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1. Multi-feature clustering of CTCF binding creates robustness for loop extrusion blocking and Topologically Associating Domain boundaries

Author

Li-Hsin Chang, Sourav Ghosh, Andrea Papale, Jennifer M. Luppino, Mélanie Miranda, Vincent Piras, Jéril Degrouard, Joanne Edouard, Mallory Poncelet, Nathan Lecouvreur, Sébastien Bloyer, Amélie Leforestier, Eric F. Joyce, David Holcman, and Daan Noordermeer

Subjects
Science
Abstract

Abstract Topologically Associating Domains (TADs) separate vertebrate genomes into insulated regulatory neighborhoods that focus genome-associated processes. TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein. Here we determine how this clustering of CTCF binding contributes to the blocking of loop extrusion and the insulation between TADs. We identify enrichment of three features of CTCF binding at strong TAD boundaries, consisting of strongly bound and closely spaced CTCF binding peaks, with a further enrichment of DNA-binding motifs within these peaks. Using multi-contact Nano-C analysis in cells with normal and perturbed CTCF binding, we establish that individual CTCF binding sites contribute to the blocking of loop extrusion, but in an incomplete manner. When clustered, individual CTCF binding sites thus create a stepwise insulation between neighboring TADs. Based on these results, we propose a model whereby multiple instances of temporal loop extrusion blocking create strong insulation between TADs.

Published
2023
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2. The Drosophila Fab-7 boundary modulates Abd-B gene activity by guiding an inversion of collinear chromatin organization and alternate promoter use

Author

Laura Moniot-Perron, Benoit Moindrot, Line Manceau, Joanne Edouard, Yan Jaszczyszyn, Pascale Gilardi-Hebenstreit, Céline Hernandez, Sébastien Bloyer, and Daan Noordermeer

Subjects
CP: Molecular biology, Biology (General), QH301-705.5
Abstract

Summary: Hox genes encode transcription factors that specify segmental identities along the anteroposterior body axis. These genes are organized in clusters, where their order corresponds to their activity along the body axis, a feature known as collinearity. In Drosophila, the BX-C cluster contains the three most posterior Hox genes, where their collinear activation incorporates progressive changes in histone modifications, chromatin architecture, and use of boundary elements and cis-regulatory regions. To dissect functional hierarchies, we compare chromatin organization in cell lines and larvae, with a focus on the Abd-B gene. Our work establishes the importance of the Fab-7 boundary for insulation between 3D domains carrying different histone modifications. Interestingly, we detect a non-canonical inversion of collinear chromatin dynamics at Abd-B, with the domain of active histone modifications progressively decreasing in size. This dynamic chromatin organization differentially activates the alternative promoters of the Abd-B gene, thereby expanding the possibilities for fine-tuning of transcriptional output.

Published
2023
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3. Eye morphogenesis in the blind Mexican cavefish

Author

Lucie Devos, François Agnès, Joanne Edouard, Victor Simon, Laurent Legendre, Naima El Khallouki, Sosthène Barbachou, Frédéric Sohm, and Sylvie Rétaux

Subjects
zic1, crispr/cas9 knock-in, live imaging, cell behaviours, optic vesicle, retinal pigmented epithelium, evo-devo, Science, Biology (General), QH301-705.5
Abstract

The morphogenesis of the vertebrate eye consists of a complex choreography of cell movements, tightly coupled to axial regionalization and cell type specification processes. Disturbances in these events can lead to developmental defects and blindness. Here, we have deciphered the sequence of defective events leading to coloboma in the embryonic eye of the blind cavefish of the species Astyanax mexicanus. Using comparative live imaging on targeted enhancer-trap Zic1:hsp70:GFP reporter lines of both the normal, river-dwelling morph and the cave morph of the species, we identified defects in migratory cell behaviours during evagination that participate in the reduced optic vesicle size in cavefish, without proliferation defect. Further, impaired optic cup invagination shifts the relative position of the lens and contributes to coloboma in cavefish. Based on these results, we propose a developmental scenario to explain the cavefish phenotype and discuss developmental constraints to morphological evolution. The cavefish eye appears as an outstanding natural mutant model to study molecular and cellular processes involved in optic region morphogenesis.

