Rapid detection of SARS-CoV-2 RNA in saliva via Cas13

Nature Biomedical Engineering · 2022 · 134 citations

• Molecular biology
• Virology
• Chemistry

Species- and site-specific genome editing in complex bacterial communities

Nature Microbiology · 2021 · 277 citations

• Biology
• Computational biology
• Genetics

The NIH Somatic Cell Genome Editing program

Nature · 2021 · 130 citations

• Computer Science
• Computer Science
• Computational biology

The move from reading to writing the human genome offers new opportunities to improve human health. The United States National Institutes of Health (NIH) Somatic Cell Genome Editing (SCGE) Consortium aims to accelerate the development of safer and more-effective methods to edit the genomes of disease-relevant somatic cells in patients, even in tissues that are difficult to reach. Here we discuss the consortium's plans to develop and benchmark approaches to induce and measure genome modifications, and to define downstream functional consequences of genome editing within human cells. Central to this effort is a rigorous and innovative approach that requires validation of the technology through third-party testing in small and large animals. New genome editors, delivery technologies and methods for tracking edited cells in vivo, as well as newly developed animal models and human biological systems, will be assembled-along with validated datasets-into an SCGE Toolkit, which will be disseminated widely to the biomedical research community. We visualize this toolkit-and the knowledge generated by its applications-as a means to accelerate the clinical development of new therapies for a wide range of conditions.

Clades of huge phages from across Earth’s ecosystems

Nature · 2020 · 533 citations

• Biology
• Genetics
• Computational biology

. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

Massively parallel kinetic profiling of natural and engineered CRISPR nucleases

Nature Biotechnology · 2020 · 143 citations

• Biology
• Computational biology
• Genetics

Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy

Cell · 2020 · 1000 citations

• Biology
• Virology
• Computational biology

The promise and challenge of therapeutic genome editing

Nature · 2020 · 1116 citations

• Computer Science
• Computational biology
• Computer Science

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling

Proceedings of the National Academy of Sciences · 2020 · 120 citations

• Biophysics
• Biology
• Computational biology

The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.

Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity

Nature Biotechnology · 2020 · 1013 citations

• Computational biology
• Biology
• Genetics

Reactions to the National Academies/Royal Society Report on <i>Heritable Human Genome Editing</i>

The CRISPR Journal · 2020 · 26 citations

• Political Science
• Computer Science
• Political Science

was published. The report offers a translational pathway for the limited approval of germline editing under limited circumstances and assuming various criteria have been met. In this perspective, some three dozen experts from the fields of genome editing, medicine, bioethics, law, and related fields offer their candid reactions to the National Academies/Royal Society report, highlighting areas of support, omissions, disagreements, and priorities moving forward.