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18 results on '"Krecsmarik, Monika"'

3. Copy number variants in patients with intellectual disability affect the regulation of ARX transcription factor gene

Author

Ishibashi, Minaka, Manning, Elizabeth, Shoubridge, Cheryl, Krecsmarik, Monika, Hawkins, Thomas A., Giacomotto, Jean, Zhao, Ting, Mueller, Thomas, Bader, Patricia I., Cheung, Sau W., Stankiewicz, Pawel, Bain, Nicole L., Hackett, Anna, Reddy, Chilamakuri C. S., Mechaly, Alejandro S., Peers, Bernard, Wilson, Stephen W., Lenhard, Boris, Bally-Cuif, Laure, Gecz, Jozef, Becker, Thomas S., and Rinkwitz, Silke

Published
2015
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4. Dynamic spatiotemporal coordination of neural stem cell fate decisions occurs through local feedback in the adult vertebrate brain

Author

Dray, Nicolas, Mancini, Laure, Binshtok, Udi, Cheysson, Felix, Supatto, Willy, Mahou, Pierre, Bedu, Sébastien, Ortica, Sara, Than-Trong, Emmanuel, Krecsmarik, Monika, Herbert, Sébastien, Masson, Jean-Baptiste, Tinevez, Jean-Yves, Lang, Gabriel, Beaurepaire, Emmanuel, Sprinzak, David, Bally-Cuif, Laure, Neurogénétique du Poisson zébré / Zebrafish Neurogenetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Collège Doctoral, Sorbonne Université (SU), Tel Aviv University (TAU), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Epidémiologie et modélisation de la résistance aux antimicrobiens - Epidemiology and modelling of bacterial escape to antimicrobials (EMAE), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de recherche en épidémiologie et santé des populations (CESP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Paul Brousse-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris-Saclay, Laboratoire d'Optique et Biosciences (LOB), École polytechnique (X)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Département de Biologie du Développement et Cellules souches - Department of Developmental and Stem Cell Biology, Institut Pasteur [Paris] (IP), Hub d'analyse d'images - Image Analysis Hub (Platform) (IAH), Département de Neuroscience - Department of Neuroscience, Département de Biologie Computationnelle - Department of Computational Biology, Work in the L.B.-C. laboratory was funded by the ANR (Labex Revive), La Ligue Nationale Contre le Cancer, CNRS, Institut Pasteur, DIM ELICIT (with E.B.), and the European Research Council (ERC) (AdG 322936). L.M. was recipient of a Ph.D. student fellowship from Labex Revive and the Fondation pour la Recherche Médicale (FRM). D.S. and U.B. acknowledge the support of the ERC under the EU Horizon 2020 research and innovation program (GA No. 682161). U.B. is the recipient of a fellowship from The Marian Gertner Institute for Medical Nanosystems at Tel Aviv University. Multiphoton equipment in E.B.’s laboratory was partly supported by the ANR (ANR-11-EQPX-0029 Morphoscope2, ANR-10-INSB-04 France BioImaging)., ANR-10-LABX-0073,REVIVE,Stem Cells in Regenerative Biology and Medicine(2010), ANR-11-EQPX-0029,MORPHOSCOPE 2,Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse)(2011), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), European Project: 322936,EC:FP7:ERC,ERC-2012-ADG_20120314,SYSTEMATICS(2013), European Project: 682161,ERC-2015-CoG ,MorphoNotch(2016), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège doctoral [Sorbonne universités], Tel Aviv University [Tel Aviv], Mathématiques et Informatique Appliquées (MIA-Paris), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris], Beaurepaire, Emmanuel, Laboratoires d'excellence - Stem Cells in Regenerative Biology and Medicine - - REVIVE2010 - ANR-10-LABX-0073 - LABX - VALID, Equipements d'excellence - Imagerie et reconstruction multiéchelles de la morphogenèse. (Plateforme d'innovation technologique et méthodologique pour l'imagerie in vivo et la reconstruction des dynamiques multiéchelles de la morphogenèse) - - MORPHOSCOPE 22011 - ANR-11-EQPX-0029 - EQPX - VALID, Développment d'une infrastructure française distribuée coordonnée - - France-BioImaging2010 - ANR-10-INBS-0004 - INBS - VALID, Dynamics and Homeostasis of Germinal Zones in the Adult Vertebrate Brain - SYSTEMATICS - - EC:FP7:ERC2013-09-01 - 2018-08-31 - 322936 - VALID, and Multi-scale analysis of the interplay between cell morphology and cell-cell signaling - MorphoNotch - - ERC-2015-CoG 2016-06-01 - 2021-05-31 - 682161 - VALID

