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1. Combining heteronuclear correlation NMR with spin-diffusion to detect relayed Cl-H-H and N-H-H proximities in molecular solids

Author

Parth Raval, Julien Trébosc, Tomasz Pawlak, Yusuke Nishiyama, Steven P. Brown, G.N. Manjunatha Reddy, UCCS Équipe RMN et matériaux inorganiques, Unité de Catalyse et Chimie du Solide - UMR 8181 (UCCS), Université d'Artois (UA)-Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université d'Artois (UA)-Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), UCCS Équipe Catalyse Supramoléculaire, Department of Bioorganic Chemistry Centre of Molecular and Macromolecular Studies Polish Academy of Sciences, Polish Academy of Sciences (PAN), RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Department of Physics [Coventry], University of Warwick [Coventry], European Project: 795091,H2020,H2020-MSCA-IF-2017,ZEOCATALYST(2019), Université d'Artois (UA)-Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut Michel Eugène Chevreul - FR 2638 (IMEC), Université d'Artois (UA)-Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre of Molecular and Macromolecular Studies, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Université de Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, Unité de Catalyse et Chimie du Solide (UCCS) - UMR 8181, and RIKEN Center for Life Science Technologies [RIKEN CLST]

Subjects
Nuclear and High Energy Physics, Magnetic Resonance Spectroscopy, Radiation, GIPAW, Dopamine, Structure elucidation, NMR crystallography, General Chemistry, [CHIM.MATE]Chemical Sciences/Material chemistry, [CHIM.THER]Chemical Sciences/Medicinal Chemistry, Fast MAS, DFT, Solid-state NMR, HMQC, Pharmaceutical, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [CHIM.CRIS]Chemical Sciences/Cristallography, QD, Histidine, Protons, Nuclear Magnetic Resonance, Biomolecular, Instrumentation, QC
Abstract

International audience; Analysis of short-to-intermediate range intermolecular interactions offers a great way of characterizing the solid-state organization of small molecules and materials. This can be achieved by two-dimensional (2D) homo- and heteronuclear correlation NMR spectroscopy, for example, by carrying out experiments at high magnetic fields in conjunction with fast magic-angle spinning (MAS) techniques. But, detecting 2D peaks for heteronuclear dipolar coupled spin pairs separated by greater than 3 Å is not always straightforward, particularly when low-gamma quadrupolar nuclei are involved. Here, we present a 2D correlation NMR experiment that combines the advantages of heteronuclear-multiple quantum coherence (HMQC) and proton-based spin-diffusion (SD) pulse sequences using radio-frequency-driven-recouping (RFDR) to probe inter and intramolecular 1H-X (X = 14N, 35Cl) interactions. This experiment can be used to acquire 2D 1H{X}-HMQC filtered 1H–1H correlation as well as 2D 1H-X HMQC spectra. Powder forms of dopamine·HCl and l-histidine·HCl·H2O are characterized at high fields (21.1 T and 18.8 T) with fast MAS (60 kHz) using the 2D HMQC-SD-RFDR approach. Solid-state NMR results are complemented with NMR crystallography analyses using the gauge-including projector augmented wave (GIPAW) approach. For histidine·HCl·H2O, 2D peaks associated with 14N–1H–1H and 35Cl–1H–1H distances of up to 4.4 and 3.9 Å have been detected. This is further corroborated by the observation of 2D peaks corresponding to 14N–1H–1H and 35Cl–1H–1H distances of up to 4.2 and 3.7 Å in dopamine·HCl, indicating the suitability of the HMQC-SD-RFDR experiments for detecting medium-range proximities in molecular solids.

Published
2022
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2. Astrocytic IP3Rs: Beyond IP3R2

Author

Mark W. Sherwood, Misa Arizono, Aude Panatier, Katsuhiko Mikoshiba, Stéphane H. R. Oliet, Oliet, Stephane, Neurocentre Magendie : Physiopathologie de la Plasticité Neuronale (U1215 Inserm - UB), Université de Bordeaux (UB)-Institut François Magendie-Institut National de la Santé et de la Recherche Médicale (INSERM), Interdisciplinary Institute for Neuroscience [Bordeaux] (IINS), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), ShanghaiTech University [Shanghai], Toho University, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), INSERM, Neurocentre Magendie, U1215, Physiopathologie de la Plasticité Neuronale, F-33000 Bordeaux, France, and Physiopathologie de la Plasticité Neuronale (Neurocentre Magendie - U1215 Inserm)

Subjects
0301 basic medicine, Gene isoform, [SDV]Life Sciences [q-bio], Mini Review, Neurosciences. Biological psychiatry. Neuropsychiatry, Biology, Neurotransmission, inositol triphosphate (IP3) receptor, 03 medical and health sciences, Cellular and Molecular Neuroscience, 0302 clinical medicine, astrocyte, GPCR, Tripartite synapse, medicine, Receptor, G protein-coupled receptor, calcium, tripartite synapse, Glutamate receptor, gliotransmission, [SDV] Life Sciences [q-bio], 030104 developmental biology, medicine.anatomical_structure, IP 3 R subtypes, IP3R subtypes, Cellular Neuroscience, Synaptic plasticity, [SDV.NEU]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC], Neuroscience, 030217 neurology & neurosurgery, Astrocyte, RC321-571
Abstract

Astrocytes are sensitive to ongoing neuronal/network activities and, accordingly, regulate neuronal functions (synaptic transmission, synaptic plasticity, behavior, etc.) by the context-dependent release of several gliotransmitters (e.g., glutamate, glycine, D-serine, ATP). To sense diverse input, astrocytes express a plethora of G-protein coupled receptors, which couple, via Gi/o and Gq, to the intracellular Ca2+ release channel IP3-receptor (IP3R). Indeed, manipulating astrocytic IP3R-Ca2+ signaling is highly consequential at the network and behavioral level: Depleting IP3R subtype 2 (IP3R2) results in reduced GPCR-Ca2+ signaling and impaired synaptic plasticity; enhancing IP3R-Ca2+ signaling affects cognitive functions such as learning and memory, sleep, and mood. However, as a result of discrepancies in the literature, the role of GPCR-IP3R-Ca2+ signaling, especially under physiological conditions, remains inconclusive. One primary reason for this could be that IP3R2 has been used to represent all astrocytic IP3Rs, including IP3R1 and IP3R3. Indeed, IP3R1 and IP3R3 are unique Ca2+ channels in their own right; they have unique biophysical properties, often display distinct distribution, and are differentially regulated. As a result, they mediate different physiological roles to IP3R2. Thus, these additional channels promise to enrich the diversity of spatiotemporal Ca2+ dynamics and provide unique opportunities for integrating neuronal input and modulating astrocyte–neuron communication. The current review weighs evidence supporting the existence of multiple astrocytic-IP3R isoforms, summarizes distinct sub-type specific properties that shape spatiotemporal Ca2+ dynamics. We also discuss existing experimental tools and future refinements to better recapitulate the endogenous activities of each IP3R isoform.

