Frequency Of Homology-directed Repair Research Articles

Efficient genome editing using modified Cas9 proteins in zebrafish.

The zebrafish (Danio rerio) is an important model organism for basic as well as applied bio-medical research. One main advantage is its genetic tractability, which was greatly enhanced by the introduction of the CRISPR/Cas method a decade ago. The generation of loss-of-function alleles via the production of small insertions or deletions in the coding sequences of genes with CRISPR/Cas systems is now routinely achieved with high efficiency. The method is based on the error prone repair of precisely targeted DNA double strand breaks by non-homologous end joining (NHEJ) in the cell nucleus. However, editing the genome with base pair precision, by homology-directed repair (HDR), is by far less efficient and therefore often requires large-scale screening of potential carriers by labour intensive genotyping. Here we confirm that the Cas9 protein variant SpRY, with relaxed PAM requirement, can be used to target some sites in the zebrafish genome. In addition, we demonstrate that the incorporation of an artificial nuclear localisation signal (aNLS) into the Cas9 protein variants not only enhances the efficiency of gene knockout but also the frequency of HDR, thereby facilitating the efficient modification of single base pairs in the genome. Our protocols provide a guide for a cost-effective generation of versatile and potent Cas9 protein variants and efficient gene editing in zebrafish.

Transient inhibition of 53BP1 increases the frequency of targeted integration in human hematopoietic stem and progenitor cells

Genome editing by homology directed repair (HDR) is leveraged to precisely modify the genome of therapeutically relevant hematopoietic stem and progenitor cells (HSPCs). Here, we present a new approach to increasing the frequency of HDR in human HSPCs by the delivery of an inhibitor of 53BP1 (named “i53”) as a recombinant peptide. We show that the use of i53 peptide effectively increases the frequency of HDR-mediated genome editing at a variety of therapeutically relevant loci in HSPCs as well as other primary human cell types. We show that incorporating the use of i53 recombinant protein allows high frequencies of HDR while lowering the amounts of AAV6 needed by 8-fold. HDR edited HSPCs were capable of long-term and bi-lineage hematopoietic reconstitution in NSG mice, suggesting that i53 recombinant protein might be safely integrated into the standard CRISPR/AAV6-mediated genome editing protocol to gain greater numbers of edited cells for transplantation of clinically meaningful cell populations.

Enhancing HR Frequency for Precise Genome Editing in Plants

Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems.

A Precise Tool to Edit Human Hematopoietic Stem Cells at High Efficiency and Decipher and Optimize the Different Double Strand Break Repair Outcomes

