Roland Kanaar

..We also provide evidence suggesting that CSB binds DNA as a dimer. DNA wrapping and unwrapping allows CSB to actively alter the DNA double helix conformation, which could influence nucleosomes and other protein-DNA interactions...

....

..Thus, paradoxically, enzymes antagonizing DNA end metabolism help to ensure that genome maintenance becomes a robust process...

..We suggest that Mus81 suppresses chromosomal instability by converting potentially detrimental replication-associated DNA structures into intermediates that are more amenable to DNA repair...

..We propose that Mus81-Eme1- and Rad54-mediated homologous recombination are involved in the same DNA replication-dependent ICL repair pathway...

..Our results show that changes in the position of PCNA result from de novo assembly of freely mobile replication factors in the nucleoplasmic pool and indicate different binding affinities for PCNA in DNA replication and repair...

..We conclude that Nbs1 and Rad54 function cooperatively, but in separate pathways to counteract this type of DNA damage and discuss mechanistic implications of these findings...

..However, the daughter cells eventually regain the general chromosomal organization pattern of their mothers, suggesting an active mechanism could be at play to reestablish chromosomal neighborhoods...

....

..In conclusion, we show that HR is important for the progression of UV-stalled replication forks in ES cells, and that protection of the fork is an interplay between HR and TLS...

..Whereas, application of low-dose 266 nm laser irradiation induced only UV-specific DNA photo-lesions allowing the study of the UV-C-induced DNA damage response in a user-defined area in cultured cells...

..Thus, even though the paralogs have similar biochemical properties, genetic analysis in mice uncovered their nonoverlapping roles...

..These findings show that due to processing of DNA lesions into a common intermediate, which occurs in a cell cycle-dependent manner, Rad9 is able to respond to different types of genotoxic stress...

..Rad51 and Mre11 foci seemed to be mutually exclusive, though a small subset of cells did show co-localization of these proteins, which suggests a possible cooperation between the proteins at a specific moment during DNA repair...

..Despite their evolutionary conservation and biochemical similarities, S. cerevisiae and mammalian Rad52 appear to differentially contribute to the DNA-damage response...

..The dynamic rearrangements of proteins and DNA within Rad51 nucleoprotein filaments could be key events driving strand exchange in homologous recombination...

..Rather, they interact with different DNA substrates produced early in DNA double-strand break repair...

..Thus, conversion of unrepaired CPD lesions into DNA breaks during DNA replication may comprise one of the principal instigators of UV-mediated cytotoxicity...

..These data show that in vitro, R, M and N form a variety of stable complexes with variable subunit composition and stoichiometry, which may be physiologically relevant in different aspects of RMN function...

..The affinity of RAD51AP1 for the central protein and DNA intermediates of recombination confers on it the ability to control the preservation of genome integrity at a number of critical mechanistic steps...

..Filament segments did not rearrange along DNA, indicating tight association of the ATP-bound protein. The kinetics of filament disassembly was defined by activating ATP hydrolysis and following individual filaments in real time...

..The challenge ahead is to uncover the relationship between the individual biochemical activities of homologous recombination proteins and their coordinated action in the context of the living cell...

....

....

..Indeed, chromatin immunoprecipitations (ChIPs) and nuclease mapping demonstrated that PREs are nucleosome depleted in vivo. We discuss the implications of these findings for models explaining PRE function...

..Interestingly, ATP binding, but not hydrolysis, increased the preference of R/M binding to DNA substrates with 3'-overhangs relative to substrates with blunt ends and 5'-overhangs...

..Our results show that the dosage of a single gene can determine the severity of aneurysm formation and imply that disturbed TGF-beta signaling underlies multiple aneurysm phenotypes...

..Our experiments reveal the versatility of this method for analysis of proteins and protein-DNA complexes...

..These proteins can occur in different quaternary arrangements: rings or helical filaments. Recent results reveal that recombinase function follows from the filamentous form...

..Collectively, these data support a role for Ercc1-Xpf in processing ICL-induced DSBs so that these cytotoxic intermediates can be repaired by homologous recombination...

..Homologous recombination uses homologous DNA sequence to repair or bypass the lesion and is therefore mainly error free. Error-prone translesion synthesis employs specialized, low fidelity polymerases to bypass the damage...

..Homologous recombination, translesion DNA synthesis and de novo reinitiation of DNA synthesis ensure robust replication by navigating it passed damaged DNA. In this review, we highlight the relationship between these three processes...

..Due to selection at the level of the DNA, the cell, and the tissue certain forms of cancer are associated with specific translocations that can be used as a tool for diagnosis and prognosis of these cancers...

