A5065280389- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Advanced Fluorescence Microscopy Techniques
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- SARS-CoV-2 and COVID-19 Research
- COVID-19 Clinical Research Studies
- SARS-CoV-2 detection and testing
- Advanced Biosensing Techniques and Applications
- Diffusion and Search Dynamics
- Herpesvirus Infections and Treatments
- CRISPR and Genetic Engineering
- Advanced biosensing and bioanalysis techniques
- Lymphoma Diagnosis and Treatment
- Gene Regulatory Network Analysis
- Biosensors and Analytical Detection
- Peroxisome Proliferator-Activated Receptors
- Dental Research and COVID-19
- bioluminescence and chemiluminescence research
- Single-cell and spatial transcriptomics
- Advanced Electron Microscopy Techniques and Applications
- Influenza Virus Research Studies
- Molecular Biology Techniques and Applications
- RNA regulation and disease
- Wound Healing and Treatments
Centre National de la Recherche Scientifique
1998-2024
Institut Jacques Monod
2004-2024
University of California, Berkeley
2015-2023
California Institute for Regenerative Medicine
2018-2019
Institut de Biologie de l'École Normale Supérieure
2013-2015
Délégation Paris 7
2013-2015
Université Paris Cité
2008-2015
École Normale Supérieure - PSL
2012-2015
Inserm
2014
Laboratoire de Géologie de l’École Normale Supérieure
2012
Phase separation and gene control Many components of eukaryotic transcription machinery—such as factors cofactors including BRD4, subunits the Mediator complex, RNA polymerase II—contain intrinsically disordered low-complexity domains. Now a conceptual framework connecting nature behavior their interactions to functions in regulation is emerging (see Perspective by Plys Kingston). Chong et al. found that domains form concentrated hubs via functionally relevant dynamic, multivalent,...
Transcription is reported to be spatially compartmentalized in nuclear transcription factories with clusters of RNA polymerase II (Pol II). However, little known about when these foci assemble or their relative stability. We developed a quantitative single-cell approach characterize protein spatiotemporal organization, single-molecule sensitivity live eukaryotic cells. observed that Pol form transiently, an average lifetime 5.1 (± 0.4) seconds, which refutes the notion they are statically...
Gene regulation relies on transcription factors (TFs) exploring the nucleus searching their targets. So far, most studies have focused how fast TFs diffuse, underestimating role of nuclear architecture. We implemented a single-molecule tracking assay to determine dynamics. found that c-Myc is global explorer nucleus. In contrast, positive elongation factor P-TEFb local oversamples its environment. Consequently, each molecule equally available for all sites while reaches targets in...
RNA Polymerase II (Pol II) and transcription factors form concentrated hubs in cells via multivalent protein-protein interactions, often mediated by proteins with intrinsically disordered regions. During Herpes Simplex Virus infection, viral replication compartments (RCs) efficiently enrich host Pol into membraneless domains, reminiscent of liquid-liquid phase separation. Despite sharing several properties phase-separated condensates, we show that RCs operate a distinct mechanism wherein...
Abstract Many cellular functions rely on DNA-binding proteins finding and associating to specific sites in the genome. Yet mechanisms underlying target search remain poorly understood, especially case of highly organized mammalian cell nucleus. Using as a model Tet repressors (TetRs) searching for multi-array locus, we quantitatively analyse process human cells with single-molecule tracking single-cell protein–DNA association measurements. We find that TetRs explore nucleus reach their by 3D...
<h2>Summary</h2> Gene activation by mammalian transcription factors (TFs) requires multivalent interactions of their low-complexity domains (LCDs), but how such regulate remains unclear. It has been proposed that extensive LCD-LCD culminating in liquid-liquid phase separation (LLPS) TFs is the dominant mechanism underlying transactivation. Here, we investigated tuning amount and localization <i>in vivo</i> affects endogenous human genes. Quantitative single-cell single-molecule imaging...
Abstract Subnuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome distinct physical biochemical environments. During X chromosome inactivation (XCI), noncoding Xist RNA coats chromosome, triggers silencing forms a dense body heterochromatin from which transcription machinery appears be excluded. Phase separation involved XCI, might explain exclusion preventing its diffusion into -coated territory....
The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast (ySAGA) have been reported, there are noteworthy functional compositional differences for this metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure human (hSAGA) show how arrangement distinct structural elements results globally divergent organization from that yeast, with different interface tethering core module to...
Summary Cells are built from vast networks of competing molecular interactions, most which have been impossible to monitor in vivo. We recently devised a new strategy, proximity-assisted photoactivation (PAPA), detect these interactions at single-molecule resolution live cells. Here we apply PAPA visualize the network that regulate central transcription elongation factor P-TEFb. between multiple pairs endogenous proteins, combined with fast tracking (fSMT), revealed inactive P-TEFb within...