The CRISPR/Cas9 discovery has revolutionized precise editing of the genome. However, Cas9-induced site-specific double-strand breaks (DSB) are predominantly repaired by the ‘error-prone’ non-homologous end-joining (NHEJ)/alternate NHEJ (aNHEJ) mechanisms, with relatively low precise correction using homology-directed repair (HDR). The HDR-corrected cells can be selected with drugs/surface reporter in cell lines, induced pluripotent cells, mouse embryonic cells. However, selection of gene edited/corrected hematopoietic stem cells (HSC) is not feasible in vitro. HSC remain the most promising targets because of their unique self-renewing, expansion and differentiation potential. Assessment and optimization of editing/correction of the rare human HSC comprising 1-2% of the CD34+ hematopoietic stem and progenitor cell (HSPC) population is particularly challenging, as their selection before/after often results in insufficient cell numbers for detailed molecular analysis; and selection post-editing for clinical translation can reduce recovery/engraftment potential from increased processing. Currently, the readout of the edited HSC is by molecular analysis for NHEJ- and aNHEJ-induced insertions/deletions and HDR detection of total CD34+ cells and assessment of long term repopulating potential (LTRP) in in vivo models. Herein, we report a unique platform that can precisely quantify NHEJ, aNHEJ, HDR and random integration of the HDR donor template in the human HSC using a flow cytometry. We targeted the CD45 surface reporter (PTPRC), present on all leukocytes and HSPC, to induce a DSB in exon 2 of the PTPRC gene using CRISPR/Cas9, and an in-frame promoter-less GFP containing homology template and a downstream tNGFR expression cassette (GFP/tNGFR HDR donor). HSC and HSPC that repaired Cas9-induced DSB via NHEJ on a single allele in diploid cells lost CD45 expression by flow cytometry. Furthermore, the gRNA/Cas9 induced DSB site was designed to have a 3bp micro-homology so that DSB repaired via aNHEJ resulted in cells express CD45 in frame, but a 6bp deletion detectable by TIDE assay. Provision of the GFP/tNGFR HDR donor repair template resulted in GFP and CD45 expressing, but not tNGFR expressing cells, but if the GFP/tNGFR HDR donor integrated randomly, cells were tNGFR+. Using this system, we optimized editing of hematopoietic progenitor cell lines (K562, Kasumi cells) and EBV transformed B-lymphoblasts to >95% efficiency, and molecular analysis of total and CD45+, and CD45- and CD45+GFP+ cell populations confirmed the precision of the flow cytometry based quantification of NHEJ, aNHEJ. In fact, molecular analysis of the CD45+ cells led to the discovery that K562 cells had a high rate of aNHEJ, while this editing via aNHEJ was absent in LCL- and Kasumi- B lymphoid cells. Inhibition of the aNHEJ pathway with small molecule inhibitors/siRNA resulted in loss of the 6bp aNHEJ-mediated deletion in K562 cells. We also found that random integration in LCL, Kasumi and CD34+ cells was a rare event, but occurred with high frequency in K562 cells. Due to the rapid detection of editing events by flow cytometry, we were able to optimize different editing and cell parameters in both cord blood and mobilized peripheral blood derived CD34+ HSPC and CD34+38-90+RA- HSC populations to achieve high viability and 80-87% editing efficiency (CD45-) in HSPC and HSC, and the FACS-based results were similar to molecular analysis. The edited CD34+ HSPC, when injected into NSG mice resulted in robust human cell engraftment, with 45±10% total engraftment, and 39±16% edited cell engraftment (n=12 mice). Using this platform, we improved HDR frequency to 30% and reduced NHEJ events to 60% in hematopoietic cell lines and similar optimization of HDR in HSPC/HSC is underway. In summary, we have developed a novel platform that allows rapid quantification of gene editing by flow cytometry of human HSC at a single cell and a single allele level, in a single step; with concurrent molecular analysis that identifies different DNA repair pathways utilized by different cell types. This platform allows rapid identification of edited events in the rare HSC population, rather than bulk CD34+ HSPC. Furthermore, ability to sort the edited HSC allows precise determination of the genotoxicity of gene editing, and optimization of DSB repair pathway needed, and optimize editing parameters that result in engraftable edited HSC with LTRP. DisclosuresNo relevant conflicts of interest to declare.

A cell cycle-dependent CRISPR-Cas9 activation system based on an anti-CRISPR protein shows improved genome editing accuracy

The development of genome editing systems based on the Cas9 endonuclease has greatly facilitated gene knockouts and targeted genetic alterations. Precise editing of target genes without off-target effects is crucial to prevent adverse effects in clinical applications. Although several methods have been reported to result in less off-target effects associated with the CRISPR technology, these often exhibit lower editing efficiency. Therefore, efficient, accurate, and innocuous CRISPR technology is still required. Anti-CRISPR proteins are natural inhibitors of CRISPR-Cas systems derived from bacteriophages. Here, the anti-CRISPR protein, AcrIIA4, was fused with the N terminal region of human Cdt1 that is degraded specifically in S and G2, the phases of the cell cycle when homology-directed repair (HDR) is dominant. Co-expression of SpyCas9 and AcrIIA4-Cdt1 not only increases the frequency of HDR but also suppress off-targets effects. Thus, the combination of SpyCas9 and AcrIIA4-Cdt1 is a cell cycle-dependent Cas9 activation system for accurate and efficient genome editing.

