Polo-like kinase 3 regulates CtIP during DNA double-strand break repair in G1

DNA double-strand breaks (DSBs) are repaired by nonhomologous end joining (NHEJ) or homologous recombination (HR). The C terminal binding protein–interacting protein (CtIP) is phosphorylated in G2 by cyclin-dependent kinases to initiate resection and promote HR. CtIP also exerts functions during NHEJ, although the mechanism phosphorylating CtIP in G1 is unknown. In this paper, we identify Plk3 (Polo-like kinase 3) as a novel DSB response factor that phosphorylates CtIP in G1 in a damage-inducible manner and impacts on various cellular processes in G1. First, Plk3 and CtIP enhance the formation of ionizing radiation-induced translocations; second, they promote large-scale genomic deletions from restriction enzyme-induced DSBs; third, they are required for resection and repair of complex DSBs; and finally, they regulate alternative NHEJ processes in Ku−/− mutants. We show that mutating CtIP at S327 or T847 to nonphosphorylatable alanine phenocopies Plk3 or CtIP loss. Plk3 binds to CtIP phosphorylated at S327 via its Polo box domains, which is necessary for robust damage-induced CtIP phosphorylation at S327 and subsequent CtIP phosphorylation at T847

PHF2 regulates homology-directed DNA repair by controlling the resection of DNA double strand breaks

Post-translational histone modifications and chromatin remodelling play a critical role controlling the integrity of the genome. Here, we identify histone lysine demethylase PHF2 as a novel regulator of the DNA damage response by regulating DNA damage-induced focus formation of 53BP1 and BRCA1, critical factors in the pathway choice for DNA double strand break repair. PHF2 knockdown leads to impaired BRCA1 focus formation and delays the resolution of 53BP1 foci. Moreover, irradiation-induced RPA phosphorylation and focus formation, as well as localization of CtIP, required for DNA end resection, to sites of DNA lesions are affected by depletion of PHF2. These results are indicative of a defective resection of double strand breaks and thereby an impaired homologous recombination upon PHF2 depletion. In accordance with these data, Rad51 focus formation and homology-directed double strand break repair is inhibited in cells depleted for PHF2. Importantly, we demonstrate that PHF2 knockdown decreases CtIP and BRCA1 protein and mRNA levels, an effect that is dependent on the demethylase activity of PHF2. Furthermore, PHF2-depleted cells display genome instability and are mildly sensitive to the inhibition of PARP. Together these results demonstrate that PHF2 promotes DNA repair by homologous recombination by controlling CtIP-dependent resection of double strand breaks.España Ministerio de Ciencia e Innovacion SAF2016-80626-REspaña, Fundación Canaria Instituto de Investigación Sanitaria de Canarias (FIISC) [PIFUN16/18

Fingering to fracturing transition in a transient gel

Fracture processes are ubiquitous in soft materials, even in complex fluids, subjected to stresses. To investigate these processes in a simple geometry, we use a model self-assembled transient gel and study the instability patterns obtained in a radial Hele-Shaw cell when a low viscosity oil pushes the more viscous transient gel. Thanks to an analysis of the morphology of the patterns, we find a discontinuous transition between the standard Saffman-Taylor fingering instability and a fracturing instability as the oil injection rate increases. Our data suggest that the flow properties of the gel ahead of the finger tip controls the transition towards fracturing. By analyzing the displacement field of the gel in the vicinity of the fingers and cracks, we show that in the fingering regime, the oil gently pushes the gel, whereas in the fracturing regime, the crack tears apart the gel, resulting in a strong drop of the gel velocity ahead of the crack tip as compared to the tip velocity. We find a unique behavior for the whole displacement field of a gel around a crack, which is drastically different from that around a finger, and reveals the solid-like behavior of the gel at short time. Our experiments and analysis provide quantitative yet simple tools to unambiguously discriminate a finger from a crack in a visco-elastic material.Comment: to appear in Soft Matte

