Chiara Vicario

Centre for Genomic Regulation

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Mathieu Coppey

Université Paris Sciences et Lettres

Maxime Dahan

Centre National de la Recherche Scientifique

Jacob Piehler

Osnabrück University

Maria Pia Cosma

Centre for Genomic Regulation

ÁC

Álvaro Castells-García

Guangdong Academy of Medical Sciences

Cornelia Monzel

Heinrich Heine University Düsseldorf

Domenik Liße

Osnabrück University

Melike Lakadamyali

California University of Pennsylvania

Fred Etoc

Rumi Scientific (United States)

Maria Victoria Neguembor

Centre for Genomic Regulation

Cooperative Institutions

Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali di Frascati

Istituto Nazionale di Fisica Nucleare

Centre National de la Recherche Scientifique

National Agency for New Technologies, Energy and Sustainable Economic Development

Sapienza University of Rome

Istituto Nazionale di Fisica Nucleare, Sezione di Milano

Université Paris-Saclay

ENEA Frascati Research Centre

Sorbonne Université

University of Milan

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Magnetogenetic Control of Intracellular Signaling Pathways

HAL (Le Centre pour la Communication Scientifique Directe) (2016)

Chiara Vicario

Controlling the spatio-temporal organization of biomolecules inside living cells is a major rerequisite for deciphering mechanisms governing cell signaling and its regulation. In this thesis project, a new method to induce a highly specific and local perturbation of signaling pathways inside living cells is presented: magnetogenetics. It is based on the use of biofunctionalized magnetic nanoparticles, to induce and maintain protein gradients inside living cells. We tailored the size and surface properties of both synthetic silica core shell nanoparticles and superparamagnetic GFP-ferritin-based nanoparticles in order to ensure unhindered mobility in the cytosol. These nanoparticles can be rapidly localized in living cells by exploiting biased diffusion at weak magnetic forces in the fN range. In combination with nanoparticles' surface functionalization for specific in situ capturing of target proteins as well as efficient delivery into the cytosplasm, this work presents a novel technology for controlling intracellular protein gradients with a spatial resolution of micrometers and a temporal resolution of a few tens of seconds. In this work we showed the possibility to precisely control the perturbation of the signaling pathways associated to the small Rho GTPases proteins with relative quantification on signal propagation in terms of effector recruitment and morphological changes.

Biomolecule

Surface Modification

Signaling proteins

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Correction: Magnetic control of cellular processes using biofunctional nanoparticles

Chemical Science (2017)

Cornelia Monzel Chiara Vicario Jacob Piehler Mathieu Coppey Maxime Dahan

[This corrects the article DOI: 10.1039/C7SC01462G.].

10.1039/c7sc90067h

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Citations (1)

Publisher Correction: Non-specific interactions govern cytosolic diffusion of nanosized objects in mammalian cells

Nature Materials (2018)

Fred Etoc Élie Balloul Chiara Vicario Davide Normanno Domenik Liße

10.1038/s41563-018-0188-0

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Citations (5)

Magnetogenetic Manipulation of Intracellular Signaling using Ferritin Nanoparticles

Biophysical Journal (2016)

Chiara Vicario Domenik Liße Cornelia Monzel Albert Ikramov Jacob Piehler

10.1016/j.bpj.2015.11.3464

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Transcription-mediated supercoiling regulates genome folding and loop formation

Molecular Cell (2021)

Maria Victoria Neguembor Laura Martin Álvaro Castells-García Pablo Aurelio Gómez-García Chiara Vicario

Transcription

10.1016/j.molcel.2021.06.009

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Citations (82)

Il Lupo Alberto y La Pimpa. Proyecto de traducción audiovisual made in Friul

Chiara Vicario

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Photonic Crystal Biosensor Based on Optical Surface Waves

Sensors (2013)

Valery N. Konopsky Tanya Karakouz E. V. Alieva Chiara Vicario S. K. Sekatskiǐ

A label-free biosensor device based on registration of photonic crystal surface waves is described. Angular interrogation of the optical surface wave resonance is used to detect changes in the thickness of an adsorbed layer, while an additional simultaneous detection of the critical angle of total internal reflection provides independent data of the liquid refractive index. The abilities of the device are demonstrated by measuring of biotin molecule binding to a streptavidin monolayer, and by measuring association and dissociation kinetics of immunoglobulin G proteins. Additionally, deposition of PSS / PAH polyelectrolytes is recorded in situ resulting calculation of PSS and PAH monolayer thicknesses separately.