Rational Selection of CRISPR-Cas9 Guide RNAs for Homology-Directed Genome Editing

Homology-directed repair (HDR) of a DNA break allows copying of genetic material from an exogenous DNA template and is frequently exploited in CRISPR-Cas9 genome editing. However, HDR is in competition with other DNA repair pathways, including non-homologous end joining (NHEJ) and microhomology-mediated end joining (MMEJ), and the efficiency of HDR outcomes is not predictable. Consequently, to optimize HDR editing, panels of CRISPR-Cas9 guide RNAs (gRNAs) and matched homology templates must be evaluated. We report here that CRISPR-Cas9 indel signatures can instead be used to identify gRNAs that maximize HDR outcomes. Specifically, we show that the frequency of deletions resulting from MMEJ repair, characterized as deletions greater than or equal to 3bp, better predicts HDR frequency than consideration of total indel frequency. We further demonstrate that tools that predict gRNA indel signatures can be repurposed to identify gRNAs to promote HDR. Finally, by comparing indels generated by S.aureus and S.pyogenes Cas9 targeted to the same site, we add to the growing body of data that the targeted DNA sequence is a major factor governing genome editing outcomes.

Methods Favoring Homology-Directed Repair Choice in Response to CRISPR/Cas9 Induced-Double Strand Breaks.

Precise gene editing is—or will soon be—in clinical use for several diseases, and more applications are under development. The programmable nuclease Cas9, directed by a single-guide RNA (sgRNA), can introduce double-strand breaks (DSBs) in target sites of genomic DNA, which constitutes the initial step of gene editing using this novel technology. In mammals, two pathways dominate the repair of the DSBs—nonhomologous end joining (NHEJ) and homology-directed repair (HDR)—and the outcome of gene editing mainly depends on the choice between these two repair pathways. Although HDR is attractive for its high fidelity, the choice of repair pathway is biased in a biological context. Mammalian cells preferentially employ NHEJ over HDR through several mechanisms: NHEJ is active throughout the cell cycle, whereas HDR is restricted to S/G2 phases; NHEJ is faster than HDR; and NHEJ suppresses the HDR process. This suggests that definitive control of outcome of the programmed DNA lesioning could be achieved through manipulating the choice of cellular repair pathway. In this review, we summarize the DSB repair pathways, the mechanisms involved in choice selection based on DNA resection, and make progress in the research investigating strategies that favor Cas9-mediated HDR based on the manipulation of repair pathway choice to increase the frequency of HDR in mammalian cells. The remaining problems in improving HDR efficiency are also discussed. This review should facilitate the development of CRISPR/Cas9 technology to achieve more precise gene editing.

Enhanced homologous recombination by the modulation of targeting vector ends

The field of genome editing was founded on the establishment of methods, such as the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR/Cas) system, used to target DNA double-strand breaks (DSBs). However, the efficiency of genome editing also largely depends on the endogenous cellular repair machinery. Here, we report that the specific modulation of targeting vectors to provide 3′ overhangs at both ends increased the efficiency of homology-directed repair (HDR) in embryonic stem cells. We applied the modulated targeting vectors to produce homologous recombinant mice directly by pronuclear injection, but the frequency of HDR was low. Furthermore, we combined our method with the CRISPR/Cas9 system, resulting in a significant increase in HDR frequency. Thus, our HDR-based method, enhanced homologous recombination for genome targeting (eHOT), is a new and powerful method for genome engineering.

The road less traveled: strategies to enhance the frequency of homology-directed repair (HDR) for increased efficiency of CRISPR/Cas-mediated transgenesis

Non-homologous end joining (NHEJ), and to a lesser extent, the error-free pathway known as homology-directed repair (HDR) are cellular mechanisms for recovery from double-strand DNA breaks (DSB) induced by RNA-guided programmable nuclease CRISPR/Cas. Since NHEJ is equivalent to using a duck tape to stick two pieces of metals together, the outcome of this repair mechanism is prone to error. Any out-of-frame mutations or premature stop codons resulting from NHEJ repair mechanism are extremely handy for loss-of-function studies. Substitution of a mutation on the genome with the correct exogenous repair DNA requires coordination via an error-free HDR, for targeted transgenesis. However, several practical limitations exist in harnessing the potential of HDR to replace a faulty mutation for therapeutic purposes in all cell types and more so in somatic cells. In germ cells after the DSB, copying occurs from the homologous chromosome, which increases the chances of incorporation of exogenous DNA with some degree of homology into the genome compared with somatic cells where copying from the identical sister chromatid is always preferred. This review summarizes several strategies that have been implemented to increase the frequency of HDR with a focus on somatic cells. It also highlights the limitations of this technology in gene therapy and suggests specific solutions to circumvent those barriers.

