Broken Ends Research Articles

Testing of the Ceramic Insulation Break for Fusion Device

Large magnet system is an essential component of most current or planned fusion devices. Axial insulation breaks are required in order to electrically isolate the cryogenic distribution system from the potential high voltage of the magnet system and bus bars. The epoxy resin based insulation break could be the weak link in magnet design, due to insulation sensitivity to high irradiation doses. The Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ceramic material instead of epoxy based material was used to manufacture the insulation break. Kovar alloy which has a similar mean coefficient of thermal expansion with Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> ceramic in the temperature range of 300-1073 K was used as two ends of the insulation breaks. The ceramic tubes and Kovar alloy tubes were vacuum brazed together using silver-based filler at 1073 K. The helium tightness, the insulation resistances and dielectric breakdown were checked at room temperature and LN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> temperature. Then 2 kN traction and compression were tested at room temperature and LN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> temperature. The maximum tensile force of 8.62 kN and 8.18 kN were measured at room temperature and LN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> temperature, respectively. The three point bending test was carried out. The test results of 4.5 kN and 3.6 kN were measured at room temperature and LN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> temperature, respectively. The 50 thermal shock cycles were performed from 77 K to 300 K to ensure that the ceramic break could operate under rapid temperature change.

The comparison of three different methods to localize nasal broken end of lacerated inferior lacrimal canaliculus

Objective To compare the clinical efficacy of three different methods to localize nasal broken end of lacerated inferior lacrimal canaliculus.Methods 24 cases of lacerated inferior lacrimal canaliculus due to trauma were treated by three different methods (pushing water into the superior punctum,finding directly under operating microscope,probing needle)to localize nasal breakage.The clinical effects were analyzed.Results The searching method of pushing water into the superior punctum was performed in 24 cases and only 7 nasal breakages were localized successfully accounting for 29.17％.The searching method of finding directly under microscope was performed in 24 cases and the nasal breakages were found in all cases and the success rate was 100％.The searching method of probing needle was performed in 24 cases.The nasal broken ends were localized in 12 cases,but 4 cases were not successful because of iatrogenic false passage.The success rate was 50％.Conclusion For the patients with lacerated inferior lacrimal canaliculus due to trauma,searching nasal broken ends directly under microscope is the preferred method.If the searching time is more than 30 minutes,pushing water into the superior punctum can be tried.Using probing needle is the last choice,but not be performed when the trauma tissue is edema. Key words: Laceration,canalicular, lacrimal; Ends, broken, nasal

Catalytic and Noncatalytic Roles of the CtIP Endonuclease in Double-Strand Break End Resection

The carboxy-terminal binding protein (CtBP)-interacting protein (CtIP) is known to function in 5' strand resection during homologous recombination, similar to the budding yeast Sae2 protein, but its role in this process is unclear. Here, we characterize recombinant human CtIP and find that it exhibits 5' flap endonuclease activity on branched DNA structures, independent of the MRN complex. Phosphorylation of CtIP at known damage-dependent sites and other sites is essential for its catalytic activity, although the S327 and T847 phosphorylation sites are dispensable. A catalytic mutant of CtIP that is deficient in endonuclease activity exhibits wild-type levels of homologous recombination at restriction enzyme-generated breaks but is deficient in processing topoisomerase adducts and radiation-induced breaks in human cells, suggesting that the nuclease activity of CtIP is specifically required for the removal of DNA adducts at sites of DNA breaks.

Regulating DNA Repair

Genetics Chromosomes carry the intricate code that makes and organizes cells and organisms. But chromosomes can break, causing a serious potential threat to cell and organismal survival. Repairing such breaks is vital, but repair can come with its own dangers, as certain repair pathways are necessarily error-prone—restoring chromosome integrity at the cost of introducing mutations into the genome. Microhomology-mediated end joining (MMEJ) is an error-prone form of repair that relies on very small (∼5 to 25 base pairs) fortuitous homologies near the broken ends of chromosomes, which allow them to come together and be rejoined. A microhomology signature is often seen in breakpoints in chromosome arrangements in cancers and other diseases, suggesting that MMEJ is commonly involved in such genome derangement. Deng et al. investigated MMEJ in the budding yeast Saccharomyces cerevisiae . They find that although resection [the trimming back of one of the DNA stands to generate a single-stranded DNA (ssDNA) tail] at the ends of the breaks is important to expose regions of microhomology internal to the break, it is not rate-limiting for repair. On the other hand, replication protein A, which binds ssDNA, actively prevents spontaneous annealing between the microhomologies and suppresses MMEJ. Nat. Struct. Mol. Biol. 10.1038/nsmb.2786 (2014).

