Nature Methods Contents: April 2013 Volume 10 pp 271 - 365

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For a limited time, you can take advantage of exceptional packages with our special trade-in, trade-up program. Learn more today. bdbiosciences.com/go/greenlight Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement RNA-Seq 2013 18-20 June 2013 | Boston, MA Your comprehensive guide to applying RNA-Seq in research and drug discovery Featuring RNA-Seq experts from... Genentech, Broad Institute, Novartis, Yale, Merck, NIH, Genzyme, BMS, GSK, AstraZeneca, AVEO, Biogen Idec, Sanofi and Stanford among others. Visit the website and download the brochure for more information. www.rna-seqsummit.com   Advertisement Nature Genetics Focus on iCOGS Nature Genetics is pleased to present the iCOGS print and online Focus advancing our understanding of the genetic susceptibility to three common hormone-related cancers-breast, ovarian and prostate cancers. This collection of 13 papers by the COGS (Collaborative Oncological Gene-environment Study) Consortium is accompanied by editorial essays highlighting and analyzing the main themes of this milestone in genetic epidemiology. View the Focus for FREE at: www.nature.com/ng/focus/iCOGS Produced with support from Illumina   In This Issue Top In This Issue Editorial Top Will technology deliver for 'big neuroscience'?   p271 doi:10.1038/nmeth.2435 European and US initiatives aiming to improve our understanding of the brain will require important leaps in technological development. This Month Top The author file: Emma Lundberg   p273 Vivien Marx doi:10.1038/nmeth.2414 A large-scale comparative study of techniques to localize proteins leads to paths through cells and forests. Points of view: Labels and callouts   p275 Martin Krzywinski doi:10.1038/nmeth.2405 Figure labels require the same consistency and alignment in their layout as text. Correspondence Top FISH-quant: automatic counting of transcripts in 3D FISH images   pp277 - 278 Florian Mueller, Adrien Senecal, Katjana Tantale, Hervé Marie-Nelly, Nathalie Ly, Olivier Collin, Eugenia Basyuk, Edouard Bertrand, Xavier Darzacq and Christophe Zimmer doi:10.1038/nmeth.2406 Protein instability following transport or storage on dry ice   pp278 - 279 Brian M Murphy, Spencer Swarts, Barbara M Mueller, Peter van der Geer, Mark C Manning and Mark I Fitchmun doi:10.1038/nmeth.2409 Research Highlights Top Mammalian genes interacting RNA interference (RNAi)-based genetic interaction screens in mammalian cells show how genes affect each other. An enhanced view of the brain A digital atlas of enhancers active in the developing mammalian brain is available for exploration. Tumors have their differences Developing tools to detect the rare mutations found in tumors demands a lot of data and rigorous benchmarking. Marked for depth An in vivo protein-labeling strategy could enable more comprehensive surveys of organelle proteomic contents. Metalloenzyme structures in a shot Researchers study the structure of the metalloenzyme photosystem II by applying femtosecond X-ray pulses to simultaneously record X-ray diffraction and X-ray emission spectroscopy data. Mouse models challenged A systematic comparison of gene expression patterns in human inflammatory conditions and in their corresponding mouse models raises troubling questions. Peering at protons Unusual properties of a diamond defect are exploited to achieve progress toward nanometer-scale magnetic resonance imaging (MRI). Methods JOBS of the week Biostatistician / Computational Biologist Lieber Institute for Brain Development Director of the Research Centre for Toxic Compounds in the Environment Masaryk University, Faculty of Science Postdoctoral Fellow Cancer Science Institute of Singapore Group Leader Postion in Bioinformatics The Institute of Genetic Diseases Imagine Postdoctoral Fellow Mount Sinai School of Medicine (Brown Lab) More Science jobs from Methods EVENT Statistical Methods for Functional Genomics 21st June 2013 New York, USA More science events from Methods in Brief Top Population mixing to finish the genome | Nanopore-based protein sequencing | Particle imaging beyond the quantum limit | Rare variants run in the family Tools in Brief Top A genome-wide TALEN resource | 'Self' peptides for enhanced delivery | Protein degradation sensors | Logic and memory integrated in a synthetic circuit Technology Feature Top Drilling into big cancer-genome data   pp293 - 297 Vivien Marx doi:10.1038/nmeth.2410 Paving roads through data mountains, consortia are developing workflows and tools for widespread use. News and Views Top Reproducibility restored—on toward the human interactome   pp301 - 303 Pascal Braun doi:10.1038/nmeth.2412 A two-laboratory study of the reproducibility of affinity purification-mass spectrometry shows that a standardized protocol results in highly reproducible interactome data. See also: Analysis by Varjosalo et al. A revolution coming to a classic model organism   pp303 - 306 David Jonah Grunwald doi:10.1038/nmeth.2415 Classic gene targeting and gene replacement can now be achieved in zebrafish after cleaving the genome with engineered nucleases in the presence of donor DNA. This simple-to-implement method enables new classes of biological study in this important model organism. See also: Brief Communication by Zu et al. Analysis Top Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS   pp307 - 314 Markku Varjosalo, Roberto Sacco, Alexey Stukalov, Audrey van Drogen, Melanie Planyavsky, Simon Hauri, Ruedi Aebersold, Keiryn L Bennett, Jacques Colinge, Matthias Gstaiger and Giulio Superti-Furga doi:10.1038/nmeth.2400 A