Research articles

HiChIP combines chromosome conformation capture with immunoprecipitation- and tagmentation-based library preparation to uncover the 3D chromatin architecture focused around a protein of interest.

A ‘conditional proteomics’ approach, as applied here to identify proteins involved in zinc homeostasis, utilizes an activatable labeling reagent to tag proteins affected by a particular biological condition in the cell, enabling them to be isolated and identified using mass spectrometry.

The combination of cellular barcoding and treatment with a library of small molecules before injecting the treated cells into mice allows the screening for compounds that inhibit metastatic seeding.

Expressing guide RNAs from a tRNA scaffold enhances mutagenesis by both Cas9 and Cpf1 and allows conditional CRISPR applications in vivo.

Packaging split Cas9 into AAVs increases cargo capacity and allows for efficient genome editing and gene activation in vivo. AAV–split-Cas9 activates the host immune system but does not trigger the extensive cellular damage observed with delivery of Cas9 via DNA electroporation.

The integration of ligand-responsive riboswitches with single guide RNAs allows Cas9–effector fusions to be targeted in response to ligands and thereby translate a cellular signal into a downstream readout of choice.

A straightforward method and tool, MetaMass, utilizes a list of subcellular markers to analyze and classify subcellular proteomics data from multiple experiments. An accompanying analysis reveals a wide variation in the results of subcellular fractionation protocols.

rG4-seq enables the mapping of RNA G-quadruplex structures across entire transcriptomes at nucleotide resolution.

Diffusion pseudotime (DPT) enables robust and scalable inference of cellular trajectories, branching events, metastable states and underlying gene dynamics from snapshot single-cell gene expression data.

Flexible mesh electronics facilitate stable long-term recordings of the same single neurons in mouse brains over months, enabling chronic recordings in behaving animals and longitudinal studies to resolve aging-dependent changes in neural activity.

A suite of tools and resources for Vibrio natriegens introduces the bacterium as a faster-growing alternative to E. coli for molecular biology and biotechnology applications.

uDISCO clearing renders whole animals transparent and capitalizes on shrinkage to image them. This method allows the analysis of intact nervous systems and whole-body screens for transplanted cells and human tissue samples after prolonged storage.

sc-GEM enables the dissection of cellular heterogeneity by simultaneously assaying the status of DNA mutations, gene expression and DNA methylation at multiple targeted loci in individual cells.

Double-strand DNA breaks capture (DSBCapture) identifies in situ DSBs via the ligation of an Illumina adaptor into the break site and shows no bias for chromatin state or base composition. A genome-wide DSB profile shows breaks occurring more frequently in euchromatin and transcriptionally active regions.

Synthetic DNA spike-ins that recapitulate genetic variation present in human genomes serve as quantitative and qualitative controls for genome sequencing and variant detection.

Synthetic spike-in standards (‘sequins’), representing spliced mRNA isoforms, provide internal controls for assessing transcript assembly and quantification within and between RNA sequencing libraries. Sequins representing fused genes can be used to determine the sensitivity limit for oncogenic fusions in cancer samples.

A network-based method and computational tool, PIUMet, reveals disease-associated molecular pathways from untargeted metabolomics data without requiring mass-spectral feature identification.

TRIC, a cross-run alignment algorithm and software tool, enables reproducible quantification of thousands of peptides across multiple targeted liquid chromatography–tandem mass spectrometry runs.

A bright and photostable far-red fluorescent protein, smURFP, was developed from a cyanobacterial phycobiliprotein. smURFP uniquely binds a highly cell-permeable biliverdin derivative to obtain fluorescence brightness comparable to that of eGFP in cells.

Virtual microfluidics uses hydrogel entrapment to make high-throughput single-cell and single-molecule amplification broadly accessible without the need for special equipment.