Nonhomologous end-joining (NHEJ) is a major DNA double-strand break (DSB) repair pathway. NHEJ is initiated through DSB recognition by the DNA end-binding heterodimer, Ku, while end-joining is accomplished by the XRCC4-DNA ligase IV (X4L4) complex. This thesis reports that APLF (Aprataxin and Polynucleotide kinase-Like Factor), an endo/exonuclease with a forkhead-associated (FHA) domain and two unique zinc fingers (ZF), interacts with both Ku and X4L4. The APLF-X4L4 interaction is FHA- and phospho-dependent, and is mediated by CK2 phosphorylation of XRCC4 in vitro. APLF binds Ku independently of the FHA and ZF domains, and complexes with Ku at DNA ends. APLF undergoes ionizing radiation induced ATM-dependent hyperphosphorylation and ATM phosphorylates APLF in vitro. Downregulation of APLF is associated with defective NHEJ and impaired DSB repair kinetics. These results suggest that APLF is an ATM target that is involved in NHEJ and facilitates DSB repair, likely via interactions with Ku and X4L4.

Nonhomologous end-joining (NHEJ) is a major DNA double-strand break (DSB) repair pathway. NHEJ is initiated through DSB recognition by the DNA end-binding heterodimer, Ku, while end-joining is accomplished by the XRCC4-DNA ligase IV (X4L4) complex. This thesis reports that APLF (Aprataxin and Polynucleotide kinase-Like Factor), an endo/exonuclease with a forkhead-associated (FHA) domain and two unique zinc fingers (ZF), interacts with both Ku and X4L4. The APLF-X4L4 interaction is FHA- and phospho-dependent, and is mediated by CK2 phosphorylation of XRCC4 in vitro. APLF binds Ku independently of the FHA and ZF domains, and complexes with Ku at DNA ends. APLF undergoes ionizing radiation induced ATM-dependent hyperphosphorylation and ATM phosphorylates APLF in vitro. Downregulation of APLF is associated with defective NHEJ and impaired DSB repair kinetics. These results suggest that APLF is an ATM target that is involved in NHEJ and facilitates DSB repair, likely via interactions with Ku and X4L4.

Indiana University-Purdue University Indianapolis (IUPUI) / Metnase is a novel bifunctional protein that contains a SET domain and a transposase domain. Metnase contains sequence-specific DNA binding activity and sequence non-specific DNA cleavage activity, as well as enhances genomic integration of exogenous DNA. Although Metnase can bind specifically to DNA sequences containing a core Terminal Inverted Repeat sequence, this does not explain how the protein could function at sites of DNA damage. Through immunoprecipitation and gel shift assays, I have identified the Pso4 protein as a binding partner of Metnase both in vitro and in vivo. Pso4 is essential for cell survival in yeast, and cells containing a mutation in Pso4 show increased sensitivity to DNA cross-linking agents. In addition, the protein has sequence-independent DNA binding activity, favoring double-stranded DNA over single-stranded DNA. I demonstrated that the two proteins form a 1:1 stochiometric complex, and once formed, Metnase can localize to DNA damage foci as shown by knockdown of Pso4 protein using in vivo immunofluorescence. In conclusion, this shows that Metnase plays an indispensable role in DNA end joining, possibly through its cleavage activity and association with DNA Ligase IV.

