Nature Structural & Molecular Biology Contents: 2017 Volume #24 pp 1007 - 1163

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Advertisement Is your organization planning a scientific event or conference for 2018?  Looking for a way to increase the number of attendees? Advertise in the Natureevents Directory 2018.  Available online and in print. Ad close deadline: 4 December, 2017  TABLE OF CONTENTS December 2017 Volume 24, Issue 12 News and Views Review Perspective Articles   Advertisement   Focus issue on Mechanobiology  Nature Reviews Molecular Cell Biology presents a focus issue highlighting the importance of mechanotransduction — the conversion of mechanical forces into biochemical signals — in morphogenesis, tissue regeneration and disease, including tumorigenesis. The articles discuss our understanding of how mechanical forces are transduced into the cell, including the nucleus, to regulate gene expression, and the therapeutic potential of modulating the mechanobiology of cells and tissues.  Free access to select content for a limited time.   Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Nature Collection: 2017 Nobel Prize in Physiology or Medicine The 2017 Nobel Prize in Physiology or Medicine was awarded to Jeffrey C. Hall, Michael Rosbash and Michael W. Young for their pioneering work in Drosophila that elucidated the molecular mechanisms controlling circadian rhythm.  Access this collection free online >>   Produced with support from:  Vanda Pharmaceuticals    Advertisement Poster on: The expanding CRISPR toolbox  The CRISPR-Cas9 system can do a lot more than gene editing. This Poster, from Nature Methods, explores the newest possibilities of CRISPR.  Available to download free online >> Produced with support from:  Dharmacon    News and Views Top Polθ helicase: drive or reverse   pp1007 - 1008 Judith L Campbell and Hongzhi Li doi:10.1038/nsmb.3510 The helicase intrinsic to DNA polymerase θ (Polθ), the versatile mediator of microhomology-based repair of DNA double-strand breaks and stalled replication forks, is now revealed to be a member of an elite group of proteins known as annealing helicases. This small family of enzymes remodels DNA intermediates in multiple repair processes that are crucial to preserving genome stability and warding off cancer and aging. See also: Article by Mateos-Gomez et al. One flexible loop in OST lassos both substrates   pp1009 - 1010 Shiteshu Shrimal, Natalia A Cherepanova and Reid Gilmore doi:10.1038/nsmb.3508 The crystal structure of an oligosaccharyltransferase in complex with a sugar donor and an acceptor peptide provides insight into the mechanism of protein glycosylation and reveals how lipid-linked oligosaccharides are positioned in the enzyme active site. See also: Article by Napiorkowska et al. Poly(A) tails: longer is not always better   pp1010 - 1011 Luciana A Castellano and Ariel A Bazzini doi:10.1038/nsmb.3509 Deadenylation of mRNAs is generally associated with translational inhibition and mRNA decay. A study now reports that, unexpectedly, highly expressed genes tend to have shorter poly(A) tails and suggests that poly(A) tails can be 'pruned', generating a 30-nucleotide-biased phased distribution, likely due to protection by poly(A)-binding proteins. See also: Article by Lima et al. Review Catching DNA with hoops—biophysical approaches to clarify the mechanism of SMC proteins   pp1012 - 1020 Jorine Eeftens and Cees Dekker doi:10.1038/nsmb.3507 In this Review, the authors consider how single-molecule biophysical approaches can inform our understanding of the ring-shaped structural maintenance of chromosome (SMC) complexes and their function in chromosome organization.   