Enhancing CRISPR/Cas9-mediated homology-directed repair in mammalian cells by expressing Saccharomyces cerevisiae Rad52.

Precise genome editing with desired point mutations can be generated by CRISPR/Cas9-mediated homology-directed repair (HDR) and is of great significance for gene function study, gene therapy and animal breeding. However, HDR efficiency is inherently low and improvements are necessitated. Herein, we determined that the HDR efficiency could be enhanced by expressing Rad52, a gene that is involved in the homologous recombination process. Both the Rad52 co-expression and Rad52-Cas9 fusion strategies yielded approximately 3-fold increase in HDR during the surrogate reporter assays in human HEK293T cells, as well as in the genome editing assays. Moreover, the enhancement effects of the Rad52-Cas9 fusion on HDR mediated by different (plasmid, PCR and ssDNA) donor templates were confirmed. We found that the HDR efficiency could be significantly improved to about 40% by the combined usage of Rad52 and Scr7. In addition, we also applied the fusion strategy for modifying the IGF2 gene of porcine PK15 cells, which further demonstrated a 2.2-fold increase in HDR frequency. In conclusion, our data suggests that Rad52-Cas9 fusion is a good option for enhancing CRISPR/Cas9-mediated HDR, which may be of use in future studies involving precise genome editing.

Optimizing the DNA Donor Template for Homology-Directed Repair of Double-Strand Breaks.

The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated proteins) technology enables rapid and precise genome editing at any desired genomic position in almost all cells and organisms. In this study, we analyzed the impact of different repair templates on the frequency of homology-directed repair (HDR) and non-homologous end joining (NHEJ). We used a stable HEK293 cell line expressing the traffic light reporter (TLR-3) system to quantify HDR and NHEJ events following transfection with Cas9, eight different guide RNAs, and a 1,000 bp donor template generated either as circular plasmid, as linearized plasmid with long 3′ or 5′ backbone overhang, or as PCR product. The sequence to be corrected was either centrally located (RS55), with a shorter 5′ homologous region (RS37), or with a shorter 3′ homologous region (RS73). Guide RNAs targeting the transcriptionally active strand (T5, T7) showed significantly higher NHEJ frequencies compared with guide RNAs targeting the transcriptionally inactive strand. HDR activity was highest when using the linearized plasmid with the short 5′ backbone overhang and the RS37 design. The results demonstrate the importance of the design of the guide RNA and template DNA on the frequency of DNA repair events and, ultimately, on the outcome of treatment approaches using HDR.

Integration-defective lentiviral vector mediates efficient gene editing through homology-directed repair in human embryonic stem cells.

Human embryonic stem cells (hESCs) are used as platforms for disease study, drug screening and cell-based therapy. To facilitate these applications, it is frequently necessary to genetically manipulate the hESC genome. Gene editing with engineered nucleases enables site-specific genetic modification of the human genome through homology-directed repair (HDR). However, the frequency of HDR remains low in hESCs. We combined efficient expression of engineered nucleases and integration-defective lentiviral vector (IDLV) transduction for donor template delivery to mediate HDR in hESC line WA09. This strategy led to highly efficient HDR with more than 80% of the selected WA09 clones harboring the transgene inserted at the targeted genomic locus. However, certain portions of the HDR clones contained the concatemeric IDLV genomic structure at the target site, probably resulted from recombination of the IDLV genomic input before HDR with the target. We found that the integrase protein of IDLV mediated the highly efficient HDR through the recruitment of a cellular protein, LEDGF/p75. This study demonstrates that IDLV-mediated HDR is a powerful and broadly applicable technology to carry out site-specific gene modification in hESCs.

