A5038281692- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Advanced Fluorescence Microscopy Techniques
- Cell Image Analysis Techniques
- Bacterial Genetics and Biotechnology
- Image Processing Techniques and Applications
- Analytical chemistry methods development
- Advanced Electron Microscopy Techniques and Applications
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- RNA modifications and cancer
- Optical Imaging and Spectroscopy Techniques
- Microtubule and mitosis dynamics
- Laser-induced spectroscopy and plasma
- DNA Repair Mechanisms
- Electrochemical Analysis and Applications
- Mass Spectrometry Techniques and Applications
- Cancer Genomics and Diagnostics
- Mercury impact and mitigation studies
- Chromosomal and Genetic Variations
- Genetics, Bioinformatics, and Biomedical Research
- Cytokine Signaling Pathways and Interactions
- DNA and Nucleic Acid Chemistry
- Gene Regulatory Network Analysis
École Polytechnique Fédérale de Lausanne
2022-2024
National Research Centre
2010-2024
University of Geneva
2024
University of Lausanne
2022-2023
Swiss Cancer Center Léman
2022-2023
Laboratoire de Biologie Moléculaire des Eucaryotes
2017-2020
Université Toulouse III - Paul Sabatier
2017-2020
Centre National de la Recherche Scientifique
2014-2020
Harvard University
2020
Advanced Imaging Research (United States)
2020
Genome dynamics are intimately linked to the regulation of gene expression, most fundamental mechanism in biology, yet we still do not know whether very process transcription drives spatial organization at specific loci. Here, have optimized ANCHOR/ParB DNA-labeling system for real-time imaging a single-copy, estrogen-inducible transgene human cells. Motion an ANCHOR3-tagged DNA locus was recorded same cell before and during appearance nascent MS2-labeled mRNA. We found that initiation by...
Advanced FIB-SEM and 3D-SIM imaging uncover cohesin-independent chromatin arrangement into structural functional modules.
Significance Central biological processes in cells and tissues are intrinsically governed by the structural order of biomolecular assemblies. It is thus a key factor to decipher how these assemblies organize complex molecular organizations, from nanometric macroscopic scale. Polarized microscopy can access such information; however, signals spatially averaged over optical diffraction limit contaminated fluorophores’ orientational flexibility their linker biomolecules. By bringing polarized...
Intrinsic dynamics of chromatin contribute to gene regulation. How mobility responds genomic processes, and whether this response relies on coordinated movement is still unclear. Here, we introduce an approach called Dense Flow reConstruction Correlation (DFCC), quantify correlation motion with sub-pixel sensitivity at the level whole nucleus. DFCC reconstructs dense global flow fields fluorescent images acquired in real-time. We applied our analyze stochastic movements DNA histones, based...
Abstract Bulk chromatin motion has not been analyzed at high resolution. We present Hi-D, a method to quantitatively map dynamics of and abundant nuclear proteins for every pixel simultaneously over the entire nucleus from fluorescence image series. Hi-D combines reconstruction classification local diffusion processes by Bayesian inference. show that DNA in interior are spatially partitioned into 0.3–3-μm domains mosaic-like pattern, uncoupled compaction. This pattern was remodeled response...
Chromatin conformation regulates gene expression and thus, constant remodeling of chromatin structure is essential to guarantee proper cell function. To gain insight into the spatiotemporal organization genome, we use high-density photoactivated localization microscopy deep learning obtain temporally resolved super-resolution images in living cells. In combination with high-resolution dense motion reconstruction, find elongated ~45- 90-nm-wide "blobs." A computational model suggests that...
The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local opening closing. However, it unclear how nucleus-wide organization responds dynamically the activity specific TFs. Here, we examined two TFs with opposite effects accessibility modulate dynamics nucleus-wide. We combine high-resolution diffusion mapping dense flow reconstruction correlation in...
Thioflavin T (ThT) is standardly used as a fluorescent marker to detect aggregation of amyloid fibrils by conventional fluorescence microscopy, including polarization resolved imaging that brings information on the orientational order fibrils. These techniques are however diffraction limited and cannot provide fine structural details at scales 10-100 nm, which lie beyond limit. In this work, we evaluate capacity ThT photoswitch when bound insulin amyloids adjusting redox properties its...