Streptavidin

Molecular binding

10.3390/s130202566

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Citations (87)

Super resolution microscopy reveals how elongating RNA polymerase II and nascent RNA interact with nucleosome clutches

Nucleic Acids Research (2021)

Álvaro Castells-García Ilyas Ed-daoui Esther González-Almela Chiara Vicario Jason Ottestrom

Abstract Transcription and genome architecture are interdependent, but it is still unclear how nucleosomes in the chromatin fiber interact with nascent RNA, and which is the relative nuclear distribution of these RNAs and elongating RNA polymerase II (RNAP II). Using super-resolution (SR) microscopy, we visualized the nascent transcriptome, in both nucleoplasm and nucleolus, with nanoscale resolution. We found that nascent RNAs organize in structures we termed RNA nanodomains, whose characteristics are independent of the number of transcripts produced over time. Dual-color SR imaging of nascent RNAs, together with elongating RNAP II and H2B, shows the physical relation between nucleosome clutches, RNAP II, and RNA nanodomains. The distance between nucleosome clutches and RNA nanodomains is larger than the distance measured between elongating RNAP II and RNA nanodomains. Elongating RNAP II stands between nascent RNAs and the small, transcriptionally active, nucleosome clutches. Moreover, RNA factories are small and largely formed by few RNAP II. Finally, we describe a novel approach to quantify the transcriptional activity at an individual gene locus. By measuring local nascent RNA accumulation upon transcriptional activation at single alleles, we confirm the measurements made at the global nuclear level.

RNA polymerase II

RNA polymerase I

10.1093/nar/gkab1215

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Citations (34)

Super-resolution microscopy reveals how histone tail acetylation affects DNA compaction within nucleosomes in vivo

Nucleic Acids Research (2019)

Jason Otterstrom Álvaro Castells-García Chiara Vicario Pablo Aurelio Gómez-García Maria Pia Cosma

Abstract Chromatin organization is crucial for regulating gene expression. Previously, we showed that nucleosomes form groups, termed clutches. Clutch size correlated with the pluripotency grade of mouse embryonic stem cells and human induced pluripotent stem cells. Recently, it was also shown that regions of the chromatin containing activating epigenetic marks were composed of small and dispersed chromatin nanodomains with lower DNA density compared to the larger silenced domains. Overall, these results suggest that clutch size may regulate DNA packing density and gene activity. To directly test this model, we carried out 3D, two-color super-resolution microscopy of histones and DNA with and without increased histone tail acetylation. Our results showed that lower percentage of DNA was associated with nucleosome clutches in hyperacetylated cells. We further showed that the radius and compaction level of clutch-associated DNA decreased in hyperacetylated cells, especially in regions containing several neighboring clutches. Importantly, this change was independent of clutch size but dependent on the acetylation state of the clutch. Our results directly link the epigenetic state of nucleosome clutches to their DNA packing density. Our results further provide in vivo support to previous in vitro models that showed a disruption of nucleosome-DNA interactions upon hyperacetylation.

10.1093/nar/gkz593

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Citations (117)

Non-specific interactions govern cytosolic diffusion of nanosized objects in mammalian cells

Nature Materials (2018)

Fred Etoc Élie Balloul Chiara Vicario Davide Normanno Domenik Liße

Macromolecular Crowding

Fluorescence Correlation Spectroscopy

Brownian dynamics

Anomalous Diffusion

10.1038/s41563-018-0120-7

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Citations (146)