Published
2021
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3. Multi‐omics analysis of hiPSCs‐derived HLCs matured on‐chip revealed patterns typical of liver regeneration

Author

Yukio Kato, Hiroyuki Kusuhara, Françoise Gilard, Johanna Bruce, Daiki Mori, Marjorie Leduc, Hiroshi Arakawa, Atsushi Miyajima, Stéphane Poulain, Karin Araya, Taketomo Kido, Mathieu Danoy, Morgane Le Gall, Charles Plessy, Eric Leclerc, Rachid Jellali, Yasuyuki Sakai, Yannick Tauran, Laboratory for Integrated Micro Mechatronics Systems (LIMMS), The University of Tokyo (UTokyo)-Centre National de la Recherche Scientifique (CNRS), The University of Tokyo (UTokyo), Laboratoire des Multimatériaux et Interfaces (LMI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Biomécanique et Bioingénierie (BMBI), Université de Technologie de Compiègne (UTC)-Centre National de la Recherche Scientifique (CNRS), Plateforme protéomique 3P5 [Institut Cochin] (3P5), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Kanazawa University (KU), Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) Japan Society for the Promotion of Science 16H06328, ANR-16-RHUS-0005,iLite,iLite(2016), JELLALI, RACHID, iLite - - iLite2016 - ANR-16-RHUS-0005 - RHUS - VALID, 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)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
0106 biological sciences, 0301 basic medicine, Induced Pluripotent Stem Cells, iPSCs, Bioengineering, [SDV.BC.BC]Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Biology, Proteomics, liver, 01 natural sciences, Applied Microbiology and Biotechnology, Transcriptome, 03 medical and health sciences, transcriptomics, Metabolomics, proteomics, 010608 biotechnology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BC.BC] Life Sciences [q-bio]/Cellular Biology/Subcellular Processes [q-bio.SC], Humans, Induced pluripotent stem cell, Biochip, Regeneration (biology), nanoCAGE, Cell Differentiation, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Genomics, differentiation, metabolomics, Liver regeneration, In vitro, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Liver Regeneration, Cell biology, 030104 developmental biology, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], hepatocytes, organ-on-chip, Biotechnology
Abstract

International audience; Maturation of human-induced pluripotent stem cells (hiPSCs)-derived hepatocytes-like cells (HLCs) toward a complete hepatocyte phenotype remains a challenge as primitiveness patterns are still commonly observed. In this study, we propose a modified differentiation protocol for those cells which includes a prematuration in Petri dishes and a maturation in microfluidic biochip. For the first time, a large range of biomolecular families has been extracted from the same sample to combine transcriptomic, proteomic, and metabolomic analysis. After integration, these datasets revealed specific molecular patterns and highlighted the hepatic regeneration profile in biochips. Overall, biochips exhibited processes of cell proliferation and inflammation (via TGFB1) coupled with anti-fibrotic signaling (via angiotensin 1-7, ATR-2, and MASR). Moreover, cultures in this condition displayed physiological lipid-carbohydrate homeostasis (notably via PPAR, cholesterol metabolism, and bile synthesis) coupled with cell respiration through advanced oxidative phosphorylation (through the overexpression of proteins from the third and fourth complex). The results presented provide an original overview of the complex mechanisms involved in liver regeneration using an advanced in vitro organ-on-chip technology.

Published
2021
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4. Analysis of hiPSCs differentiation toward hepatocyte-like cells upon extended exposition to oncostatin

Author

Hiroshi Arakawa, Hiroyuki Kusuhara, Yukio Kato, Eric Leclerc, Mathieu Danoy, Karin Araya, Yasuyuki Sakai, Charles Plessy, Taketomo Kido, Yannick Tauran, Stéphane Poulain, Sachi Kato, Atsushi Miyajima, Daiki Mori, Laboratory for Integrated Micro Mechatronics Systems (LIMMS), The University of Tokyo (UTokyo)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Multimatériaux et Interfaces (LMI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Centre de Ressources Biologiques - [Nancy] (CRB Nancy), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), The University of Tokyo (UTokyo), Laboratory of Pharmacokinetics, Kanazawa University (KU), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biomécanique et génie biomédical (BIM), and Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Cancer Research, Epithelial-Mesenchymal Transition, [SDV]Life Sciences [q-bio], Induced Pluripotent Stem Cells, Drug Evaluation, Preclinical, Oncostatin M, Biology, Transcriptome, Cytochrome P-450 CYP2C8, 03 medical and health sciences, 0302 clinical medicine, Cytochrome P-450 CYP1A2, medicine, Cytochrome P-450 CYP3A, Humans, NRF1, Induced pluripotent stem cell, Molecular Biology, Transcription factor, ComputingMilieux_MISCELLANEOUS, Cell Proliferation, Nuclear Respiratory Factor 1, Liver cell, Cell Differentiation, Cell Biology, Liver regeneration, 3. Good health, HNF1A, Cell biology, Liver Regeneration, Cytochrome P-450 CYP2B6, 030104 developmental biology, medicine.anatomical_structure, Sp3 Transcription Factor, Cytochrome P-450 CYP2D6, Liver, Hepatocyte, Hepatocytes, 030217 neurology & neurosurgery, Developmental Biology
Abstract

The capability to produce and maintain functional human adult hepatocytes remains one of the major challenges for the use of in-vitro models toward liver cell therapy and industrial drug-screening applications. Among the suggested strategies to solve this issue, the use of human-induced pluripotent stem cells (hiPSCs), differentiated toward hepatocyte-like cells (HLCs) is promising. In this work, we propose a 31-day long protocol, that includes a final 14-day long phase of oncostatin treatment, as opposed to a 7-day treatment which led to the formation of a hepatic tissue functional for CYP1A2, CYP2B6, CYP2C8, CYP2D6, and CYP3A4. The production of albumin, as well as bile acid metabolism and transport, were also detected. Transcriptome profile comparisons and liver transcription factors (TFs) motif dynamics revealed increased expression of typical hepatic markers such as HNF1A and of important metabolic markers like PPARA. The performed analysis has allowed for the extraction of potential targets and pathways which would allow enhanced hepatic maturation in-vitro. From this investigation, NRF1 and SP3 appeared as transcription factors of importance. Complex epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) patterns were also observed during the differentiation process. Moreover, whole transcriptome analysis highlighted a response typical of the one observed in liver regeneration and hepatocyte proliferation. While a complete maturation of hepatocytes was yet to be obtained, the results presented in this work provide new insights into the process of liver development and highlight potential targets aimed to improve in-vitro liver regeneration.

