A5058356244- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Advanced Fluorescence Microscopy Techniques
- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Single-cell and spatial transcriptomics
- CRISPR and Genetic Engineering
- Gene Regulatory Network Analysis
- Advanced biosensing and bioanalysis techniques
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Cell Image Analysis Techniques
- Plant Molecular Biology Research
- Force Microscopy Techniques and Applications
- Advanced Biosensing Techniques and Applications
- Engineering and Materials Science Studies
- Click Chemistry and Applications
- Chromosomal and Genetic Variations
- Viral Infectious Diseases and Gene Expression in Insects
- DNA Repair Mechanisms
- Mechanical and Optical Resonators
- Cancer-related molecular mechanisms research
- RNA Interference and Gene Delivery
- Neurobiology and Insect Physiology Research
- Nanopore and Nanochannel Transport Studies
Institute for Systems Biology
2018-2024
New York University
2019-2024
Indiana University School of Medicine
2024
NYU Langone Health
2017-2022
Janelia Research Campus
2009-2017
Howard Hughes Medical Institute
2009-2017
Helix (United States)
2013-2016
Albert Einstein College of Medicine
2009-2015
Cold Spring Harbor Laboratory
2011
Yeshiva University
2009-2010
Although messenger RNA (mRNA) translation is a fundamental biological process, it has never been imaged in real time vivo with single-molecule precision. To achieve this, we developed nascent chain tracking (NCT), technique that uses multi-epitope tags and antibody-based fluorescent probes to quantify protein synthesis dynamics at the single-mRNA level. NCT reveals an elongation rate of ~10 amino acids per second, initiation occurring stochastically every ~30 seconds. Polysomes contain ~1...
Measuring translation in space and time The ribosome translates the information contained within messenger RNAs (mRNAs) into proteins. When where ribosomes encounter mRNAs can regulate gene expression. Halstead et al. developed an RNA biosensor that allows single molecules of have never been translated to be distinguished from ones undergone by living cells (see Perspective Popp Maquat). authors demonstrated utility their technique examining spatial temporal regulation Drosophila oocytes...
Protein clustering is a hallmark of genome regulation in mammalian cells. However, the dynamic molecular processes involved make it difficult to correlate with functional consequences vivo. We developed live-cell super-resolution approach uncover correlation between mRNA synthesis and dynamics RNA Polymerase II (Pol II) clusters at gene locus. For endogenous β-actin genes mouse embryonic fibroblasts, we observe that short-lived (~8 s) Pol basal output. During serum stimulation, stereotyped...
Significance We have derived a new technology for the detection of genes within undisturbed nuclei fixed cells and tissues. Previous approaches used fluorescent DNA probes to hybridize interest, requiring treatment heat disruptive chemicals that distort natural organization nucleus. Instead, we bacterial protein, CRISPR (clustered regularly interspaced short palindromic repeats), combined with an RNA sequence as find interest in intact genome. This approach preserves spatial relationships...
Cys2His2 zinc finger (ZF) domains engineered to bind specific target sequences in the genome provide an effective strategy for programmable regulation of gene expression, with many potential therapeutic applications. However, structurally intricate engagement ZF DNA has made their design challenging. Here we describe screening 49 billion protein-DNA interactions and development a deep-learning model, ZFDesign, that solves any genomic target. ZFDesign is modern machine learning method models...
DNA helicases are enzymes capable of unwinding double-stranded (dsDNA) to provide the single-stranded template required in many biological processes. Among these, UvrD, an essential repair enzyme, has been shown unwind dsDNA while moving 3′-5′ on one strand. Here, we use a single-molecule manipulation technique monitor real-time changes extension single, stretched, nicked substrate as it is unwound by single enzyme. This offers means for measuring rate, lifetime, and processivity enzymatic...
Abstract Germ granules, specialized ribonucleoprotein particles, are a hallmark of all germ cells. In Drosophila , an estimated 200 mRNAs enriched in the plasm, and some these have important, often conserved roles cell formation, specification, survival migration. How spatially distributed within granule whether their position defines functional properties is unclear. Here we show, using single-molecule FISH structured illumination microscopy, super-resolution approach, that organized...
How RNA-binding proteins recognize specific sets of target mRNAs remains poorly understood because current approaches depend primarily on sequence information. In this study, we demonstrate that recognition messenger RNAs (mRNAs) by requires the correct spatial positioning these sequences. We characterized both cis -acting elements and restraints define mode RNA binding zipcode-binding protein 1 (ZBP1/IMP1/IGF2BP1) to β-actin zipcode. The third fourth KH (hnRNP K homology) domains ZBP1...
The chiral nature of DNA plays a crucial role in cellular processes. Here we use magnetic tweezers to explore one the signatures this chirality, coupling between stretch and twist deformations. We show that extension stretched molecule increases linearly by 0.42 nm per excess turn applied double helix. This result contradicts intuition should lengthen as it is unwound get shorter with overwinding. then present numerical results energy minimizations torsionally restrained display behavior...
Single-molecule micromanipulation techniques traditionally have been developed for biophysical applications, but they are being increasingly employed in materials science applications such as rheology and polymer dynamics. Continuing developments improvements single-molecule manipulation afford new opportunities a broad range of fields. In this review we present an overview current techniques, with emphasis on optical magnetic tweezers, followed by description the elastic properties single...
The Influenza A virus genome consists of eight negative sense, single-stranded RNA segments. Although it has been established that most particles contain a single copy each the viral RNAs, packaging selection mechanism remains poorly understood. RNAs are synthesized in nucleus, exported into cytoplasm and travel to plasma membrane where budding occurs. Due difficulties analyzing associated vRNPs while preserving information about their positions within cell, remained unclear how during...
Messenger RNA localization is important for cell motility by local protein translation. However, while single mRNAs can be imaged and their movements tracked in cells, it has not yet been possible to determine whether these are actively translating. Therefore, we β-actin tagged with MS2 stem loops colocalizing labeled ribosomes when polysomes formed. A dataset of tracking information consisting thousands trajectories per demonstrated that co-moving have significantly different diffusion...
ABSTRACT Histone post-translational modifications are key gene expression regulators, but their rapid dynamics during development remain difficult to capture. We applied a Fab-based live endogenous modification labeling technique monitor the changes in histone levels zygotic genome activation (ZGA) living zebrafish embryos. Among various modifications, H3 Lys27 acetylation (H3K27ac) exhibited most drastic changes, accumulating two nuclear foci 64- 1k-cell-stage The elongating form of RNA...
The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. deposited by the SWR1 chromatin remodeler and evicted unclear mechanisms. We tracked living yeast at single-molecule resolution, found that eviction dependent on RNA Polymerase II (Pol II) Kin28/Cdk7 kinase, which phosphorylates Serine 5 heptapeptide repeats carboxy-terminal domain largest Pol subunit Rpb1. These findings link to initiation, promoter escape...