Volume 11 Issue 1, January 2014

Building an approach to quantify chinks in a protein's armor.

Chromosome conformation capture data provide scaffolds for de novo genome assemblies.

Applying tiny forces to single molecules at high speed reveals the mechanics behind molecule unfolding.

Electron diffraction using three-dimensional (3D) crystals may expand the reach of this technique.

Two groups use nanopore sequencing through a protein pore to detect methylcytosine and hydroxymethylcytosine.

Genome-wide, in vivo RNA structure probing helps reveal how RNA structure regulates gene expression.

Single-cell genome and transcriptome sequencing methods are generating a fresh wave of biological insights into development, cancer and neuroscience. Kelly Rae Chi reports.

A brief overview of how to derive a genome or transcriptome from a single cell.

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.

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.

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.

Precise alterations to the epigenome with targeted enzymes.

A boost to neuroscience technology development could be transformative.

Biologists need methods for sequencing genetic material directly from intact tissues.

Imaging-based sensors are used to map mechanical forces exerted by cells.

Single-particle electron cryomicroscopy reaches for atomic resolution.

Small, genetically encoded probes for real-time detection and perturbation of cellular events are gaining attention.

For some applications, a crowd of people is superior to the best computational tools available.

Tissue-like organoids with surprisingly complex structures can be formed by stem cells in vitro.

A variety of liquid-handling methods are available for labs large and small. Selecting an approach is not just a matter of budget.

New methods for measuring the sensitivity of chromatin to DNase digestion and Tn5 transposition help us map and interpret the genome's regulatory sequences.

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.

Protein-lipid interactions can be systematically analyzed using a quantitative, multiplexed liposome microarray–based assay (LiMA).

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.

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.

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.

A method and software tool, ResMap, for quantifying the local resolution across 3D electron cryo-microscopy density maps is reported.

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.

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.

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.

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.

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 chemically defined diet for Drosophila melanogaster is described. It should enable a variety of behavioral, metabolic and fitness studies where controlled nutrition is important.

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.

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.