The final publication is available at http://dx.doi.org/10.1073/pnas.1402391111. Ashraf S. Yousif, Andre Stanlie, Samiran Mondal, Tasuku Honjo, and Nasim A. Begum. Differential regulation of S-region hypermutation and class-switch recombination by noncanonical functions of uracil DNA glycosylase. PNAS 2014 111 (11) E1016-E1024; published ahead of print March 3, 2014. / 京都大学 / 0048 / 新制・課程博士 / 博士(医科学) / 甲第18464号 / 医科博第55号 / 新制||医科||4(附属図書館) / 31342 / 京都大学大学院医学研究科医科学専攻 / (主査)教授 清水 章, 教授 萩原 正敏, 教授 武田 俊一 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

<p>If not efficiently repaired, DNA double-stranded breaks can result in cell death. A major contributor to the repair of this DNA damage is the non-homologous end joining pathway (NHEJ) which depends on the proteins: X-ray cross complementing protein 4 (XRCC4) and XLF. These proteins form a complex that can bridge DNA substrates <em>in vitro. </em>Analysis of these proteins has demonstrated that the C-terminal region of XRCC4 is necessary for this bridging function. However, this region is also critical for both tetramerization and DNA binding abilities of XRCC4, making the interpretation of XRCC4's role in the DNA-bridging unclear. Here, we intend to further characterize the tetramerization of XRCC4 and find a functionally independent mutant. Our studies suggest that regions in the N-terminus of XRCC4 may be important for the tetramerization of the protein but not for its DNA binding ability. These mutants were also analyzed by circular dichroism and mobility shift assays to verify for the integrity of their secondary structure composition and show that they are able to interact with its known binding partner, DNA Ligase IV. Additionally, we have shown that the XRCC4:XLF complex as well as XLF alone are able to interact with DNA substrates as short as 36 base pairs. Taking the data together, we expect to be able to construct a structural model for the XRCC4:XLF complex with DNA and obtain a better understanding on the role of XRCC4’s tetramerization in the NHEJ pathway. As deficiency of XRCC4 has been implicated with tumourigenesis and immunodeficiency, understanding its role will be helpful for the development of treatments for such complications.</p> / Master of Science (MSc)

La polymicrogyrie est un type de malformation corticale dans laquelle on retrouve un excès de gyrations et une surface corticale irrégulière. La polymicrogyrie peut être provoquée par des causes environnementales ou génétiques. C'est ces dernières auxquelles nous nous sommes intéressés et que nous avons étudié afin d'approfondir nos connaissances sur les bases génétiques de la polymicrogyrie. Nous traitons trois projets qui se situent à trois niveaux de recherche différents : étude d'un gène dont la pathogénicité est établie pour le premier, étude de gènes candidats pour le deuxième et recherche de nouveaux gènes candidats pour le troisième. Dans le premier projet, nous avons réussi à prouver l'implication du gène NHEJ1 dans le développement du cortex cérébral. Nous avons montré, grâce à l'ARN interférence in utero que la dérégulation de Nhej1 chez le rat perturbe la migration neuronale, déclenche un phénomène de mort neuronale massive et désorganise les couches corticales. Dans le deuxième projet, après une étude par hybridation génomique comparative sur puce d'ADN, nous avons identifié une duplication dans la région 1p36 chez un patient présentant une polymicrogyrie bilatérale. Nous avons montré que cette duplication casse le gène ENO1 et diminue son expression. L'expression spatio-temporelle d'ENO1 est en accord avec un rôle de celui-ci pendant le développement cérébral. Nous avons également montré que la diminution de l'expression du gène Eno1 perturbe la migration neuronale radiale. / Polymicrogyria is a cortical malformation characterized by excessive gyration and an irregular cortex surface. Environmental and genetic causes can be responsible for this disorder. Our principal aim was to better understand the genetic basis of polymicrogyria. Three projects were conducted. The first focused on the NHEJ1 gene. Using RNA interference and in utero electroporation, we showed that deregulation of NHEJ1 disrupts neuronal migration, triggers massive neuronal cell death and disorganizes the cortical layers. In the second project, we identified by comparative genomic hybridization microarray, a duplication in the 1p36 region in a patient with bilateral polymicrogyria. We have shown that this duplication breaks the ENO1 gene and reduces its expression. The spatio-temporal expression of ENO1 and the fact that its deregulation disrupts neuronal migration indicates that ENO1 is a good candidate gene for cortical development. Finally, in the third project, we identified by exome sequencing of familial cases of bilateral polymicrogyria, one coding variation in the GABRA3 gene. Our work allowed us to generate new knowledge for several candidate genes for polymicrogyria.