Published
2020
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5. Characterization of liver zonation‐like transcriptomic patterns in HLCs derived from hiPSCs in a microfluidic biochip environment

Author

Taketomo Kido, Eric Leclerc, Atsushi Miyajima, Benedikt Scheidecker, Stéphane Poulain, Sachi Kato, Charles Plessy, Mathieu Danoy, Myriam Lereau-Bernier, Yasuyuki Sakai, Laboratory for Integrated Micro Mechatronics Systems (LIMMS), The University of Tokyo (UTokyo)-Centre National de la Recherche Scientifique (CNRS), Centre de Ressources Biologiques - [Nancy] (CRB Nancy), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), The University of Tokyo (UTokyo), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Biomécanique et génie biomédical (BIM), Centre National de la Recherche Scientifique (CNRS), Leclerc, Eric, Centre National de la Recherche Scientifique (CNRS)-The University of Tokyo (UTokyo), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I

Subjects
[SDV]Life Sciences [q-bio], Cellular detoxification, Induced Pluripotent Stem Cells, SMAD, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Downregulation and upregulation, Mesenchymal–epithelial transition, Humans, Epithelial–mesenchymal transition, Transcription factor, Cells, Cultured, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Tissue Engineering, Chemistry, Wnt signaling pathway, Cell Differentiation, Microfluidic Analytical Techniques, Cell biology, Nanostructures, [SDV] Life Sciences [q-bio], Liver, 030220 oncology & carcinogenesis, Hepatocytes, Biotechnology
Abstract

The liver zonation is an important phenomenon characterized by a gradient of several functions along the liver acinus. However, this gradient remains difficult to reproduce in in-vitro conditions, making the obtention of an in-vitro method to recapitulate the liver zonation a challenging issue. In this study, we evaluated the spatial evolution of the transcriptome profile of human induced pluripotent stem cells (hiPSCs) differentiated toward hepatocytes-like cells (HLCs) phenotype in a microfluidic biochip environment. Cells collected at the inlet of the biochip, where the oxygen concentration is higher, were identified by the expression of genes involved in metabolic pathways related to cellular reorganization and cell proliferation. Cells collected in the middle and at the outlet of the biochips, where oxygen concentrations are lower, were characterized by the upregulation of genes involved in cellular detoxification processes (CYP450), PPAR signaling or arginine biosynthesis. A subset of 16 transcription factors (TFs) was extracted and identified as upstream regulators to HNF1A and PPARA. These TFs are also known as regulators to target genes engaged in the Wnt/βcatenin pathway, in the TGFβ/BMP/SMAD signaling, in the transition between epithelial mesenchymal transition (EMT) and mesenchymal epithelial transition (MET), in the homeostasis of lipids, bile acids and carbohydrates homeostasis, in drug metabolism, in the estrogen processing and in the oxidative stress response. Overall, the analysis allowed to confirm a partial zonation-like pattern in hiPSCs-derived HLCs in the microfluidic biochip environment. These results provide important insights into the reproduction of liver zonation in-vitro for a better understanding of the phenomenon.

Published
2020
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6. Integration of metabolomic and transcriptomic profiles of hiPSCs-derived hepatocytes in a microfluidic environment

Author

Taketomo Kido, Yasuyuki Sakai, Rachid Jellali, Charles Plessy, Françoise Gilard, Stéphane Poulain, Mathieu Danoy, Eric Leclerc, Atsushi Miyajima, Sachi Kato, Laboratory for Integrated Micro Mechatronics Systems (LIMMS), The University of Tokyo-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Life Science Technologies, Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), The University of Tokyo, Centre National de la Recherche Scientifique (CNRS), The University of Tokyo (UTokyo)-Centre National de la Recherche Scientifique (CNRS), Centre de Ressources Biologiques - [Nancy] (CRB Nancy), Centre Hospitalier Régional Universitaire de Nancy (CHRU Nancy), Biomécanique et Bioingénierie (BMBI), Université de Technologie de Compiègne (UTC)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), The University of Tokyo (UTokyo), ANR-16-RHUS-0005,iLite,iLite(2016), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0303 health sciences, Environmental Engineering, Chemistry, [SDV]Life Sciences [q-bio], Biomedical Engineering, Bioengineering, Pentose phosphate pathway, Fatty acid beta-oxidation, 01 natural sciences, Cell biology, Transcriptome, Spermidine, 03 medical and health sciences, chemistry.chemical_compound, Metabolomics, In vivo, 010608 biotechnology, Glycolysis, Biochip, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Biotechnology
Abstract

International audience; The differentiation of human induced pluripotent stem cells (hiPSCs) into functional hepatocytes has the potential to solve the shortage of human primary liver cells and would be of use in drug screening. In this frame, we developed a hiPSCs maturation strategy in microfluidic biochips, using a liver-on-chip approach, a promising technology mimicking in vivo physiology. Hepato-like tissues differentiated in biochips presented advanced liver features, including ALB and CYP3A4 expressing cells. The metabolomics and transcriptomics profiles of hepato-likes cells differentiated either in biochips or Petri dishes were integrated to compare their functionalities. The multi-omics analysis revealed 41 metabolites and 302 genes differentially expressed. Overall, biochip environment lead to higher degree of hepatic differentiation demonstrated by an increase in the metabolic production of lipids, fatty acids and biliary acids, which was confirmed at the transcriptome level by the modulation of expression for genes involved in related signaling pathways. This observation was correlated with higher production of fructose in biochips, together with down-regulation of genes engaged in glycolysis. In parallel, increased activity of the Krebs cycle, pentose phosphate shuffle, and fatty acid beta oxidation was observed in tissues cultured in Petri. Besides, the modulation of nitrogen metabolism was observed in transcriptomic data and confirmed by an intense production of glutamine, putrescine and creatinine and by the higher consumption of spermidine measured in Petri.

Published
2020
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7. Integration of metabolomic and transcriptomic profiling to compare two protocols of differentiation of human induced pluripotent stem cells into hepatocytes

Author

Stéphane Poulain, Yasuyuki Sakai, Charles Plessy, Eric Leclerc, Françoise Gilard, Sachi Kato, Myriam Lereau Bernier, Taketomo Kido, Yannick Tauran, Mathieu Danoy, Bertrand-David Segard, Atsushi Miyajima, Rachid Jellali, Biomécanique et Bioingénierie (BMBI), Université de Technologie de Compiègne (UTC)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Laboratory for Integrated Micro Mechatronics Systems (LIMMS), The University of Tokyo (UTokyo)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Multimatériaux et Interfaces (LMI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), The University of Tokyo (UTokyo), Center for International Research on Integrative Biomedical Systems [University of Tokyo] (CIBiS), Institute of Industrial Science (IIS), The University of Tokyo (UTokyo)-The University of Tokyo (UTokyo), ANR-16-RHUS-0005,iLite,iLite(2016), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV]Life Sciences [q-bio], Bioengineering, Metabolomic, Oxidative phosphorylation, Biology, Applied Microbiology and Biotechnology, Biochemistry, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Metabolomics, Biochemistry Manuscript category Cell Culture Technology, Extracellular, Molecular Biology, 030304 developmental biology, NanoCAGE, 0303 health sciences, Messenger RNA, CYP3A4, In vitro, Cell biology, Induced pluripotent stem cells, 030220 oncology & carcinogenesis, Lipogenesis, Hepatocyte-like cells, induced pluripotent stem cells Taxonomy Metabolome Analysis, hepatocytes like cells
Abstract

International audience; Human hepatocyte-like cells derived from human induced pluripotent stem cells (hiPSC) may provide an unlimited supply of cells for in vitro liver models. However, hiPSC differentiation remains a major challenge due to immaturity of the hepatocytes obtained and the high cost of differentiation protocols currently proposed. Here, we studied the efficacy of new protocol, with reduction of growth factors, for the generation of hepatocyte-like cells from hiPSC. We performed metabolomic and mRNA analysis by RTqPCR and nanoCAGE processing to identify and understand key metabolisms during differentiation. By reducing the change frequency of the culture medium in the new protocol, we successfully generated hepatocyte-like cells producing albumin, urea, and CYP3A4 positive. The metabolomic analysis successfully extracted both signatures, common and specific, for each differentiation step. Integrating the metabolomic data with transcriptomic contributed to explaining the kinetics of carbohydrate, lipid and nitrogen metabolism throughout differentiation. The information extracted during differentiation showed that the cells moved from an aerobic-like respiration pattern to a mitochondrial oxidative respiration pattern in both protocols. Reducing culture medium renewal led to reduced glucose consumption, followed by fructose production and significant extracellular lipogenesis throughout differentiation. We believe that the overall dataset can provide information on the sequence of process.