Subjects
Multiphoton microscopy MPM, [SDV]Life Sciences [q-bio], zebrafish, analytical modeling, population behavior, intrinsic niche, spatial statistics, [SDV] Life Sciences [q-bio], pallium, nervous system, Adult neural stem cell, In vivo imaging, quiescence, spatiotemporal homeostasis, reproductive and urinary physiology, Notch signaling
Abstract

International audience; Neural stem cell (NSC) populations persist in the adult vertebrate brain over a lifetime, and their homeostasis is controlled at the population level through unknown mechanisms. Here, we combine dynamic imaging of entire NSC populations in their in vivo niche over several weeks with pharmacological manipulations, mathematical modeling, and spatial statistics and demonstrate that NSCs use spatiotemporally resolved local feedback signals to coordinate their decision to divide in adult zebrafish brains. These involve Notch-mediated short-range inhibition from transient neural progenitors and a dispersion effect from the dividing NSCs themselves exerted with a delay of 9–12 days. Simulations from a stochastic NSC lattice model capturing these interactions demonstrate that these signals are linked by lineage progression and control the spatiotemporal distribution of output neurons. These results highlight how local and temporally delayed interactions occurring between brain germinal cells generate self-propagating dynamics that maintain NSC population homeostasis and coordinate specific spatiotemporal correlations.

Published
2021

5. Dynamic spatiotemporal coordination of neural stem cell fate decisions through local feedback in the adult vertebrate brain

Author

Dray, Nicolas, primary, Mancini, Laure, additional, Binshtok, Udi, additional, Cheysson, Felix, additional, Supatto, Willy, additional, Mahou, Pierre, additional, Bedu, Sébastien, additional, Ortica, Sara, additional, Krecsmarik, Monika, additional, Herbert, Sébastien, additional, Masson, Jean-Baptiste, additional, Tinevez, Jean-Yves, additional, Lang, Gabriel, additional, Beaurepaire, Emmanuel, additional, Sprinzak, David, additional, and Bally-Cuif, Laure, additional

Published
2020
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8. An optimised pipeline for parallel image-based quantification of gene expression and genotyping after in situ hybridisation

Author

Dobrzycki, Tomasz, Krecsmarik, Monika, Bonkhofer, Florian, Patient, Roger, and Monteiro, Rui

Subjects
Genotyping, Bias, QH301-705.5, Methods & Techniques, hemic and lymphatic diseases, Science, Image quantification, Mutant, virus diseases, Biology (General), neoplasms, Zebrafish
Abstract

Advances in genome engineering have resulted in the generation of numerous zebrafish mutant lines. A commonly used method to assess gene expression in the mutants is in situ hybridisation (ISH). Because the embryos can be distinguished by genotype after ISH, comparing gene expression between wild-type and mutant siblings can be done blinded and in parallel. Such experimental design reduces the technical variation between samples and minimises the risk of bias. This approach, however, requires an efficient method of genomic DNA extraction from post-ISH fixed zebrafish samples to ascribe phenotype to genotype. Here we describe a method to obtain PCR-quality DNA from 95-100% of zebrafish embryos, suitable for genotyping after ISH. In addition, we provide an image analysis protocol for quantifying gene expression of ISH-probed embryos, adaptable for the analysis of different expression patterns. Finally, we show that intensity-based image analysis enables accurate representation of the variability of gene expression detected by ISH and that it can complement quantitative methods like qRT-PCR. By combining genotyping after ISH and computer-based image analysis, we have established a high-confidence, unbiased methodology to assign gene expression levels to specific genotypes, and applied it to the analysis of molecular phenotypes of newly generated lmo4a mutants., Summary: Our optimised protocol to genotype zebrafish mutant embryos after in situ hybridisation and digitally quantify the in situ signal will help to standardise existing experimental designs and methods of analysis.