Structural basis for translocation by AddAB helicase–nuclease and its arrest at χ sites

In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence Chi1,2 and is catalysed by either an AddAB or RecBCD-type helicase-nuclease (reviewed in refs 3, 4). These enzyme complexes unwind and digest the DNA duplex from the broken end until they encounter a Chi sequence5 whereupon they produce a 3′-single-stranded DNA tail onto which they initiate loading of the RecA protein6. Consequently, regulation of the AddAB/RecBCD complex by Chi is a key control point in DNA repair and other processes involving genetic recombination. Here, we report crystal structures of AddAB in complex with different Chi-containing DNA substrates either with or without a nonhydrolysable ATP analogue. Comparison of these structures suggests a mechanism for DNA translocation and unwinding, how the enzyme binds specifically to Chi sequences, and explains how Chi recognition leads to the arrest of AddAB (and RecBCD) translocation that is observed in single molecule experiments7-9.

Structural Insights Into DNA Repair by RNase T—An Exonuclease Processing 3′ End of Structured DNA in Repair Pathways

Author SummaryDNA repair relies on various enzymes, including exonucleases that bind and trim DNA at broken ends. However, we know little about how an exonuclease precisely selects and trims a DNA broken end in specific repair pathways. In this study, the enzyme RNase T, previously known for its involvement in processing RNA substrates, is shown to also possess DNase activity. RNase T is a DnaQ-like exonuclease and is characterized in this work as the exoDNase responsible for trimming the 3′ ends of structured DNA in various DNA repair pathways. Based on the high-resolution crystal structures of RNase T-DNA complexes, an insightful working model is provided showing how RNase T processes bulge, bubble, and Y- structured DNA in various DNA repair pathways. RNase T thus represents a unique structure-specific exonuclease with multiple functions not only in processing 3′ overhangs of duplex RNA during RNA maturation, but also in processing 3′ ends of bubble, bulge, and Y-structured DNA during DNA repair. These findings advance our understanding of the precise function of an exonuclease in DNA repair and suggest possible roles for thousands of members of DnaQ superfamily exonucleases in DNA repair and replication.

MBAND analysis of early and late damages in the chromosome of human lymphocytes after exposures to gamma rays and Fe ions

Stable-type chromosome aberrations that survive multiple generations of cell division include translocation and inversions. An efficient method to detect an inversion is multi-color banding fluorescent in situ hybridization (mBAND) which allows identification of both inter- and intra-chromosome aberrations simultaneously. Post irradiation, chromosome aberrations may also arise after multiple cell divisions as a result of genomic instability. This study was aimed at investigating stable or late-arising chromosome aberrations in human lymphocytes induced after low- and high-LET radiation exposure.Human lymphocytes were exposed in vitro to gamma ray doses of 2 or 4 Gy using a 137Cs source at a dose rate of 0.5 Gy/min. For high LET radiation, cells were exposed to Fe ions (600 MeV/nucleon) of 0.05, 0.5 or 1 Gy at NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL). Chromosomes were collected at 48 h which represented the first mitosis, and 7 and 14 days after irradiation using a premature chromosome condensation (PCC) technique as described previously [ 1]. Chromosome 3 was painted with the XCyte3 mBAND kit (MetaSystems), and intra- and inter-chromosomal aberrations were analyzed with the mBAND analysis system (MetaSystems).With gamma irradiation, about half of the damages observed at first mitosis remained after 7- and 14-day culture, suggesting transmissibility of damages to the surviving progeny. With Fe ions irradiation, at the doses that produced similar frequencies of gamma-induced chromosome aberrations as observed at first mitosis, a significantly lower yield of aberrations remained at the same population doublings after Fe ion exposure. At these equitoxic doses, more complex-type aberrations were observed for Fe ions, indicating that Fe ion-induced initial chromosome damages are more severe and may lead to cell death.Comparison of the number of breaks indicates that Fe ions produced three or more breaks in ∼20% of the damaged chromosome 3, whereas ∼10% or a less fraction of cells with three or more breaks in chromosome 3 were found after gamma ray exposures. Unlike gamma rays, increasing doses of Fe ions did not produce more breaks in a damaged chromosome 3, indicating that damages from Fe ions exposures were mostly due to the single track effect, in agreement with the results of Hada et al. [ 1, 2].Increasing doses of exposure resulted in less fraction of chromosome break ends involved in intra-chromosomal exchange induced by either gamma rays or Fe ions in the first mitosis.Interestingly, simple inversions in chromosome 3 were found in only the 7 and 14-day samples after 4 Gy gamma irradiation. It is not clear whether cells containing simple inversions had already progressed through the first cell division at 48 h, or the simple inversions were induced after the first cell division.Detailed analysis of breaks participating in total chromosome exchanges within the first cell cycle post-irradiation revealed a common hot spot located in the 3p21 region, which is a known fragile site corresponding to Band 6 in the mBand analysis [ 2]. The breakpoint distribution in chromosomes collected at 7 days, but not at 14 days, post-irradiation appeared similar to the distribution in cells collected within the first cell cycle post-irradiation. The breakpoint distribution for human lymphocytes after radiation exposure was different from the previously published distribution for human mammary epithelial cells [ 2], indicating that interphase chromatin folding structures play a role in the distribution of radiation-induced breaks.

