A5026847124- CRISPR and Genetic Engineering
- Advanced biosensing and bioanalysis techniques
- RNA and protein synthesis mechanisms
- Virus-based gene therapy research
- RNA regulation and disease
- Cytomegalovirus and herpesvirus research
- Evolution and Genetic Dynamics
- Bacteriophages and microbial interactions
- Gut microbiota and health
- CAR-T cell therapy research
- Cancer, Hypoxia, and Metabolism
- Epigenetics and DNA Methylation
- Retinal Development and Disorders
- HIV Research and Treatment
- Barrier Structure and Function Studies
- SARS-CoV-2 and COVID-19 Research
- Viral Infections and Immunology Research
- Immune Cell Function and Interaction
- Cancer-related molecular mechanisms research
- Plant Virus Research Studies
- RNA modifications and cancer
- Genetics, Aging, and Longevity in Model Organisms
Agricultural Genomics Institute at Shenzhen
2018-2024
Chinese Academy of Agricultural Sciences
2018-2024
Ministry of Agriculture and Rural Affairs
2023-2024
Shanghai Institutes for Biological Sciences
2015-2018
University of Chinese Academy of Sciences
2018
Chinese Academy of Sciences
2015
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...
Engineered base editors convert the second nucleotide C to T in context of 5′-CC-3′ with high precision and targeting fidelity.
Abstract Efficient and precise base editors (BEs) for C-to-G transversion are highly desirable. However, the sequence context affecting editing outcome largely remains unclear. Here we report engineered BEs of high efficiency fidelity, with predictable via machine-learning methods. By changing species origin relative position uracil-DNA glycosylase deaminase, together codon optimization, obtain optimized (OPTI-CGBEs) efficient transversion. The motif preference OPTI-CGBEs 100 endogenous...
Abstract Base editors have been reported to induce off-target mutations in cultured cells, mouse embryos and rice, but their long-term effects vivo remain unknown. Here, we develop a Systematic evaluation Approach For gene Editing tools by Transgenic mIce (SAFETI), evaluate the of BE3, high fidelity version CBE (YE1-BE3-FNLS) ABE (ABE7.10 F148A ) ~400 transgenic mice over 15 months. Whole-genome sequence analysis reveals BE3 expression generated de novo offspring mice. RNA-seq both...
Abstract Adenine base editors (ABEs) and cytosine (CBEs) enable the single nucleotide editing of targeted DNA sites avoiding generation double strand breaks, however, genomic features that influence outcomes in vivo still remain to be characterized. High-throughput datasets from lentiviral integrated libraries were used investigate sequence affecting outcomes, but effects endogenous factors beyond sequences are largely unknown. Here ABE CBE evaluated mammalian cells for 5012 11,868...
Prolyl hydroxylase domain proteins (PHDs) control cellular adaptation to hypoxia. PHDs are found involved in inflammatory bowel disease (IBD); however, the exact role of PHD3, a member PHD family, IBD remains unknown. We show here that PHD3 plays critical maintaining intestinal epithelial barrier function. genetic ablation Phd3 cells led spontaneous colitis mice. Deletion decreases level tight junction protein occludin, leading failure Further studies indicate stabilizes occludin by...
Abstract The applicability of cytosine base editors is hindered by their dependence on sequence context and off-target effects. Here, using AlphaFold2 to predict the three-dimensional structure 1,483 cytidine deaminases experimentally characterizing representative (selected from each structural cluster after categorizing them via partitional clustering), we report discovery a few with high editing efficiencies, diverse windows increased ratios on-target Specifically, several induced C-to-T...
The safety of CRISPR-based gene editing methods is the utmost priority in clinical applications. Previous studies have reported that Cas9 cleavage induced frequent aneuploidy primary human T cells, but whether cleavage-mediated base editors would generate off-target structure variations remains unknown. Here, we investigate potential structural associated with CRISPR/Cas9, ABE, and CBE mouse embryos cells by whole-genome sequencing single-cell RNA-seq analyses.
Abstract Genome editing tools including CRISPR/Cas9 and base editors hold great promise for correcting pathogenic mutations. Unbiased genome-wide off-target effects of the in mammalian cells is required before clinical applications, but determination extent has been difficult due to existence single nucleotide polymorphisms (SNPs) individuals. Here, we developed a method named GOTI (Genome-wide Off-target analysis by Two-cell embryo Injection) detect mutations without interference SNPs. We...
Abstract The FokI catalytic domain can be fused to various DNA binding architectures improve the precision of genome editing tools. However, evaluation off-target effects is essential for developing these We use Genome-wide Off-target analysis by Two-cell embryo Injection (GOTI) detect low-frequency events in mouse embryos injected with FokI-based architectures. Specifically, we test FokI-heterodimers TALENs, homodimers RYdCas9, or domains alone resulting no significant effects. These...
The engineered TadA variants used in cytosine base editors (CBEs) present distinctive advantages, including a smaller size and fewer off-target effects compared to that rely on natural deaminases. However, the current demonstrate preference for editing DNA with specific motif sequences possess dual deaminase activity, acting both adenosine adjacent positions, limiting their application scope. To address these issues, we employ orthologs screening multi sequence alignment (MSA)-guided protein...
Base editors hold promise for correcting pathogenic mutations, while substantial single nucleotide variations (SNVs) on both DNA and RNA were generated by cytosine base (CBEs). Here we examined possibilities to reduce off-target effects engineering deaminases. By screening 24 CBEs harboring various rAPOBEC1 (BE3) or human APOBEC3A (BE3-hA3A) mutations the ssDNA binding domain, found 8 CBE could maintain high on-target editing efficiency. Using Genome-wide Off-target analysis Two-cell embryo...
Abstract Recently emerging SARS-CoV-2 virus has caused a global pandemic, with millions of infections and over 200, 000 deaths1. However, development effective anti-coronavirus treatments lagged behind. Competitive co-evolution between microbes viruses led to the diversification microbe’s CRISPR/Cas defense systems against infectious viruses2,3. Among class-2 single effector systems, Cas13 is in combating RNA phages4. Previous studies have discovered novel Cas9 Cas12 from metagenomic...
Prolyl hydroxylases (PHD1-3) hydroxylate hypoxia inducible factor α (HIFα), leading to HIFα ubiquitination and degradation. Recent studies indicated that administration of generic inhibitors PHDs improved mice colitis, suggesting suppression PHD activity by these may be a potential strategy for the treatment inflammatory bowel diseases. However, exact role each member family in homeostasis intestinal epithelium remains elusive. The aim this work is study possible PHD2 using with genetic...