News & Views in 2013

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

RNA-seq is a recent and immensely popular technology for cataloging and comparing gene expression. Two papers from the international RGASP consortium report on large-scale competitions to identify the best algorithms for RNA-seq analysis, with surprising variability in the results.

Network-based stratification (NBS) enables the subtyping of tumors on the basis of their mutational profiles, providing new avenues for cancer research and precision oncology.

Use of helper interactions to encourage weak heteromeric interactions between fluorescent protein pairs helps ensure optimal fluorescence resonance energy transfer (FRET) signals and minimizes the impact on target protein interactions.

An algorithm called CONTACT identifies correlated side-chain motions in proteins from X-ray crystallographic data, providing insights into dynamics and function.

With a flood of new tools for genome engineering, we can benefit from choosing the tool that best fits the job.

Massive parallelization of scanning-based super-resolution imaging allows fast imaging of large fields of view.

Methods for high-throughput and high-resolution dissection of enhancers in Drosophila are described by two independent groups.

Two approaches to serially enrich protein post-translational modifications allow the detection of multiple modifications in a single biological sample using mass spectrometry.

More than 40 years after the invention of semiconductor pH microtransducers known as ISFETs, this transistor-based technology may revolutionize quantitative PCR.

A synthetic biology terminator toolkit enables more sophisticated circuit design and gives insight into the mechanism of transcriptional termination.

Two reports describing the use of direct-conversion electron detectors and algorithms that correct for beam-induced sample motion in single-particle electron cryomicroscopy demonstrate that this technique can solve structures of macromolecules at near-atomic resolution.

An approach for analyzing gene expression data identifies putative lineage-specifying transcription factors that may prove useful in cellular reprogramming.

Three RNA interference–based methods probe genetic interactions in mammalian cells at large scale.

Zinc-finger DNA-binding domains are expressed on the surface of cells so that the cells can be tagged with fluorescently labeled oligonucleotides, enabling many possible applications in complex cell populations.

A two-laboratory study of the reproducibility of affinity purification–mass spectrometry shows that a standardized protocol results in highly reproducible interactome data.

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.

Synthetic transcription factors act synergistically.

Statistical analysis of single-molecule tracking data maps the number of states occupied by a molecule in a bacterial cell.

Classification of proteins by ligand binding similarity offers an alternative approach to evolutionary methods for organizing and understanding biology, allowing new insights into protein function and physiological signal transduction.