David A Knowles, Joe R Davis, Hilary Edgington, Anil Raj, Marie-Julie Favé, Xiaowei Zhu, James B Potash, Myrna M Weissman, Jianxin Shi, Douglas F Levinson, Philip Awadalla, Sara Mostafavi, Stephen B Montgomery & Alexis Battle
Iterative oxidation, elimination and dephosphorylation steps remove nucleotides from the 3′ end of RNA until a 2′-O-methylated ribose that cannot be oxidized is encountered and brings the process to a stop. High-throughput sequencing of these fragments exposes 2′-O-methyl sites at base resolution.
Nan Yang, Soham Chanda, Samuele Marro, Yi-Han Ng, Justyna A Janas, Daniel Haag, Cheen Euong Ang, Yunshuo Tang, Quetzal Flores, Moritz Mall, Orly Wapinski, Mavis Li, Henrik Ahlenius, John L Rubenstein, Howard Y Chang, Arturo Alvarez Buylla, Thomas C Südhof & Marius Wernig
Transient transcription factor expression rapidly induces a homogenous population of mature GABAergic neurons from human pluripotent stem cells, aiding the study of inhibitory neuron function and disease.
Adaptive optics can counteract optical aberrations within tissues, but the field of view is typically limited. Multi-pupil adaptive optics expands the area that can be imaged, and this is demonstrated by multiple applications in the mouse brain imaging.
Peter Cameron, Chris K Fuller, Paul D Donohoue, Brittnee N Jones, Matthew S Thompson, Matthew M Carter, Scott Gradia, Bastien Vidal, Elizabeth Garner, Euan M Slorach, Elaine Lau, Lynda M Banh, Alexandra M Lied, Leslie S Edwards, Alexander H Settle, Daniel Capurso, Victor Llaca, Stéphane Deschamps, Mark Cigan, Joshua K Young & Andrew P May
CIRCLE-seq is an in vitro assay for selectively sequencing off-target sites cleaved by Cas9–sgRNA in genomic DNA. It sensitively profiles genome-wide off-target cut sites and characterizes the contribution of SNPs to these cleavage events.
A gain-of-function mutation in a sodium/potassium pump renders cells resistant to a small-molecule drug and provides an efficient coselection strategy to enrich for CRISPR-induced mutations at an independent locus.
CREST-seq allows functional screening of cis-regulatory elements through the use of sgRNA pairs to introduce tiled deletions in regions of interest. The analysis of a 2-megabase target region shows that promoters can act as distal enhancers for unrelated genes.
Iterative expansion microscopy (iExM) is a strategy that achieves high resolution expansion microscopy by expanding samples multiple times. Expanding a sample twice enables ∼4.5 × 4.5 ∼20× physical expansion and ∼25 nm resolution.
An ultrafast, fragment-ion indexing–based database search tool, MSFragger, makes open searching practical and enables comprehensive identification of modified peptides in mass spectrometry–based proteomics data sets.
Martin Harterink, Marta Esteves da Silva, Lena Will, Julia Turan, Adiljan Ibrahim, Alexander E Lang, Eljo Y van Battum, R Jeroen Pasterkamp, Lukas C Kapitein, Dmitri Kudryashov, Ben A Barres, Casper C Hoogenraad & J Bradley Zuchero
DeActs are genetically encoded tools that perturb the actin cytoskeleton. In contrast to drugs such as latrunculin, they can be targeted to specific cell types, which is demonstrated in the developing mouse brain and in Caenorhabditis elegans.
iTango confers access to neuromodulation-sensitive subsets of neurons in a functionally defined and temporally controlled manner. The tool allows for manipulating the subset of neurons that are activated by dopamine during a behavior of interest.