Superconducting parity effect across the Anderson limit

How small superconductors can be? For isolated nanoparticles subject to quantum size effects, P.W. Anderson conjectured in 1959 that superconductivity could only exist when the electronic level spacing $\delta$ is smaller than the superconducting gap energy $\Delta$. Here, we report a scanning tunneling spectroscopy study of superconducting lead (Pb) nanocrystals grown on the (110) surface of InAs. We find that for nanocrystals of lateral size smaller than the Fermi wavelength of the 2D electron gas at the surface of InAs, the electronic transmission of the interface is weak; this leads to Coulomb blockade and enables the extraction of the electron addition energy of the nanocrystals. For large nanocrystals, the addition energy displays superconducting parity effect, a direct consequence of Cooper pairing. Studying this parity effect as function of nanocrystal volume, we find the suppression of Cooper pairing when the mean electronic level spacing overcomes the superconducting gap energy, thus demonstrating unambiguously the validity of the Anderson criterion.Comment: 25 pages, 5 figures in main articles, 9 in supplementar

The structure of an LIM-only protein 4 (LMO4) and deformed epidermal autoregulatory factor-1 (DEAF1) complex reveals a common mode of binding to LMO4

LIM-domain only protein 4 (LMO4) is a widely expressed protein with important roles in embryonic development and breast cancer. It has been reported to bind many partners, including the transcription factor Deformed epidermal autoregulatory factor-1 (DEAF1), with which LMO4 shares many biological parallels. We used yeast two-hybrid assays to show that DEAF1 binds both LIM domains of LMO4 and that DEAF1 binds the same face on LMO4 as two other LMO4-binding partners, namely LIM domain binding protein 1 (LDB1) and C-terminal binding protein interacting protein (CtIP/RBBP8). Mutagenic screening analysed by the same method, indicates that the key residues in the interaction lie in LMO4LIM2 and the N-terminal half of the LMO4-binding domain in DEAF1. We generated a stable LMO4LIM2-DEAF1 complex and determined the solution structure of that complex. Although the LMO4-binding domain from DEAF1 is intrinsically disordered, it becomes structured on binding. The structure confirms that LDB1, CtIP and DEAF1 all bind to the same face on LMO4. LMO4 appears to form a hub in protein-protein interaction networks, linking numerous pathways within cells. Competitive binding for LMO4 therefore most likely provides a level of regulation between those different pathways.SJ was funded by an Australian Postgraduate Award (education.gov.au/australian-postgraduate-awards). JPM and JMM were awarded Senior Research Fellowships from the Australian National and Medical Research Council (www.nhmrc.gov.au). This project was funded by an Australian Research Council (www. arc.gov.au) Discovery Project Grant (DP110104332) to JMM and LC

Scanning Tunneling Spectroscopy of Suspended Single-Wall Carbon Nanotubes

We have performed low-temperature STM measurements on single-wall carbon nanotubes that are freely suspended over a trench. The nanotubes were grown by CVD on a Pt substrate with predefined trenches etched into it. Atomic resolution was obtained on the freestanding portions of the nanotubes. Spatially resolved spectroscopy on the suspended portion of both metallic and semiconducting nanotubes was also achieved, showing a Coulomb-staircase behavior superimposed on the local density of states. The spacing of the Coulomb blockade peaks changed with tip position reflecting a changing tip-tube capacitance

hSSB1 rapidly binds at the sites of DNA double-strand breaks and is required for the efficient recruitment of the MRN complex

hSSB1 is a newly discovered single-stranded DNA (ssDNA)-binding protein that is essential for efficient DNA double-strand break signalling through ATM. However, the mechanism by which hSSB1 functions to allow efficient signalling is unknown. Here, we show that hSSB1 is recruited rapidly to sites of double-strand DNA breaks (DSBs) in all interphase cells (G1, S and G2) independently of, CtIP, MDC1 and the MRN complex (Rad50, Mre11, NBS1). However expansion of hSSB1 from the DSB site requires the function of MRN. Strikingly, silencing of hSSB1 prevents foci formation as well as recruitment of MRN to sites of DSBs and leads to a subsequent defect in resection of DSBs as evident by defective RPA and ssDNA generation. Our data suggests that hSSB1 functions upstream of MRN to promote its recruitment at DSBs and is required for efficient resection of DSBs. These findings, together with previous work establish essential roles of hSSB1 in controlling ATM activation and activity, and subsequent DSB resection and homologous recombination (HR).Peer reviewe