Structural & Molecular Biology JOBS of the week MRC WIMM Prize PhD Studentships Weatherall Institute of Molecular Medicine, University of Oxford Posdoctoral position CNRS & Bordeaux University NIDDK / NIH Post-Doctoral Fellowship position National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK) Research Assistant - FMI Group Liberali Friedrich Miescher Institute for Biomedical Research (FMI) Postdoctoral Fellowship in Metabolism or Tissue Fibrosis University of California - San Francisco More Science jobs from Structural & Molecular Biology EVENT International conference on plant and molecular biology 22.02.18 Paris, France More science events from Perspective Top The ribosome moves: RNA mechanics and translocation   pp1021 - 1027 Harry F Noller, Laura Lancaster, Jie Zhou and Srividya Mohan doi:10.1038/nsmb.3505 The mechanics and mechanisms of ribosomal translocation, including the conformational rearrangements in the ribosome and the roles of EF-G and tRNAs, are discussed in this Perspective by Mohan, Noller and colleagues.   Advertisement Nature Collection: 2017 Nobel Prize in Chemistry  Nature Research present this Collection of articles celebrating the 2017 Nobel Prize in Chemistry to Jacques Dubochet, Joachim Frank and Richard Henderson, recognised "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution".  Access the collection here >>  Produced with support from:  Thermo Fisher Scientific   Articles Top Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA   pp1028 - 1038 Xueyin Wang, Richard D Paucek, Anne R Gooding, Zachary Z Brown, Eva J Ge et al. doi:10.1038/nsmb.3487 Biochemical reconstitution of PRC2 interactions with chromatinized templates demonstrates that protein-free linker DNA dominates the PRC2-nucleosome interaction, while RNA inhibits binding.   DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation   pp1039 - 1047 Jeongyoon Choi, Andreas Linus Bachmann, Katharina Tauscher, Christian Benda, Beat Fierz et al. doi:10.1038/nsmb.3488 The DNA-binding activity of the winged-helix domain of PHF1 stabilizes PRC2 on chromatin, thereby permitting efficient H3K27 trimethylation.   Histone propionylation is a mark of active chromatin   pp1048 - 1056 Adam F Kebede, Anna Nieborak, Lara Zorro Shahidian, Stephanie Le Gras, Florian Richter et al. doi:10.1038/nsmb.3490 Histone H3 lysine 14 is propionylated and butyrylated in vivo in a metabolic-state-dependent manner and these modifications promote high levels of transcription.   Short poly(A) tails are a conserved feature of highly expressed genes   pp1057 - 1063 Sarah Azoubel Lima, Laura B Chipman, Angela L Nicholson, Ying-Hsin Chen, Brian A Yee et al. doi:10.1038/nsmb.3499 Although deadenylation induces translational inhibition and mRNA decay, well-expressed transcripts are now shown to possess short, well-defined poly(A) tails, suggesting that pruned tails may be ideal for protective and translational functions. See also: News and Views by Castellano & Bazzini Dissecting the telomere-inner nuclear membrane interface formed in meiosis   pp1064 - 1072 Devon F Pendlebury, Yasuhiro Fujiwara, Valerie M Tesmer, Eric M Smith, Hiroki Shibuya et al. doi:10.1038/nsmb.3493 Structural and functional analyses of human TRF1 in complex with meiosis-specific protein TERB1 reveal the basis for telomere tethering to the inner nuclear membrane and offer insight into the mechanism of dissociation in late pachytene.   Telomeric TERB1-TRF1 interaction is crucial for male meiosis   pp1073 - 1080 Juanjuan Long, Chenhui Huang, Yanyan Chen, Ying Zhang, Shaohua Shi et al. doi:10.1038/nsmb.3496 Disrupting the interaction between telomere protein TRF1 with meiosis-specific protein TERB1 impairs the pairing of X and Y chromosomes via their telomere-adjacent pseudoautosomal regions in pachytene, leading to spermatocyte apoptosis and male infertility in mice.   Dynamic regulation of CD28 conformation and signaling by charged lipids and ions   pp1081 - 1092 Wei Yang, Weiling Pan, Shuokai Chen, Nicola Trendel, Shutan Jiang et al. doi:10.1038/nsmb.3489 CD28 signaling motifs are sequestered within the membrane via interactions with phospholipids. TCR activation increases the local Ca2+ concentration, which disrupts CD28-lipid interactions.   A consensus model of human apolipoprotein A-I in its monomeric and lipid-free state   pp1093 - 1099 John T Melchior, Ryan G Walker, Allison L Cooke, Jamie Morris, Mark Castleberry et al. doi:10.1038/nsmb.3501 Apolipoprotein A-I (apoA-I) is the scaffold protein that is essential for the assembly and function of HDL particles. A structural model for monomeric, lipid-free apoA-I, based on previous and new data, is now presented.   