A5013172884- Telomeres, Telomerase, and Senescence
- CRISPR and Genetic Engineering
- SARS-CoV-2 and COVID-19 Research
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Advanced biosensing and bioanalysis techniques
- interferon and immune responses
- Bacterial Genetics and Biotechnology
- Digestive system and related health
- RNA modifications and cancer
- Science, Research, and Medicine
- Microtubule and mitosis dynamics
- Cancer Cells and Metastasis
- Genomics and Chromatin Dynamics
- DNA Repair Mechanisms
- Blood disorders and treatments
- Genetics, Aging, and Longevity in Model Organisms
- Animal Virus Infections Studies
- Chromatin Remodeling and Cancer
- Epigenetics and DNA Methylation
- Cytokine Signaling Pathways and Interactions
- Virus-based gene therapy research
- Innovation and Socioeconomic Development
- Insect symbiosis and bacterial influences
- Chromosomal and Genetic Variations
New York University
2013-2023
New York Genome Center
2019-2023
A novel variant of the SARS-CoV-2 virus carrying a point mutation in Spike protein (D614G) has recently emerged and rapidly surpassed others prevalence. This is linkage disequilibrium with an ORF1b (P314L), making it difficult to discern functional significance D614G from population genetics alone. Here, we perform site-directed mutagenesis on wild-type human-codon-optimized introduce variant. Using multiple human cell lines, including lung epithelial cells, found that lentiviral particles...
Most variants associated with complex traits and diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome unknown effects. Using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR screens, single-cell transcriptomic proteomic sequencing, we discovered 124
Abstract A novel isolate of the SARS-CoV-2 virus carrying a point mutation in Spike protein (D614G) has recently emerged and rapidly surpassed others prevalence. This is linkage disequilibrium with an ORF1b variant (P314L), making it difficult to discern functional significance D614G from population genetics alone. Here, we perform site-directed mutagenesis introduce show that multiple cell lines, including human lung epithelial cells, up 8-fold more effective at transducing cells than...
A key limitation of the widely used CRISPR enzyme S. pyogenes Cas9 is strict requirement an NGG protospacer-adjacent motif (PAM) at target site. This constraint can be limiting for genome editing applications that require precise positioning. Recently, two variants with a relaxed PAM (NG) have been developed (xCas9 and Cas9-NG), but their activity has measured only small number endogenous sites. Here, we devise high-throughput pooled competition screen to compare performance thousands...
Abstract To date, the locus with most robust human genetic association to COVID-19 severity is 3p21.31. Here, we integrate genome-scale CRISPR loss-of-function screens and eQTLs in diverse cell types tissues pinpoint genes underlying risk. Our findings identify SLC6A20 CXCR6 as putative causal that modulate risk highlight usefulness of this integrative approach bridge divide between correlational studies biology.
Sister chromatid cohesion relies on cohesin, a complex comprising tri-partite ring and peripheral subunit Scc3, which is found as two related isoforms SA1 SA2 in vertebrates. There division of labor between the vertebrate cohesin complexes; SA1-cohesin required at telomeres SA2-cohesin centromeres. Depletion has dramatic consequences for telomere function genome integrity, but mechanism by mediates not well understood. Here we dissect individual contribution subunits to show that rely...
Functional mechanisms remain unknown for most genetic loci associated to complex human traits and diseases. In this study, we first mapped trans-eQTLs in a data set of primary monocytes stimulated with LPS, discovered that risk variant autoimmune disease, rs17622517 an intron C5ORF56, affects the expression transcription factor IRF1 20 kb away. The cis-regulatory effect specific is active under early immune stimulus, large number trans-eQTL effects across genome late LPS response. Using...
Sister chromatids are held together by cohesin, a tripartite ring with peripheral SA1/2 subunit, where SA1 is required for telomere cohesion and SA2 centromere cohesion. The STAG2 gene encoding often inactivated in human cancer, but not manner associated aneuploidy. Thus, how these tumors maintain chromosomal loss contributes to tumorigenesis remain open questions. Here we show that, despite cohesion, sister mutant tumor cells mitosis at chromosome arms telomeres. Telomere maintenance...
