Nature Methods Contents: January 2014 Volume 11 pp 1 - 112

Advertisement Successful experiments happen with Reichert Surface Plasmon Resonance (SPR) instruments Reichert SPR systems generate precise kinetics (on/off rates), affinity and thermodynamics data for lead optimization. The ultra-sensitive systems are flexible and affordable. Discover the importance of rate constants and read about the TraceDrawer data analysis program in the SPR Insider Blog ReichertSPR.com  TABLE OF CONTENTS January 2014 Volume 11, Issue 1 In This Issue Special Feature Editorial This Month Research Highlights News Feature Technology Feature News and Views Analysis Brief Communications Articles Advertisement Special Offer: Enhanced BD Horizon™ Brilliant Violet™ Reagents Buy enhanced BD Horizon™ Brilliant Violet™ reagents and receive a free bandpass filter. Brighter than traditional dyes, these reagents can help you to resolve rare and dim cell populations, revealing nature's secrets with unprecedented clarity. Special offer details, tools, and information available now. bdbiosciences.com/go/brilliant Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Nature Collections  LIGHT-SHEET MICROSCOPY  The use of a planar sheet of light for illumination in light-sheet fluorescence microscopy allows researchers to image sample volumes faster than is possible with other current methods, while limiting light dosage. A collection of articles from Nature Methods, Nature Communications and Nature Reviews Molecular Cell Biology provides a brief overview of this exciting imaging technology and the biological research applications that it makes possible. Produced with support from:  Carl Zeiss Microscopy    In This Issue Top InThisIssue    Special Feature Top Method of the Year 2013 Contents Editorial News Feature Primer Commentary Methods to Watch Nature Methods' choice for Method of the Year 2013 is single-cell sequencing. A collection of articles present the unique considerations related to sequencing single cells and highlight recent applications in biology and medicine. The Methods to Watch feature provides a look at possible future Methods of the Year. Editorial Top Special feature: Method of the Year 2013 Method of the Year 2013   p1 doi:10.1038/nmeth.2801 Methods to sequence the DNA and RNA of single cells are poised to transform many areas of biology and medicine. This Month Top Benjamin F. Cravatt   p3 Vivien Marx doi:10.1038/nmeth.2774 Building an approach to quantify chinks in a protein's armor. Research Highlights Top Genomes in 3D improve one-dimensional assemblies Chromosome conformation capture data provide scaffolds for de novo genome assemblies. Unfolding to force Applying tiny forces to single molecules at high speed reveals the mechanics behind molecule unfolding. Electron crystallography goes 3D WITH MicroED Electron diffraction using three-dimensional (3D) crystals may expand the reach of this technique. Protein nanopores to detect DNA methylation Two groups use nanopore sequencing through a protein pore to detect methylcytosine and hydroxymethylcytosine. The in vivo RNA structurome Genome-wide, in vivo RNA structure probing helps reveal how RNA structure regulates gene expression. Methods in Brief Bias in ChIP-seq data | A solution to the phasing problem | Transcriptome of a single nucleus | Engineering detergent-stable membrane proteins Tools in Brief Chemically probing GPCR-ligand interactions | 3D expansion of human pluripotent stem cells | TALENs knock out human microRNAs | Seeing the brain through a prism Methods JOBS of the week Postdoc position in top-down proteomics UVic-Genome BC Proteomics Centre PhD student position Goethe University Frankfurt a.M Postdoctoral Fellow Icahn School of Medicine at Mount Sinai Postdoctoral position in Bioinformatics (Dr. Zoghbi Lab) Baylor College of Medicine (BCM) Biostatistical / Computational Postdoctoral Fellow Brigham & Women's Hospital - Harvard Medical School More Science jobs from Methods EVENT Modern Synthetic Methods in Organofluorine Chemistry 6th March 2014 London, UK More science events from News Feature Top Special feature: Method of the Year 2013 Singled out for sequencing   pp13 - 17 Kelly Rae Chi doi:10.1038/nmeth.2768 Single-cell genome and transcriptome sequencing methods are generating a fresh wave of biological insights into development, cancer and neuroscience. Kelly Rae Chi reports. Primer Top Special feature: Method of the Year 2013 Single-cell sequencing   p18 Tal Nawy doi:10.1038/nmeth.2771 A brief overview of how to derive a genome or transcriptome from a