Published
2019
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8. Optimized protocol for the hepatic differentiation of induced pluripotent stem cells in a fluidic microenvironment

Author

Stéphane Poulain, Myriam Lereau Bernier, Hiroyuki Kusuhara, Taketomo Kido, Eric Leclerc, Sachi Kato, Mathieu Danoy, Charles Plessy, Daiki Mori, Atsushi Miyajima, Yasuyuki Sakai, Keiichi Kimura, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Louis Pasteur - Strasbourg I, The University of Tokyo (UTokyo), and Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Induced Pluripotent Stem Cells, Bioengineering, 01 natural sciences, Applied Microbiology and Biotechnology, Transcriptome, Extracellular matrix, 03 medical and health sciences, 010608 biotechnology, CEBPA, Humans, Progenitor cell, Stem Cell Niche, Biochip, Induced pluripotent stem cell, Transcription factor, ComputingMilieux_MISCELLANEOUS, Chemistry, Cell Differentiation, TCF4, Hep G2 Cells, Microfluidic Analytical Techniques, Cell biology, 030104 developmental biology, Gene Expression Regulation, Liver, Hepatocytes, Biotechnology, Transcription Factors
Abstract

In the present study, we evaluated the performance of different protocols for the hepatic differentiation of human-induced pluripotent stem cells (hiPSCs) in microfluidic biochips. Strategies for complete and partial on-chip differentiation were tested. Unlike full on-chip differentiation, the transfer of iPSCs from Petri dishes to biochips during the differentiation process produced a heterogeneous tissue with enhanced hepatic features compared with control cultures in Petri dishes. The tissue in biochips was constituted of cells expressing either stabilin-1 or albumin, while no stabilin-1 was detected in controls. Functional analysis also revealed double the production rate for albumin in biochips (about 2,000 ng per day per 106 cells). Besides this, tissues obtained in biochips and controls exhibited the metabolism of a specific bile acid. Whole transcriptome analysis with nanoCAGE exhibited a differential expression of 302 genes between control and biochip cultures and a higher degree of hepatic differentiation in biochips, together with increased promoter motif activity for typical liver transcription factors such as estrogen related receptor alpha ( ESRRA), hepatic nuclear factor 1 ( HNF1A), hepatic nuclear factor 4 ( HNF4A), transcription factor 4 ( TCF4), and CCAAT enhancer binding protein alpha ( CEBPA). Gene set enrichment analysis identified several pathways related to the extracellular matrix, tissue reorganization, hypoxia-inducible transcription factor, and glycolysis that were differentially modulated in biochip cultures. However, the presence of CK19/ALB-positive cells and the ɑ-fetoprotein levels measured in the cultures still reflect primitive differentiation patterns. Overall, we identified key parameters for improved hepatic differentiation on-chip, including the maturation stage of hepatic progenitors, inoculation density, adhesion time, and perfusion flow rate. Optimization of these parameters further led to establish a protocol for reproducible differentiation of hiPSCs into hepatocyte-like cells in microfluidic biochips with significant improvements over Petri dish cultures.

Published
2019
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9. Profiling of derived-hepatocyte progenitors from induced pluripotent stem cells using nanoCAGE promoter analysis

Author

Myriam Lereau Bernier, Eric Leclerc, Sachi Kato, Stéphane Poulain, Keiichi Kimura, Yasuyuki Sakai, Charles Plessy, Atsushi Miyajima, Marie Shinohara, Taketomo Kido, Mathieu Danoy, Yannick Tauran, Bertrand-David Segard, Laboratory for Integrated Micro Mechatronics Systems (LIMMS), The University of Tokyo (UTokyo)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Laboratoire des Multimatériaux et Interfaces (LMI), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Center for International Research on Integrative Biomedical Systems [University of Tokyo] (CIBiS), Institute of Industrial Science (IIS), The University of Tokyo (UTokyo)-The University of Tokyo (UTokyo), Institute of Molecular and Cellular Biosciences, and The University of Tokyo (UTokyo)

Subjects
0106 biological sciences, 0303 health sciences, Environmental Engineering, [SDV]Life Sciences [q-bio], nanoCAGE, Biomedical Engineering, Bioengineering, Promoter, Hepatic differentiation, Biology, 01 natural sciences, 3. Good health, Cell biology, Chromatin, hiPS, Transcriptome, 03 medical and health sciences, 010608 biotechnology, Gene expression, Glucose homeostasis, Progenitor cell, Induced pluripotent stem cell, Transcription factor, 030304 developmental biology, Biotechnology
Abstract

International audience; Human induced pluripotent stem (hiPS) cells represent a potential source of human cells for regenerative and personalized medicine applications. It is envisioned that hiPS cells could be an efficient tool for disease modelling and drug therapy testings. However, the successful derivation of hiPS cells to mature hepatocytes remains a challenge as far as the current proposed protocols lead to immature patterns and are very expensive (due to growth factors cost). In this work, we have compared two protocols of differentiation to produce hepatocyte-like cells. The first protocol is the conventional protocol adapted from Si-Tayeb et al. in 2010. By changing the frequency of culture medium exchange, we reduced the use of growth factors in the second protocol by 40%. Both protocols lead to hepatocyte-like characteristics including albumin (ALB) and cytochrome P450/3A4 (CYP3A4) expression in cells. Albumin production reached 2500 ng/mL/day for both protocols. The transcription factor motif activity analysis via transcriptomic data obtained with the Cap Analysis Gene Expression (CAGE) technology confirmed a typical hepatic profile for both protocols (such as activation of HNF1 A and HNF1B promoters). However, specific patterns were also detected with higher mRNA levels of WT1, MTF1, HCFC1, and PGCα1 in protocol 2. The overall transcriptomic analysis also revealed a modulation of targets involved in glucose homeostasis, in cell remodeling, lipid pathways and chromatin processing. However, the alpha-fetoprotein (AFP) production remained very high and the function of CYP3A4 was weak in both protocols illustrating still an immature profile in both protocols.