Published
2021
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4. Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases

Author

Jean-Baptiste Renaud, Charlotte Boix, Marine Charpentier, Anne De Cian, Julien Cochennec, Evelyne Duvernois-Berthet, Loïc Perrouault, Laurent Tesson, Joanne Edouard, Reynald Thinard, Yacine Cherifi, Séverine Menoret, Sandra Fontanière, Noémie de Crozé, Alexandre Fraichard, Frédéric Sohm, Ignacio Anegon, Jean-Paul Concordet, and Carine Giovannangeli

Subjects
Biology (General), QH301-705.5
Abstract

Genome editing has now been reported in many systems using TALEN and CRISPR-Cas9 nucleases. Precise mutations can be introduced during homology-directed repair with donor DNA carrying the wanted sequence edit, but efficiency is usually lower than for gene knockout and optimal strategies have not been extensively investigated. Here, we show that using phosphorothioate-modified oligonucleotides strongly enhances genome editing efficiency of single-stranded oligonucleotide donors in cultured cells. In addition, it provides better design flexibility, allowing insertions more than 100 bp long. Despite previous reports of phosphorothioate-modified oligonucleotide toxicity, clones of edited cells are readily isolated and targeted sequence insertions are achieved in rats and mice with very high frequency, allowing for homozygous loxP site insertion at the mouse ROSA locus in particular. Finally, when detected, imprecise knockin events exhibit indels that are asymmetrically positioned, consistent with genome editing taking place by two steps of single-strand annealing.

Published
2016
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5. The Drosophila Fab-7 boundary element modulates Abd-B gene activity in the genital disc by guiding an inversion of collinear chromatin organization and alternative promoter use

Author

Laura Moniot-Perron, Benoit Moindrot, Line Manceau, Joanne Edouard, Yan Jaszczyszyn, Pascale Gilardi-Hebenstreit, Céline Hernandez, Sébastien Bloyer, Daan Noordermeer, Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
Hox genes, single-cell RNA-seq, histone modifications, 3D genome organization, contact domain, Boundary Element, Drosophila, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, collinearity, alternative promoter use, Fab-7
Abstract

SummaryHox genes encode transcription factors that specify segmental identities along the Antero-Posterior body axis. These genes are organized in clusters, where their order corresponds to their activity along the body axis, an evolutionary conserved feature known as collinearity. In Drosophila, the BX-C cluster contains the three most posterior Hox genes, where their collinear activation incorporates progressive replacement of histone modifications, reorganization of 3D chromatin architecture and sequential activation of boundary elements and cis-regulatory regions. To dissect functional hierarchies, we compared chromatin organization in larvae and in cell lines, with a focus on the Abd-B gene. Our work establishes the importance of the Fab-7 boundary element for insulation between 3D domains marked by different histone modifications. Interestingly, we detected a non-canonical inversion of collinear chromatin dynamics at the Abd-B gene, with the active histone domain decreasing in size. This chromatin organization differentially instructed alternative Abd-B promoter use, thereby expanding the possibilities to regulate transcriptional output.

Published
2022

6. Eye morphogenesis in the blind Mexican cavefish

Author

Laurent Legendre, François Agnès, Lucie Devos, Naima El Khallouki, Frédéric Sohm, Victor Simon, Joanne Edouard, Sosthène Barbachou, Sylvie Rétaux, Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Animaux Modèles Aquatiques : ingéniérie GENétique (AMAGEN), and Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
genetic structures, QH301-705.5, Science, Morphogenesis, Cavefish, Biology, Optic cup (anatomical), Blindness, Eye, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, 0302 clinical medicine, biology.animal, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, medicine, Animals, Optic vesicle, Biology (General), Cell behaviours, Live imaging, 030304 developmental biology, 0303 health sciences, Coloboma, Eye morphogenesis, Evo-devo, Fishes, Vertebrate, [SDV.BDD.MOR]Life Sciences [q-bio]/Development Biology/Morphogenesis, CRISPR/Cas9 knock-in, medicine.disease, eye diseases, 3. Good health, medicine.anatomical_structure, Evolutionary biology, Lens (anatomy), Evolutionary developmental biology, Zic1, Retinal pigmented epithelium, sense organs, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery, Research Article
Abstract

