Rad9/53BP1 promotes DNA repair via crossover recombination by limiting the Sgs1 and Mph1 helicases

In budding yeast, the 53BP1 ortholog Rad9 limits the resection nucleolytic processing of DNA double strand breaks. Here the authors reveal that Rad9 promotes long tract gene conversions, BIR and CO, during the HR repair of a DSB via modulation of Sgs1 and Mph1 helicases

Comparison of Hi-C results using in-solution versus in-nucleus ligation

BACKGROUND: Chromosome conformation capture and various derivative methods such as 4C, 5C and Hi-C have emerged as standard tools to analyze the three-dimensional organization of the genome in the nucleus. These methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. During development of single-cell Hi-C, we devised an alternative Hi-C protocol with ligation in preserved nuclei rather than in solution. Here we directly compare Hi-C methods employing in-nucleus ligation with the standard in-solution ligation. RESULTS: We show in-nucleus ligation results in consistently lower levels of inter-chromosomal contacts. Through chromatin mixing experiments we show that a significantly large fraction of inter-chromosomal contacts are the result of spurious ligation events formed during in-solution ligation. In-nucleus ligation significantly reduces this source of experimental noise, and results in improved reproducibility between replicates. We also find that in-nucleus ligation eliminates restriction fragment length bias found with in-solution ligation. These improvements result in greater reproducibility of long-range intra-chromosomal and inter-chromosomal contacts, as well as enhanced detection of structural features such as topologically associated domain boundaries. CONCLUSIONS: We conclude that in-nucleus ligation captures chromatin interactions more consistently over a wider range of distances, and significantly reduces both experimental noise and bias. In-nucleus ligation creates higher quality Hi-C libraries while simplifying the experimental procedure. We suggest that the entire range of 3C applications are likely to show similar benefits from in-nucleus ligation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0753-7) contains supplementary material, which is available to authorized users

MAGIC observation of the GRB 080430 afterglow

Context. Gamma-ray bursts are cosmological sources emitting radiation from the gamma-rays to the radio band. Substantial observational efforts have been devoted to the study of gamma-ray bursts during the prompt phase, i.e. the initial burst of high-energy radiation, and during the long-lasting afterglows. In spite of many successes in interpreting these phenomena, there are still several open key questions about the fundamental emission processes, their energetics and the environment. Aims. Independently of specific gamma-ray burst theoretical recipes, spectra in the GeV/TeV range are predicted to be remarkably simple, being satisfactorily modeled with power-laws, and therefore offer a very valuable tool to probe the extragalactic background light distribution. Furthermore, the simple detection of a component at very-high energies, i.e. at similar to 100GeV, would solve the ambiguity about the importance of various possible emission processes, which provide barely distinguishable scenarios at lower energies. Methods. We used the results of the MAGIC telescope observation of the moderate resdhift (z similar to 0.76) GRB 080430 at energies above about 80 GeV, to evaluate the perspective for late-afterglow observations with ground based GeV/TeV telescopes. Results. We obtained an upper limit of F(95% CL) = 5.5 x 10(-11) erg cm(-2) s(-1) for the very-high energy emission of GRB 080430, which cannot set further constraints on the theoretical scenarios proposed for this object also due to the difficulties in modeling the low-energy afterglow. Nonetheless, our observations show that Cherenkov telescopes have already reached the required sensitivity to detect the GeV/TeV emission of GRBs at moderate redshift (z less than or similar to 0.8), provided the observations are carried out at early times, close to the onset of their afterglow phase