single cell. Commentary Top Special feature: Method of the Year 2013 Dissecting genomic diversity, one cell at a time   pp19 - 21 Paul C Blainey and Stephen R Quake doi:10.1038/nmeth.2783 Emerging technologies are bringing single-cell genome sequencing into the mainstream; this field has already yielded insights into the genetic architecture and variability between cells that highlight the dynamic nature of the genome. Special feature: Method of the Year 2013 Entering the era of single-cell transcriptomics in biology and medicine   pp22 - 24 Rickard Sandberg doi:10.1038/nmeth.2764 Recent technical advances have enabled RNA sequencing (RNA-seq) in single cells. Exploratory studies have already led to insights into the dynamics of differentiation, cellular responses to stimulation and the stochastic nature of transcription. We are entering an era of single-cell transcriptomics that holds promise to substantially impact biology and medicine. Special feature: Method of the Year 2013 The promise of single-cell sequencing   pp25 - 27 James Eberwine, Jai-Yoon Sul, Tamas Bartfai and Junhyong Kim doi:10.1038/nmeth.2769 Individual cells of the same phenotype are commonly viewed as identical functional units of a tissue or organ. However, the deep sequencing of DNA and RNA from single cells suggests a more complex ecology of heterogeneous cell states that together produce emergent system-level function. Continuing development of high-content, real-time, multimodal single-cell measurement technologies will lead to the ultimate goal of understanding the function of an individual cell in the context of its microenvironment. Methods to Watch Top Special feature: Method of the Year 2013 CRISPRs and epigenome editing   p28 Nicole Rusk doi:10.1038/nmeth.2775 Precise alterations to the epigenome with targeted enzymes. Special feature: Method of the Year 2013 Bring on the neuro tools   p28 Erika Pastrana doi:10.1038/nmeth.2776 A boost to neuroscience technology development could be transformative. Special feature: Method of the Year 2013 In situ sequencing   p29 Tal Nawy doi:10.1038/nmeth.2777 Biologists need methods for sequencing genetic material directly from intact tissues. Special feature: Method of the Year 2013 Tiny tools to measure force   p29 Natalie de Souza doi:10.1038/nmeth.2778 Imaging-based sensors are used to map mechanical forces exerted by cells. Special feature: Method of the Year 2013 Single-particle electron cryomicroscopy   p30 Allison Doerr doi:10.1038/nmeth.2779 Single-particle electron cryomicroscopy reaches for atomic resolution. Special feature: Method of the Year 2013 Intracellular mini-binders   p30 Erika Pastrana doi:10.1038/nmeth.2780 Small, genetically encoded probes for real-time detection and perturbation of cellular events are gaining attention. Special feature: Method of the Year 2013 The power of a crowd   p31 Daniel Evanko doi:10.1038/nmeth.2781 For some applications, a crowd of people is superior to the best computational tools available. Special feature: Method of the Year 2013 Self-organizing stem cells   p31 Natalie de Souza doi:10.1038/nmeth.2782 Tissue-like organoids with surprisingly complex structures can be formed by stem cells in vitro. Technology Feature Top Pouring over liquid handling   pp33 - 38 Vivien Marx doi:10.1038/nmeth.2785 A variety of liquid-handling methods are available for labs large and small. Selecting an approach is not just a matter of budget. News and Views Top The genome shows its sensitive side   pp39 - 40 Anil Raj and Graham McVicker doi:10.1038/nmeth.2770 New methods for measuring the sensitivity of chromatin to DNase digestion and Tn5 transposition help us map and interpret the genome's regulatory sequences. See also: Article by Vierstra et al. | Article by He et al. Analysis Top Quantitative assessment of single-cell RNA-sequencing methods   pp41 - 46 Angela R Wu, Norma F Neff, Tomer Kalisky, Piero Dalerba, Barbara Treutlein et al. doi:10.1038/nmeth.2694 A systematic evaluation of various single-cell RNA-seq approaches reports their sensitivity, accuracy and reproducibility and establishes the high performance of a high-throughput microfluidic method. Brief Communications Top A quantitative liposome microarray to systematically characterize protein-lipid interactions   pp47 - 50 Antoine-Emmanuel Saliba, Ivana Vonkova, Stefano Ceschia, Greg M Findlay, Kenji Maeda et al. doi:10.1038/nmeth.2734 Protein-lipid interactions can be systematically analyzed using a quantitative, multiplexed liposome microarray-based assay (LiMA). Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing   pp51 - 54 Rui Zhang, Xin Li, Gokul Ramaswami, Kevin S Smith, Gustavo Turecki et al. doi:10.1038/nmeth.2736 For allele-specific expression and RNA editing studies, targeted RNA sequencing using microfluidic multiplexed PCR (mmPCR-seq) gives robust high-throughput measurements of allelic ratios across the dynamic range of gene expression, even for low-quantity or low-quality RNA. Deciphering laminar-specific neural inputs with line-scanning fMRI   pp55 - 58 Xin Yu, Chunqi Qian, Der-yow Chen, Stephen J Dodd and Alan P Koretsky doi:10.1038/nmeth.2730 A line-scanning method is applied to obtain onset times of fMRI responses in rats. The authors show that onset time of the fMRI response can be used to infer information about which cortical layers receive the connectivity input from other brain areas. HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics   pp59 - 62 Rui M M Branca, Lukas M Orre, Henrik J Johansson, Viktor Granholm, Mikael Huss et al. doi:10.1038/nmeth.2732 High-resolution isoelectric focusing (HiRIEF) of peptides followed by mass spectrometry analysis, combined with accurate peptide pI prediction, allows a reduction of protein database search space, enabling deep proteome coverage and the discovery of protein-coding loci in human and mouse. Quantifying the local resolution of cryo-EM density maps   pp63 - 65 Alp Kucukelbir, Fred J Sigworth and Hemant D Tagare doi:10.1038/nmeth.2727 A method and software tool, ResMap, for quantifying the local resolution across 3D electron cryo-microscopy density maps is reported. Articles Top Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH   pp66 - 72 Jeff Vierstra, Hao Wang, Sam John, Richard Sandstrom and John A Stamatoyannopoulos doi:10.1038/nmeth.2713 By separately sequencing and mapping smaller and larger DNase I fragments from the same DNase I digestion experiment, the approach allows simultaneous profiling of transcription factor footprints relative to nucleosome occupancy. See also: News and Views by Raj & McVicker Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification   pp73 - 78 Housheng Hansen He, Clifford A Meyer, Sheng'en Shawn Hu, Mei-Wei Chen, Chongzhi Zang et al. doi:10.1038/nmeth.2762 Detailed analysis of DNase-seq protocols reveals the importance of choosing the right enzyme concentration and fragment length and cautions that many transcription factor footprints may represent cutting bias. See also: News and Views by Raj & McVicker A chemoproteomic platform to quantitatively map targets of lipid-derived electrophiles   pp79 - 85 Chu Wang, Eranthie Weerapana, Megan M Blewett and Benjamin F Cravatt doi:10.1038/nmeth.2759 A competitive activity-based protein profiling method is reported for quantifying the reactivity of lipid-derived electrophilic compounds with cysteine residues in the human proteome. Parallel measurement of dynamic changes in translation rates in single cells   pp86 - 93 Kyuho Han, Ariel Jaimovich, Gautam Dey, Davide Ruggero, Oded Meyuhas et al. doi:10.1038/nmeth.2729 A system to monitor translation regulation in living cells is reported. By fusing a fluorescent reporter that has a controllable destabilization domain to translation regulatory motifs, the authors analyze the contribution of these motifs to changes in translation in individual cells under different experimental situations. Integrating protein-protein interaction networks with phenotypes reveals signs of interactions   pp94 - 99 Arunachalam Vinayagam, Jonathan Zirin, Charles Roesel, Yanhui Hu, Bahar Yilmazel et al. doi:10.1038/nmeth.2733 An approach is presented for predicting the nature of the relationship (activating or inhibiting) between interacting proteins via integration of phenotypic information with protein-protein interaction networks. A holidic medium for Drosophila melanogaster   pp100 - 105 Matthew D W Piper, Eric Blanc, Ricardo Leitão-Gonçla;alves, Mingyao Yang, Xiaoli He et al. doi:10.1038/nmeth.2731 A chemically defined diet for Drosophila melanogaster is described. It should enable a variety of behavioral, metabolic and fitness studies where controlled nutrition is important. Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny   pp106 - 112 Xiaolei Yin, Henner F Farin, Johan H van Es, Hans Clevers, Robert Langer et al. doi:10.1038/nmeth.2737 This paper reports culture conditions for the expansion of near-homogeneous populations of mouse Lgr5+ intestinal stem cells. These methods will enable the study of intestinal biology and potentially that of other tissues. 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