343. Repair of the Sickle-Cell Disease Mutation in Human Stem Cells Using CRISPR/Cas9 and Single-Stranded Oligodeoxynucleotides

Sickle cell disease is a hereditary anemia caused by a homozygous point mutation in the β-globin gene resulting in a glutamic acid to valine change at position 6 in the globin β-chain. Association of the mutated β-chain with α-chain results in the formation of hemoglobin S, which polymerizes intracellularly thus causing erythrocyte sickling. One promising therapy relies on the transplantation of autologous hematopoietic stem cells transduced with a lentiviral vector encoding a wild-type or mutant β-globin gene. However, one of the main concerns associated with the use of recombinant retroviruses to deliver therapeutic genes in stem cells is the risk of insertional mutagenesis following semi-random retroviral DNA integration. Alternatively, gene repair by homology-directed repair (HDR) is recognized as a potentially less genotoxic approach to repair mutations. Although HDR is intrinsically inefficient in human cells, enzymes that create specific DNA double-strand breaks can efficiently increase HDR frequency. Our long-term goal is to develop an efficient HDR approach to repair the sickle cell anemia mutation in stem cells. We have previously evaluated meganucleases and TALEN-based approaches to edit the β-globin gene in a human induced pluripotent stem (iPS) cell line carrying a homozygous sickle cell mutation. Here, we investigate the use of CRISPR/Cas9 system in combination with single-stranded oligodeoxynucleotides (ssODNs) to repair the sickle mutation in the above mentioned sickle iPS line (sciPS). Based on gene alignment analysis with the highly homologous Δ-globin gene, we have designed two β-globin-gene-specific CRISPR guide RNAs (gRNAs). Using these gRNAs, along with Cas9 and ssODNs, we show repair of the sickle cell mutation in sciPS cells. In the short term, we expect to translate these genome editing technologies to repair the sickle mutation in patient-specific cells, such as CD34+ hematopoietic cells, an approach that holds promise for future autologous stem cell therapies.

Correct End Use during End Joining of Multiple Chromosomal Double Strand Breaks Is Influenced by Repair Protein RAD50, DNA-dependent Protein Kinase DNA-PKcs, and Transcription Context

During repair of multiple chromosomal double strand breaks (DSBs), matching the correct DSB ends is essential to limit rearrangements. To investigate the maintenance of correct end use, we examined repair of two tandem noncohesive DSBs generated by endonuclease I-SceI and the 3' nonprocessive exonuclease Trex2, which can be expressed as an I-SceI-Trex2 fusion. We examined end joining (EJ) repair that maintains correct ends (proximal-EJ) versus using incorrect ends (distal-EJ), which provides a relative measure of incorrect end use (distal end use). Previous studies showed that ATM is important to limit distal end use. Here we show that DNA-PKcs kinase activity and RAD50 are also important to limit distal end use, but that H2AX is dispensable. In contrast, we find that ATM, DNA-PKcs, and RAD50 have distinct effects on repair events requiring end processing. Furthermore, we developed reporters to examine the effects of the transcription context on DSB repair, using an inducible promoter. We find that a DSB downstream from an active promoter shows a higher frequency of distal end use, and a greater reliance on ATM for limiting incorrect end use. Conversely, DSB transcription context does not affect end processing during EJ, the frequency of homology-directed repair, or the role of RAD50 and DNA-PKcs in limiting distal end use. We suggest that RAD50, DNA-PKcs kinase activity, and transcription context are each important to limit incorrect end use during EJ repair of multiple DSBs, but that these factors and conditions have distinct roles during repair events requiring end processing.

BCR-ABL Induces Error-Prone Single Strand Annealing in Transformed Cells.