Chk2 and P53 Regulate the Transmission of Healed Chromosomes in the Drosophila Male Germline

When a dicentric chromosome breaks in mitosis, the broken ends cannot be repaired by normal mechanisms that join two broken ends since each end is in a separate daughter cell. However, in the male germline of Drosophila melanogaster, a broken end may be healed by de novo telomere addition. We find that Chk2 (encoded by lok) and P53, major mediators of the DNA damage response, have strong and opposite influences on the transmission of broken-and-healed chromosomes: lok mutants exhibit a large increase in the recovery of healed chromosomes relative to wildtype control males, but p53 mutants show a strong reduction. This contrasts with the soma, where mutations in lok and p53 have the nearly identical effect of allowing survival and proliferation of cells with irreparable DNA damage. Examination of testes revealed a transient depletion of germline cells after dicentric chromosome induction in the wildtype controls, and further showed that P53 is required for the germline to recover. Although lok mutant males transmit healed chromosomes at a high rate, broken chromosome ends can also persist through spermatogonial divisions without healing in lok mutants, giving rise to frequent dicentric bridges in Meiosis II. Cytological and genetic analyses show that spermatid nuclei derived from such meiotic divisions are eliminated during spermiogenesis, resulting in strong meiotic drive. We conclude that the primary responsibility for maintaining genome integrity in the male germline lies with Chk2, and that P53 is required to reconstitute the germline when cells are eliminated owing to unrepaired DNA damage.

Expression of FGF-2 and IGF-1 in diabetic rats with fracture

ObjectiveTo observe the change of fibroblast growth factor-2 (FGF-2), insulin-like growth factor-1 (IGF-1) in serum and bone callus after fracture in diabetic rats, and to explore molecular biological mechanism of healing of diabetic fracture. MethodsThirty male SD rats were designed into normal (n=15) and control (n=15) groups randomly. Venous blood was extracted on the lst, 2nd, 4th, 6th, 8th week after surgery. It was certificated and the serum was obtained. Left lower extremity was observed by X- ray. Bone callus at broken ends was observed under light microscope. Expressions of FGF-2 and IGF-1 in tissue were detected by immunohistochemistry method, and ELISA was used to detect expression of FGF-2 and IGF-1 in serum. ResultsThe results showed a significant increase in the density and area of newly formed bone in the distraction gaps of normal rats compared to control rats. Increased cell proliferation was also found in the distraction gaps of normal rats versus control rats. There was significant difference in serum levels of FGF-2 and IGF-1 between two groups. ConclusionsThe decrease of FGF-2 and IGF-1 both in the serum and in the fracture region is one of the reasons for bad bone healing or delayed union in rats' fracture with diabetes. There are some synergistic effects possibly between FGF-2 and IGF-1.

Tracking the processing of damaged DNA double-strand break ends by ligation-mediated PCR: increased persistence of 3′-phosphoglycolate termini in SCAN1 cells