..In this review, we focus on the biological relevance of DSB repair in mammalian cells and the potential overlap between nonhomologous end-joining and homologous recombination in different tissues...

..Rad54 binds duplex DNA distant from the site that will be unwound. Translocation of Rad54 along the duplex DNA increases superhelical stress thereby promoting duplex DNA unwinding...

..In this issue of Molecular Cell, Barlow et al. (2008) show that not all DNA double-strand breaks are processed equally and that the chemical nature of DNA ends guides different paths to DNA repair...

..Recently published crystal structures of different Mre11 and Rad50 complexes show the arrangement of these proteins and imply dramatic ligand-induced rearrangements with important functional consequences...

..It plays important roles in central processes in the cell such as genome duplication and DNA damage repair. Recent experiments reveal the surprising versatility of one of its central actors, the Rad54 protein...

..We propose that the putative function of the XRCC4 tetramer is distinct from its DNA ligase IV-associated function...

..This is an important step forward in the study of mucositis and the development of treatment and prevention strategies, proving once more the power and clinical importance of tissue engineering...

..The eukaryotic complexes were similar to each other and differed from their prokaryotic and archaeal homologs. These similarities and differences are discussed with respect to their diverse mechanistic roles in chromosome metabolism...

..We highlight recent advances in in vivo imaging that greatly expand our knowledge on the relationships between DNA damage checkpoints and DNA repair...

..In the case of DNA repair, for example, it will facilitate cross-talk between different DNA repair pathways and coupling to other DNA transactions, such as replication...

..Buis et al. (2008) and Williams et al. (2008) now reveal the importance of the nuclease activity of Mre11 for mammalian genome maintenance and present a molecular view of its active site...

....

..New information on the architecture of protein complexes involved in the dynamic organization of chromosomes challenges existing models of their structures and provides fresh insight into their mechanisms of action...

....

..We deduce a maximum built-up torsion of 10.1 +/- 0.7 k(b)T. In vivo this built-up torsion may be used to favor regression of a stalled replication fork or to free the chromosomal DNA in E.coli from its condensing proteins...

....

..However, centrosome formation was not affected. Intriguingly, a reduced level of sister chromatid cohesion was found in CL-V4B cells. These results reveal a role for Rad51C that is unique among the Rad51 paralogs...

..The substantially increased DNA damage response in the double mutants implies a cooperation of the two DSB repair pathways for survival and genomic integrity in the animal...

..We conclude that, although highly conserved, Brctx is not essential for the above-mentioned processes and may be redundant...

..These findings demonstrate a role for NHEJ in the repair of DSBs that occur spontaneously during or after DNA replication, and reveal overlapping functions for NHEJ and Rad54-dependent HR in the repair of such DSBs...

..In those forty years the Holliday junction has gone from a hypothetical structure to models for its atomic structure and visualization of its dynamics at the single molecule level...

..These studies demonstrate a critical role for the proper biallelic expression of the mammalian Mus81 in the maintenance of genomic integrity and tumor suppression...

..Our results support the breakage-first theory to explain the origin of chromosomal translocations...

..These results illustrate the power of adding sensitive fluorescence imaging to optical tweezers instrumentation...

..Indeed, in Rad50 coiled-coils, two positions of increased flexibility are observed. We discuss how this dynamic structural feature is integral to Rad50 function...

..The hR/M/N complex thus is an example of a biological nanomachine in which binding to its ligand, in this case DNA, affects the functional conformation of a domain located 50 nm distant...

..Most importantly, Eme1 deficiency led to spontaneous genomic instability. These results reveal that mammalian Eme1 plays a key role in DNA repair and the maintenance of genome integrity...

..Thus, mice deficient in NHEJ provide excellent models to study the etiology of unbalanced translocations and amplification events during tumorigenesis...

....

..Instead each nucleoprotein filament consists of a string of many small filament patches that are only a few tens of monomers long. The high flexibility and dynamic nature of this arrangement is likely to facilitate strand exchange...

..Thus, our data indicate that Rad54 and Rad54B-mediated HR is not essential for SHM. In addition, the finding that the ablation of RAD51 paralogues causes an increase in SHM argues against a direct involvement of HR in promoting SHM...

..Instead, the mechanism of attenuation of retroviral infection by RAD52 appears to be based upon competition between the RAD52 protein and active integration complexes for the retroviral cDNA genome...

..We found that instability over generations depends not only on parental germinal instability, but also on a second event taking place after fertilization...

..Because the live-cell procedure requires more hands-on experience, we recommend starting with the fixed-cell application...