Volume 14 Issue 2, February 2017

Swimming to a way of testing thousands of guide RNAs at once.

Isolation of nuclei in an isotonic buffer retains chromosome loops and allows the probing of intrinsic loop conformation.

Researchers have engineered a protease specific for a post-translational modification.

Donor age impacts the epigenetic state and mutational burden of induced pluripotent stem cells.

Researchers identify biological inhibitors of Cas9 nuclease activity and block genome editing in cultured human cells.

Genetically encoded reporters can be used for noninvasive cell tracking or molecular imaging with magnetic resonance imaging technologies.

In this Commentary, Ascoli et al. discuss recipes for setting up public data sharing initiatives based on their experiences with NeuroMorpho.Org.

Efforts to pare away cellular genomes are yielding streamlined biosynthetic factories and deeper insights into the core processes of biology.

New methods exploit single-molecule measurements to study protein structure and dynamics.

In this Review, the authors compare commonly used chromosome conformation capture techniques, describing their respective strengths and weaknesses, and provide advice for the end user on which approach and analysis method to use.

Benchmarking on synthetic data reveals differences between common RNA-seq alignment software tools, particularly for complex genomic regions.

The positions of fluorophores can be localized in single proteins with Angstrom-scale resolution using Cryogenic Optical Localization in 3D (COLD), a complementary approach to traditional structural biology techniques.

Standardized driver and effector lines that use optimized GAL4 from a cryophilic yeast species enable bipartite control of transgene expression in Caenorhabditis elegans.

Hyper-Spectral Phasors allow unmixing of multiple signals even under conditions with low signal-to-noise ratios, and they enable highly multiplexed 5D imaging of live zebrafish embryos labeled with conventional fluorophores.

A lentiviral library expressing Cpf1 guide RNAs and containing target sequences allows high-throughput profiling of highly active guide RNAs and is the basis for cindel, a webtool to predict the activity at any given target sequence.

Stroke is often modeled in rodents by surgically occluding vessels. SIMPLE is an alternative approach that involves the magnet-induced accumulation of nanoparticles. Because of its reversible nature, this method can be used to study both occlusion and subsequent reperfusion of blood vessels.

Direct library preparation (DLP) is a robust and economic method for preparing large numbers of single-cell whole-genome sequencing libraries without preamplification, to study copy-number heterogeneity at the cell level and other variant types at the clone or population level.

A hybrid approach merges networks of time-correlated distances determined by single-molecule FRET to uncover local and global dynamics of the multidomain protein Hsp90 in solution at multiple timescales.

The mechanical properties of tissues can be measured by deforming magnetically responsive microdroplets that are implanted in the tissue. Serwane et al. apply this method to study the mechanical properties of tissues in the living zebrafish embryo.

A method to screen proteins for enzymatic activity by incubating purified or overexpressed proteins with a metabolite extract and measuring changes in metabolite abundance using mass spectrometry enables high-throughput characterization of functionally uncharacterized proteins in Escherichia coli.

Homing guide RNAs that target Cas9 to their own loci generate diverse barcodes that can trace the lineage of cells.

The RNA-element selection assay (RESA) probes regulatory elements in vivo and identifies protein binding partners and the nucleotides that contribute most to the regulation.