ALBERT

Description: DNA Topoisomerases are essential to resolve topological problems during DNA metabolism in all species. However, the prevalence and function of RNA topoisomerases remain uncertain. Here, we show that RNA topoisomerase activity is prevalent in Type IA topoisomerases from bacteria, archaea, and eukarya. Moreover, this activity always requires the conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; however, it does not absolutely require the non-conserved carboxyl-terminal domain (CTD), which is necessary for relaxation reactions of supercoiled DNA. The RNA topoisomerase activity of human Top3β differs from that of Escherichia coli topoisomerase I in that the former but not the latter requires the CTD, indicating that topoisomerases have developed distinct mechanisms during evolution to catalyze RNA topoisomerase reactions. Notably, Top3β proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3β-polyribosome association requires TDRD3, which directly interacts with Top3β and is present in animals but not bacteria or yeast. We propose that RNA topoisomerases arose in the early RNA world, and that they are retained through all domains of DNA-based life, where they mediate mRNA translation as part of polyribosomes in animals.

Description: RNase J is a conserved ribonuclease that belongs to the β-CASP family of nucleases. It possesses both endo- and exo-ribonuclease activities, which play a key role in pre-rRNA maturation and mRNA decay. Here we report high-resolution crystal structures of Deinococcus radiodurans RNase J complexed with RNA or uridine 5'-monophosphate in the presence of manganese ions. Biochemical and structural studies revealed that RNase J uses zinc ions for two-metal-ion catalysis. One residue conserved among RNase J orthologues (motif B) forms specific electrostatic interactions with the scissile phosphate of the RNA that is critical for the catalysis and product stabilization. The additional manganese ion, which is coordinated by conserved residues at the dimer interface, is critical for RNase J dimerization and exonuclease activity. The structures may also shed light on the mechanism of RNase J exo- and endonucleolytic activity switch.

Description: There are the two major pathways responsible for the repair of DNA double-strand breaks (DSBs): non-homologous end-joining (NHEJ) and homologous recombination (HR). NHEJ operates throughout the cell-cycle, while HR is primarily active in the S/G2 phases suggesting that there are cell cycle-specific mechanisms that regulate the balance between NHEJ and HR. Here we reported that CDK2 could phosphorylate RNF4 on T26 and T112 and enhance RNF4 E3 ligase activity, which is important for MDC1 degradation and proper HR repair during S phase. Mutation of the RNF4 phosphorylation sites results in MDC1 stabilization, which in turn compromised HR during S-phase. These results suggest that in addition to drive cell cycle progression, CDK also targets RNF4, which is involved in the regulatory network of DSBs repair.

Description: In order to perform gas exploration and determine the distribution pattern of gas in the Yanchang Oil Field in the eastern part of the North Shaanxi Slope, Ordos Basin, China, gravity and magnetic survey data were systemically collated, processed and interpreted in combination with the drilling data and recent seismic data. The genesis of gravity and magnetic anomalies and the relationship between the characteristics of the gravity and magnetic fields and known gas distribution were explored in order to predict the favourable exploration targets for gas. Gravity anomalies resulted both from the lateral variation in density of the basement rock and lateral lithologic transformation in the sedimentary cover. The regional magnetic anomalies were mainly caused by the basement metamorphic rocks and the residual magnetic anomalies may reflect the amount and general location of the volcanic materials in the overlying strata. The residual gravity and magnetic anomalies generated by high-density sandstone and high content of volcanics in the gas reservoir of the upper Paleozoic distorted and deformed the anomaly curves when they were stacked onto the primary background anomaly. The gas wells were generally found to be located in the anomaly gradient zones, or the distorted part of contour lines, and the flanks of high and low anomalies, or the transitional zones between anomaly highs and lows. The characteristics of gravity and magnetic fields provide significant information that can be used for guidance when exploring the distribution of gas. Based on these characteristics, five favourable areas for gas exploration were identified; these are quasi-equally spaced like a strip extending from the southeast to the northwest.