Chronic myelogenous leukemia (CML) is a hematopoietic stem cell disorder, caused by the BCR-ABL tyrosine kinase oncogene. BCR-ABL kinase activity is required for all aspects of transformation, including abnormal proliferation and neoplastic expansion of stem cells, activation of signaling pathways and genomic instability. We have recently shown that BCR-ABL kinase activity also causes elevated intracellular levels of reactive oxygen species (ROS). These chronically elevated ROS levels have been implicated in the induction of DNA double-strand breaks (DSB) and therapy-related drug resistance, mainly through low- fidelity homology-directed repair (HDR) of DNA lesions. We have utilized GFP-based reporters in BCR-ABL transformed cells to measure both HDR and single-strand annealing (SSA), a mutagenic pathway of homologous repair between repetitive sequences. Repair rates of a single DSB by each of these pathways was measured in BCR-ABL expressing BaF3 cells (BaF3.p210), which have previously been shown to be an excellent system to model the induction of imatinib resistant mutations. We found that inhibition of BCR-ABL kinase activity by imatinib decreased the frequency of SSA by 73 ± 2% (n=3) and increased the frequency of HDR by 70 ± 11% (n=3) in BaF3.p210, compared to untreated cells. Treatment with imatinib did not affect HDR or SSA in BaF3 cells that do not express BCR-ABL. We also determined the fidelity of both SSA and HDR in our model system using clonal populations that stably express the repaired GFP+ reporters (n=20). As expected, sequencing of GFP+ repair products from cells containing the SSA reporter confirmed the expected sequence deletions, consistent with an error-prone mechanism. In contrast, sequencing of GFP+ repair products from the HDR reporter indicated a high-fidelity repair mechanism, without any mutations. It should be noted that this reporter assay does not account for potentially imprecise HDR, leading to a non-functional GFP. Nevertheless, point mutations at the previously reported rate were not detected. Thus, altered HDR fidelity may not be a universal mechanism for the induction of point mutations by BCR-ABL. Our data suggests a unique and alternative pathway, whereby BCR-ABL alters the balance between the SSA and HDR pathways. Moreover, in the presence of interleukin-3 at a concentration that supports not only viability but also cell growth (1ng/ml), imatinib was ineffective at protecting cells from error-prone SSA. In vivo, stromal cells may provide these additional growth signals. Our in vitro data show that stromal cell conditioned medium is not only sufficient to support growth and viability of CML cell lines in the presence of imatinib, but it can also lead to elevated levels of ROS. An abnormal increase in ROS is sufficient by itself to cause genomic mutations (transitions and/or transversions) as a result of single strand oxidative DNA lesions, even in the absence of altered DSB or single strand lesion repair mechanisms. Thus, therapy-related resistance and additional genomic abnormalities may not only be a result of BCR-ABL dependent ROS induction but may also occur within the stromal cell microenvironment through ROS induction by growth factors.

Alternative Pathways for the Repair of RAG-Induced DNA Breaks

RAG1 and RAG2 cleave DNA to generate blunt signal ends and hairpin coding ends at antigen receptor loci in lymphoid cells. During V(D)J recombination, repair of these RAG-generated double-strand breaks (DSBs) by the nonhomologous end-joining (NHEJ) pathway contributes substantially to the antigen receptor diversity necessary for immune system function, although recent evidence also supports the ability of RAG-generated breaks to undergo homology-directed repair (HDR). We have determined that RAG-generated chromosomal breaks can be repaired by pathways other than NHEJ in mouse embryonic stem (ES) cells, although repair by these pathways occurs at a significantly lower frequency than NHEJ. HDR frequency was estimated to be >or=40-fold lower than NHEJ frequency for both coding end and signal end reporters. Repair by single-strand annealing was estimated to occur at a comparable or lower frequency than HDR. As expected, V(D)J recombination was substantially impaired in cells deficient for the NHEJ components Ku70, XRCC4, and DNA-PKcs. Concomitant with decreased NHEJ, RAG-induced HDR was increased in each of the mutants, including cells lacking DNA-PKcs, which has been implicated in hairpin opening. HDR was increased to the largest extent in Ku70-/- cells, implicating the Ku70/80 DNA end-binding protein in regulating pathway choice. Thus, RAG-generated DSBs are typically repaired by the NHEJ pathway in ES cells, but in the absence of NHEJ components, a substantial fraction of breaks can be efficiently channeled into alternative pathways in these cells.

Ku DNA end-binding protein modulates homologous repair of double-strand breaks in mammalian cells.

Chromosomal double-strand breaks (DSBs) in mammalian cells are repaired by either homology-directed repair (HDR), using a homologous sequence as a repair template, or nonhomologous end-joining (NHEJ), which often involves sequence alterations at the DSB site. To characterize the interrelationship of these two pathways, we analyzed HDR of a DSB in cells deficient for NHEJ components. We find that the HDR frequency is enhanced in Ku70(-/-), XRCC4(-/-), and DNA-PKcs(-/-) cells, with the increase being particularly striking in Ku70(-/-) cells. Neither sister-chromatid exchange nor gene-targeting frequencies show a dependence on these NHEJ proteins. A Ku-modulated two-ended versus one-ended chromosome break model is presented to explain these results.