Reviews & Analysis

Dual sequencing of the epigenome and genome could have broad implications in oncology.

Genetically encoded concentric barcodes function as multiplexed electron microscopy (EM) gene reporters (EMcapsulins) for cell culture and in vivo models. These barcodes can be used to visualize gene expression information as automatically labeled overlays on volume EM data.

Nano-tRNAseq is a nanopore-based, cost-effective and high-throughput approach to quantify transfer RNA (tRNA) abundances and modifications simultaneously, providing a framework to study the ‘tRNAome’ at single-molecule resolution. We envision that Nano-tRNAseq will enable us to study the role of tRNA molecules and their modifications in a wide variety of contexts.

We present the Schmidt objective, a novel astronomy-inspired concept for designing multi-immersion microscope objectives with high numerical aperture, long working distance and large field of view. The Schmidt objective uses a spherical mirror and a correction plate to focus light. It is well suited for high-resolution imaging deep inside cleared biological samples.

The ability to create in vivo genomic medicines for tissues other than the liver has been impeded by difficulties in delivery. Using a high-throughput platform, we developed lipid nanoparticles that can effectively deliver mRNA and CRISPR–Cas9 gene editing tools to the lungs through intratracheal administration, expanding the potential clinical uses of gene editing and mRNA-based technologies.

CRISPR RNA is delivered to the mouse lung by inhalation using improved lipid nanoparticles.

We have designed a method, binding affinities to native chromatin by sequencing (BANC-seq), to determine the transcription factor concentrations required for binding to regulatory elements across the genome. Our study shows that chromatin context and DNA accessibility are key regulators of transcription factor binding.

Leveraging advances in hardware and probes, we have combined innovations in optics and algorithms to allow automated single-molecule-based super-resolution imaging at unprecedented throughput. This approach allows us to obtain nanoscale information from large cell populations, bridging the gap between imaging and indirect ensemble methods.

Fine-tuning gene expression is crucial for generating quantitative phenotypic changes and crop improvement. Using CRISPR–Cas base editing and prime editing, we engineered upstream open reading frames — eukaryotic translational control elements — in rice to incrementally downregulate translation to predictable and desired levels.

Sequencing individual cells in a sample enables scientists to infer the unique characteristics of important subsets. Single-cell sequencing methods that rely on microfluidics for cell barcoding are limited in speed, scale and flexibility. We developed a technique that uses particle-templated emulsification instead of microfluidics and can process millions of cells within minutes.

We developed TACCO, a versatile and efficient computational annotation framework, leveraging growing single-cell and spatial omics data to identify cell types and states, decipher molecular and cellular tissue structure, and resolve differentiation trajectories.

Ultrasensitive sequential fluorescence in situ hybridization (USeqFISH) enables multiplexed detection of the expression of endogenous and exogenous genes delivered by adeno-associated virus (AAV) vectors in intact tissue. USeqFISH provides a spatial map of AAV tropism with high throughput and resolution.

Functional proteins with limited homology to natural proteins are designed using a large language model.

CLASH is a CRISPR-based platform that enables the parallel knock-in via homology-directed repair of a large pool of transgene variants encoded in adeno-associated virus vectors. CLASH can be applied to the systematic and unbiased selection of favorable features in T cells and, in principle, other cell types.

Targeted RNA degradation remains a challenge using existing methods owing to off-target effects and toxicity. We adapted the CRISPR-Csm complex, a multi-protein effector from type III CRISPR systems, for precise knockdown of nuclear or cytoplasmic transcripts in eukaryotic cells with minimal side effects.

Sequencing of proteins is a technically difficult task that typically requires digestion into short peptides before detection and identification. We developed a digestion-free method to chemically unfold and ‘scan’ full-length proteins through a nanopore, producing electrical fingerprints unique to individual protein molecules that are useful in their identification.

The collection of RNAs in a cell reflects its identity and behavior. Although probing these RNAs in the present is commonplace, peering into the past remains challenging. We developed TIGER (transcribed RNAs inferred by genetically encoded records) to record selected RNAs at the single-cell level, enabling us to connect the past with the present.

Edited, transgene-free plants are produced without tissue culture by RNA migration from rootstocks to grafts.

Elongating protein fibers record the transcriptional activity of single cells for later readout by imaging.

By screening natural prokaryotic gas vesicle gene clusters, we found and engineered new acoustic reporter genes (ARGs) that give bacteria and mammalian cells brighter ultrasound contrast for real-time noninvasive imaging. Expressing these ARGs in engineered cells enabled us to image tumor-homing bacteria and perform genetically guided tumor biopsies in vivo.