Published
2018

12. Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome

Author

Naville, Magali, Ishibashi, Minaka, Ferg, Marco, Bengani, Hemant, Rinkwitz, Silke, Krecsmarik, Monika, Hawkins, Thomas A., Wilson, Stephen W., Manning, Elizabeth, Chilamakuri, Chandra S. R., Wilson, David I., Louis, Alexandra, Lucy Raymond, F., Rastegar, Sepand, Strähle, Uwe, Lenhard, Boris, Bally-Cuif, Laure, van Heyningen, Veronica, FitzPatrick, David R., Becker, Thomas S., Roest Crollius, Hugues, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Brain and Mind Research Institute, University of Technology Sydney (UTS), Karlsruhe Institute of Technology (KIT), MRC Human Genetics Unit, MRC Institute of Medical Genetic and Molecular Medicine, Institut des Neurosciences de Paris-Saclay (Neuro-PSI), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), C.D.B. Division of Biosciences, Anatomy building UCL, Department of Tumor Biology, The Norwegian Radium Hospital, University of Southampton and University Hospital Southampton NHS Foundation Trust, Centre for Human Development, Stem Cells and Regeneration, MP808, Faculty of Medicine, Cambridge Institute for Medical Research (CIMR), University of Cambridge [UK] (CAM), Institute of Clinical Sciences, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, University of Bergen (UIB), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut des Neurosciences Paris-Saclay (NeuroPSI), University of Bergen (UiB), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris

Subjects
Life sciences, biology, Genetic Linkage, DATABASE, Evolution, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, Gene Expression, Article, DISEASE, Animals, Genetically Modified, Evolution, Molecular, Midical sciences: 700::Basic medical, dental and veterinary sciences: 710::Medical genetics: 714 [VDP], Medisinske Fag: 700 [VDP], ddc:570, ELEMENTS, Genetics, Animals, Humans, Selection, Genetic, Zebrafish, GENE-EXPRESSION, Gene Rearrangement, TOOLS, Chromosomes, Human, X, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, GENOMIC SEQUENCES, IN-SITU HYBRIDIZATION, ENHANCERS, Biological sciences, Medisinske fag: 700::Basale medisinske, odontologiske og veterinærmedisinske fag: 710::Medisinsk genetikk: 714 [VDP], Enhancer Elements, Genetic, HUMAN CELL-TYPES, CONSERVED SYNTENY
Abstract

Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test this concept experimentally using the human X chromosome. We describe a scoring method to identify evolutionary maintenance of linkage between conserved noncoding elements and neighbouring genes. Chromatin marks associated with enhancer function are strongly correlated with this linkage score. We test >1,000 putative enhancers by transgenesis assays in zebrafish to ascertain the identity of the target gene. The majority of active enhancers drive a transgenic expression in a pattern consistent with the known expression of a linked gene. These results show that evolutionary maintenance of linkage is a reliable predictor of an enhancer's function, and provide new information to discover the genetic basis of diseases caused by the mis-regulation of gene expression., Enhancers regulate the transcription of genes over long genomic distances. Here, the authors show that enhancer function is correlated with maintenance of linkage between non-coding elements and neighbouring genes in the human X chromosome and that enhancers in zebrafish drive expression in a pattern consistent with the expression of a linked gene.

Published
2015
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16. Large-scale live imaging of adult neural stem cells in their endogenous niche.