To track the processing of damaged DNA double-strand break (DSB) ends in vivo, a method was devised for quantitative measurement of 3′-phosphoglycolate (PG) termini on DSBs induced by the non-protein chromophore of neocarzinostatin (NCS-C) in the human Alu repeat. Following exposure of cells to NCS-C, DNA was isolated, and labile lesions were chemically stabilized. All 3′-phosphate and 3′-hydroxyl ends were enzymatically capped with dideoxy termini, whereas 3′-PG ends were rendered ligatable, linked to an anchor, and quantified by real-time Taqman polymerase chain reaction. Using this assay and variations thereof, 3′-PG and 3′-phosphate termini on 1-base 3′ overhangs of NCS-C-induced DSBs were readily detected in DNA from the treated lymphoblastoid cells, and both were largely eliminated from cellular DNA within 1 h. However, the 3′-PG termini were processed more slowly than 3′-phosphate termini, and were more persistent in tyrosyl-DNA phosphodiesterase 1-mutant SCAN1 than in normal cells, suggesting a significant role for tyrosyl-DNA phosphodiesterase 1 in removing 3′-PG blocking groups for DSB repair. DSBs with 3′-hydroxyl termini, which are not directly induced by NCS-C, were formed rapidly in cells, and largely eliminated by further processing within 1 h, both in Alu repeats and in heterochromatic α-satellite DNA. Moreover, absence of DNA-PK in M059J cells appeared to accelerate resolution of 3′-PG ends.

Solution for the difficuties in the anastomosis of lacerated canaliculus

Objective To explore the difficulties and its solutions in treatment of canalicular laceration.Methods Fifty four eyes of 54 cases were enrolled in this retrospective study.The steps of surgery included searching the broken end of the canaliculus under operating microscope,deep fixation of the canaliculus,safe suturing of stent and preventing the contraction of scar on the lower lid.Results The follow up of these cases were from 6 months to 2 years.The result of surgeries was successful in 46 cases (85.2％),improved in 4 cases (7.4％) and failure in 4 cases (7.4％).Conclusion The key points of the success are the search and inosculation of the broken end of the lacrimal canaliculus,the fixation of the stent,prevention of the contraction of scar on the lower eyelid. Key words: Laceration, lacrimal canaliculus; Surgery; Key points

Alternative Lengthening of Telomeres: Recurrent Cytogenetic Aberrations and Chromosome Stability under Extreme Telomere Dysfunction

Human tumors using the alternative lengthening of telomeres (ALT) exert high rates of telomere dysfunction. Numerical chromosomal aberrations are very frequent, and structural rearrangements are widely scattered among the genome. This challenging context allows the study of telomere dysfunction-driven chromosomal instability in neoplasia (CIN) in a massive scale. We used molecular cytogenetics to achieve detailed karyotyping in 10 human ALT neoplastic cell lines.We identified 518 clonal recombinant chromosomes affected by 649 structural rearrangements. While all human chromosomes were involved in random or clonal, terminal, or pericentromeric rearrangements and were capable to undergo telomere healing at broken ends, a differential recombinatorial propensity of specific genomic regions was noted.We show that ALT cells undergo epigenetic modifications rendering polycentric chromosomes functionally monocentric, and because of increased terminal recombinogenicity, they generate clonal recombinant chromosomes with interstitial telomeric repeats. Losses of chromosomes 13, X, and 22, gains of 2, 3, 5, and 20, and translocation/deletion events involving several common chromosomal fragile sites (CFSs) were recurrent. Long-term reconstitution of telomerase activity in ALT cells reduced significantly the rates of random ongoing telomeric and pericentromeric CIN. However, the contribution of CFS in overall CIN remained unaffected, suggesting that in ALT cells whole-genome replication stress is not suppressed by telomerase activation. Our results provide novel insights into ALT-driven CIN, unveiling in parallel specific genomic sites that may harbor genes critical for ALT cancerous cell growth.

Clustering and Protein Dynamics ofDrosophila melanogasterTelomeres

Telomeres are obligatory chromosomal landmarks that demarcate the ends of linear chromosomes to distinguish them from broken ends and can also serve to organize the genome. In both budding and fission yeast, they cluster at the periphery of the nucleus, potentially to establish a compartment of silent chromatin. To gain insight into telomere organization in higher organisms, we investigated their distribution in interphase nuclei of Drosophila melanogaster. We focused on the syncytial blastoderm, an excellent developmental stage for live imaging due to the synchronous division of the nuclei at this time. We followed the EGFP-labeled telomeric protein HOAP in vivo and found that the 16 telomeres yield four to six foci per nucleus, indicative of clustering. Furthermore, we confirmed clustering in other somatic tissues. Importantly, we observed that HOAP signal intensity in the clusters increases in interphase, potentially due to loading of HOAP to newly replicated telomeres. To determine the rules governing clustering, we used in vivo imaging and fluorescence in situ hybridization to test several predictions. First, we inspected mutant embryos that develop as haploids and found that clustering is not mediated by associations between homologs. Second, we probed specifically for a telomere of novel sequence and found strong evidence against DNA sequence identity and homology as critical factors. Third, we ruled out predominance of intrachromosomal interactions by marking both ends of a chromosome. Based on these results, we propose that clustering is independent of sequence and is likely maintained by an as yet undetermined factor.