Description: MDC1 is a key mediator of the DNA-damage response in mammals with several phosphorylation-dependent protein interaction domains. The function of its N-terminal forkhead-associated (FHA) domain remains elusive. Here, we show with structural, biochemical and cellular data that the FHA domain mediates phosphorylation-dependent dimerization of MDC1 in response to DNA damage. Crystal structures of the FHA domain reveal a face-to-face dimer with pseudo-dyad symmetry. We found that the FHA domain recognizes phosphothreonine 4 (pT4) at the N-terminus of MDC1 and determined its crystal structure in complex with a pT4 peptide. Biochemical analysis further revealed that in the dimer, the FHA domain binds in trans to pT4 from the other subunit, which greatly stabilizes the otherwise unstable dimer. We show that T4 is phosphorylated primarily by ATM upon DNA damage. MDC1 mutants with the FHA domain deleted or impaired in its ability to dimerize formed fewer foci at DNA-damage sites, but the localization defect was largely rescued by an artificial dimerization module, suggesting that dimerization is the primary function of the MDC1 FHA domain. Our results suggest a novel mechanism for the regulation of MDC1 function through T4 phosphorylation and FHA-mediated dimerization.

Description: Aims The Miyun Reservoir is the most important drinking water source for Beijing—the capital of China with a population of more than 16 million. Since the 1980s, the inflow to the reservoir has been decreasing, which seriously threatens the security of water use in Beijing. Our goal was to analyze the impact of land use and cover change (LUCC) on run-off yield in the upstream of the Miyun Reservoir. Methods In this study, the Soil andWater Assessment Tool (SWAT) was used to simulate the impacts of LUCC on the run-off yield in the Bai River catchment—upstream of the Miyun Reservoir basin in northern China. The investigation was conducted using two 6-year historical streamflow records: from 1986 to 1991 and from 2000 to 2005. A split sample procedure was used for model calibration and validation. The data from 1986 to 1988 and from 2000 to 2002 were used for calibration, while those from 1989 to 1991 and from 2003 to 2005 for validation. The SWAT calibration was based on monthly measured discharge at Zhangjiafen station at the catchment outlet from Bai River catchment. Additionally, the influence of LUCC on the surface run-off was distinguished from that of climate change on the surface runoff through SWAT scenarios modeling, the two-way analysis of variance (ANOVA), and the rainfall–run-off double-mass analysis in the Bai River catchment. Important Findings We found that the SWAT model could be used successfully to accurately simulate run-off yield and different LUCC patterns affecting water quantity in this catchment. During calibraion for the two periods the simulated monthly run-off satisfactorily matched the observed values, with the Nash–Sutcliffe coefficient 〉0.9 and 0.7 and a coefficient of determination of 0.9 and 0.65 at the outlet station (Zhangjiafen station), while during validation for the two periods the obtained values were 0.85, 0.65 and 0.9, 0.65, respectively. During the period of 1986–91, both the SWAT scenarios modeling and the analysis of the two-way ANOVA method showed that LUCC and climate change had some impact on run-off, and the impact of climate change was more significant than that of LUCC. Compared with the period during 1986–91, the run-off yield in the period during 2000–05 significantly decreased. The obtained results from the rainfall–run-off double-mass analysis indicate that since 1998 LUCC has had an increasing influence on the run-off, while the response of the run-off to rainfall has been decreasing. Since 1998, the LUCC has been a major driving force for run-off change in Bai River catchment.

Description: Gordon Holmes syndrome (GHS) is a rare Mendelian neurodegenerative disorder characterized by ataxia and hypogonadism. Recently, it was suggested that disordered ubiquitination underlies GHS though the discovery of exome mutations in the E3 ligase RNF216 and deubiquitinase OTUD4 . We performed exome sequencing in a family with two of three siblings afflicted with ataxia and hypogonadism and identified a homozygous mutation in STUB1 (NM_005861) c.737C-〉T, p.Thr246Met, a gene that encodes the protein CHIP (C-terminus of HSC70-interacting protein). CHIP plays a central role in regulating protein quality control, in part through its ability to function as an E3 ligase. Loss of CHIP function has long been associated with protein misfolding and aggregation in several genetic mouse models of neurodegenerative disorders; however, a role for CHIP in human neurological disease has yet to be identified. Introduction of the Thr246Met mutation into CHIP results in a loss of ubiquitin ligase activity measured directly using recombinant proteins as well as in cell culture models. Loss of CHIP function in mice resulted in behavioral and reproductive impairments that mimic human ataxia and hypogonadism. We conclude that GHS can be caused by a loss-of-function mutation in CHIP. Our findings further highlight the role of disordered ubiquitination and protein quality control in the pathogenesis of neurodegenerative disease and demonstrate the utility of combining whole-exome sequencing with molecular analyses and animal models to define causal disease polymorphisms.