The morphogenesis of the vertebrate eye consists of a complex choreography of cell movements, tightly coupled to axial regionalization and cell type specification processes. Disturbances in these events can lead to developmental defects and blindness. Here, we have deciphered the sequence of defective events leading to coloboma in the embryonic eye of the blind cavefish of the species Astyanax mexicanus. Using comparative live imaging on targeted enhancer-trap Zic1:hsp70:GFP reporter lines of both the normal, river-dwelling morph and the cave morph of the species, we identified defects in migratory cell behaviours during evagination that participate in the reduced optic vesicle size in cavefish, without proliferation defect. Further, impaired optic cup invagination shifts the relative position of the lens and contributes to coloboma in cavefish. Based on these results, we propose a developmental scenario to explain the cavefish phenotype and discuss developmental constraints to morphological evolution. The cavefish eye appears as an outstanding natural mutant model to study molecular and cellular processes involved in optic region morphogenesis., Summary: We show that the developing embryonic eye of the blind Mexican cavefish suffers multiple tissue morphogenesis and cell behaviour defects that lead to coloboma.

Published
2021

7. Fgfr3 Is a Positive Regulator of Osteoblast Expansion and Differentiation During Zebrafish Skull Vault Development

Author

Laurence Legeai-Mallet, Ghaith Abdessalem, Emilie Dambroise, Joanne Edouard, E. Elizabeth Patton, Björn Busse, Olivier Pellé, Frédéric Sohm, Alessandro Brombin, Olivia Binder, Ivan Ktorza, Imke A. K. Fiedler, Marine Luka, Mickaël M. Ménager, Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), MRC Human Genetics Unit, University of Edinburgh-Western General Hospital, Cancer Research UK Edinburgh Centre [Edinburgh, UK], University of Edinburgh-MRC Institute of Genetics and Molecular Medicine [Edinburgh] (IGMM), University of Edinburgh-Medical Research Council-Medical Research Council, Animaux Modèles Aquatiques : ingéniérie GENétique (AMAGEN), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Plateforme (PF I2BC), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Osteology and Biomechanics, Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), Structure Fédérative de Recherche Necker (SFR Necker - UMS 3633 / US24), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Inflammasome NLRP3 – NLRP3 Inflammasome, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), French National Research Agency (ANR)ANR-10-EQPX-03ANR10-INBS-09-08European Commission602300UK Research & Innovation (UKRI)Medical Research Council UK (MRC)MC_UU_000007/9European Research Council (ERC)European CommissionZF-MEL-CHEMBIO-648489L'Oreal Melanoma Research Alliance 401181l'Association des Gueules Cassees Region Ile-de-France, Lallemant, Christopher, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, musculoskeletal diseases, congenital, hereditary, and neonatal diseases and abnormalities, Endocrinology, Diabetes and Metabolism, Fgfr3, Regulator, Cranial Vault Defects, 030209 endocrinology & metabolism, Extracellular matrix, 03 medical and health sciences, 0302 clinical medicine, Osteogenesis, Cranial vault, medicine, Animals, Receptor, Fibroblast Growth Factor, Type 3, Orthopedics and Sports Medicine, Zebrafish, 030304 developmental biology, [SDV.MHEP.EM] Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, 0303 health sciences, Osteoblasts, biology, Skull, Cell Differentiation, Osteoblast, Zebrafish Proteins, Fibroblast growth factor receptor 3, [SDV.MHEP.EM]Life Sciences [q-bio]/Human health and pathology/Endocrinology and metabolism, biology.organism_classification, Cell biology, stomatognathic diseases, 030104 developmental biology, medicine.anatomical_structure, Intramembranous ossification, 030217 neurology & neurosurgery
Abstract