systematic study of the intra- and interlaboratory reproducibility of a standardized affinity purification-mass spectrometry protocol demonstrates the high reproducibility of this technique and hints at the feasibility of a large-scale human interactome project through interlaboratory efforts. See also: News and Views by Braun Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells   pp315 - 323 Charlotte Stadler, Elton Rexhepaj, Vasanth R Singan, Robert F Murphy, Rainer Pepperkok, Mathias Uhlén, Jeremy C Simpson and Emma Lundberg doi:10.1038/nmeth.2377 In this analysis, the authors directly compared immunofluorescence and fluorescent-protein tagging of 506 human proteins and studied their subcellular localization. They conclude that the two methodologies are highly complementary and propose an integrative strategy for the characterization of newly identified proteins. Brief Communications Top Predicting the molecular complexity of sequencing libraries   pp325 - 327 Timothy Daley and Andrew D Smith doi:10.1038/nmeth.2375 A statistical method and software yields accurate predictions of sequencing library complexity on the basis of initial shallow sequencing surveys, allowing robust estimates of how deep to sequence for adequate coverage. TALEN-mediated precise genome modification by homologous recombination in zebrafish   pp329 - 331 Yao Zu, Xiangjun Tong, Zhanxiang Wang, Da Liu, Ruochuan Pan, Zhe Li, Yingying Hu, Zhou Luo, Peng Huang, Qian Wu, Zuoyan Zhu, Bo Zhang and Shuo Lin doi:10.1038/nmeth.2374 Gene targeting via homologous recombination is achieved in the zebrafish with TALENs and double-stranded DNA donors, expanding the range of experimental possibilities in this organism. See also: News and Views by Grunwald Neutron-encoded mass signatures for multiplexed proteome quantification   pp332 - 334 Alexander S Hebert, Anna E Merrill, Derek J Bailey, Amelia J Still, Michael S Westphall, Eric R Strieter, David J Pagliarini and Joshua J Coon doi:10.1038/nmeth.2378 A method called neutron-encoding SILAC will enable higher-order multiplexing with high accuracy in quantitative proteomics experiments. Ultrahigh accuracy imaging modality for super-localization microscopy   pp335 - 338 Jerry Chao, Sripad Ram, E Sally Ward and Raimund J Ober doi:10.1038/nmeth.2396 An imaging modality that restricts the number of photons detected in each pixel of an electron-multiplying CCD to an average of <1 allows single-fluorophore localization accuracies that approach the ultimate limit. A Y2H-seq approach defines the human protein methyltransferase interactome   pp339 - 342 Mareike Weimann, Arndt Grossmann, Jonathan Woodsmith, Ziya Özkan, Petra Birth, David Meierhofer, Nouhad Benlasfer, Taras Valovka, Bernd Timmermann, Erich E Wanker, Sascha Sauer and Ulrich Stelzl doi:10.1038/nmeth.2397 A high-sensitivity, high-quality yeast two-hybrid screen using short-read sequencing as its readout is used to map the interactome of human methyltransferases. QuaNCAT: quantitating proteome dynamics in primary cells   pp343 - 346 Andrew J M Howden, Vincent Geoghegan, Kristin Katsch, Georgios Efstathiou, Bhaskar Bhushan, Omar Boutureira, Benjamin Thomas, David C Trudgian, Benedikt M Kessler, Daniela C Dieterich, Benjamin G Davis and Oreste Acuto doi:10.1038/nmeth.2401 Combining a method to label newly synthesized proteins and a strategy to distinguish two populations in cell culture allows quantitative assessment of intracellular protein dynamics. Advertisement Achieve cDNA Success. Your challenge: overcome long targets, secondary structure & limited research budget to get full-length cDNA. The solution: PrimeScript™ RTase - fast, affordable, powerful, RNase H-. Learn how PrimeScript RTase can help your cDNA mission: Download the Application Note   Articles Top Quantitative estimation of activity and quality for collections of functional genetic elements   pp347 - 353 Vivek K Mutalik, Joao C Guimaraes, Guillaume Cambray, Quynh-Anh Mai, Marc Juul Christoffersen, Lance Martin, Ayumi Yu, Colin Lam, Cesar Rodriguez, Gaymon Bennett, Jay D Keasling, Drew Endy and Adam P Arkin doi:10.1038/nmeth.2403 This linear ANOVA-based method quantifies the activity of different combinations of genetic elements and assigns a score that indicates the variation in performance across changing contexts. Precise and reliable gene expression via standard transcription and translation initiation elements   pp354 - 360 Vivek K Mutalik, Joao C Guimaraes, Guillaume Cambray, Colin Lam, Marc Juul Christoffersen, Quynh-Anh Mai, Andrew B Tran, Morgan Paull, Jay D Keasling, Adam P Arkin and Drew Endy doi:10.1038/nmeth.2404 By using a bicistronic design, with a leader peptide that overlaps with and contains the Shine-Dalgarno site for a downstream gene of interest, the authors demonstrate reliable, context-independent gene expression. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing   pp361 - 365 Nicola Crosetto, Abhishek Mitra, Maria Joao Silva, Magda Bienko, Norbert Dojer, Qi Wang, Elif Karaca, Roberto Chiarle, Magdalena Skrzypczak, Krzysztof Ginalski, Philippe Pasero, Maga Rowicka and Ivan Dikic doi:10.1038/nmeth.2408 Biotinylated tags bind double-strand breaks in genomic DNA; after enrichment and sequencing, this allows precise, genome-wide mapping of the breaks. Advertisement CNIO, Nature, Nature Cell Biology and Nature Reviews Cancer present: CNIO Cancer Symposium: Frontiers in Tumor Heterogeneity and Plasticity October 27-30, 2013 Madrid, Spain Click here for more information or to register for this conference today!   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. 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