Published
2019
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10. Amphioxus functional genomics and the origins of vertebrate gene regulation

Author

Patrick Wincker, Pierre Pontarotti, Elisa de la Calle-Mustienes, Zbynek Kozmik, Malcolm Perry, José Luis Gómez-Skarmeta, Cristian Cañestro, Stéphanie Bertrand, Yamile Marquez, Èlia Benito-Gutiérrez, Juan J. Tena, Hector Escriva, Alexandra Louis, Anthony Leon, Matthew T. Weirauch, Juan Ramón Martínez-Morales, Panos N. Firbas, Peter W. H. Holland, Iryna Kozmikova, Daniel Aldea, Sandra Jiménez-Gancedo, Jordi Garcia-Fernàndez, Jean-Marc Aury, Michael Schubert, Paul Edward Duckett, Beatriz Albuixech-Crespo, Simon J. van Heeringen, Boris Lenhard, Piero Carninci, Carlos Herrera-Úbeda, Olivier Mirabeau, Demian Burguera, Lorena Buono, Tokiharu Takahashi, Rafael D. Acemel, Silvia Naranjo, Ryan Lister, Sophie Mangenot, Lucie Subirana, Ksenia Skvortsova, Jr-Kai Yu, Hugues Roest Crollius, Ildiko M. L. Somorjai, Vincent Laudet, Piotr J. Balwierz, Gabriel A. B. Marais, Ignacio Maeso, Anlong Xu, Christopher D. R. Wyatt, Shengfeng Huang, Ozren Bogdanovic, David E. K. Ferrier, Ferdinand Marlétaz, Salvatore D'Aniello, Jon Permanyer, Filipe Castro, Manuel Irimia, Ricard Albalat, Yann Le Petillon, Ensieh Farahani, Hervé Seitz, Okinawa Institute of Science and Technology Graduate University (OIST), Department of Zoology [Oxford], University of Oxford, Centro Andaluz de Biología del Desarrollo, Universidad Pablo Olavide, University of New South Wales [Sydney] (UNSW), The University of Western Australia (UWA), Imperial College London, Universitat Pompeu Fabra [Barcelona] (UPF), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Barcelona Institute of Science and Technology (BIST), Universidad Pablo de Olavide [Sevilla] (UPO), Radboud University [Nijmegen], University of Barcelona, Garvan Institute of medical research, Institute of Molecular Genetics of the Czech Academy of Sciences (IMG / CAS), Czech Academy of Sciences [Prague] (CAS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), 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-PSL), 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 National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Genetics and IrBio, University of Cambridge [UK] (CAM), Universidade do Porto = University of Porto, Stazione Zoologica Anton Dohrn (SZN), University of St Andrews [Scotland], Sun Yat-Sen University [Guangzhou] (SYSU), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Microbes évolution phylogénie et infections (MEPHI), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), University of Manchester [Manchester], Université Paris sciences et lettres (PSL), Academia Sinica, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), University of Cincinnati (UC), University of Bergen (UiB), ANR-16-CE12-0008,CHORELAND,Détermination de la conservation du landscape génomique de régulation au cours de l'embryogenèse des chordés(2016), European Project: 637591,H2020,ERC-2014-STG,NEURAL AS(2015), European Project: 658521,H2020,H2020-MSCA-IF-2014,EVOREL(2016), European Project: 268513,EC:FP7:ERC,ERC-2010-AdG_20100317,GENEVA(2011), European Commission, The Leverhulme Trust, University of St Andrews. School of Biology, University of St Andrews. Marine Alliance for Science & Technology Scotland, University of St Andrews. Scottish Oceans Institute, University of St Andrews. Biomedical Sciences Research Complex, University of Oxford [Oxford], Radboud university [Nijmegen], Garvan Institute of Medical Research, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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), Universidade do Porto, Commission of the European Communities, Biotechnology and Biological Sciences Research Council (BBSRC), Wellcome Trust, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - 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), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), Departament de Genetica, Facultat de Biologia, Universitat de Barcelona (UB), Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Max F. Perutz Laboratories, University of Vienna [Vienna], DYnamique et Organisation des GENomes - Equipe de l'IBENS (DYOGEN), 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)-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), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-IFR140-Centre National de la Recherche Scientifique (CNRS), Stress, Immunité, Pathogènes (SIMPA), Université de Lorraine (UL), Unité de Biométrie et Intelligence Artificielle (UBIA), Institut National de la Recherche Agronomique (INRA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique d'Evry (IG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Departament de Genètica, Universitat Autònoma de Barcelona [Barcelona] (UAB), Texas A&M University [College Station], Sun Yat-Sen University (SYSU), Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup (VAS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Analyse, Topologie, Probabilités (LATP), Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Centre National de la Recherche Scientifique (CNRS), Unité de génétique et biologie des cancers (U830), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie-Institut National de la Santé et de la Recherche Médicale (INSERM), University of Medical Sciences / Beijing, Institute of Cellular and Organismic Biology, Ctr Life Sci Technol, Div Gen Technol, Tsurumi Ku, RIKEN, Centre of Excellence in Plant Energy Biology (ARC), Australian National University (ANU)-School of Biochemistry and Molecular Biology, SARS International Centre for Marine Molecular Biology, Modèles en biologie cellulaire et évolutive (MBCE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), European Research Council, Ministerio de Economía y Competitividad (España), Australian Research Council, Maeso, Ignacio [0000-0002-6440-8457], Tena, Juan J [0000-0001-8165-7984], Perry, Malcolm [0000-0001-5228-3434], Wyatt, Christopher DR [0000-0001-8033-2213], de la Calle-Mustienes, Elisa [0000-0002-8975-6503], Bertrand, Stephanie [0000-0002-0689-0126], Naranjo, Silvia [0000-0002-4529-3332], Jimenez-Gancedo, Sandra [0000-0002-2247-1319], Aldea, Daniel [0000-0001-5101-0194], Buono, Lorena [0000-0002-5457-4515], Louis, Alexandra [0000-0001-7032-5650], Balwierz, Piotr J [0000-0002-1548-4605], Aury, Jean-Marc [0000-0003-1718-3010], Albalat, Ricard [0000-0003-0282-9595], Benito-Gutiérrez, Èlia [0000-0003-2435-0948], Cañestro, Cristian [0000-0003-4623-8105], Castro, Filipe [0000-0001-7697-386X], Ferrier, David EK [0000-0003-3247-6233], Schubert, Michael [0000-0002-2341-712X], Seitz, Hervé [0000-0001-8172-5393], Somorjai, Ildiko [0000-0001-5243-6664], Takahashi, Tokiharu [0000-0002-5785-8660], Yu, Jr-Kai [0000-0001-8591-0529], Carninci, Piero [0000-0001-7202-7243], Martinez-Morales, Juan Ramon [0000-0002-4650-4293], Garcia-Fernàndez, Jordi [0000-0001-5677-5970], Lister, Ryan [0000-0001-6637-7239], Escriva, Hector [0000-0001-7577-5028], Irimia, Manuel [0000-0002-2179-2567], Apollo - University of Cambridge Repository, CIIMAR - Centro Interdisciplinar de Investigação Marinha e Ambiental, COMBE, Isabelle, Détermination de la conservation du landscape génomique de régulation au cours de l'embryogenèse des chordés - - CHORELAND2016 - ANR-16-CE12-0008 - AAPG2016 - VALID, Functions and evolutionary impact of transcriptomic novelties in the vertebrate brain - NEURAL AS - - H20202015-04-01 - 2020-03-31 - 637591 - VALID, Evolution of Regulatory Landscapes in Chordates - EVOREL - - H20202016-01-01 - 2017-12-31 - 658521 - VALID, Genome Evolution in the Animal Kingdom - GENEVA - - EC:FP7:ERC2011-06-01 - 2016-05-31 - 268513 - VALID, Institute of Molecular Genetics of the Czech Academy of Sciences, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA) - Grenoble, Laboratoire de Biologie Moléculaire de la Cellule (LBMC), 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), Institut de Mathématiques de Marseille (I2M), Centre National de la Recherche Scientifique (CNRS)-Ecole Centrale de Marseille (ECM)-Aix Marseille Université (AMU), Riken Omics Science Center, Riken Yokohama Institute, Cincinnati Children's Hospital Medical Center, and Computational Regulatory Genomics

