU (2 mM) for 24 hr (left) or with I-SceI (right) and assayed 72 hr later. In E, right, a model for end resection and processing of structure-forming sequences (such as Flex1) at DSB ends to generate clean 3’ ends for strand invasion. See also Figure S1.) In all experiments, error bars represent standard deviation (s.d.) of three independent experiments.

Figure 2. CtIP is associated with an endonuclease activity

A–C. Internally ³²P-labeled (asterisk) DNA hairpin substrates with two 30 bp ssDNA tails (A), ssDNA and/or dsDNA tails (B), or Y-shaped branched substrates with ssDNA tails (C) were used for nuclease assays with CtIP at concentrations 20 and 60 nM (A), or 5, 20 and 60 nM (B and C) or without at 37°C for 30 min. Sub: substrates, Prod: products. DNA hairpin substrates with one 3’ tail or no tail were run on the gel as markers in A. D. Internally ³²P-labeled 66-bp ssDNA or a hairpin substrate with ssDNA tails were incubated with 5, 20, 60 nM CtIP or without at 37°C for 30 min. E. dsDNA with blunt, or 3’ or 5’ overhangs were internally labeled with ³²P and used as substrates for nuclease assays with CtIP concentrations of 70 and 200 nM or without at 37°C for 1 hr. F and G. CtIP fragments of indicated lengths (in F) and CtIP fragment 45–461 containing various point mutations (in G) were assayed for nuclease activity at CtIP concentrations of 20 and 60 nM or without using the hairpin substrate from A. Coomassie blue staining of these purified CtIP fragments is shown in Figure S2D. H. Gel mobility shift was performed with CtIP (45-461) WT or N181A/R185A mutant at 2, 5, 20 and 60 nM or without and using 3 nM hairpin DNA substrate from A, with BSA (100 and 200 nM) as control. I and J. U2OS cells carrying HR-Flex or HR-Luc (in I) or EGFP-SSA (in J, Figure S2N) and expressing HA-CtIP (WT, N181A/R185A or E267A/E268A) or vector, with endogenous CtIP silenced, were induced with I-SceI and assayed. See also Figure S2.) In all experiments, error bars represent standard deviation (s.d.) of three independent experiments.

Figure 3. CtIP exhibits a conserved function required for IRs-induced mitotic recombination

A. The HR-Alu substrates (left). Southern blot analysis of HR-Alu substrates (see also Figure S3B), to distinguish DR-Alu and Luc-Alu from IR-Alu and Luc/rev-Alu, respectively (right). B. U2OS cells carrying HR-DR-Alu or HR-IR-Alu or control HR-Luc-Alu and HR-Luc/rev-Alu were assayed for spontaneous HR of non-green cells after sorting and 2- or 3-week culturing. C–E. U2OS (HR-IR-Alu) cells were expressed with indicated shRNAs or control MKO (in C) or expressed with HA-Mre11 (WT or H129N), with endogenous Mre11 silenced (in D), or with HA-CtIP (WT or indicated mutants), with endogenous CtIP silenced (in E). Spontaneous HR was assayed after 3-week culturing. F. Top: Alignment of human CtIP and its homologues from indicated species, with the conserved NxxxR/K motif shown. Bottom: Alu-IRs-induced recombination between two lys2 alleles as described (Lobachev et al., 2002) was assayed in S. cerevisiae Δsae2 yeast strain expressing Sae2 (WT or N123A/R127A) or vector. G. Clonogenic survival assay was performed in U2OS cells expressing HA-CtIP (WT or indicated mutants), with endogenous CtIP silenced, after CPT treatment with indicated concentrations for 1hr. (See also Figure S3.) In all experiments, error bars represent standard deviation (s.d.) of three independent experiments.

Figure 4. Mre11 and CtIP are important for CFS protection

A. Metaphase spread of HCT116 cells before (Aph−) and after aphidicolin (Aph+) treatment (Aph, 0.4 µM, 24 hr), with arrows indicating chromosomal breakages. B. Overall chromosome gaps and breaks per cell in HCT116 cells expressing shRNAs against Mre11, CtIP or control MKO, before and after Aph treatment. C. FISH analysis of HCT116 cells using probes against FRA3B (top panels) or FRA16D (bottom panels), with DAPI staining (left) and FISH probe hybridization (right). Red and yellow arrows indicate broken and normal chromosomes, respectively. D–E. Frequency of CFS expression at FRA3B or FRA16D in HCT116 cells expressing Mre11, CtIP or control MKO shRNAs (in D) or expressing HA-Mre11 (WT or H129N), with endogenous Mre11 silenced (in E, left), or HA-CtIP (WT or indicated mutants), with endogenous CtIP silenced (in E, right), before and after Aph treatment. F. Proposed model for HR-mediated DSB repair and replication restart at collapsed replication forks due to structure-forming DNA (such as hairpins). See Discussion. See also Figure S4.) In all experiments, error bars represent standard deviation (s.d.) of three independent experiments.