Nature Structural & Molecular Biology Contents: 2014 Volume #21 pp 841-943

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TABLE OF CONTENTS October 2014 Volume 21, Issue 10 Commentary News and Views Articles Resource Technical Report Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Nature Communications soon to be fully open access   From 20th October Nature Communications, will become fully open access for all new submissions. If an author has a manuscript they wish to submit to the journal via the subscription route, they must submit before 20th October. After this date all new submissions, if accepted, will be published open access and an article processing charge (APC) will apply. For any questions on the switch, open access or advice on policies and funding, visit our website, read the press release or contact our dedicated support team at openaccess@nature.com.   Commentary Top A 3D cellular context for the macromolecular world OPEN   pp841 - 845 Ardan Patwardhan, Alun Ashton, Robert Brandt, Sarah Butcher, Raffaella Carzaniga et al. doi:10.1038/nsmb.2897 We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community. News and Views Top The timing is right   pp846 - 847 R Magnus N Friis and Michael C Schultz doi:10.1038/nsmb.2898 Yeast cells display synchronized oscillation between phases of high and low oxygen consumption accompanied by a program of cyclical gene expression. A study monitoring mRNA levels, histone modifications and chromatin occupancy of histone modifiers during the yeast metabolic cycle (YMC) at high temporal resolution reveals both 'just-in-time' supply of YMC gene products and new patterns of chromatin reconfiguration associated with transcriptional regulation. See also: Article by Kuang et al. Articles Energetic dissection of Gleevec's selectivity toward human tyrosine kinases   pp848 - 853 Roman V Agafonov, Christopher Wilson, Renee Otten, Vanessa Buosi and Dorothee Kern doi:10.1038/nsmb.2891 Chemotherapeutic drug Gleevec (imatinib) is a potent and specific inhibitor of Abl kinase. NMR and fast kinetic analyses now reveal that Abl undergoes an induced-fit conformational change upon Gleevec binding. High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast   pp854 - 863 Zheng Kuang, Ling Cai, Xuekui Zhang, Hongkai Ji, Benjamin P Tu et al. doi:10.1038/nsmb.2881 Analyses of transcription and chromatin states during the yeast metabolic cycle reveal the links between different chromatin modifications and gene expression. The data also show that chromatin-modifier occupancies do not precisely match modification patterns. See also: News and Views by Friis & Schultz Structure of cohesin subcomplex pinpoints direct shugoshin-Wapl antagonism in centromeric cohesion   pp864 - 870 Kodai Hara, Ge Zheng, Qianhui Qu, Hong Liu, Zhuqing Ouyang et al. doi:10.1038/nsmb.2880 The crystal structure of a human cohesin subcomplex, SA2–Scc1, guides mutagenesis analyses to dissect the antagonistic roles of shugoshin and Wapl in regulating centromeric functions during mitosis. Structural & Molecular Biology JOBS of the week Faculty Positions Memorial Sloan Kettering Cancer Center (MSKCC) Faculty Position in Signaling, Chromatin, and Gene Regulation The University of Texas Southwestern Medical Center Postdoctoral fellow Harvard Medical School Tenure-Track Faculty Positions University of Colorado Anschutz Medical Campus Postdoctoral Researcher in Biochemistry & Biophysics Ludwig-Maximilians Universitaet Muenchen, Germany More Science jobs from Structural & Molecular Biology EVENT In Silico Drug Discovery Conference 03.12.14 Research Triangle Park, USA More science events from Mechanochemical basis of protein degradation by a double-ring AAA+ machine   pp871 - 875 Adrian O Olivares, Andrew R Nager, Ohad Iosefson, Robert T Sauer and Tania A Baker doi:10.1038/nsmb.2885 A single-molecule optical-trapping approach is used to examine protein unfolding and translocation by double-ring AAA+ machine ClpA. Although ClpA can unfold some substrates faster