Subjects
Epigenomics, Branchiostoma, genetic analysis, animal cell, transcriptomics, 0302 clinical medicine, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, vertebrate, zebra fish, histone modification, Branchiostoma lanceolatum, ComputingMilieux_MISCELLANEOUS, comparative study, Lancelets, Regulation of gene expression, DDC model, DNA methylation, adult, Vertebrate, Genomics, priority journal, Science & Technology - Other Topics, Molecular Developmental Biology, LANDSCAPES, whole genome duplication, Functional genomics, chordate evolution, CONSERVATION, embryo, gene sequence, PLURIPOTENCY, Article, animal tissue, 03 medical and health sciences, regulatory genomics, biology.animal, genomics, Humans, genome, mouse, Science & Technology, Molecular Sequence Annotation, TRANSGENESIS, DNA Methylation, Ancestral expression, developmental stage, 030104 developmental biology, hourglass model, Amfiox, Evolutionary biology, molecular genetics, chromatin, Subfunctionalization, transcriptome, 030217 neurology & neurosurgery, CHROMATIN, 0301 basic medicine, Branchiostoma Lanceolatum, Genome, specialization, Gene duplication, Vertebrats, Promoter Regions, Genetic, Whole-genome Duplication (WGD), Multidisciplinary, gene control, BRANCHIOSTOMA-LANCEOLATUM, innovation, Multidisciplinary Sciences, female, SEQ, Vertebrates, [SDV.MHEP.MI] Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Phylotypic Period, General Science & Technology, invertebrate, QH426 Genetics, Biology, DNA DEMETHYLATION, male, evolution, Animals, controlled study, gene, QH426, multigene family, Body Patterning, Vertebrata, nonhuman, Amphioxus, ZEBRAFISH, gene duplication, embryo development, DAS, biology.organism_classification, EVOLUTION, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, Gene Expression Regulation, gene expression, Molecular evolution, Transcriptome
Abstract

Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome duplications. Here we sequence the genome of the Mediterranean amphioxus (Branchiostoma lanceolatum) and characterize DNA methylation, chromatin accessibility, histone modifications and transcriptomes across multiple developmental stages and adult tissues to investigate the evolution of the regulation of the chordate genome. Comparisons with vertebrates identify an intermediate stage in the evolution of differentially methylated enhancers, and a high conservation of gene expression and its cis-regulatory logic between amphioxus and vertebrates that occurs maximally at an earlier mid-embryonic phylotypic period. We analyse regulatory evolution after whole-genome duplications, and find that—in vertebrates—over 80% of broadly expressed gene families with multiple paralogues derived from whole-genome duplications have members that restricted their ancestral expression, and underwent specialization rather than subfunctionalization. Counter-intuitively, paralogues that restricted their expression increased the complexity of their regulatory landscapes. These data pave the way for a better understanding of the regulatory principles that underlie key vertebrate innovations., This research was funded primarily by the European Research Council (ERC) under the European Union’s Horizon 2020 and Seventh Framework Program FP7 research and innovation programs (ERC-AdG-LS8-740041 to J.L.G.-S., ERC-StG-LS2-637591 to M.I., a Marie Sklodowska-Curie Grant (658521) to I.M. and a FP7/2007-2013-ERC-268513 to P.W.H.H.), the Spanish Ministerio de Economía y Competitividad (BFU2016-74961-P to J.L.G.-S., RYC-2016-20089 to I.M., BFU2014-55076-P and BFU2017-89201-P to M.I. and BFU2014-55738-REDT to J.L.G.-S, M.I. and J.R.M.-M), the ‘Centro de Excelencia Severo Ochoa 2013-2017’(SEV-2012-0208), the ‘Unidad de Excelencia María de Maetzu 2017-2021’(MDM-2016-0687), the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Program FP7 under REA grant agreement number 607142 (DevCom) to J.L.G.-S., and the CNRS and the ANR (ANR16-CE12-0008-01) to H.E. O.B. was supported by an Australian Research Council Discovery Early Career Researcher Award (DECRA; DE140101962).

Published
2018
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11. Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress

Author

Diego di Bernardo, Ali Tebbi, Annamaria Carissimo, Kosuke Hashimoto, Piero Carninci, Florence Levillayer, Nesrine Boudjadja, Yu Wei, Hugo Varet, Grégory Jouvion, Laurence Fiette, Guillaume Soubigou, Stefano Cairo, Ana Maria Suzuki, Pathogenèse des Virus de l'Hépatite B (PVHB), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Hépacivirus et Immunité innée, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Histopathologie humaine et Modèles animaux, Institut Pasteur [Paris] (IP), Centre d'Informatique pour la Biologie, XenTech, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Telethon Institute of Genetics and Medicine, European Union’s Seventh Framework Program (FP7) under grant agreement No. 259743 (MODHEP consortium) to the Institut Pasteur (A.T., F.L., Y.W.), RIKEN Center (K.H., A.M.S., P.C.) and Telethon Institute of Genetics and Medicine (D.B.)., European Project: 259743,EC:FP7:HEALTH,FP7-HEALTH-2010-two-stage,MODHEP(2011), Wei, Yu, Systems biology of liver cancer: an integrative genomic-epigenomic approach - MODHEP - - EC:FP7:HEALTH2011-01-01 - 2016-06-30 - 259743 - VALID, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris], Institut Pasteur [Paris], Tebbi, Ali, Levillayer, Florence, Jouvion, Grégory, Fiette, Laurence, Soubigou, Guillaume, Varet, Hugo, Boudjadja, Nesrine, Cairo, Stefano, Hashimoto, Kosuke, Suzuki, Ana Maria, Carninci, Piero, Carissimo, Annamaria, and DI BERNARDO, Diego

Subjects
0301 basic medicine, Male, Cancer Research, Nude, Apoptosis, medicine.disease_cause, Cell Transformation, Lipid peroxidation, chemistry.chemical_compound, Mice, Adenomatous Polyposis Coli, Animals, Cell Transformation, Neoplastic, Cells, Cultured, DNA Damage, Female, Fibroblasts, Intestinal Neoplasms, Lipid Peroxidation, Liver, Mice, Inbred BALB C, Mice, Knockout, Mice, Nude, Oxidative Stress, P-Glycoproteins, Reactive Oxygen Species, Inbred BALB C, Cultured, Bile acid, General Medicine, 3. Good health, Biochemistry, ATP Binding Cassette Transporter, Subfamily B, DNA damage, medicine.drug_class, Cells, Knockout, [SDV.CAN]Life Sciences [q-bio]/Cancer, Original Manuscript, Biology, NO, 03 medical and health sciences, [SDV.CAN] Life Sciences [q-bio]/Cancer, Lipid biosynthesis, medicine, Neoplastic, Fatty acid metabolism, Microarray analysis techniques, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, HCCS, Molecular biology, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, 030104 developmental biology, chemistry, Carcinogenesis
Abstract