Author

Dray, Nicolas, Bedu, Sébastien, Vuillemin, Nelly, Alunni, Alessandro, Coolen, Marion, Krecsmarik, Monika, Supatto, Willy, Beaurepaire, Emmanuel, and Bally-Cuif, Laure

Subjects
NEURAL stem cells, BRAIN imaging, GERMINAL centers, CEREBRAL cortex, LABORATORY zebrafish
Abstract

Live imaging of adult neural stem cells (aNSCs) in vivo is a technical challenge in the vertebrate brain. Here, we achieve long-term imaging of the adult zebrafish telencephalic neurogenic niche and track a population of >1000 aNSCs over weeks, by taking advantage of fish transparency at near-infrared wavelengths and of intrinsic multiphoton landmarks. This methodology enables us to describe the frequency, distribution and modes of aNSCs divisions across the entire germinal zone of the adult pallium, and to highlight regional differences in these parameters. [ABSTRACT FROM AUTHOR]

Published
2015
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17. Dynamic spatiotemporal coordination of neural stem cell fate decisions occurs through local feedback in the adult vertebrate brain.

Author

Dray N, Mancini L, Binshtok U, Cheysson F, Supatto W, Mahou P, Bedu S, Ortica S, Than-Trong E, Krecsmarik M, Herbert S, Masson JB, Tinevez JY, Lang G, Beaurepaire E, Sprinzak D, and Bally-Cuif L

Subjects
Animals, Brain, Cell Proliferation, Feedback, Zebrafish, Neural Stem Cells, Neurogenesis
Abstract

Neural stem cell (NSC) populations persist in the adult vertebrate brain over a lifetime, and their homeostasis is controlled at the population level through unknown mechanisms. Here, we combine dynamic imaging of entire NSC populations in their in vivo niche over several weeks with pharmacological manipulations, mathematical modeling, and spatial statistics and demonstrate that NSCs use spatiotemporally resolved local feedback signals to coordinate their decision to divide in adult zebrafish brains. These involve Notch-mediated short-range inhibition from transient neural progenitors and a dispersion effect from the dividing NSCs themselves exerted with a delay of 9-12 days. Simulations from a stochastic NSC lattice model capturing these interactions demonstrate that these signals are linked by lineage progression and control the spatiotemporal distribution of output neurons. These results highlight how local and temporally delayed interactions occurring between brain germinal cells generate self-propagating dynamics that maintain NSC population homeostasis and coordinate specific spatiotemporal correlations., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)

Published
2021
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18. Long-range evolutionary constraints reveal cis-regulatory interactions on the human X chromosome.

Author

Naville M, Ishibashi M, Ferg M, Bengani H, Rinkwitz S, Krecsmarik M, Hawkins TA, Wilson SW, Manning E, Chilamakuri CS, Wilson DI, Louis A, Lucy Raymond F, Rastegar S, Strähle U, Lenhard B, Bally-Cuif L, van Heyningen V, FitzPatrick DR, Becker TS, and Roest Crollius H

Subjects
Animals, Animals, Genetically Modified, Evolution, Molecular, Gene Rearrangement genetics, Humans, Zebrafish, Chromosomes, Human, X genetics, Enhancer Elements, Genetic genetics, Gene Expression genetics, Genetic Linkage genetics, Selection, Genetic genetics
Abstract

Enhancers can regulate the transcription of genes over long genomic distances. This is thought to lead to selection against genomic rearrangements within such regions that may disrupt this functional linkage. Here we test this concept experimentally using the human X chromosome. We describe a scoring method to identify evolutionary maintenance of linkage between conserved noncoding elements and neighbouring genes. Chromatin marks associated with enhancer function are strongly correlated with this linkage score. We test >1,000 putative enhancers by transgenesis assays in zebrafish to ascertain the identity of the target gene. The majority of active enhancers drive a transgenic expression in a pattern consistent with the known expression of a linked gene. These results show that evolutionary maintenance of linkage is a reliable predictor of an enhancer's function, and provide new information to discover the genetic basis of diseases caused by the mis-regulation of gene expression.

Published
2015
Full Text
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