O DNA está constantemente exposto a danos causados tanto por agentes endógenos quanto exógenos. Estes podem causar diferentes tipos de lesões incluindo modificações de bases e do açúcar, além de quebras de fitas simples ou duplas. As quebras de duplas fitas, quando comparadas às demais, constituem as mais citotóxicas e podem resultar em deleções no DNA e instabilidade genética. Deleções no DNA mitocondrial (mtDNA) causam diversas doenças e estão envolvidas no processo de envelhecimento. No núcleo, as quebras de duplas fitas no DNA podem ser reparadas por recombinação homóloga (HR), ligação de pontas não homólogas (NHEJ) e anelamento de fita simples (SSA). No entanto, em mitocôndrias de células de mamíferos, o reparo de quebras de duplas fitas ainda não foi completamente caracterizado. Experimentos in vitro usando extratos mitocondriais de células de roedores mostraram que estes são capazes de reparar essas quebras, no entanto pouco é sabido sobre quais proteínas são responsáveis por cada etapa de reparo, bem como sua implicação na manutenção da integridade do genoma mitocondrial. Sendo assim, nesse trabalho investigamos a localização e função mitocondrial das proteínas ATM, Rad51, Rad52, Ku70/86 e DNA-PKCs, que são sabidamente envolvidas em reparo de quebras de duplas fitas no núcleo. Para identificar essas proteínas em mitocôndrias de células de mamíferos, mitocôndrias foram isoladas a partir de células da linhagem HEK293T, usando centrifugação diferencial seguida por gradiente de Percoll. Para as proteínas de recombinação homóloga, ATM e Rad51, imunodetectamos isoformas semelhantes em todos os compartimentos celulares. Já para a proteína Rad52 o mesmo anticorpo imunodetectou duas bandas distintas na mitocôndria ao passo que no núcleo foram quatro. Além disso, verificamos que baixos níveis de proteína Rad52, induzidos pela expressão de shRNA (short hairping RNA) específico, resultam em diminuição do número de cópias de mtDNA bem como acúmulo de deleções no genoma mitocondrial. Para as proteínas de NHEJ, DNA-PKCs e a subunidade Ku70, identificamos isoformas semelhantes em todos os compartimentos celulares. Já para a subunidade 86 do heterodímero Ku70/86 o anticorpo detectou, somente em mitocôndrias, uma banda menor de 50 kDa, a qual difere na região N-terminal da subunidade detectada no núcleo (86 KDa). Experimentos de co-imunprecitação de proteínas mostraram que essa isoforma menor compõe o heterodímero mitocondrial juntamente com a subunidade 70 (mtKu70/50) e que esse interage com DNA ligase III mitocondrial. Nossos resultados também mostraram que a estabilidade proteica de mtKu70/50 é regulada por ATM. Tratamento das células com peróxido de hidrogênio, que induz quebras de duplas fitas, aumentou a associação do heterodímero mtKu70/50 com o mtDNA, de forma independente de aumento da concentração proteica intra-mitocondrial. Já a diminuição dos níveis proteicos de Ku, induzida através de shRNA, resultou em diminuição do número de cópias de mtDNA e acumulo de danos nesse genoma. Extratos mitocondriais de células knockdown para Ku apresentaram menor atividade de reparo NHEJ em um ensaio in vitro, sugerindo que o acúmulo de danos nestas células é provavelmente devido a deficiências na via de NHEJ. Em conjunto, nossos dados sugerem que tanto HR quanto NHEJ operam em mitocôndrias. Além disso, a via de NHEJ mitocondrial utiliza o heterodímero mitocondrial Ku70/50 o qual está envolvido na manutenção do mtDNA. Ademais, nossos resultados mostram uma grande conservação molecular e funcional entre as vias de reparo de NHEJ e HR no núcleo e na mitocôndria, o que reforça sua importância para a manutenção da estabilidade genômica mitocondrial e, provavelmente a função mitocondrial. / DNA is constantly exposed to damaging agents from both endogenous and exogenous sources. These can cause different types of DNA lesions that include base and sugar modifications and single and double strand breaks. DNA doublestrand breaks (DSBs) are among the most cytotoxic DNA lesions, which can result in deletions and genetic instability. Deletions in the mitochondrial DNA (mtDNA) cause numerous human diseases and drive normal aging. DSBs in the nuclear DNA are repaired by non-homologous DNA end joining (NHEJ), homologous recombination (HR) or Single Strand Annealing (SSA). Yet, repair of DSBs in mammalian mitochondria has not been fully characterized. Mitochondrial extracts from rodent cells are proficient in ligating DNA ends in vitro, but little is known about which proteins are responsible for each enzymatic step and its implication in mitochondrial genome maintenance. Thus, we investigated mitochondrial localization and function of DSBR (double strand break repair) proteins ATM, Rad51, Rad52, the Ku70/86 heterodimer and DNA-PKCs.To identify DSBR proteins in mammalian mitochondria, highly purified mitochondria from HEK293T cells were isolated using differential centrifugation followed by Percoll gradient. For HR proteins, we detected similar isoforms for ATM and Rad51 proteins in all cellular compartments. Two mitochondriaspecific isoforms of Rad52 were detected, while the same antibody detected four isoforms in the nucleus. In addition, lower Rad52 protein levels, induced by specific shRNA expression, result in decreased mtDNA copy number and accumulation of deleted mitochondrial genomes. For NHEJ proteins, similar isoforms of DNA-PKcs and the Ku70 subunit were detected in all cellular compartments. On the other hand, antibodies against the Ku86 subunit detected a smaller band in mitochondrial extracts (50 KDa), lacking the N-terminal region of the canonical isoform detected in the nucleus (86 KDa). The mitochondrial Ku70/50 heterodimer interacts with mitochondrial DNA ligase III, suggesting a role in DSBR. Moreover, stability of the mtKu heterodimer is regulated by ATM. Hydrogen peroxide treatment, which induces DSBs, increases mtKu70/50 association with the mtDNA and cells with reduced Ku levels, also induced by shRNA transfection, have lower mtDNA copy number and accumulate mtDNA damage. Moreover, mitochondrial extracts from Ku knockdown cells show lower NHEJ repair activity in an in vitro assay, suggesting that damage accumulation in these cells is likely due to deficiencies in NHEJ. Together, our data suggest that both HR and NHEJ operate in mitochondria. Also, mtNHEJ requires the Ku heterodimer and is involved in mtDNA maintenance. Moreover, our results indicate that there is a significant molecular and functional conservation between NHEJ and HR repair pathways in the nucleus and in mitochondria, which reinforces their importance for maintenance of mitochondrial genomic stability and, likely mitochondrial function.