Gain- or loss-of-function mutations in fibroblast growth factor receptor 3 (FGFR3) result in cranial vault defects - highlighting the protein’s role in membranous ossification. Zebrafish express high levels of fgfr3 during skull development; in order to study FGFR3’s role in cranial vault development, we generated the first fgfr3 loss-of-function zebrafish (fgfr3lof/lof). The mutant fish exhibited major changes in the craniofacial skeleton, with a lack of sutures, abnormal frontal and parietal bones, and the presence of ectopic bones. Integrated analyses (in vivo imaging, and single-cell RNA sequencing of the osteoblast lineage) of zebrafish fgfr3lof/lof revealed a delay in osteoblast expansion and differentiation, together with changes in the extracellular matrix. These findings demonstrate that fgfr3 is a positive regulator of osteogenesis. We hypothesize that changes in the extracellular matrix within growing bone impair cell-cell communication, mineralization, and new osteoblast recruitment.

Published
2020

8. TRIM8 is required for virus-induced IFN response in human plasmacytoid dendritic cells

Author

Olivier Moncorgé, Sarah Maillet, Jean-Philippe Herbeuval, Nikaïa Smith, Joanne Edouard, Ghizlane Maarifi, Nathalie J. Arhel, Jean-Pierre Levraud, Frédéric Sohm, Georges Lutfalla, Fabien Blanchet, Sébastien Nisole, Célia Chamontin, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Universitätsklinikum Ulm - University Hospital of Ulm, Equipe Chimie et Biologie, Modélisation et Immunologie pour la Thérapie (CBMIT), Université Paris Descartes - Paris 5 (UPD5)-Université Paris Descartes - Paris 5 (UPD5), Animaux Modèles Aquatiques : ingéniérie GENétique (AMAGEN), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques (LCBPT - UMR 8601), Université Paris Descartes - Paris 5 (UPD5)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Dynamique des interactions membranaires normales et pathologiques (DIMNP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université Montpellier 1 (UM1), Macrophages et Développement de l’Immunité, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Funding: This work was supported by Labex EpiGenMed, an Investissements d’avenir program (ANR-10-LABX-12-01 to N.J.A. and S.N.), the Agence National de la Recherche sur le SIDA et les Hépatites virales, ANRS (AO2017-1 to J.-P.H.), the European Community’s Seventh Framework Program (FP7- PEOPLE-2011-ITN) under the Marie-Curie Initial Training Network FishForPharma (PITN-GA-2011-289209 to G.L.), the European Community’s H2020 Program Marie-Curie Innovative Training Network ImageInLife (721537 to G.L. and J.-P.L.), the Agence Nationale de la Recherche (ANR-16-CE20-0002-03 and ANR-10-MDI-009 to J.-P.L.), and the Région Occitanie (REPERE2017ImageInLife to G.L.). G.M. (AO2018-2), N.S. (AO2016-1), O.M. (AO2017-1), and S.M. (AO2017-2) were supported by grants from the ANRS. This work received help and expertise from TACGene, which is supported by the program Investissement d’avenir TEFOR (ANR-II-INSB-0014). N.S. acknowledges support from the European Molecular Biology Organization EMBO for Fellowship (LT-834-2017), the start-up funding program 'Baustein' of the Medical Faculty of Ulm University (LSBN.0147), and the Deutsche Forschungsgemeinschaft DFG (SM 544/1-1)., ANR-10-LABX-0012,EpiGenMed,From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow(2010), ANR-16-CE20-0002,Fish-RNAvax,Vaccins ARN éco-compatibles pour l'induction de réponses immunitaires protectrices chez le poisson d'élevage(2016), ANR-10-MIDI-0009,ZebraFlam,Signaux et cellules de la réponse inflammatoire: suivi en temps réel chez un vertébré entier, le danio zébré(2010), ANR-11-INBS-0014,TEFOR,Transgenèse pour les Etudes Fonctionnelles sur les Organismes modèles(2011), European Project: 289209,EC:FP7:PEOPLE,FP7-PEOPLE-2011-ITN,FISHFORPHARMA(2012), European Project: 721537,ImageInLife(2017), Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Centre National de la Recherche Scientifique (CNRS), ANR-10-LABX-0012/10-LABX-0012,EpiGenMed,From Genome and Epigenome to Molecular Medicine: turning new paradigms in biology into the therapeutic strategies of tomorrow(2010), ANR: 11-INBS-0014,TEFOR,Transgenèse pour les Etudes Fonctionnelles sur les Organismes modèles(2011), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)