than ClpX can, it translocates the unfolded polypeptide more slowly. TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release   pp876 - 883 Heeyoun Bunch, Xiaofeng Zheng, Adam Burkholder, Simon T Dillon, Shmulik Motola et al. doi:10.1038/nsmb.2878 The protein TRIM28 is identified as a factor that modulates RNA polymerase II pausing and transcriptional elongation at a large number of mammalian genes. This function is regulated by transcription-coupled phosphorylation of TRIM28 at Ser824. Visualization of recombination-mediated damage bypass by template switching   pp884 - 892 Michele Giannattasio, Katharina Zwicky, Cindy Follonier, Marco Foiani, Massimo Lopes et al. doi:10.1038/nsmb.2888 A combination of two-dimensional gel electrophoresis and EM is used to isolate and characterize multiple template-switching intermediates generated in budding yeast during replication of damaged DNA. Protein dynamics during presynaptic-complex assembly on individual single-stranded DNA molecules   pp893 - 900 Bryan Gibb, Ling F Ye, YoungHo Kwon, Hengyao Niu, Patrick Sung et al. doi:10.1038/nsmb.2886 New single-molecule imaging analyses reveal how dynamic interactions of RPA, Rad52 and Rad51 on single-stranded DNA direct assembly of the presynaptic complex that promotes strand invasion during homologous recombination. Rbfox3 controls the biogenesis of a subset of microRNAs   pp901 - 910 Kee K Kim, Yanqin Yang, Jun Zhu, Robert S Adelstein and Sachiyo Kawamoto doi:10.1038/nsmb.2892 The RNA-binding protein Rbfox is an established regulator of alternative splicing. Here, Kawamoto and colleagues identify transcriptome-wide targets of Rbfox3 in neuronal cells and tissues to uncover an unexpected role in pri-miRNA processing Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex   pp911 - 918 Piotr Wysoczański, Cornelius Schneider, ShengQi Xiang, Francesca Munari, Simon Trowitzsch et al. doi:10.1038/nsmb.2889 A solution NMR structure of the pre-mRNA retention and splicing (RES) core complex from budding yeast now reveals how the trimer stabilizes the RRM of its Snu17 subunit to promote pre-mRNA interactions within the spliceosome. The RNA exosome promotes transcription termination of backtracked RNA polymerase II   pp919 - 926 Jean-François Lemay, Marc Larochelle, Samuel Marguerat, Sophie Atkinson, Jürg Bähler et al. doi:10.1038/nsmb.2893 New in vivo analyses in Schizosaccharomyces pombe suggest that the RNA exosome promotes transcription termination by targeting the 3' end of nascent transcripts associated with 'backtracked' RNA polymerase II, revealing a new link between mRNA surveillance and termination. Resource Top Uncovering global SUMOylation signaling networks in a site-specific manner   pp927 - 936 Ivo A Hendriks, Rochelle C J D'Souza, Bing Yang, Matty Verlaan-de Vries, Matthias Mann et al. doi:10.1038/nsmb.2890 High-resolution MS identifies >4,300 SUMOylation sites in >1,600 proteins in human cells under standard growth conditions and after proteasome inhibition or heat shock. The data reveal cross-talk between SUMO and other post-translational modifications. Technical Report Top Multiple in vivo pathways for Escherichia coli small ribosomal subunit assembly occur on one pre-rRNA   pp937 - 943 Neha Gupta and Gloria M Culver doi:10.1038/nsmb.2887 Using the M2 stem-loop region to tag 16S pre-rRNA allows one-step isolation of assembly intermediates of the small ribosomal subunit from wild-type Escherichia coli. Characterization of these RNPs reveals multiple independent pathways for rRNA maturation. Top Advertisement Scientific Reports is now accepting submissions from all scientific fields. Online and open access, Scientific Reports is a primary research publication from the publishers of Nature, covering all areas of the natural and clinical sciences. The scope of the journal has been broadened to include all fields of medical research. Submit your manuscript now.     Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. 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