Les translocations chromosomiques qui consistent en l’échange de morceaux de chromosomes sont une des caractéristiques génétiques de nombreux cancers. Les séquences des jonctions des chromosomes transloqués chez les patients correspondent à une réparation par NHEJ. Nous avons étudié le rôle du complexe de ligation XRCC4/LigaseIV du C-NHEJ dans la formation de ces réarrangements chromosomiques dans les cellules humaines. Nous avons utilisé différentes nucléases artificielles (ZFN, TALEN, et CRISPR/Cas9) afin d'introduire deux CDB sur deux chromosomes et nous avons ainsi réussi à générer différentes translocations. Des lignées sauvages et mutantes pour ce complexe de ligation ont été utilisées et la fréquence formation de translocations a été quantifiée par PCR. Nous avons pu observer que celle-ci est souvent diminuée dans les différentes lignées mutantes. Les jonctions des translocations obtenues par séquençage sont modifiées dans des cellules déficientes pour ce complexe. En effet, elles présentent de longues délétions et un biais d’utilisation de microhomologies, indiquant l’utilisation d’un mécanisme alt-NHEJ. Une altération de cette voie dans les cellules humaines n’affecte d’ailleurs pas la formation de ces réarrangements chromosomiques. Ainsi, contrairement aux cellules de souris, les translocations dans les cellules humaines sont générées par le C-NHEJ. / Chromosomal translocations involve the exchange of chromosome pieces and are often associated with oncogenesis. It has been shown that breakpoint junctions of translocated chromosomes found in patients are typical of a repair by NHEJ. Here we investigated the specific role of XRCC4/LigaseIV, the ligation complex of C-NHEJ, on chromosomal translocation formation in human cells. Using different nucleases (ZFN, TALEN, et CRISPR/Cas9) targeting two chromosomes, we studied the induction of translocation in wt and KO human cells, expressing or not the XRCC4/LigaseIV complex. We found that translocation frequency was mostly reduced in XRCC4/LigaseIV deficient cells when we quantified the induction of translocation by PCR. In addition, we analyzed the breakpoint junctions by sequencing. Strikingly, we found that junctions of translocations show large deletions, and a bias towards the use of longer microhomologies only in XRCC4/LigaseIV KO cells, signature of the alt-NHEJ activity. In contrast, translocation formation was not affected in alt-NHEJ deficient cells. Thus conflicting with results obtained in rodent cells where alt-NHEJ promotes translocation formation, translocations in human cells are generated by the C-NHEJ.