ABSTRACT Three-dimensional (3D) chromatin organization plays a key role in regulating mammalian genome function, however many of its physical features at the single-cell level remain underexplored. Here we use 3D super-resolution and scanning electron microscopy to analyze structural functional nuclear somatic cells. We identify linked domains (CDs) composed irregular ∼200-300-nm-wide aggregates nucleosomes that can overlap with individual topologically associating are distinct from...
Chromatin 'blobs' were recently identified by live super-resolution imaging of labeled nucleosomes as pervasive but fleeting structural entities. However, the mechanisms leading to formation these blobs and their functional implications are unknown. We explore here whether causal relationships exist between parameters that characterize chromatin blob dynamics structure, adapting a framework for spatio-temporal Granger-causality inference. Our analysis reveals is key determinant both area...
Laser-induced breakdown spectroscopy (LIBS) has been used for brass plasma diagnostic using a Nd:YAG laser at 1064 nm. Optimal experimental conditions were evaluated, including repetition rate, number of shots on sample, and energy. The temperatures the electron densities determined from emission spectra LIBS. Cu Zn spectral lines excitation temperature calculation Saha-Boltzmann distribution as well line pair ratio. It was found that, calculated by ratio methods are not same. density...
ABSTRACT Bulk chromatin motion has not been analysed at high resolution. We present Hi-D, a method to quantitatively map dynamics of and abundant nuclear proteins for every pixel simultaneously over the entire nucleus from fluorescence image series. Hi-D combines reconstruction motion, classification local diffusion processes by Bayesian inference. show that DNA in interior are spatially partitioned into 0.3 – 3 μm domains mosaic-like pattern, uncoupled compaction. This pattern was...
Gene transcription by RNA polymerase II (RNAPol II) is a tightly regulated process in the genomic, temporal, and spatial context. Recently, we have shown that chromatin exhibits spatially coherently moving regions over entire nucleus, which enhanced transcription. Yet, it remains unclear how mobility of Pol molecules affected regulation whether this response depends on coordinated movement. We applied our Dense Flow reConstruction Correlation method to analyze nucleus-wide coherent movements...
Abstract Genome dynamics relate to regulation of gene expression, the most fundamental process in biology. Yet we still do not know whether very transcription drives spatial organization and chromatin conformation at specific loci. To address this issue, have optimized ANCHOR/ParB DNA labeling system for real-time imaging quantitative analysis a single-copy transgene human cells. Transcription under control endogenous Cyclin D1 promoter was induced by addition 17β-estradiol. Motion...
Abstract Intrinsic dynamics of chromatin contribute to gene regulation. How mobility responds genomic processes and whether this response relies on coordinated movement is still unclear. Here, we introduce an approach called Dense Flow reConstruction Correlation (DFCC) quantify correlation motion with sub-pixel sensitivity at the level whole nucleus. DFCC based reconstructing dense global flow fields fluorescent images acquired in real-time. By simulating variations microscopic dynamic...
Abstract Chromatin conformation regulates gene expression and thus constant remodeling of chromatin structure is essential to guarantee proper cell function. To gain insight into the spatio-temporal organization genome, we employ high-density photo-activated localization microscopy deep learning obtain temporally resolved super-resolution images in living cells. In combination with high-resolution dense motion reconstruction, confirm existence elongated ~ 45 90 nm wide ‘blobs’. A...
Abstract The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local opening closing. However, it unclear how nucleus-wide organization responds dynamically the activity specific TFs. Here we examined two TFs with opposite effects accessibility modulate dynamics nucleus-wide. We combine High-resolution Diffusion mapping (Hi-D) Dense Flow reConstruction...
Abstract Access to scientific meetings and conferences is limited in low‐ middle‐income countries (LMIC). Efforts are being implemented rectify this issue through short workshops, seminars, conferences. Sena Institute of Technology (SIT), a nonprofit research institute based Ghana, one such organization championing initiative. Through partnership with the Federation American Societies for Experimental Biology (FASEB), SIT hosted first FASEB conference Africa from August 27–30, 2023 Ghana....