Summary The transporter of phosphatidylcholine Mdr2/MDR3 not only plays an essential role for bile formation but also is involved in the maintenance of lipid homeostasis. Deficiency of Mdr2 leads to accumulation of ROS, cell transformation and susceptibility to intestinal carcinogenesis., Multidrug resistance 2 (Mdr2), also called adenosine triphosphate-binding cassette B4 (ABCB4), is the transporter of phosphatidylcholine (PC) at the canalicular membrane of mouse hepatocytes, which plays an essential role for bile formation. Mutations in human homologue MDR3 are associated with several liver diseases. Knockout of Mdr2 results in hepatic inflammation, liver fibrosis and hepatocellular carcinoma (HCC). Whereas the pathogenesis in Mdr2 −/− mice has been largely attributed to the toxicity of bile acids due to the absence of PC in the bile, the question of whether Mdr2 deficiency per se perturbs biological functions in the cell has been poorly addressed. As Mdr2 is expressed in many cell types, we used mouse embryonic fibroblasts (MEF) derived from Mdr2 −/− embryos to show that deficiency of Mdr2 increases reactive oxygen species accumulation, lipid peroxidation and DNA damage. We found that Mdr2 −/− MEFs undergo spontaneous transformation and that Mdr2 −/− mice are more susceptible to chemical carcinogen-induced intestinal tumorigenesis. Microarray analysis in Mdr2−/− MEFs and cap analysis of gene expression in Mdr2 −/− HCCs revealed extensively deregulated genes involved in oxidation reduction, fatty acid metabolism and lipid biosynthesis. Our findings imply a close link between Mdr2 −/−-associated tumorigenesis and perturbation of these biological processes and suggest potential extrahepatic functions of Mdr2/MDR3.

Published
2015
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12. Capillary-Inserted Rotor Design for HRµMAS NMR-Based Metabolomics on Mass-Limited Neurospheres

Author

Yosky Kataoka, Alan Wong, Masayuki Nakano, Yasuhisa Tamura, Masanori Yamato, Satoshi Kume, Nghia Tuan Duong, Yusuke Nishiyama, Advanced Solid-State NMR Unit (RIKEN CLST-JEOL), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Multi-Modal Microstructure Analysis Unit (RIKEN CLST-JEOL), RIKEN Center for Life Science Technologies (RIKEN CLST), Osaka City University Graduate Medical School, Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), JEOL Ltd, 1156 Nakagami, Akishima, Tokyo 196-0022, Japan., ANR-16-CE11-0023,HRmicroMAS,SPECTROSCOPIE RMN MICROSCOPIC SPECIMENS(2016), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Magnetic Resonance Spectroscopy, Capillary action, Analytical chemistry, Pharmaceutical Science, capillary-inserted rotor, Standard solution, 01 natural sciences, Article, Spectral line, Analytical Chemistry, law.invention, lcsh:QD241-441, 03 medical and health sciences, Nuclear magnetic resonance, Metabolomics, lcsh:Organic chemistry, law, Drug Discovery, mass-limited neurospheres, Magic angle spinning, Physical and Theoretical Chemistry, Spectroscopy, NMR, metabolomics, metabolites, HRµMAS, Rotor (electric), Chemistry, 010401 analytical chemistry, Organic Chemistry, Analytical technique, [CHIM.MATE]Chemical Sciences/Material chemistry, 0104 chemical sciences, 030104 developmental biology, Chemistry (miscellaneous), Molecular Medicine
Abstract

International audience; Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical technique and has been widely used in metabolomics. However, the intrinsic low sensitivity of NMR prevents its applications to systems with limited sample availabilities. In this study, a new experimental approach is presented to analyze mass-scarce samples in limited volumes of less than 300 nL with simple handling. The sample is loaded into the glass capillary, and this capillary is then inserted into a Kel-F rotor. The experimental performance of the capillary-inserted rotor (capillary-insert) is investigated on an isotropic solution of sucrose by the use of a high-resolution micro-sized magic angle spinning (HRµMAS) probe. The acquired NMR signal's sensitivity to a given sample amount is comparable or even higher in comparison to that recorded by the standard solution NMR probe. More importantly, this capillary-insert coupled with the HRµMAS probe allows in-depth studies of heterogeneous samples as the MAS removes the line broadening caused by the heterogeneity. The NMR analyses of mass-limited cultured neurospheres have been demonstrated, resulting in high quality spectra where numerous metabolites are unambiguously identified.

Published
2017
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13. A three-dimensional movie of structural changes in bacteriorhodopsin

Author

Eriko Nango, Jörg Standfuss, Shigeki Owada, Takanori Nakane, Petra Båth, Robert Dods, Ayumi Yamashita, Byeonghyun Jeon, Minoru Kubo, Takaaki Fujiwara, Jan Davidsson, Rebecka Andersson, Dohyun Im, Michihiro Sugahara, Yasuaki Yamanaka, Kazumasa Oda, Makina Yabashi, Osamu Nureki, Takaki Hatsui, Kensuke Tono, Tomoyuki Tanaka, Michio Murata, Gebhard F. X. Schertler, Antoine Royant, Daewoong Nam, Takashi Nomura, Eiichi Mizohata, Satoshi Kawatake, Tetsunari Kimura, So Iwata, Przemyslaw Nogly, Tatsuro Shimamura, Takashi Kameshima, Changyong Song, Masahiro Fukuda, Jun Kobayashi, Shigeru Matsuoka, Yasumasa Joti, Ana-Nicoleta Bondar, Richard Neutze, Cecilia Wickstrand, Toshiaki Hosaka, Rie Tanaka, Toshi Arima, Tomohiro Nishizawa, RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), European Synchrotron Radiation Facility (ESRF), Department of Biological Sciences, The University of Tokyo (UTokyo), Department of Chemistry and Molecular Biology [Gothenburg], University of Gothenburg (GU), Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN)-RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Department of Applied Chemistry, Osaka University [Osaka], Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute (PSI), Institut Armand Frappier (INRS-IAF), Institut National de la Recherche Scientifique [Québec] (INRS)-Réseau International des Instituts Pasteur (RIIP), Department of Physics, Pohang University of Science and Technology (POSTECH), Department of Cell Biology, Graduate School of Medicine, Kyoto University [Kyoto], Angström Laboratory, Uppsala University, JST-Exploratory Research for Advanced Technology (ERATO), Japan Synchrotron Radiation Research Institute [Hyogo] (JASRI), Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, ANR-11-JSV5-0009,SOxygen,Oxygène singulet : du dégât sur les protéines vers le développement de bio-détecteurs et générateurs(2011), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Kyoto University

Subjects
Protein Conformation, alpha-Helical, 0301 basic medicine, Cytoplasm, Proton, Motion Pictures, Biophysics, 02 engineering and technology, 03 medical and health sciences, Imaging, Three-Dimensional, Nuclear magnetic resonance, Proton transport, Molecule, fluorescent protein, Branchiostoma lanceolatum, Crystallography, Multidisciplinary, biology, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Membrane transport protein, Chemistry, Lasers, Spectrum Analysis, Biochemistry and Molecular Biology, Bacteriorhodopsin, specific radiation damage, 021001 nanoscience & nanotechnology, Transmembrane protein, Biofysik, Time resolved crystallography, Transmembrane domain, 030104 developmental biology, in crystallo optical spectroscopy, Bacteriorhodopsins, Retinaldehyde, biology.protein, Protons, online Raman spectroscopy, 0210 nano-technology, Biokemi och molekylärbiologi
Abstract