The complexity of DNA double strand breaks is a critical factor enhancing end-resection

DNA double strand breaks (DSBs) induced by ionizing radiation (IR) are deleterious damages. Two major pathways repair DSBs in human cells, DNA non-homologous end-joining (NHEJ) and homologous recombination (HR). It has been suggested that the balance between the two repair pathways varies depending on the chromatin structure surrounding the damage site and/or the complexity of damage at the DNA break ends. Heavy ion radiation is known to induce complex-type DSBs, and the efficiency of NHEJ in repairing these DSBs was shown to be diminished. Taking advantage of the ability of high linear energy transfer (LET) radiation to produce complex DSBs effectively, we investigated how the complexity of DSB end structure influences DNA damage responses. An early step in HR is the generation of 3'-single strand DNA (SSD) via a process of DNA end resection that requires CtIP. To assess this process, we analyzed the level of phosphorylated CtIP, as well as RPA phosphorylation and focus formation, which occur on the exposed SSD. We show that complex DSBs efficiently activate DNA end resection. After heavy ion beam irradiation, resection signals appear both in the vicinity of heterochromatic areas, which is also observed after X-irradiation, and additionally in euchromatic areas. Consequently, ~85% of complex DSBs are subjected to resection in heavy ion particle tracks. Furthermore, around 20-40% of G1 cells exhibit resection signals. Taken together, our observations reveal that the complexity of DSB ends is a critical factor regulating the choice of DSB repair pathway and drastically alters the balance toward resection-mediated rejoining. As demonstrated here, studies on DNA damage responses induced by heavy ion radiation provide an important tool to shed light on mechanisms regulating DNA end resection.

Migrating bubble during break-induced replication drives conservative DNA synthesis

The repair of chromosomal double strand breaks (DSBs) is crucial in the maintenance of genomic integrity. However, the repair of DSBs can also destabilize the genome by causing mutations and chromosomal rearrangements, the driving forces for carcinogenesis and hereditary diseases. Break induced replication (BIR) is one of the DSB repair pathways that is highly prone to genetic instability1–3. BIR proceeds by invasion of one broken end into a homologous DNA sequence followed by replication that can copy hundreds of kilobasepairs of DNA from a donor molecule all the way through its telomere4,5. The resulting repaired chromosome comes at a great cost to the cell, as BIR promotes mutagenesis, loss of heterozygosity, translocations, and copy number variations, all hallmarks of carcinogenesis4–9. BIR employs the majority of known replication proteins to copy large portions of DNA, similar to S-phase replication10,11. It has thus been suggested that BIR proceeds by semiconservative replication; however, the model of a bona-fide, stable replication fork contradicts the known instabilities associated with BIR such as a 1000-fold increase in mutation rate compared to normal replication9. Here we demonstrate that the mechanism of replication during BIR is significantly different from S-phase replication, as it proceeds via an unusual bubble-like replication fork that results in conservative inheritance of the new genetic material. We provide the evidence that this atypical mode of DNA replication, dependent on Pif1 helicase, is responsible for the dramatic increase in BIR-associated mutations. We propose that the BIR-mode of synthesis presents a powerful mechanism that can initiate bursts of genetic instability in eukaryotes including humans.

DNA double-strand breaks: linking gene expression to chromosome morphology and mobility

Ionizing radiation can lead to DNA double-strand breaks (DSBs) which belong to the most dangerous forms of damage to the DNA. Cells possess elaborate repair mechanisms and react in a complex manner to the emergence of DSBs. Experiments have shown that gene expression levels in irradiated cells are changed, and thousands of radiation-responsive genes have been identified. On the other hand, recent studies have shown that gene expression is tightly connected to the three-dimensional organization of the genome. In this work, we analyzed the chromatin organization in the cell nuclei before and after exposure to ionizing radiation with an expression-dependent folding model. Our results indicate that the alteration of the chromosome organization on the scale of a complete chromosome is rather limited despite the expression level change of a large number of genes. We further modelled breaks within sub-compartments of the model chromosomes and showed that entropic changes caused by a break lead to increased mobility of the break sites and help to locate break ends further to the periphery of the sub-compartments. We conclude that the changes in the chromatin structure after irradiation are limited to local scales and demonstrate the importance of entropy for the behaviour of break ends.