Subjects
Small interfering RNA, Interferon Regulatory Factor-7, Ubiquitin-Protein Ligases, [SDV]Life Sciences [q-bio], Immunology, Regulator, Nerve Tissue Proteins, Cell Line, 03 medical and health sciences, 0302 clinical medicine, Ubiquitin, Interferon, medicine, Animals, Humans, Phosphorylation, RNA, Small Interfering, Research Articles, Zebrafish, 030304 developmental biology, 0303 health sciences, Multidisciplinary, Innate immune system, biology, Influenza A Virus, H3N2 Subtype, SciAdv r-articles, hemic and immune systems, Dendritic Cells, Tripartite motif family, Immunity, Innate, 3. Good health, Cell biology, NIMA-Interacting Peptidylprolyl Isomerase, HEK293 Cells, Interferon Type I, biology.protein, PIN1, HIV-1, IRF7, [SDV.IMM]Life Sciences [q-bio]/Immunology, RNA Interference, Carrier Proteins, Chikungunya virus, 030215 immunology, medicine.drug, Research Article, Signal Transduction
Abstract

TRIM8 and Pin1 oppositely control IRF7-induced interferon production., Plasmacytoid dendritic cells (pDCs) play a crucial role in antiviral innate immunity through their unique capacity to produce large amounts of type I interferons (IFNs) upon viral detection. Tripartite motif (TRIM) proteins have recently come forth as important modulators of innate signaling, but their involvement in pDCs has not been investigated. Here, we performed a rationally streamlined small interfering RNA (siRNA)–based screen of TRIM proteins in human primary pDCs to identify those that are critical for the IFN response. Among candidate hits, TRIM8 emerged as an essential regulator of IFN regulatory factor 7 (IRF7) function. Mechanistically, TRIM8 protects phosphorylated IRF7 (pIRF7) from proteasomal degradation in an E3 ubiquitin ligase–independent manner by preventing its recognition by the peptidyl-prolyl isomerase Pin1. Our findings uncover a previously unknown regulatory mechanism of type I IFN production in pDCs by which TRIM8 and Pin1 oppositely regulate the stability of pIRF7.

Published
2019

9. Postembryonic Fish Brain Proliferation Zones Exhibit Neuroepithelial-Type Gene Expression Profile

Author

Julia Jouralet, Aurélie Heuzé, Barbara Rizzi, Stéphanie Bouffard, Eric Reiter, Claude Thermes, Jean-Stéphane Joly, Joanne Edouard, Franck Bourrat, Yan Jaszczyszyn, Frédéric Sohm, Matthieu Simion, Spencer Brown, Anne Poupon, Pierre Affaticati, Mickael Bourge, Emilie Dambroise, Thomas Bourquard, Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Plateforme intégrée IMAGIF, Centre National de la Recherche Scientifique (CNRS), Animaux Modèles Aquatiques : ingéniérie GENétique (AMAGEN), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), FINEST project (ANR-11-BSV2-0029), Institut des Neurosciences de Paris-Saclay (Neuro-PSI), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut des Neurosciences de Paris-Saclay ( Neuro-PSI ), Université Paris-Sud - Paris 11 ( UP11 ) -Centre National de la Recherche Scientifique ( CNRS ), Physiologie de la reproduction et des comportements [Nouzilly] ( PRC ), Institut National de la Recherche Agronomique ( INRA ) -Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique ( CNRS ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Centre National de la Recherche Scientifique ( CNRS ), AMAGEN CNRS UMS3504 / INRA UMS1374 ( AMAGEN ), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, G2 Phase, Cell type, Optic tectum, Superior Colliculi, DNA Repair, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Green Fluorescent Proteins, Neuroepithelial Cells, Oryzias, Neuroepithelial cell, Biology, Cell cycle, [ SDV.NEU.PC ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Animals, Genetically Modified, 03 medical and health sciences, [ SDV.NEU.SC ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, RNA seq, Animals, Progenitor cell, Cell Proliferation, Genetics, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Sequence Analysis, RNA, Gene Expression Profiling, Neurogenesis, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, Brain, Gene Expression Regulation, Developmental, Cell Biology, Cell sorting, Embryonic stem cell, Neural stem cell, Cell biology, Up-Regulation, 030104 developmental biology, [ SDV.NEU.NB ] Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Microcephaly, Molecular Medicine, Stem cell, Biomarkers, Developmental Biology
Abstract

