Nature Structural & Molecular Biology Contents: January 2014 Volume #21 pp 1-112

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Read more about how you can be part of the future of research publication TABLE OF CONTENTS January 2014 Volume 21, Issue 1 Editorial Correspondence News and Views Research Highlights Perspective Articles Brief Communication Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement nature.com webcasts Macmillan Science Communication presents a custom webcast series: Drugging the Human Methylome Two independent, but complimentary, webcasts and live Q & A's broadcasting on:  21 January   23 January Sponsored by:     Editorial Top Taking stock in the New Year   p1 doi:10.1038/nsmb.2755 As 2014 begins, we look back at our performance over the previous year. Correspondence Top CENP-A octamers do not confer a reduction in nucleosome height by AFM   pp2 - 3 Marcin P Walkiewicz, Emilios K Dimitriadis and Yamini Dalal doi:10.1038/nsmb.2742 CENP-A octamers do not confer a reduction in nucleosome height by AFM   pp4 - 5 Christine A Codomo, Takehito Furuyama and Steven Henikoff doi:10.1038/nsmb.2743 Reply to "CENP-A octamers do not confer a reduction in nucleosome height by AFM"   pp5 - 8 Matthew D D Miell, Aaron F Straight and Robin C Allshire doi:10.1038/nsmb.2744 Centromere chromatin: a loose grip on the nucleosome?   p8 Yuri L Lyubchenko doi:10.1038/nsmb.2745 News and Views Top Good cap/bad cap: how the cap-binding complex determines RNA fate   pp9 - 12 Michaela Muller-McNicoll and Karla M Neugebauer doi:10.1038/nsmb.2751 Every RNA polymerase II transcript receives a 5′-end 7-methylguanosine (m7G) cap, which is rapidly bound by the nuclear cap-binding complex (CBC). Two recent studies now reveal that the CBC associates with a variety of effector proteins that enable it to interrogate nascent RNA, discriminating between distinct RNA subclasses and routing them either toward distinct maturation pathways or toward decay. Thus, the CBC has an early role in policing cellular RNA. Look Ma, no PCNA: how DNA polymerase ε synthesizes long stretches of DNA without a processivity factor   pp12 - 14 Karl E Zahn and Sylvie Doublié doi:10.1038/nsmb.2749 The long-awaited crystal structure of Saccharomyces cerevisiae DNA polymerase ε reveals a unique domain never before observed in B-family DNA polymerases. This novel domain endows polymerase ε with a capacity for highly processive DNA synthesis. See also: Article by Hogg et al. Chromatin remodeling: a collaborative effort   pp14 - 16 Patrick D Varga-Weisz doi:10.1038/nsmb.2748 Enzymes that alter nucleosome structure or position are at the very center of gene and genome regulation, and understanding how, and to what extent, these diverse activities collaborate and control each other to shape the genome for dynamic regulation is a major challenge. A new study provides an important step in this direction by illustrating the cooperative nature of ATP-dependent chromatin-remodeling systems in mammalian cells. See also: Article by Morris et al. Looking into the barrel of the RNA exosome   pp17 - 18 Claudia Schneider and David Tollervey doi:10.1038/nsmb.2750 The exosome complex has key roles in RNA processing and quality control. Single-particle EM analyses now provide compelling evidence for two distinct pathways by which substrate RNAs can pass through the exosome structure to reach the catalytic site for exonuclease digestion. See also: Article by Liu et al. Structural & Molecular Biology JOBS of the week Postdoctoral Associate in Molecular Biology University of Minnesota - Twin Cities PhD in Molecular Biology and Bioinformatics Universität Basel Molecular Biology - Postdoctoral Associate State University of New York Postdoctoral Position in Molecular Biology Roswell Park Cancer Institute(RPCI) Plant / Molecular Biology Research Assistant (JBEI) Lawrence Berkeley National Laboratory (LBNL) More Science jobs from Structural & Molecular Biology EVENT The Molecular and Developmental Biology of Drosophila 22.06.14 Kolymbari, Greece More science events from Research Highlights Top Targeting huntingtin | Babysitting the clock | TALlying lipid-protein interactions | Mind your pols and Qs Perspective Top Prereplication-complex formation: a molecular double take?   pp20 - 25 Hasan Yardimci and Johannes C Walter doi:10.1038/nsmb.2738 DNA replication begins with prereplication-complex formation at origins and is followed by helicase activation to unwind DNA at the replication fork. This Perspective compares bacterial DnaB and eukaryotic MCM2-7 helicase-loading mechanisms and discusses emerging data supporting current models of how two MCM2-7 complexes are loaded to form a double hexamer. Articles Top Staufen1 senses overall transcript secondary structure to regulate translation   pp26 - 35 Emiliano P Ricci, Alper Kucukural, Can Cenik, Blandine C Mercier, Guramrit Singh et al. doi:10.1038/nsmb.2739 Human Staufen1 (Stau1) is a double-stranded RNA-binding protein implicated in various post-transcriptional gene-regulatory processes. Genome-wide mapping of Stau1-binding sites, combined with Stau1 knockdown and overexpression analyses, has revealed a new role for Stau1 in regulating translation of GC-rich mRNAs by sensing overall transcript secondary structure. A phospho-BAD BH3 helix activates glucokinase by a mechanism distinct from that of allosteric activators   pp36 - 42 Benjamin Szlyk, Craig R Braun, Sanda Ljubicic, Elaura Patton, Gregory H Bird et al. doi:10.1038/nsmb.2717 Glucokinase activators are attractive therapeutics in diabetes, but their benefits can be offset by hypoglycemia, owing to the allosteric enhancement of the enzyme's glucose affinity. The biochemical and structural dissection of the interaction between