O DNA está constantemente exposto a danos causados tanto por agentes endógenos quanto exógenos. Estes podem causar diferentes tipos de lesões incluindo modificações de bases e do açúcar, além de quebras de fitas simples ou duplas. As quebras de duplas fitas, quando comparadas às demais, constituem as mais citotóxicas e podem resultar em deleções no DNA e instabilidade genética. Deleções no DNA mitocondrial (mtDNA) causam diversas doenças e estão envolvidas no processo de envelhecimento. No núcleo, as quebras de duplas fitas no DNA podem ser reparadas por recombinação homóloga (HR), ligação de pontas não homólogas (NHEJ) e anelamento de fita simples (SSA). No entanto, em mitocôndrias de células de mamíferos, o reparo de quebras de duplas fitas ainda não foi completamente caracterizado. Experimentos in vitro usando extratos mitocondriais de células de roedores mostraram que estes são capazes de reparar essas quebras, no entanto pouco é sabido sobre quais proteínas são responsáveis por cada etapa de reparo, bem como sua implicação na manutenção da integridade do genoma mitocondrial. Sendo assim, nesse trabalho investigamos a localização e função mitocondrial das proteínas ATM, Rad51, Rad52, Ku70/86 e DNA-PKCs, que são sabidamente envolvidas em reparo de quebras de duplas fitas no núcleo. Para identificar essas proteínas em mitocôndrias de células de mamíferos, mitocôndrias foram isoladas a partir de células da linhagem HEK293T, usando centrifugação diferencial seguida por gradiente de Percoll. Para as proteínas de recombinação homóloga, ATM e Rad51, imunodetectamos isoformas semelhantes em todos os compartimentos celulares. Já para a proteína Rad52 o mesmo anticorpo imunodetectou duas bandas distintas na mitocôndria ao passo que no núcleo foram quatro. Além disso, verificamos que baixos níveis de proteína Rad52, induzidos pela expressão de shRNA (short hairping RNA) específico, resultam em diminuição do número de cópias de mtDNA bem como acúmulo de deleções no genoma mitocondrial. Para as proteínas de NHEJ, DNA-PKCs e a subunidade Ku70, identificamos isoformas semelhantes em todos os compartimentos celulares. Já para a subunidade 86 do heterodímero Ku70/86 o anticorpo detectou, somente em mitocôndrias, uma banda menor de 50 kDa, a qual difere na região N-terminal da subunidade detectada no núcleo (86 KDa). Experimentos de co-imunprecitação de proteínas mostraram que essa isoforma menor compõe o heterodímero mitocondrial juntamente com a subunidade 70 (mtKu70/50) e que esse interage com DNA ligase III mitocondrial. Nossos resultados também mostraram que a estabilidade proteica de mtKu70/50 é regulada por ATM. Tratamento das células com peróxido de hidrogênio, que induz quebras de duplas fitas, aumentou a associação do heterodímero mtKu70/50 com o mtDNA, de forma independente de aumento da concentração proteica intra-mitocondrial. Já a diminuição dos níveis proteicos de Ku, induzida através de shRNA, resultou em diminuição do número de cópias de mtDNA e acumulo de danos nesse genoma. Extratos mitocondriais de células knockdown para Ku apresentaram menor atividade de reparo NHEJ em um ensaio in vitro, sugerindo que o acúmulo de danos nestas células é provavelmente devido a deficiências na via de NHEJ. Em conjunto, nossos dados sugerem que tanto HR quanto NHEJ operam em mitocôndrias. Além disso, a via de NHEJ mitocondrial utiliza o heterodímero mitocondrial Ku70/50 o qual está envolvido na manutenção do mtDNA. Ademais, nossos resultados mostram uma grande conservação molecular e funcional entre as vias de reparo de NHEJ e HR no núcleo e na mitocôndria, o que reforça sua importância para a manutenção da estabilidade genômica mitocondrial e, provavelmente a função mitocondrial. / DNA is constantly exposed to damaging agents from both endogenous and exogenous sources. These can cause different types of DNA lesions that include base and sugar modifications and single and double strand breaks. DNA doublestrand breaks (DSBs) are among the most cytotoxic DNA lesions, which can result in deletions and genetic instability. Deletions in the mitochondrial DNA (mtDNA) cause numerous human diseases and drive normal aging. DSBs in the nuclear DNA are repaired by non-homologous DNA end joining (NHEJ), homologous recombination (HR) or Single Strand Annealing (SSA). Yet, repair of DSBs in mammalian mitochondria has not been fully characterized. Mitochondrial extracts from rodent cells are proficient in ligating DNA ends in vitro, but little is known about which proteins are responsible for each enzymatic step and its implication in mitochondrial genome maintenance. Thus, we investigated mitochondrial localization and function of DSBR (double strand break repair) proteins ATM, Rad51, Rad52, the Ku70/86 heterodimer and DNA-PKCs.To identify DSBR proteins in mammalian mitochondria, highly purified mitochondria from HEK293T cells were isolated using differential centrifugation followed by Percoll gradient. For HR proteins, we detected