A5007449696- CRISPR and Genetic Engineering
- Immune Cell Function and Interaction
- Pluripotent Stem Cells Research
- Genomics and Chromatin Dynamics
- Genetics, Aging, and Longevity in Model Organisms
- T-cell and B-cell Immunology
- Diabetes and associated disorders
- DNA Repair Mechanisms
- Retinal Development and Disorders
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Immunotherapy and Immune Responses
- Cancer Immunotherapy and Biomarkers
- Single-cell and spatial transcriptomics
- Cytomegalovirus and herpesvirus research
- interferon and immune responses
- IL-33, ST2, and ILC Pathways
- Innovation and Socioeconomic Development
- CAR-T cell therapy research
- Hepatitis B Virus Studies
- Mycobacterium research and diagnosis
- Bacteriophages and microbial interactions
- Liver Disease Diagnosis and Treatment
- Immune cells in cancer
- Adipose Tissue and Metabolism
University of California, San Diego
2020-2025
University of California, Berkeley
2017-2020
Innovative Genomics Institute
2017-2020
University of California, Los Angeles
2015-2019
Spotting off-targets from gene editing Unintended genomic modifications limit the potential therapeutic use of gene-editing tools. Available methods to find generally do not work in vivo or detect single-nucleotide changes. Three papers this issue report new for monitoring tools (see Perspective by Kempton and Qi). Wienert et al. followed recruitment a DNA repair protein breaks induced CRISPR-Cas9, enabling unbiased detection off-target cellular animal models. Zuo identified without...
Abstract Repair of double strand DNA breaks (DSBs) can result in gene disruption or modification via homology directed repair (HDR) from donor DNA. Altering cellular responses to DSBs may rebalance editing outcomes towards HDR and away other outcomes. Here, we utilize a pooled CRISPR screen define host cell involvement between Cas9 DSB plasmid stranded (dsDonor). We find that the Fanconi Anemia (FA) pathway is required for dsDonor genes act repress HDR. Small molecule inhibition one these...
Abstract Type I Interferons (IFN-I) are central to host protection against viral infections, with plasmacytoid dendritic cells (pDC) being the most significant source, yet pDCs lose their IFN-I production capacity following an initial burst of IFN-I, resulting in susceptibility secondary infections. The underlying mechanisms these dynamics not well understood. Here we find that infection reduces engage both oxidative and glycolytic metabolism. Mechanistically, identify lactate dehydrogenase...
During a microbial infection, responding CD8+ T cells give rise to effector that provide acute host defense and memory sustained protection. An alternative outcome is exhaustion, state of cell dysfunction occurs in the context chronic infections cancer. Although it evident exhausted (TEX) are phenotypically molecularly distinct from cells, factors regulating earliest events differentiation process TEX remain incompletely understood. Here, we performed single-cell RNA-sequencing...
Abstract CRISPR-Cas9 genome editing creates targeted double strand breaks (DSBs) in eukaryotic cells that are processed by cellular DNA repair pathways. Co-administration of single stranded oligonucleotide donor (ssODN) during can result high-efficiency (>20%) incorporation ssODN sequences into the break site. This process is commonly referred to as homology directed (HDR) and here template (SSTR) distinguish it from using a (dsDonor). The high efficacy SSTR makes promising avenue for...
Abstract Chronic infections drive a CD8 T cell program termed exhaustion, characterized by reduced effector functions. While cell-intrinsic mechanisms underlying exhaustion have been extensively studied, the impact of metabolic environment in which exhausted cells (Tex) operate remains less clear. Using untargeted metabolomics and murine lymphocytic choriomeningitis virus infection model we investigated systemic metabolite changes early late following acute versus chronic viral infections....
Infections elicit immune adaptations to enable pathogen resistance and/or tolerance and are associated with compositional shifts of the intestinal microbiome. However, a comprehensive understanding how infections pathogens that exhibit distinct capability spread persist differentially change microbiome, underlying mechanisms, relative contribution individual commensal species cell is still lacking. Here, we discovered mouse infection fast-spreading persistent (but not slow-spreading acute)...
Abstract Type I Interferons (IFN-I) are central to host protection against viral infections 1 . While any cell can produce IFN-I, Plasmacytoid Dendritic Cells (pDCs) make greater quantities and more varieties of these cytokines than other type 2 However, following an initial burst IFN- I, pDCs lose their exceptional IFN-I production capacity become “exhausted”, a phenotype that associates with enhanced susceptibility secondary 3–5 Despite this apparent cost for the host, pDC exhaustion is...
Abstract Genome editing using nucleases such as CRISPR-Cas induces programmable DNA damage at a target genomic site but can also affect off-target sites. Here, we develop powerful, sensitive assay for the unbiased identification of sites that term DISCOVER-Seq. This approach takes advantage recruitment endogenous repair factors genome-wide Cas-induced double-strand breaks. One factor, MRE11, is recruited precisely to breaks, enabling molecular characterization nuclease cut with single-base...
ABSTRACT The challenge of linking intergenic mutations to target genes has limited molecular understanding human diseases. Here, we show that H3K27ac HiChIP generates high-resolution contact maps active enhancers and in rare primary T cell subtypes coronary artery smooth muscle cells. Differentiation naïve cells helper 17 or regulatory creates subtype-specific enhancer-promoter interactions, specifically at regions shared DNA accessibility. These data provide a principled means assigning...
Mycobacteriophages Deby, LaterM, LilPharaoh, Paola, SgtBeansprout, and Sulley were isolated from soil using Mycobacterium smegmatis mc 2 155. Genomic analysis indicated that they belong to subclusters K1 K5.
Repair of double strand DNA breaks (DSBs) can result in gene disruption or precise modification via homology directed repair (HDR) from a templating donor DNA. During genome editing, altering cellular responses to DSBs may be an effective strategy rebalance editing outcomes towards HDR and away other pathways. To identify factors that regulate double-stranded (dsDonor), we utilized pooled screen define the consequences thousands individual knockdowns during Cas9-initiated plasmid donor. We...
Summary Cas9 is a prokaryotic RNA-guided DNA endonuclease that binds substrates tightly in vitro but turns over rapidly when used to manipulate genomes eukaryotic cells. Little known about the factors responsible for dislodging or how they influence genome engineering. Using proximity labeling system unbiased detection of transient protein interactions cell-free Xenopus laevis egg extract, we identified dimeric histone chaperone FACT as an interactor substrate-bound Cas9. Immunodepletion...