Nature Methods Contents: March 2017 Volume 14 pp 209 - 323

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Advertisement MagCapture™ Exosome Isolation Kit PS Wako is has developed an exosome isolation kit using a novel affinity molecule. High yield high purity exosomes can be isolated by PS affinity method. Exosomes can be recovered from culture media containing FBS. TABLE OF CONTENTS March 2017 Volume 14, Issue 3 In This Issue Editorial This Month Correspondence Research Highlights Commentary Technology Feature News and Views Review Resource Brief Communications Articles Corrigendum Errata Advertisement Nikon is offering special pricing on our award winning Eclipse Ts2 inverted tissue culture microscope with phase contrast optics. The Ts2 features intuitive controls, a compact body, LED illumination, and smart accessories such as the Contrast Shield which allows fluorescent samples to be easily observed in brightly lit labs. For more information, go to www.nikoninstruments.com/ts2-promo Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Secreted Luciferase Reporter for Live Cell Analysis  $99 / Cloning Vector Secreted luciferase assays: Gaussia Luciferase (GLuc) and Secreted Alkaline Phosphatase (SEAP) enable live cell analysis Reporter vectors and clones: Cloning vectors Promoter reporter clones 3' UTR miRNA target clones Transcriptional response element reporter clones Learn more >>   Advertisement nature.com webcasts Springer Nature presents a custom webcast on: Advances in neuroscience research utilizing modern in situ RNA gene expression techniques. Date: 23rd March 2017 Time: 10AM PDT | 1PM EDT | 5PM GMT | 6PM CET Register for FREE and discover how Dr. Jerold Chun has used RNAscope to investigate the human brain Sponsor:  Advanced Cell Diagnostics     In This Issue Top In This Issue Editorial Top Responsible referencing   p209 doi:10.1038/nmeth.4219 Careful construction of reference lists is the responsibility of every scientist. This Month Top The Author File: Bart Deplancke   p211 Vivien Marx doi:10.1038/nmeth.4188 An engineered approach to study gene regulation, and why home is where the heart is. Points of Significance: Interpreting P values   pp213 - 214 Naomi Altman and Martin Krzywinski doi:10.1038/nmeth.4210 A P value measures a sample's compatibility with a hypothesis, not the truth of the hypothesis. Correspondence Top Should we ignore western blots when selecting antibodies for other applications?   p215 Fridtjof Lund-Johansen and Michael D Browning doi:10.1038/nmeth.4192 See also: Correspondence by Uhlen Response to: Should we ignore western blots when selecting antibodies for other applications?   pp215 - 216 Mathias Uhlen doi:10.1038/nmeth.4194 See also: Correspondence by Lund-Johansen & Browning Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses   pp216 - 217 Shijie C Zheng, Stephan Beck, Andrew E Jaffe, Devin C Koestler, Kasper D Hansen et al. doi:10.1038/nmeth.4187 See also: Correspondence by Rahmani et al. | Correspondence Correcting for cell-type heterogeneity in DNA methylation: a comprehensive evaluation   pp218 - 219 Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu et al. doi:10.1038/nmeth.4190 See also: Correspondence by Zheng et al. | Correspondence Editor's note on Zheng et al. and Rahmani et al.   p219 doi:10.1038/nmeth.4208 See also: Correspondence by Zheng et al. | Correspondence by Rahmani et al. Research Highlights Top Taking nanoscopy to the limit MINFLUX nanoscopy can obtain 1-nm localization precision with orders of magnitude fewer emitted photons. Cerebral organoids enter the fold Two groups use cerebral organoids to model brain development and disease. Another player for RNA-guided RNA cleavage Cas13b relies on activator and repressor proteins to regulate RNA cleavage. Precision switches for protein control Light- or drug-dependent switches enable precise control over signaling pathways in living cells. Protein holography Low-energy holography enables imaging single proteins and protein complexes. Methods in Brief Improved 3D single-molecule imaging | Cell-based fragment screening | Biomechanical properties measured in vivo | Faster Bayesian localization microscopy Tools in Brief CRiNCL unveils noncoding RNA functions | Crystal Skull—a panoramic view of the brain | Microbial genomes on a chip | Sequence covariation predicts the effects of mutation Methods JOBS of the week Post-doctoral positions / Scientist (m/f) in Physics/Chemistry The Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. Protein Trafficking Expert Astex Pharmaceuticals Senior Scientific Editor at D. E. Shaw Research D. E. Shaw Research Associate Director Center for Patient Derived Models Dana-Farber Cancer Institute Two Junior Group Leader Positions Centre for Genomic Regulation More Science jobs from Methods EVENT Materials, Methods & Technologies 2017, 19th International Conference 26 - 30 June 2017 Elenite, Bulgaria More science events from Commentary Top EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research   pp228 - 232 EV-TRACK Consortium:  Jan Van Deun, Pieter Mestdagh, Patrizia Agostinis, Ozden Akay et al. doi:10.1038/nmeth.4185 Technology Feature Top Cell biology: tracking a cell's cycle   pp233 - 236 Vivien Marx doi:10.1038/nmeth.4186 The tools that clock a cell's everyday affairs reveal plenty that's out of the ordinary. News and Views Top Genetic screening enters the single-cell era   pp237 - 238 Daniel E Wagner and Allon M Klein doi:10.1038/nmeth.4196 Four studies overcome the limitations of pooled and arrayed genetic screens by integrating single-cell transcriptomics. See also: Article by Datlinger et al. Stratifying tissue heterogeneity with scalable single-cell assays   pp238 - 239 Kun Zhang doi:10.1038/nmeth.4209 Three methods dramatically improve the scale of single-cell genomic sequencing and structural assays, allowing for the hierarchical partitioning of cell populations within a tissue. See also: Brief Communication by Ramani et al. | Article by Vitak et al. Synthetic human proteomes for accelerating protein research   pp240 - 242 Yasset Perez-Riverol and Juan Antonio Vizcaino doi:10.1038/nmeth.4191 The generation of synthetic human proteomes and future derived tools will expand knowledge in protein biology. See also: Resource by Matsumoto et al. | Brief Communication by Zolg et al. Review Top A guide to designing germline-dependent epigenetic inheritance experiments in mammals   pp243 - 249 Johannes Bohacek and Isabelle M Mansuy doi:10.1038/nmeth.4181 This Review discusses key aspects of experimental design to evaluate intergenerational and transgenerational epigenetic inheritance. It describes advantages of patrilineal and matrilineal design, and it offers advice for selecting animals for breeding and for determining the weaning scheme and group size. Resource Top A large-scale targeted proteomics assay resource based on an in vitro human proteome   pp251 - 258 Masaki Matsumoto, Fumiko Matsuzaki, Kiyotaka Oshikawa, Naoki Goshima, Masatoshi Mori et al. doi:10.1038/nmeth.4116 A large-scale resource, iMPAQT, provides multiple reaction monitoring (MRM)-mass spectrometry assays for targeted quantitative analysis of mTRAQ-labeled human proteins. See also: News and Views by Perez-Riverol & Vizcaino Brief Communications Top Building ProteomeTools based on a complete synthetic human proteome   pp259 - 262 Daniel P Zolg, Mathias Wilhelm, Karsten Schnatbaum, Johannes Zerweck, Tobias Knaute et al. doi:10.1038/nmeth.4153 The ProteomeTools project provides the proteomics community with a physical synthetic tryptic peptide resource and a digital LC-MS/MS data resource covering all human proteins. See also: News and Views by Perez-Riverol & Vizcaino Massively multiplex single-cell Hi-C   pp263 - 266 Vijay Ramani, Xinxian Deng, Ruolan Qiu, Kevin L Gunderson, Frank J Steemers et al. doi:10.1038/nmeth.4155 Single-cell combinatorial indexed Hi-C (sciHi-C) is a streamlined protocol for generating thousands of high-quality single-cell chromosome conformation data sets that resemble bulk Hi-C data in aggregate. See also: News and Views by Zhang Effective detection of variation in single-cell transcriptomes using MATQ-seq   pp267 - 270 Kuanwei Sheng, Wenjian Cao, Yichi Niu, Qing Deng and Chenghang Zong doi:10.1038/nmeth.4145 MATQ-seq is a highly sensitive single-cell RNA-seq protocol that enables the detection of true subtle biological variations among single cells as well as the capture of nonpolyadenylated RNA. Optogenetic inhibition of behavior with anion channelrhodopsins   pp271 - 274 Farhan Mohammad, James C Stewart, Stanislav Ott, Katarina Chlebikova, Jia Yi Chua et al. doi:10.1038/nmeth.4148 Anion channelrhodopsins are light-sensitive chloride channels that can be used as optogenetic inhibitors. Mohammad et al. report their application in Drosophila, showing that various behaviors can be inhibited in a light-dependent