Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain
the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in
Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles
and JavaScript.
Huang, Qin, Shang et al. profile double-strand breaks (DSBs) generated by C-to-G base editors (CGBEs) and find that HMCES protects abasic sites and reduces CGBE-triggered DSBs.
Noack and Vangelisti et al. present 3DRAM-seq, which simultaneously profiles genome organization, chromatin accessibility and DNA methylation at high resolution and allows mapping cell-type-specific epigenetic regulation in human neurogenesis.
Huang et al. provide a method to generate human gastric stem cell-derived pancreatic islet-like organoids that are capable of restoring glucose homeostasis in diabetic mice.
Berg et al. describe Metaboverse, a tool for automated discovery and visualization of metabolic data. Metaboverse enhances the user’s ability to extract meaningful patterns from multi-omics datasets to describe metabolic responses and signatures.
Lotfollahi et al. present ExpiMap, a deep-learning model enabling interpretable reference mapping of RNA sequencing data using biologically defined entities, offering end-to-end analysis from dataset integration to functional interpretation.
Stewart-Morgan et al. present isolation of DNA by 5-ethynyl-deoxyuridine labelling for mass spectrometry, a highly sensitive, quantitative mass spectrometry-based method for measuring DNA modifications on metabolically labelled DNA. They apply it to study DNA methylation and hydroxymethylation propagation.
Lim et al. developed a fluorescence resonance energy transfer-based assay to identify anti-CRISPR molecules and discovered an SpCas9 inhibitor that is twofold more efficient in inhibiting Cas9 at diverse genomic loci than existing inhibitors and easy to synthesize.
Truong et al. report a system to monitor RNA expression by modifying an intron within a gene of interest. This additional engineered transcript then hijacks nuclear export machinery for subsequent translation of a reporter gene.
Zou et al. use a single multi-target guide RNA to direct Cas9 to a high number of loci mapped by high-throughput short-read sequencing. This multi-target CRISPR system allows detailed studies of genome editing and DNA repair.
Rosebrock, Arora et al. report a method to overcome limited cortical cellular diversity in human organoids, thus mirroring fundamental features of cortical development and offering a basis for organoid-based disease modelling.
John Peter et al. develop METALIC (Mass tagging-Enabled TrAcking of Lipids In Cells), an approach to track interorganelle lipid flux in live cells using organelle-targeted enzymatic labelling of lipid subpopulations and mass spectrometry.
Lummertz da Rocha et al. present CellComm, an algorithm that analyses cell–cell communication to predict signalling and regulatory networks, and identify regulators of haematopoietic development in the aorta–gonad–mesonephros region.
Through structure-guided protein engineering, Guo et al. developed a Lachnospiraceae bacterium Cas12a variant with enhanced editing efficiency and applied the enzyme-dead version of this variant for multiplex gene activation in the mouse retina.
Wang, Qu et al. developed a genome-editing system, utilizing catalytically inactive Cas9 fused to microbial single-strand annealing proteins, for kilobase-scale insertion in human cells without introducing DNA nicks or breaks.
Chowdhury, Sau and Musser report a multicolour imaging approach that enables the 3D visualization of cargo transport trajectories relative to a super-resolved nuclear pore complex scaffold in non-fixed permeabilized cells.
Jo et al. develop a broadly applicable deep-learning approach to predict fluorescence (FL) based on label-free refractive index (RI) measurements, ‘RI2FL’ (RI to FL). The trained model can be used across cell types without retraining.
Xue and colleagues developed LACE-seq to globally profile RNA targets of RNA-binding proteins at single-nucleotide resolution in low-input cells or even single oocytes.
Truong et al. developed a cell-based reporter system, EXSISERS, that enables non-invasive quantification of the protein expression levels of exon-specific isoforms via intein-mediated protein splicing.
Li et al. develop reversible shearing DNA-based tension probes to quantify molecular piconewton-scale forces, estimate the number of mechanically active receptors with single-molecule sensitivity and study mechanisms of force transduction in live cells.