Re-opening of communities in the midst ongoing COVID-19 pandemic has ignited new waves infections many places around world. Mitigating risk reopening will require widespread SARS-CoV-2 testing, which would be greatly facilitated by simple, rapid, and inexpensive testing methods. This study evaluates several protocols for RNA extraction RT-qPCR that are simpler less expensive than prevailing First, isopropanol precipitation is shown to provide an effective means from nasopharyngeal (NP) swab...
Abstract SARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with significant mortality and morbidity. At this time, the only FDA-approved therapeutic for COVID-19 is remdesivir, a broad-spectrum antiviral nucleoside analog. Efficacy moderate, improved treatment strategies are urgently needed. To accomplish goal, we devised strategy to identify compounds that act synergistically remdesivir in preventing SARS-CoV-2 replication. We conducted combinatorial high-throughput...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of disease 2019 (COVID-19), has emerged as a major global health threat. The COVID-19 pandemic resulted in over 168 million cases and 3.4 deaths to date, while number continues rise. With limited therapeutic options, identification safe effective therapeutics is urgently needed. repurposing known clinical compounds holds potential for rapid drugs against SARS-CoV-2. Here, we utilized library FDA-approved...
Abstract Understanding how transcription factors regulate organized cellular diversity in developing tissues remains a major challenge due to their pleiotropic functions. We addressed this by monitoring and genetically modulating the activity of PAX3 PAX7 during specification neural progenitor pools embryonic spinal cord. Using mouse models, we show that balance between transcriptional activating repressing functions these is modulated along dorsoventral axis instructive patterning pools. By...
We recently described an unconventional mode of gene regulation in budding yeast by which transcriptional and translational interference collaborate to down-regulate protein expression. Developmentally timed inhibited production a well translated mRNA isoform resulted the containing inhibitory upstream open reading frames (uORFs) that prevented translation main ORF. Transcriptional uORF-based repression are established mechanisms outside yeast, but whether this type integrated was conserved...
Fibroblasts are important players in regulating tissue homeostasis. In the dermis, they involved wound healing where differentiate into contractile myofibroblasts leading to closure. nonhealing chronic wounds, fibroblasts fail undertake differentiation. We established and used a human ex vivo model of wounds can undergo normal myofibroblast differentiation, or take on nondifferentiable pathological state. At whole genome scale, we identified genes that differentially regulated these two cell...
The SARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with currently 29 million confirmed cases and close to a deaths. At this time, there are no FDA-approved vaccines or therapeutics for COVID-19, but Emergency Use Authorization been granted remdesivir, broad-spectrum antiviral nucleoside analog. However, remdesivir is only moderately efficacious against SARS-CoV-2 in the clinic, improved treatment strategies urgently needed. To accomplish goal, we devised strategy...
Article8 February 2021Open Access Transparent process Transcription activation depends on the length of RNA polymerase II C-terminal domain Anna Sawicka Department Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany Search more papers by this author Gabriel Villamil Michael Lidschreiber orcid.org/0000-0002-6740-2755 Xavier Darzacq orcid.org/0000-0003-2537-8395 and Cell University California, Berkeley, CA, USA CIRM Center Excellence, Claire Dugast-Darzacq...
Regular surveillance testing of asymptomatic individuals for SARS-CoV-2 has been center to outbreak prevention on college and university campuses. Here we describe the voluntary saliva program instituted at University California, Berkeley during an early period pandemic in 2020. The was administered as a research study ahead clinical implementation, enabling us launch while continuing optimize assay. Results both protocol itself participants’ experience show how succeeded providing routine,...
Abstract Sub-nuclear compartmentalization has been proposed to play an important role in gene regulation by segregating active and inactive parts of the genome distinct physical biochemical environments, where transcription epigenetic factors are either concentrated or depleted. The X chromosome offers a paradigm for studying sub-nuclear compartmentalization. When non-coding Xist RNA coats chromosome, it recruits repressors chromatin that trigger silencing, forms dense body heterochromatin...
The carboxy-terminal domain (CTD) of RNA polymerase (Pol) II is an intrinsically disordered low-complexity region that critical for pre-mRNA transcription and processing. CTD consists hepta-amino acid repeats varying in number from 52 humans to 26 yeast. Here we report human yeast CTDs undergo cooperative liquid phase separation at increasing protein concentration, with the shorter forming less stable droplets. In cells, truncation length decreases Pol clustering chromatin association...
Abstract Human SAGA is an essential co-activator complex that regulates gene expression by interacting with enhancer-bound activators, recruiting transcriptional machinery, and modifying chromatin near promoters. Subunit variations the metazoan-specific requirement of in development hinted at unique structural features human complex. Our 2.9 Å structure reveals intertwined functional modules flexibly connected to a core distinctively integrates mammalian paralogs, incorporates U2 splicing...