Molecular basis of lipid-linked oligosaccharide recognition and processing by bacterial oligosaccharyltransferase   pp1100 - 1106 Maja Napiorkowska, Jeremy Boilevin, Tina Sovdat, Tamis Darbre, Jean-Louis Reymond et al. doi:10.1038/nsmb.3491 The crystal structure of the single-subunit oligosaccharyltransferase PglB in complex with acceptor peptide and a synthetic lipid-linked oligosaccharide analog reveals a key intermediate in the reaction mechanism. See also: News and Views by Shrimal et al. Preribosomes escaping from the nucleus are caught during translation by cytoplasmic quality control   pp1107 - 1115 Anshuk Sarkar, Matthias Thoms, Clara Barrio-Garcia, Emma Thomson, Dirk Flemming et al. doi:10.1038/nsmb.3495 Abnormal pre-60S particles are able to escape nuclear quality control and join mature 40S subunits to catalyze cytoplasmic protein synthesis, but the resulting translation defects trigger the cytoplasmic surveillance machineries RQC and the Ski-exosome.   The helicase domain of Polθ counteracts RPA to promote alt-NHEJ   pp1116 - 1123 Pedro A Mateos-Gomez, Tatiana Kent, Sarah K Deng, Shane McDevitt, Ekaterina Kashkina et al. doi:10.1038/nsmb.3494 Biochemical and cellular analyses reveal that the helicase activity of DNA polymerase theta (Polθ) antagonizes RPA to promote DNA strand annealing and double-strand break repair via alt-NHEJ in mouse ES cells. See also: News and Views by Campbell & Li Extrachromosomal telomere repeat DNA is linked to ALT development via cGAS-STING DNA sensing pathway   pp1124 - 1131 Yi-An Chen, Yi-Ling Shen, Hsuan-Yu Hsia, Yee-Peng Tiang, Tzu-Ling Sung et al. doi:10.1038/nsmb.3498 The cGAS-STING cytoplasmic-DNA-sensing pathway is activated by accumulation of extrachromosomal telomere repeats, and this proliferation-inhibition mechanism is defective in ALT cancer cells.   Programming asynchronous replication in stem cells   pp1132 - 1138 Hagit Masika, Marganit Farago, Merav Hecht, Reba Condiotti, Kirill Makedonski et al. doi:10.1038/nsmb.3503 Asynchronous replication-timing patterns undergo programmed switching between maternal and paternal alleles in embryonic and adult stem cells.   TFIIH generates a six-base-pair open complex during RNAP II transcription initiation and start-site scanning   pp1139 - 1145 Eric J Tomko, James Fishburn, Steven Hahn and Eric A Galburt doi:10.1038/nsmb.3500 During transcription initiation, Ssl2, the dsDNA translocase of TFIIH, opens a 6-bp DNA bubble, suggesting a two-step model wherein Ssl2 triggers a 6-bp open complex that RNA polymerase II expands via NTP-dependent RNA transcription.   Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states   pp1146 - 1154 Xiaoyuan Zhou, Minghui Li, Deyuan Su, Qi Jia, Huan Li et al. doi:10.1038/nsmb.3502 Cryo-EM analyses of human TRPML3 reveal this channel in three different states—closed, agonist-activated and low-pH-inhibited—and suggest mechanisms for regulation.   Encoding optical control in LCK kinase to quantitatively investigate its activity in live cells   pp1155 - 1163 Ardiyanto Liaunardy-Jopeace, Ben L Murton, Mohan Mahesh, Jason W Chin and John R James doi:10.1038/nsmb.3492 Engineering an LCK mutant, in which an active-site lysine is replaced by a photocaged equivalent via genetic code expansion, allows quantitation of phosphorylation kinetics in situ and provides insights into LCK activation dynamics.   Advertisement npj Molecular Phenomics is an online-only, open access journal that provides a forum for cutting-edge scientific advances in the emerging field of phenomics, the study of the physical and chemical characteristics of an individual in quantitative terms. Part of the Nature Partner Journals series, npj Molecular Phenomics is published in partnership with Fudan University. The journal is now open for submissions. Find out more >>>   Top Advertisement 40 years of Sanger DNA sequencing  Research and Commentary reflecting on the evolution and future of Sanger DNA sequencing  Access the Collection online >>    Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

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