Formation of individualized sister chromatids is essential for their accurate segregation. In budding yeast, while most the genome segregates at metaphase to anaphase transition, resolution ribosomal DNA (rDNA) repeats delayed. The timing and mechanism in human cells unknown. Here we show that rDNA occurs after bulk genome, dependent on tankyrase 1, condensin II, topoisomerase IIα. Defective leads bridges, damage, aneuploidy an rDNA-containing acrocentric chromosome. Thus, temporal...
CRISPR-Cas transcriptional tools have been widely applied for programmable regulation of complex biological networks. In comparison to eukaryotic systems, bacterial CRISPR activation (CRISPRa) has stringent target site requirements effective gene activation. While genes may not always an NGG protospacer adjacent motif (PAM) at the appropriate position, PAM-flexible dCas9 variants can expand range targetable sites. Here we systematically evaluate a panel their ability activate genes. We...
Abstract The majority of variants associated with complex traits and common diseases identified by genome-wide association studies (GWAS) map to noncoding regions the genome unknown regulatory effects in cis trans . By leveraging biobank-scale GWAS data, massively parallel CRISPR screens single cell transcriptome sequencing, we discovered target genes for blood trait loci. closest gene was often gene, but this not always case. We also -effects networks when encoded transcription factors,...
Abstract To date the locus with most robust human genetic association to COVID-19 susceptibility is 3p21.31. Here, we integrate genome-scale CRISPR loss-of-function screens and eQTLs in diverse cell types tissues pinpoint genes underlying risk. Our findings identify SLC6A20 CXCR6 as putative causal that mediate risk highlight usefulness of this integrative approach bridge divide between correlational studies biology.
Abstract A key limitation of the commonly-used CRISPR enzyme S. pyogenes Cas9 is strict requirement an NGG protospacer-adjacent motif (PAM) at target site, which reduces number accessible genomic loci. This constraint can be limiting for genome editing applications that require precise positioning. Recently, two variants with a relaxed PAM (NG) have been developed (xCas9 and Cas9-NG) but their activity has measured only small endogenous sites. Here we devised high-throughput pooled...
Abstract Type VI CRISPR enzymes have recently been identified as programmable RNA-guided, RNA-targeting Cas proteins with nuclease activity that allow for specific and robust target gene knock-down without altering the genome. However, we currently lack information about optimal Cas13 guide RNA designs high efficacy. To close this gap, conducted four massively-parallel screens targeting mRNA of a destabilized green fluorescent protein (GFP) transgene CD46, CD55 CD71 cell surface in human...
<div>Abstract<p>Sister chromatids are held together by cohesin, a tripartite ring with peripheral SA1/2 subunit, where SA1 is required for telomere cohesion and SA2 centromere cohesion. The <i>STAG2</i> gene encoding often inactivated in human cancer, but not manner associated aneuploidy. Thus, how these tumors maintain chromosomal loss contributes to tumorigenesis remain open questions. Here we show that, despite cohesion, sister mutant tumor cells mitosis at...
<p>Figure Legends for Supplemental Figures 1-3. Figure 1: S1 provides a list of the STAG2 tumor cell lines used in this study and immunoblot analysis SA1 SA2 protein expression relates to 1. Supplementary 2: S2 telomere sister chromatid exchange HCT116 WT KO cells 3. 3: S3 cohesion, exchange, growth, DNA damage, senescence, length, aneuploidy BJ-1 BJ-2 SA2-depleted stable 6.</p>
<p>Figure S2 provides analysis of telomere sister chromatid exchange in HCT116 WT and SA2 KO cells relates to Figure 3.</p>
<p>The supplemental materials and methods provides details of plasmids, general transfection infection, use for the figures, references.</p>
<p>Figure S1 provides a list of the STAG2 tumor cell lines used in this study and immunoblot analysis SA1 SA2 protein expression relates to Figure 1.</p>
<p>Figure S3 provides analysis of telomere cohesion, sister chromatid exchange, growth, DNA damage, senescence, length, and aneuploidy BJ-1 BJ-2 SA2-depleted stable cell lines relates to Figure 6.</p>
<p>Figure S3 provides analysis of telomere cohesion, sister chromatid exchange, growth, DNA damage, senescence, length, and aneuploidy BJ-1 BJ-2 SA2-depleted stable cell lines relates to Figure 6.</p>