similar isoforms for ATM and Rad51 proteins in all cellular compartments. Two mitochondriaspecific isoforms of Rad52 were detected, while the same antibody detected four isoforms in the nucleus. In addition, lower Rad52 protein levels, induced by specific shRNA expression, result in decreased mtDNA copy number and accumulation of deleted mitochondrial genomes. For NHEJ proteins, similar isoforms of DNA-PKcs and the Ku70 subunit were detected in all cellular compartments. On the other hand, antibodies against the Ku86 subunit detected a smaller band in mitochondrial extracts (50 KDa), lacking the N-terminal region of the canonical isoform detected in the nucleus (86 KDa). The mitochondrial Ku70/50 heterodimer interacts with mitochondrial DNA ligase III, suggesting a role in DSBR. Moreover, stability of the mtKu heterodimer is regulated by ATM. Hydrogen peroxide treatment, which induces DSBs, increases mtKu70/50 association with the mtDNA and cells with reduced Ku levels, also induced by shRNA transfection, have lower mtDNA copy number and accumulate mtDNA damage. Moreover, mitochondrial extracts from Ku knockdown cells show lower NHEJ repair activity in an in vitro assay, suggesting that damage accumulation in these cells is likely due to deficiencies in NHEJ. Together, our data suggest that both HR and NHEJ operate in mitochondria. Also, mtNHEJ requires the Ku heterodimer and is involved in mtDNA maintenance. Moreover, our results indicate that there is a significant molecular and functional conservation between NHEJ and HR repair pathways in the nucleus and in mitochondria, which reinforces their importance for maintenance of mitochondrial genomic stability and, likely mitochondrial function.

Au cours de la réplication, la réparation des cassures double brin (CDB) par recombinaison homologue (RH), basée sur la synthèse d’ADN à partir de la chromatide sœur, permet le maintien de la stabilité du génome. La religature d’extrémités (EJ) éloignées de CDB peut quant à elle générer des réarrangements menaçant son intégrité. Nous avons étudié le mécanisme de réparation par EJ en fonction de la distance séparant deux cassures double brin. En utilisant des substrats intra-chromosomiques permettant la mesure de l’efficacité et de la fidélité du EJ après ligature d’extrémités éloignées ou proximales, nous avons mis en évidence l’implication du complexe de cohésion dans l’inhibition du EJ d’extrémités distales. Le complexe de cohésion joue donc un rôle central dans l’interface réplication/réparation ; la cohésion des chromatides sœurs favorise la réparation par RH et permet l’inhibition spécifique du EJ d’extrémités éloignées, probablement en limitant la mobilité de la chromatine endommagée et la formation d’une synapse propice au rapprochement des extrémités. La religature d’extrémités éloignées est également nécessaire aux mécanismes de diversification des gènes des immunoglobulines tels que la recombinaison V(D)J et la commutation de classe. L’étude de souris Rad21+/- a également démontré une implication du complexe de cohésion dans ces mécanismes essentiels à la diversité de l’information génétique. Le complexe de cohésion étant impliqué dans ces mécanismes et dans l’inhibition des réarrangements complexes tels que les translocations et insertions il est un acteur essentiel de la diversité et de la stabilité génomique. / DNA double-strand breaks (DSBs) repair is essential for genome stability/diversity, but can also generate genome rearrangements. Although non-homologous end-joining (NHEJ) is required for genome stability maintenance, the joining of distant double strand ends (DSE) should inexorably lead to genetic rearrangements. We analyzed the efficiency and accurency of close or distal EJ repair. Our data show that global end-joining is more efficient on close ends (34bp) compared to distal ends (3200bp) and that C-NHEJ is favored on close ends, resulting in more accurate outcome, compared to distal ends where more mutagenic A-EJ events takes place. In addition, the joining of distal ends favors the insertion/capture of DNA sequences. These data show only few kb distances between two DSEs are sufficient to jeopardize DSB repair efficiency and accuracy, leading to complex scars at the re-sealed junctions, and cell response is sufficiently sensitive to differently process such distal ends. We next addressed the question of the mechanisms preventing the joining of distant DSE. We show that depletion of the cohesin complex proteins specifically stimulates the end-joining of I-SceI-induced DSBs distant of 3200bp, while the joining of close DSEs (34bp) remained unaffected. Consistently, exome sequencing and cytogenetic analysis revealed that RAD21 ablation generates large chromosome rearrangements and a strong induction of replication stress-induced chromosome fusions. These data reveal a role for the cohesin complex in the protection against profound genome rearrangements arising through ligation of distant DSEs.