A5052382465- Signaling Pathways in Disease
- Plant Molecular Biology Research
- Genomics and Chromatin Dynamics
- Adipose Tissue and Metabolism
- Analytical Chemistry and Chromatography
- Plant Gene Expression Analysis
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Receptor Mechanisms and Signaling
- Pancreatic function and diabetes
- Computational Drug Discovery Methods
- RNA Interference and Gene Delivery
- Birth, Development, and Health
- Neuroendocrine regulation and behavior
- Synthesis and Characterization of Heterocyclic Compounds
- Plant nutrient uptake and metabolism
- Epigenetics and DNA Methylation
- Genetic diversity and population structure
- Animal Behavior and Reproduction
- Developmental Biology and Gene Regulation
- Single-cell and spatial transcriptomics
- Cholinesterase and Neurodegenerative Diseases
- Mass Spectrometry Techniques and Applications
- Pharmacogenetics and Drug Metabolism
- T-cell and B-cell Immunology
Salk Institute for Biological Studies
2022-2024
University of California, San Diego
1996-2024
Cold Spring Harbor Laboratory
2024
University of California, Los Angeles
2015-2023
Australian Regenerative Medicine Institute
2023
Monash University
2023
University of Kansas
1994-2001
Wilmington University
1995
Abstract DNA methylation has been utilized for target gene silencing in plants. However, it is not well understood whether other pathways can be also used to manipulate expression. Here we performed a gain-of-function screen proteins that could silence when fused an artificial zinc finger. We uncovered many suppressed expression through methylation, histone H3K27me3 deposition, H3K4me3 demethylation, deacetylation, inhibition of RNA polymerase II transcription elongation or Ser-5...
The microrchidia (MORC) proteins are a family of evolutionarily conserved GHKL-type ATPases involved in chromatin compaction and gene silencing. Arabidopsis MORC act the RNA-directed DNA methylation (RdDM) pathway, where they as molecular tethers to ensure efficient establishment RdDM de novo However, also have RdDM-independent functions although their underlying mechanisms unknown.
Arabidopsis telomeric repeat binding factors (TRBs) can bind DNA sequences to protect telomeres from degradation. TRBs also recruit Polycomb Repressive Complex 2 (PRC2) deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that associate and colocalize with JUMONJI14 (JMJ14) trigger H3K4me3 demethylation at some The trb1/2/3 triple mutant the jmj14-1 show an increased level TRB JMJ14 sites, resulting in up-regulation their genes. Furthermore,...
Abstract The amygdala processes positive and negative valence contributes to addiction, but the cell-type-specific gene regulatory programs involved are unknown. We generated an atlas of single-nucleus expression chromatin accessibility in outbred rats with high low cocaine addiction-like behaviors following prolonged abstinence. Differentially expressed genes between groups were enriched for energy metabolism across cell types. Rats addiction index (AI) showed increased relapse-like...
Summary A single gene may have multiple enhancers, but how they work in concert to regulate transcription is poorly understood. To analyze enhancer interactions throughout the genome, we developed a generalized linear modeling framework, GLiMMIRS, for interrogating effects from single-cell CRISPR experiments. We applied GLiMMIRS published dataset and tested between 46,166 pairs corresponding genes, including 264 ’high-confidence’ pairs. found that combine multiplicatively with limited...
Abstract The amygdala processes positive and negative valence contributes to the development of addiction, but underlying cell type-specific gene regulatory programs are unknown. We generated an atlas single nucleus expression chromatin accessibility in outbred rats with low high cocaine addiction-like behaviors following prolonged abstinence. Between different addiction indexes, we identified thousands differentially expressed genes enriched for energy metabolism-related pathways that known...
A single gene may have multiple enhancers, but how they work in concert to regulate transcription is poorly understood. To analyze enhancer interactions throughout the genome, we developed a generalized linear modeling framework, GLiMMIRS, for interrogating effects from single-cell CRISPR experiments. We applied GLiMMIRS published dataset and tested between 46,166 pairs corresponding genes, including 264 "high-confidence" pairs. found that combine multiplicatively with limited evidence...
Deep neural networks (DNNs) have advanced predictive modeling for regulatory genomics, but challenges remain in ensuring the reliability of their predictions and understanding key factors behind decision making. Here we introduce DEGU (Distilling Ensembles Genomic Uncertainty-aware models), a method that integrates ensemble learning knowledge distillation to improve robustness explainability DNN predictions. distills an DNNs into single model, capturing both average ensemble's variability...
Abstract Arabidopsis telomeric repeat binding factors (TRBs) can bind DNA sequences to protect telomeres from degradation. TRBs also recruit Polycomb Repressive Complex 2 (PRC2) deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that associate and colocalize with JUMONJI14 (JMJ14) trigger H3K4me3 demethylation at some The trb1/2/3 triple mutant the jmj14-1 show an increased level TRB JMJ14 sites, resulting in up-regulation their genes....
Introducing functional macromolecules into a variety of living cells is challenging but important for biology research and cell-based therapies. We report novel cell delivery platform based on rotating shape anisotropic magnetic particles (SAMPs), which make very small cuts membranes macromolecule with high efficiency survivability. SAMP performed by placing commercially available nickel powder onto grown in standard culture dishes. Application uniform field causes the to rotate because...
We report a novel intracellular delivery system based on aligning Shape-Anisotropic Magnetic Particles (SAMP) to deliver functional molecules into mammalian cells with high efficiency and viability. A broad range of (calcein, dextran 3K, 40K, GFP plasmid, SiRNA, β-lactamase) have been successfully delivered primary preserved functions. achieved enzyme human dermal fibroblast (NHDF), other large macromolecules (dextran 40K) mouse cortical neurons.
Mitonuclear interactions have been proposed as evolutionary drivers of sexual reproduction, selection, adaptation, and speciation. We investigated the role pre-mating isolation in maintaining functional mitonuclear a wild population with divergent sets co-adapted genotypes. Two lineages identified eastern yellow robin Eopsaltria australis - putatively climate-adapted to ‘inland’ ‘coastal’ climates. The differ by ~7% mitochondrial DNA positions, whereas nuclear genome differences are...