Fluorescence Technologies for Evaluating Male Gamete (Dys)Function

For many years, andrologists have sought ways of assessing sperm fertility, especially of new sires entering the breeding chain. As knowledge of the complex processes that enable sperm to fertilize eggs has increased, it has become clearer that quantitative estimation of the fertilizing potential of a sire or an ejaculate is actually unlikely ever to be fully realized. Here, we propose that a better approach is to identify substandard males and semen samples. During the past decades, the use of fluorescence technologies in biomedical science has burgeoned, with the development of very powerful instrumentation such as confocal microscopy and flow cytometers of ever-increasing capabilities together with a vast range of fluorochromes and fluorochrome conjugates. This technology has been applied to andrology but thus far in only a relatively simple way. In this review, we offer strategies for assessing a large range of sperm functions thought to be related to fertilizing ability over a temporal window rather than at a single time point. From such an assessment profile, sperm samples that over-respond or do not respond sufficiently could be identified, termed dysfunctional and rejected. We outline the rationales behind such tests, present information on new potentially useful fluorochromes and current flow cytometer models that would be suitable for the multicolour multifunctional tests we propose, and we offer suggestions as to how andrologists might design such multicolour tests for themselves.

Modelling organelle transport after traumatic axonal injury

This paper is motivated by recent experimental research (Tang-Schomer et al. 2012) on the formation of periodic varicosities in axons after traumatic brain injury (TBI). TBI leads to the formation of undulated distortions in the axons due to their dynamic deformation. These distortions result in the breakage of some microtubules (MTs) near the peaks of undulations. The breakage is followed by catastrophic MT depolymerisation around the broken ends. Although after relaxation axons regain their straight geometry, the structure of the axon after TBI is characterised by the presence of periodic regions where the density of MTs has been decreased due to depolymerisation. We modelled organelle transport in an axon segment with such a damaged MT structure and investigated how this structure affects the distributions of organelle concentrations and fluxes. The modelling results suggest that organelles accumulate at the boundaries of the region where the density of MTs has been decreased by depolymerisation. According to the model, the presence of such damaged regions decreases the organelle flux by only about 12%. This provides evidence that axon degradation after TBI may be caused by organelle accumulation rather than by starvation due to insufficient organelle flux.

PCNA promotes processive DNA end resection by Exo1

Exo1-mediated resection of DNA double-strand break ends generates 3′ single-stranded DNA overhangs required for homology-based DNA repair and activation of the ATR-dependent checkpoint. Despite its critical importance in inducing the overall DNA damage response, the mechanisms and regulation of the Exo1 resection pathway remain incompletely understood. Here, we identify the ring-shaped DNA clamp PCNA as a new factor in the Exo1 resection pathway. Using mammalian cells, Xenopus nuclear extracts and purified proteins, we show that after DNA damage, PCNA loads onto double-strand breaks and promotes Exo1 damage association through direct interaction with Exo1. By tethering Exo1 to the DNA substrate, PCNA confers processivity to Exo1 in resection. This role of PCNA in DNA resection is analogous to its function in DNA replication where PCNA serves as a processivity co-factor for DNA polymerases.

ATM Release at Resected Double-Strand Breaks Provides Heterochromatin Reconstitution to Facilitate Homologous Recombination

Non-homologous end-joining (NHEJ) and homologous recombination (HR) represent the two main pathways for repairing DNA double-strand breaks (DSBs). During the G2 phase of the mammalian cell cycle, both processes can operate and chromatin structure is one important factor which determines DSB repair pathway choice. ATM facilitates the repair of heterochromatic DSBs by phosphorylating and inactivating the heterochromatin building factor KAP-1, leading to local chromatin relaxation. Here, we show that ATM accumulation and activity is strongly diminished at DSBs undergoing end-resection during HR. Such DSBs remain unrepaired in cells devoid of the HR factors BRCA2, XRCC3 or RAD51. Strikingly, depletion of KAP-1 or expression of phospho-mimic KAP-1 allows repair of resected DSBs in the absence of BRCA2, XRCC3 or RAD51 by an erroneous PARP-dependent alt-NHEJ process. We suggest that DSBs in heterochromatin elicit initial local heterochromatin relaxation which is reversed during HR due to the release of ATM from resection break ends. The restored heterochromatic structure facilitates HR and prevents usage of error-prone alternative processes.