A5054259097- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- DNA and Nucleic Acid Chemistry
- Plant Molecular Biology Research
- Bioinformatics and Genomic Networks
- Plant and Biological Electrophysiology Studies
- Advanced biosensing and bioanalysis techniques
- Material Dynamics and Properties
- DNA Repair Mechanisms
- nanoparticles nucleation surface interactions
- Single-cell and spatial transcriptomics
- Nonlinear Dynamics and Pattern Formation
- Diatoms and Algae Research
- CRISPR and Genetic Engineering
- stochastic dynamics and bifurcation
- Diffusion and Search Dynamics
- Biomedical Text Mining and Ontologies
- Plant Reproductive Biology
- Theoretical and Computational Physics
- Advanced Fluorescence Microscopy Techniques
- Genomics and Phylogenetic Studies
Massachusetts Institute of Technology
2017-2020
Technical University of Munich
2014-2018
Centre National de la Recherche Scientifique
2006
Aix-Marseille Université
2006
Institut de Recherche sur les Phénomènes Hors Équilibre
2005
Tracking mitotic chromosome formation How cells pack DNA into fully compact, rod-shaped chromosomes during mitosis has fascinated cell biologists for more than a century. Gibcus et al. delineated the conformational transition trajectory from interphase chromatin to minute by cycle. The is organized in spiral staircase architecture which loops emanate radially centrally located helical scaffold. molecular machines condensin I and II play distinct roles these processes: Condensin essential...
Significance Human DNA is 2 m long and folded into a 10-μm-sized cellular nucleus. Experiments have revealed two major features of genome organization: Segregation alternating active inactive regions compartments, formation compacted local domains. These were hypothesized to be formed by different mechanisms: Compartments can microphase separation domains active, motor-driven, loop extrusion. Here, we integrate these mechanisms polymer model show that their interplay coherently explains...
The spatial organization of chromatin in the nucleus has been implicated regulating gene expression. Maps high-frequency interactions between different segments have revealed topologically associating domains (TADs), within which most regulatory are thought to occur. TADs not homogeneous structural units but appear be organized into a hierarchy. We present OnTAD, an optimized nested TAD caller from Hi-C data, identify hierarchical TADs. OnTAD reveals new biological insights role levels,...
Arrays of regularly spaced nucleosomes are a hallmark chromatin, but it remains unclear how they generated. Recent genome-wide studies, in vitro and vivo, showed constant nucleosome spacing even if the histone concentration was experimentally reduced. This counters long-held assumption that density determines calls for factors keeping regardless density. We call this clamping activity. Here, we show purified system ISWI- CHD1-type remodelers have activity such not only generate arrays also...
Faithful genome transmission in dividing cells requires that the two copies of each chromosome's DNA package into separate but physically linked sister chromatids. The linkage between chromatids is mediated by cohesin, yet where are and how they resolve during cell cycle progression has remained unclear. In this study, we investigated chromatid organization live human using dCas9-mEGFP labeling endogenous genomic loci. We detected substantial locus separation G2 phase irrespective proximity...
Abstract Mammalian chromatin is organized on length scales ranging from individual nucleosomes to chromosomal territories. At intermediate two dominant features emerge in interphase: (i) alternating regions (<5Mb) of active and inactive that spatially segregate into different compartments, (ii) domains (<1Mb), i.e. preferentially interact internally, which are also termed topologically associating (TADs) central gene regulation. There growing evidence TADs formed by extrusion loops...
The first level of genome packaging in eukaryotic cells involves the formation dense nucleosome arrays, with DNA coverage near 90% yeasts. How achieve such high within a short time, e.g. after replication, remains poorly understood. It is known that random sequential adsorption impenetrable particles on line reaches density extremely slowly, due to jamming phenomenon. nucleosome-shifting action remodeling enzymes has been proposed as mechanism resolve jams. Here, we suggest two biophysical...
Adsorption-desorption processes are ubiquitous in physics, chemistry, and biology. Models usually assume hard particles, but within the realm of soft matter physics adsorbing particles compressible. A minimal 1D model reveals that softness fundamentally changes kinetics: Below desorption time scale, a logarithmic increase particle density replaces usual Rényi jamming plateau, subsequent relaxation to equilibrium can be nonmonotonic much faster than for particles. These effects will impact...
Stationary spatiotemporal pattern formation emerging from the electric activity of biological membranes is widespread in cells and tissues. A known key instability comes self-aggregation membrane channels. In a two-dimensional geometry, we show that primary undergoes four secondary instabilities: Eckhaus-like, period-halving, drift instabilities, global oscillation. The stability diagram determined. parity-breaking (drift) bifurcation channel density characterized analytically numerically.
Abstract The spatial organization of chromatin in the nucleus has been implicated many aspects regulated gene expression. Maps high frequency interactions between different segments have revealed Topologically Associating Domains (TADs), within which most regulatory are thought to occur. Recent studies shown that TADs not homogeneous structural units, but rather they appear be organized into a hierarchy. However, precise identification hierarchical TAD structures remains challenge. We...
A salient feature of stationary patterns in tip-growing cells is the key role played by symports and antiports, membrane proteins that translocate two ionic species at same time. It shown these cotransporters destabilize generically voltage if translocated ions diffuse differently carry a charge opposite (same) sign for (antiports). The orders magnitude obtained time length scale are agreement with experiments. weakly nonlinear analysis characterizes bifurcation.
Faithful genome transmission in dividing cells requires that the two copies of each chromosome’s DNA package into separate, but physically linked, sister chromatids. The linkage between chromatids is mediated by cohesin, yet where are linked and how they resolve during cell cycle progression has remained unclear. Here, we investigated chromatid organization live human using dCas9-mEGFP labelling endogenous genomic loci. We detected substantial locus separation G2 phase, irrespective...
Abstract Proper positioning of nucleosomes in eukaryotic cells is determined by a complex interplay factors, including nucleosome-nucleosome interactions, DNA sequence, and active chromatin remodeling. Yet, characteristic features nucleosome positioning, such as gene-averaged patterns, are surprisingly robust across perturbations, conditions, species. Here, we explore how this robustness arises despite the underlying complexity. We leverage mathematical models to show that large class...