Description: Vaccination against hepatitis B virus is an effective and routine practice that can prevent infection. However, 5–10% of healthy adults fail to produce protective levels of antibody against the hepatitis B vaccination. It has been reported that host genetic variants might affect the immune response to hepatitis B vaccination. Here, we reported a genome-wide association study in a Chinese Han population consisting of 108 primary high-responders and 77 booster non-responders to hepatitis B vaccination using the Illumina HumanOmniExpress Beadchip. We identified 21 SNPs at 6p21.32 were significantly associated with non-response to booster hepatitis B vaccination ( P -value 〈1 x 10 –6 ). The most significant SNP in the region was rs477515, located ~12 kb upstream of the HLA-DRB1 gene. Its P- value (4.81 x 10 –8 ) exceeded the Bonferroni-corrected genome-wide significance threshold. Four tagging SNPs (rs477515, rs28366298, rs3763316 and rs13204672) that capture genetic information of these 21 SNPs were validated in three additional Chinese Han populations, consisting of 1336 primary high-responders and 420 primary non-responders. The four SNPs continued to show significant associations with non-response to hepatitis B vaccination ( P -combined = 3.98 x 10 –13 – 1.42 x 10 –8 ). Further analysis showed that the rs477515 was independently associated with non-response to hepatitis B vaccination with correction for other three SNPs in our GWAS and the known hepatitis B vaccine immunity associated SNP in previous GWAS. Our findings suggest that the rs477515 was an independent marker associated with non-response to hepatitis B vaccination and HLA-DR region might be a critical susceptibility locus of hepatitis B vaccine-induced immunity.

Description: Previous studies have emphasized ethnically heterogeneous human leukocyte antigen (HLA) classical allele associations to rheumatoid arthritis (RA) risk. We fine-mapped RA risk alleles within the major histocompatibility complex (MHC) in 2782 seropositive RA cases and 4315 controls of Asian descent. We applied imputation to determine genotypes for eight class I and II HLA genes to Asian populations for the first time using a newly constructed pan-Asian reference panel. First, we empirically measured high imputation accuracy in Asian samples. Then we observed the most significant association in HLA-DRβ1 at amino acid position 13, located outside the classical shared epitope ( P omnibus = 6.9 x 10 –135 ). The individual residues at position 13 have relative effects that are consistent with published effects in European populations (His 〉 Phe 〉 Arg 〉 Tyr Gly 〉 Ser)—but the observed effects in Asians are generally smaller. Applying stepwise conditional analysis, we identified additional independent associations at positions 57 (conditional P omnibus = 2.2 x 10 –33 ) and 74 (conditional P omnibus = 1.1 x 10 –8 ). Outside of HLA-DRβ1, we observed independent effects for amino acid polymorphisms within HLA-B (Asp9, conditional P = 3.8 x 10 –6 ) and HLA-DPβ1 (Phe9, conditional P = 3.0 x 10 –5 ) concordant with European populations. Our trans-ethnic HLA fine-mapping study reveals that (i) a common set of amino acid residues confer shared effects in European and Asian populations and (ii) these same effects can explain ethnically heterogeneous classical allelic associations (e.g. HLA-DRB1*09:01 ) due to allele frequency differences between populations. Our study illustrates the value of high-resolution imputation for fine-mapping causal variants in the MHC.

Description: We use about 15 000 F/G nearby dwarf stars selected from the LAMOST pilot survey to map the U – V velocity distribution in the solar neighbourhood. An extreme deconvolution algorithm is applied to reconstruct an empirical multi-Gaussian model. In addition to the well-known substructures, e.g. Sirius, Coma Berenices, Hyades–Pleiades overdensities, several new substructures are unveiled. A ripple-like structure from ( U , V ) = (–120, –5) to (103, –32) km s –1 is clearly seen in the U – V distribution. This structure seems associated with resonance induced by the Galactic bar, since it is extended in U while having a small dispersion in V at the same time. A ridge structure between ( U , V ) = (–60, 40) and (–15, 15) km s –1 is also found. Although similar substructures have been seen in the Hipparcos data, their origin is still unclear. Another compact overdensity is seen at ( U , V ) = (–102, –24). With this large data sample, we find that the substructure located at V  ~ –70 km s –1 and the Arcturus group are essentially parallel in V , which may indicate that they originate from an unrelaxed disc component perturbed by the rotating bar.