International audience; In mammals, neuroepithelial cells play an essential role in embryonic neurogenesis, whereas glial stem cells are the principal source of neurons at post-embryonic stages. By contrast, neuroepithelial-like stem/progenitor (NE) cells have been shown to be present throughout life in teleosts. We used 3-dimensional (3D) reconstructions of cleared transgenic wdr12:GFP medaka brains to demonstrate that this cell type is widespread in juvenile and to identify new regions containing NE cells. We established the gene expression profile of optic tectum (OT) NE cells by cell sorting followed by RNA-seq. Our results demonstrate that most OT NE cells are indeed active stem cells and that some of them exhibit long G2 phases. We identified several novel pathways (e.g., DNA repair pathways) potentially involved in NE cell homeostasis. In situ hybridization studies showed that all NE populations in the post-embryonic medaka brain have a similar molecular signature. Our findings highlight the importance of NE progenitors in medaka and improve our understanding of NE-cell biology. These cells are potentially useful not only for neural stem cell studies, but also for improving the characterization of neurodevelopmental diseases, such as microcephaly. This article is protected by copyright. All rights reserved.

Published
2016

10. Identification of the CCR5-Delta32 HIV resistance allele and new mutations of the CCR5 gene in different Tunisian populations

Author

Karima Fadhlaoui-Zid, Asma Jlizi, Amine Slim, Joanne Edouard, Sabah Frigi, Ioannis Theodorou, Wassila Carpentier, Patrice Debré, and Amel Ben Ammar El Gaaied

Subjects
Adult, Male, Tunisia, Genotype, Receptors, CCR5, Immunology, Population, Single-nucleotide polymorphism, HIV Infections, Biology, medicine.disease_cause, Gene Frequency, medicine, Immunology and Allergy, Humans, Allele, education, Allele frequency, Alleles, Genetics, Mutation, education.field_of_study, Polymorphism, Genetic, Point mutation, Haplotype, General Medicine, Virology, Immunity, Innate, Haplotypes, HIV-1, Female
Abstract

Polymorphisms in some chemokine receptor genes are associated with susceptibility to and progression of human immunodeficiency virus-1 (HIV-1) infection. Most mutations detected in the CC-chemokine receptor 5 (CCR5) gene are specific to different populations. In this study, we focused on polymorphisms of the CCR5 coding region in three healthy populations from Tunisia, corresponding to a cosmopolitan population from Tunis, and two isolated Berber populations. In addition to the CCR5-Delta32 deletion, eleven single nucleotide polymorphisms were detected. Some of these point mutations were associated with the same genotype and even the same haplotype. The (L55Q-C101X), I124, V131F, T143N, A159V, I237, T239A and G301R alleles have not been described previously, whereas the CCR5-Delta32, L55Q, A335V and Y339F variants have already been reported in the literature. The distribution and frequency of these variants were different among the three groups studied, a result in agreement with the mosaic genetic structure of the Tunisian population. To determine whether these alleles affect HIV-1 transmission, we compared allele frequencies between healthy and HIV-1 infected individuals from Tunis. The frequency of the CCR5-Delta32 variant was significantly different between the two groups, leading us to conclude that this mutation might confer protection against HIV infection in Tunisian populations.

Published
2007

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