glucokinase and a phosphomimetic of the BH3 a-helix derived from human BAD, a glucokinase-binding partner, demonstrates a new binding region and distinct mode of enzyme activation. Copper-transporting P-type ATPases use a unique ion-release pathway   pp43 - 48 Magnus Andersson, Daniel Mattle, Oleg Sitsel, Tetyana Klymchuk, Anna Marie Nielsen et al. doi:10.1038/nsmb.2721 P-type ATPases adopt different conformations during their transport cycle, including autophosphorylated forms. The structure of type IB P-type ATPase CopA is now solved in its E2P state. Comparison with a previous E2Pi structure indicates that dephosphorylation is not coupled to ion extrusion, in contrast to mechanisms in type IIA SERCA. The findings explain the effect of disease-related mutations in human Cu+ transporters. Structural basis for processive DNA synthesis by yeast DNA polymerase ε   pp49 - 55 Matthew Hogg, Pia Osterman, Göran O Bylund, Rais A Ganai, Else-Britt Lundström et al. doi:10.1038/nsmb.2712 The first X-ray crystal structure of the catalytic core of Saccharomyces cerevisiae DNA polymerase ε with a primed DNA template and an incoming dNTP reveals a new 'P domain' that encircles the DNA and contributes to the high processivity of this replicative polymerase. See also: News and Views by Zahn & Doublie Energetic analysis of the rhodopsin–G-protein complex links the a5 helix to GDP release   pp56 - 63 Nathan S Alexander, Anita M Preininger, Ali I Kaya, Richard A Stein, Heidi E Hamm et al. doi:10.1038/nsmb.2705 Activated G protein–coupled receptors promote GDP release by their cognate G proteins, through an allosteric mechanism that remains to be fully determined. Now DEER analyses are integrated with previously available structural data and computational work, thus generating a unified model for receptor-mediated G-protein activation. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis   pp64 - 72 Hume Stroud, Truman Do, Jiamu Du, Xuehua Zhong, Suhua Feng et al. doi:10.1038/nsmb.2735 Non-CG methylation is abundant in plants, but its functions are poorly understood. A new study has uncovered the contributions of each non-CG methyltransferase, including the poorly characterized methyltransferase CMT2, to DNA methylation patterning and gene silencing. The results suggest that non-CG methyltransferases participate in self-reinforcing loop mechanisms with histone H3 K9 methylation and small RNAs to control gene silencing throughout the Arabidopsis genome. Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions   pp73 - 81 Stephanie A Morris, Songjoon Baek, Myong-Hee Sung, Sam John, Malgorzata Wiench et al. doi:10.1038/nsmb.2718 ATP-dependent chromatin remodeling is essential for the dynamic organization of chromatin structure. Genome-wide localization and activity analyses now suggest that remodeler complexes substantially overlap in the mouse genome and that many regions require the activity of more than one remodeler to regulate chromatin accessibility. See also: News and Views by Varga-Weisz Structure of a pathogenic type 3 secretion system in action   pp82 - 87 Julia Radics, Lisa Königsmaier and Thomas C Marlovits doi:10.1038/nsmb.2722 The type III secretion systems of infectious bacteria use the needle-like injectisome to secrete proteins from the bacterial cytoplasm into host cells. Cryo-electron tomography and single-particle cryo-EM reveal for the first time the path of unfolded protein substrates through the narrow bore of the injectisome. Transcription-generated torsional stress destabilizes nucleosomes   pp88 - 94 Sheila S Teves and Steven Henikoff doi:10.1038/nsmb.2723 To test the effect of transcription-generated torsional stress on nucleosome dynamics and RNA polymerase II (Pol II) kinetics in Drosophila cells, a new study reports a genome-wide sequencing-based assay to measure torsional states at the gene level. Inhibition of topoisomerases leads to rapid accumulation of torsional strain accompanied by changes in Pol II kinetics and destabilization of nucleosomes. Visualization of distinct substrate-recruitment pathways in the yeast exosome by EM   pp95 - 102 Jun-Jie Liu, Matthew A Bratkowski, Xueqi Liu, Chu-Ya Niu, Ailong Ke et al. doi:10.1038/nsmb.2736 A combination of single-particle EM and biochemical analyses provides direct evidence for two distinct, substrate-specific recruitment pathways that channel RNAs for degradation by the eukaryotic exosome. See also: News and Views by Schneider & Tollervey Dynamics of yeast histone H2A and H2B phosphorylation in response to a double-strand break   pp103 - 109 Cheng-Sheng Lee, Kihoon Lee, Gaëlle Legube and James E Haber doi:10.1038/nsmb.2737 Histone H2A is rapidly phosphorylated to γH2AX at the site of DNA double-strand breaks (DSBs). A new, genome-wide analysis in Saccharomyces cerevisiae reports a second histone phosphorylation, γH2B, and examines the modification kinetics and chromosomal distribution of both γH2AX and γH2B and their propagation from DSBs to other genomic loci. Brief Communication Top Establishment of methylation patterns in ES cells   pp110 - 112 Ofra Sabag, Ayelet Zamir, Ilana Keshet, Merav Hecht, Guy Ludwig et al. doi:10.1038/nsmb.2734 Using embryonic stem cells as a model system for studying the basic bimodal DNA methylation pattern in vivo, a new study now indicates that demethylation is not required for generating unmethylated regions such as CpG islands as part of the overall bimodal methylation pattern but is involved in resetting methylation patterns during somatic-cell reprogramming. Top Advertisement Discover a world of scientific events.  The 2014 Natureevents Directory is now online and waiting to connect you with events vital to your career, worldwide. 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