A role for chromatin remodellers in replication of damaged DNA

In eukaryotic cells, replication past damaged sites in DNA is regulated by the ubiquitination of proliferating cell nuclear antigen (PCNA). Little is known about how this process is affected by chromatin structure. There are two isoforms of the Remodels the Structure of Chromatin (RSC) remodelling complex in yeast. We show that deletion of RSC2 results in a dramatic reduction in the level of PCNA ubiquitination after DNA-damaging treatments, whereas no such effect was observed after deletion of RSC1. Similarly, depletion of the BAF180 component of the corresponding PBAF (Polybromo BRG1 (Brahma-Related Gene 1) Associated Factor) complex in human cells led to a similar reduction in PCNA ubiquitination. Remarkably, we found that depletion of BAF180 resulted after UV-irradiation, in a reduction not only of ubiquitinated PCNA but also of chromatin-associated unmodified PCNA and Rad18 (the E3 ligase that ubiquitinates PCNA). This was accompanied by a modest decrease in fork progression. We propose a model to account for these findings that postulates an involvement of PBAF in repriming of replication downstream from replication forks blocked at sites of DNA damage. In support of this model, chromatin immunoprecipitation data show that the RSC complex in yeast is present in the vicinity of the replication forks, and by extrapolation, this is also likely to be the case for the PBAF complex in human cells

Ubiquitination and deubiquitination of PCNA in response to stalling of the replication fork

Following exposure of human cells to DNA damaging agents that block the progress of the replication fork, mono-ubiquitination of PCNA mediates the switch from replicative DNA polymerases to polymerases specialised for translesion synthesis. We have shown that this modification of PCNA is necessary for the survival of cells after UV-irradiation and methyl methanesulfonate, that it is independent of cell cycle checkpoint activation, and that it persists after UV damage has been removed. In this Extra-view, we compare the regulation and biological significance of PCNA ubiquitination following treatments with UV light and the replication inhibitor hydroxyurea. We show that ubiquitination persists after removal of the replication block in both cases. With UV however, the persistence of ubiquitinated PCNA correlates with disappearance of the PCNA deubiquitinating enzyme USP1, whereas this is not the case for HU. Prevention of PCNA ubiquitination sensitises the cells to killing by both UV and HU

Scanning tunneling microscopy and spectroscopy of the electronic local density of states of graphite surfaces near monoatomic step edges

We measured the electronic local density of states (LDOS) of graphite surfaces near monoatomic step edges, which consist of either the zigzag or armchair edge, with the scanning tunneling microscopy (STM) and spectroscopy (STS) techniques. The STM data reveal that the $(\sqrt{3} \times \sqrt{3}) R 30^{\circ}$ and honeycomb superstructures coexist over a length scale of 3-4 nm from both the edges. By comparing with density-functional derived nonorthogonal tight-binding calculations, we show that the coexistence is due to a slight admixing of the two types of edges at the graphite surfaces. In the STS measurements, a clear peak in the LDOS at negative bias voltages from -100 to -20 mV was observed near the zigzag edges, while such a peak was not observed near the armchair edges. We concluded that this peak corresponds to the graphite "edge state" theoretically predicted by Fujita \textit{et al.} [J. Phys. Soc. Jpn. {\bf 65}, 1920 (1996)] with a tight-binding model for graphene ribbons. The existence of the edge state only at the zigzag type edge was also confirmed by our first-principles calculations with different edge terminations.Comment: 20 pages, 11 figure

Magnetism as a mass term of the edge states in graphene

The magnetism by the edge states in graphene is investigated theoretically. An instability of the pseudo-spin order of the edge states induces ferrimagnetic order in the presence of the Coulomb interaction. Although the next nearest-neighbor hopping can stabilize the pseudo-spin order, a strong Coulomb interaction makes the pseudo-spin unpolarized and real spin polarized. The magnetism of the edge states makes two peaks of the density of states in the conduction and valence energy bands near the Fermi point. Using a continuous model of the Weyl equation, we show that the edge-induced gauge field and the spin dependent mass terms are keys to make the magnetism of the edge states. A relationship between the magnetism of the edge states and the parity anomaly is discussed.Comment: 7 pages, 5 figure

Three DNA polymerases, recruited by different mechanisms, carry out NER repair synthesis in human cells

Nucleotide excision repair (NER) is the most versatile DNA repair system that deals with the major UV photoproducts in DNA, as well as many other DNA adducts. The early steps of NER are well understood, whereas the later steps of repair synthesis and ligation are not. In particular, which polymerases are definitely involved in repair synthesis and how they are recruited to the damaged sites has not yet been established. We report that, in human fibroblasts, approximately half of the repair synthesis requires both polκ and polδ, and both polymerases can be recovered in the same repair complexes. Polκ is recruited to repair sites by ubiquitinated PCNA and XRCC1 and polδ by the classical replication factor complex RFC1-RFC, together with a polymerase accessory factor, p66, and unmodified PCNA. The remaining repair synthesis is dependent on polɛ, recruitment of which is dependent on the alternative clamp loader CTF18-RFC

Room-temperature ferromagnetism in graphite driven by 2D networks of point defects

Ferromagnetism in carbon-based materials is appealing for both applications and fundamental science purposes because carbon is a light and bio-compatible material that contains only s and p electrons in contrast to traditional ferromagnets based on 3d or 4f electrons. Here we demonstrate direct evidence for ferromagnetic order locally at defect structures in highly oriented pyrolytic graphite (HOPG) with magnetic force microscopy and in bulk magnetization measurements at room temperature. Magnetic impurities have been excluded as the origin of the magnetic signal after careful analysis supporting an intrinsic magnetic behavior of carbon. The observed ferromagnetism has been attributed to originate from unpaired electron spins localized at grain boundaries of HOPG. Grain boundaries form two-dimensional arrays of point defects, where their spacing depends on the mutual orientation of two grains. Depending on the distance between these point defects, scanning tunneling spectroscopy of grain boundaries showed two intense split localized states for small distances between defects (< 4 nm) and one localized state at the Fermi level for large distances between defects (> 4 nm).Comment: 19 pages, 5 figure

Gauge field for edge state in graphene

By considering the continuous model for graphene, we analytically study a special gauge field for the edge state. The gauge field explains the properties of the edge state such as the existence only on the zigzag edge, the partial appearance in the $k$-space, and the energy position around the Fermi energy. It is demonstrated utilizing the gauge field that the edge state is robust for surface reconstruction, and the next nearest-neighbor interaction which breaks the particle-hole symmetry stabilizes the edge state.Comment: 9 pages, 5 figure

ATR-mediated phosphorylation of DNA polymerase η is needed for efficient recovery from UV damage

DNA polymerase η (polη) belongs to the Y-family of DNA polymerases and facilitates translesion synthesis past UV damage. We show that, after UV irradiation, polη becomes phosphorylated at Ser601 by the ataxia-telangiectasia mutated and Rad3-related (ATR) kinase. DNA damage–induced phosphorylation of polη depends on its physical interaction with Rad18 but is independent of PCNA monoubiquitination. It requires the ubiquitin-binding domain of polη but not its PCNA-interacting motif. ATR-dependent phosphorylation of polη is necessary to restore normal survival and postreplication repair after ultraviolet irradiation in xeroderma pigmentosum variant fibroblasts, and is involved in the checkpoint response to UV damage. Taken together, our results provide evidence for a link between DNA damage–induced checkpoint activation and translesion synthesis in mammalian cells