manner. Characterizing cell subsets using marker enrichment modeling   pp275 - 278 Kirsten E Diggins, Allison R  Greenplate, Nalin Leelatian, Cara E Wogsland and Jonathan M Irish doi:10.1038/nmeth.4149 Marker enrichment modeling (MEM) provides an objective metric for characterizing cell populations from high-content single-cell analysis. The MEM score outperforms standard metrics and provides a machine-readeable label for cell subsets. Post-translational selective intracellular silencing of acetylated proteins with de novo selected intrabodies   pp279 - 282 Michele Chirichella, Simonetta Lisi, Marco Fantini, Martina Goracci, Mariantonietta Calvello et al. doi:10.1038/nmeth.4144 PISA, generates intrabodies that selectively bind and interfere with the intracellular function of an acetylated version of a target protein. High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles   pp283 - 286 Michiel van de Waterbeemd, Kyle L Fort, Dmitriy Boll, Maria Reinhardt-Szyba, Andrew Routh et al. doi:10.1038/nmeth.4147 Instrumental modifications enable native mass spectrometry analysis with unprecedented mass resolution, especially at high mass-to-charge ratios, as illustrated through the analysis of intact ribosome particles. One-step generation of conditional and reversible gene knockouts   pp287 - 289 Amanda Andersson-Rolf, Roxana C Mustata, Alessandra Merenda, Jihoon Kim, Sajith Perera et al. doi:10.1038/nmeth.4156 The combination of knocking one allele out with CRISPR-mediated NHEJ and targeting the other with a conditionally inactivating cassette allows rapid generation of conditional alleles. Advertisement nature.com webcasts Custom webcast on: Analyzing Ebola virus glycoprotein and its interactions with therapeutic antibodies using CG-MALS Date: Wednesday, March 15, 2017 Time: 8am PDT | 11am EDT | 3pm GMT | 4pm CET Register for Free Sponsor:  Sponsor: Wyatt Technology Corporation     Articles Top cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination   pp290 - 296 Ali Punjani, John L Rubinstein, David J Fleet and Marcus A Brubaker doi:10.1038/nmeth.4169 A software tool, cryoSPARC, addresses the speed bottleneck in cryo-EM image processing, enabling automated macromolecular structure determination in hours on a desktop computer without requiring a starting model. Pooled CRISPR screening with single-cell transcriptome readout   pp297 - 301 Paul Datlinger, Andre F Rendeiro, Christian Schmidl, Thomas Krausgruber, Peter Traxler et al. doi:10.1038/nmeth.4177 CROP-seq enables pooled CRISPR screens for complex transcriptome signatures by making gRNA expression detectable in single-cell RNA sequencing. See also: News and Views by Wagner & Klein Sequencing thousands of single-cell genomes with combinatorial indexing   pp302 - 308 Sarah A Vitak, Kristof A Torkenczy, Jimi L Rosenkrantz, Andrew J Fields, Lena Christiansen et al. doi:10.1038/nmeth.4154 Single-cell combinatorial indexed sequencing (SCI-seq) resolves genomic heterogeneity by generating thousands of low-pass single-cell libraries at once for somatic copy number variant detection. See also: News and Views by Zhang Single-cell mRNA quantification and differential analysis with Census   pp309 - 315 Xiaojie Qiu, Andrew Hill, Jonathan Packer, Dejun Lin, Yi-An Ma et al. doi:10.1038/nmeth.4150 The Census tool converts single-cell RNA-seq relative read counts to relative transcript counts for more accurate differential gene expression and analysis in the absence of spike-ins or molecular barcodes. SMiLE-seq identifies binding motifs of single and dimeric transcription factors   pp316 - 322 Alina Isakova, Romain Groux, Michael Imbeault, Pernille Rainer, Daniel Alpern et al. doi:10.1038/nmeth.4143 The Microfluidic-based Ligand Enrichment (SMiLE) sequencing strategy probes DNA binding of single and heterodimeric transcription factors over a wide affinity range. Corrigendum Top Corrigendum: eC-CLEM: flexible multidimensional registration software for correlative microscopies   p323 Perrine Paul-Gilloteaux, Xavier Heiligenstein, Martin Belle, Marie-Charlotte Domart, Banafshe Larijani et al. doi:10.1038/nmeth0317-323a Errata Top Erratum: Faster brain imaging   p323 Nina Vogt doi:10.1038/nmeth0317-323b Erratum: Epitranscriptome sequencing technologies: decoding RNA modifications   p323 Xiaoyu Li, Xushen Xiong and Chengqi Yi doi:10.1038/nmeth0317-323c Top 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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