A5036678164- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- CRISPR and Genetic Engineering
- Genetics, Aging, and Longevity in Model Organisms
- Plant Molecular Biology Research
- Gene Regulatory Network Analysis
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Developmental Biology and Gene Regulation
- Advanced Biosensing Techniques and Applications
- Cell Image Analysis Techniques
- RNA modifications and cancer
- Cytokine Signaling Pathways and Interactions
- MicroRNA in disease regulation
- Mast cells and histamine
- Insect Resistance and Genetics
- Plant Reproductive Biology
- Advanced Fluorescence Microscopy Techniques
- Protist diversity and phylogeny
- interferon and immune responses
- Bacteriophages and microbial interactions
University of California, Berkeley
2017-2023
Stanford University
2010-2018
Howard Hughes Medical Institute
2018
Pediatrics and Genetics
2012
Hôpital Saint-Louis
1995
Centre National de la Recherche Scientifique
1995
Morphogen gradients direct the spatial patterning of developing embryos; however, mechanisms by which these are interpreted remain elusive. Here we used lattice light-sheet microscopy to perform in vivo single-molecule imaging early
The regulation of transcription requires the coordination numerous activities on DNA, yet how factors mediate these remains poorly understood. Here, we use lattice light-sheet microscopy to integrate single-molecule and high-speed 4D imaging in developing Drosophila embryos study nuclear organization interactions key Zelda Bicoid. In contrast previous studies suggesting stable, cooperative binding, show that both interact with DNA surprisingly high off-rates. We find form dynamic subnuclear...
In the universal genetic code, most amino acids can be encoded by multiple trinucleotide codons, and choice among available codons influence position-specific translation elongation rates. By using sequence-based ribosome profiling, we obtained transcriptome-wide profiles of in vivo occupancy as a function codon identity Caenorhabditis elegans human cells. Particularly striking these was trend higher for translated via G:U wobble base-pairing compared with synonymous that pair same tRNA...
High-throughput assays of three-dimensional interactions chromosomes have shed considerable light on the structure animal chromatin. Despite this progress, precise physical nature observed structures and forces that govern their establishment remain poorly understood. Here we present high resolution Hi-C data from early Drosophila embryos. We demonstrate boundaries between topological domains various sizes map to DNA elements resemble classical insulator elements: short genomic regions...
More than half of Caenorhabditis elegans pre-mRNAs lose their original 5′ ends in a process termed “ trans -splicing” which the RNA extending from transcription start site (TSS) to -splicing primary transcript, “outron,” is replaced with 22-nt spliced leader. This complicates mapping TSSs, leading lack available TSS data for these genes. We used growth at low temperature and nuclear isolation enrich transcripts still containing outrons, applying modified SAGE capture procedure...
miRNAs are post-transcriptional regulators of gene activity that reduce protein accumulation from target mRNAs. Elucidating precise molecular effects animal have on transcripts has proven complex, with varied evidence indicating miRNA regulation may produce different outcomes in species, systems, and/or physiological conditions. Here we use high-throughput ribosome profiling to analyze detailed translational parameters for five well-studied targets regulate C. elegans developmental timing....
Nematodes of the genus Caenorhabditis enter a developmental diapause state after hatching in absence food. To better understand relative contributions distinct regulatory modalities to gene expression changes associated with this transition, we characterized genome-wide mRNA abundance and translational efficiency L1 exit four species using ribosome profiling mRNA-seq. We found strong tendency for regulation processes act synergistically, together effecting dramatic remodeling program. While...
We have used a combination of three high-throughput RNA capture and sequencing methods to refine augment the transcriptome map well-studied genetic model, Caenorhabditis elegans . The include standard (non-directional) library preparation protocol relying on cDNA priming foldback that has been in several previous studies for characterization this species, two directional protocols, one involving direct single-stranded fragments circular-template PCR (CircLigase). find each RNA-seq approach...
Our current understanding of the regulation gene expression in early Drosophila melanogaster embryo comes from observations a few genes at time, as with situ hybridizations, or observation levels without regards to patterning, RNA-sequencing. Single-nucleus RNA-sequencing however, has potential provide new insights into for many once while simultaneously retaining information regarding position each nucleus prior dissociation based on patterned expression. In order establish use...
Next generation high-throughput sequencing has enabled sensitive and unambiguous analysis of RNA populations in cells. Here, we describe a method for isolation strand-specific small pools from bacteria that can be multiplexed to accommodate multiple biological samples single experiment. Small RNAs are isolated by polyacrylamide gel electrophoresis treated with T4 polynucleotide kinase. This allows 3' adapter ligation CRISPR RNAs, which don't have pre-existing 3'-OH ends. Pre-adenylated...
Abstract Insulator proteins bind to specific genomic loci and have been shown play a role in partitioning genomes into independent domains of gene expression chromatin structure. Despite decades study, the mechanism by which insulators establish these remains elusive. Here, we use genome-wide conformation capture (Hi-C) generate high-resolution map spatial interactions from Drosophila melanogaster embryos. We show that earliest stages development genome is divided distinct topologically...
Abstract/Summary The eukaryotic genome is organized to enable the precise regulation of gene expression required for development. This organization established during early development when embryo transitions from a fertilized germ cell totipotent zygote. To understand factors and processes that drive genomic organization, we focused on pioneer factor GAGA (GAF) embryonic in Drosophila. GAF transcriptionally activates zygotic localized subnuclear foci. We show this non-uniform distribution...
Abstract Our current understanding of the regulation gene expression in early Drosophila melanogaster embryo comes from observations a few genes at time, as with situ hybridizations, or observation levels without regards to patterning, RNA-sequencing. Single-nucleus RNA-sequencing however, has potential provide new insights into for many once while simultaneously retaining information regarding position each nucleus prior dissociation based on patterned expression. In order establish...