Snapshots of bacteriorhodopsin Bacteriorhodopsin is a membrane protein that harvests the energy content from light to transport protons out of the cell against a transmembrane potential. Nango et al. used timeresolved serial femtosecond crystallography at an x-ray free electron laser to provide 13 structural snapshots of the conformational changes that occur in the nanoseconds to milliseconds after photoactivation. These changes begin at the active site, propagate toward the extracellular side of the protein, and mediate internal protonation exchanges that achieve proton transport. Science , this issue p. 1552

Published
2016
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14. Green computing on graphics processing units

Author

Magoulès, Frédéric, Cheik Ahamed, Abal-Kassim, Suzuki, Atsushi, Mathématiques et Informatique pour la Complexité et les Systèmes (MICS), CentraleSupélec, Laboratoire d'Informatique et de Mathématiques (LIM), Université de La Réunion (UR), RIKEN Center for Life Science Technologies (RIKEN CLST), and RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN)

Subjects
[INFO.INFO-DM]Computer Science [cs]/Discrete Mathematics [cs.DM], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2016
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15. Evaluation of a high-resolution micro-sized magic angle spinning (HR[small mu ]MAS) probe for NMR-based metabolomic studies of nanoliter samples

Author

Takahiro Nemoto, Yusuke Nishiyama, Hiroshi Kato, Nghia Tuan Duong, Yuki Endo, Anne-Karine Bouzier-Sore, Alan Wong, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), JEOL Ltd, 1156 Nakagami, Akishima, Tokyo 196-0022, Japan., Centre de résonance magnétique des systèmes biologiques (CRMSB), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Chemistry, General Chemical Engineering, 010401 analytical chemistry, General Engineering, Analytical chemistry, Nanotechnology, Repeatability, [CHIM.MATE]Chemical Sciences/Material chemistry, 010402 general chemistry, 01 natural sciences, 0104 chemical sciences, Analytical Chemistry, Metabolomics, Magic angle spinning, Sample preparation, Spectral data
Abstract

International audience; This study evaluates the performances of a recently introduced 1 mm HR[small mu ]MAS NMR probe for metabolic profiling of nanoliter samples. It examines essential NMR criteria such as spectral data qualities and repeatability, and experimental practicality. The report also discusses the difficulties related to the sample preparation in HR[small mu ]MAS experiments and considers possible solutions and improvements.

Published
2016
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16. Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs

Author

Ferenc Müller, Vidar M. Steen, Jesper B. Andersen, Laure Bally-Cuif, Chirag Nepal, Marion Coolen, Boris Lenhard, Piotr Mydel, Piero Carninci, Yavor Hadzhiev, Delphine Cussigh, Biotech Research and Innovation Centre (BRIC), University of Copenhagen = Københavns Universitet (KU), Institut des Neurosciences Paris-Saclay (NeuroPSI), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), School of Clinical and Experimental Medicine, College of Medical and Dental Science, Broegelmann Research Laboratory, Department of Clinical Science, University of Oslo (UiO), RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Institute of Clinical Sciences, MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, and Commission of the European Communities

Subjects
0301 basic medicine, Ribonuclease III, Transcription, Genetic, [SDV.NEU.NB]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Neurobiology, 05 Environmental Sciences, Embryonic Development, RNA polymerase II, Histones, 03 medical and health sciences, microRNA, Genetics, Transcriptional regulation, RNA Precursors, Animals, RNA Processing, Post-Transcriptional, Promoter Regions, Genetic, Drosha, Zebrafish, Regulation of gene expression, 08 Information And Computing Sciences, biology, [SDV.NEU.PC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Psychology and behavior, Gene regulation, Chromatin and Epigenetics, [SDV.NEU.SC]Life Sciences [q-bio]/Neurons and Cognition [q-bio.NC]/Cognitive Sciences, Promoter, 06 Biological Sciences, Chromatin, Cell biology, MicroRNAs, 030104 developmental biology, Histone, Gene Expression Regulation, biology.protein, RNA, Small Untranslated, RNA Polymerase II, Transcription Initiation Site, Developmental Biology
Abstract

International audience; MicroRNAs (miRNAs) play a major role in the post-transcriptional regulation of target genes, especially in development and differentiation. Our understanding about the transcriptional regulation of miRNA genes is limited by inadequate annotation of primary miRNA (pri-miRNA) transcripts. Here, we used CAGE-seq and RNA-seq to provide genome-wide identification of the pri-miRNA core promoter repertoire and its dynamic usage during zebrafish embryogenesis. We assigned pri-miRNA promoters to 152 precursor-miRNAs (pre-miRNAs), the majority of which were supported by promoter associated post-translational histone modifications (H3K4me3, H2A.Z) and RNA polymerase II (RNAPII) occupancy. We validated seven miR-9 pri-miRNAs by in situ hybridization and showed similar expression patterns as mature miR-9. In addition, processing of an alternative intronic promoter of miR-9-5 was validated by 5' RACE PCR. Developmental profiling revealed a subset of pri-miRNAs that are maternally inherited. Moreover, we show that promoter-associated H3K4me3, H2A.Z and RNAPII marks are not only present at pri-miRNA promoters but are also specifically enriched at pre-miRNAs, suggesting chromatin level regulation of pre-miRNAs. Furthermore, we demonstrated that CAGE-seq also detects 3'-end processing of pre-miRNAs on Drosha cleavage site that correlates with miRNA-offset RNAs (moRNAs) production and provides a new tool for detecting Drosha processing events and predicting pre-miRNA processing by a genome-wide assay.

Published
2016
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17. Evolutionary diversification of retinoic acid receptor ligand-binding pocket structure by molecular tinkering

Author

Romain A. Studer, Susana Alvarez, William Bourguet, Juliana Gutierrez-Mazariegos, Michael Schubert, Shigehiro Kuraku, Vincent Laudet, Angel R. de Lera, Eswar Kumar Nadendla, Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolution, Université de Lausanne (UNIL), Departamento de Química Orgánica, Universidate de Vigo, Genome Resource and Analysis Unit (GRAS), RIKEN Center for Developmental Biology, Centre de Biochimie Structurale [Montpellier] (CBS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), HAL UPMC, Gestionnaire, Molecular Zoology Team, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Universidade de Vigo, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), CNRS, ENS de Lyon, UPMC (Universite Paris 06), Agence Nationale de la Recherche [ANR-2010-BLAN-1234-01, ANR-11-JSV2-002-01], MINECO (FEDER) [SAF2013-48397-R], Xunta de Galicia (Consolidacion, INBIOMED-FEDER 'Unha maneira de facer Galicia'), European Union (FP7) [BIOCAPS 316265/REGPOT-2012-2013.1], École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), RIKEN Center for Life Science Technologies, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-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 Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Schubert, Michael, and Laudet, Vincent

Subjects
0301 basic medicine, Lineage (evolution), Paralogous Gene, Corrections, nuclear hormone receptor signalling, cyclostomes, 03 medical and health sciences, biology.animal, Gene duplication, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, vertebrate evolution, lcsh:Science, neoplasms, emergence of evolutionary novelty, ComputingMilieux_MISCELLANEOUS, Genetics, gene and whole genome duplication, hagfish and lamprey, Multidisciplinary, biology, Lamprey, organic chemicals, Biology (Whole Organism), Vertebrate, [SDV.BDD.EO] Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, biology.organism_classification, biological factors, body regions, Retinoic acid receptor, 030104 developmental biology, [SDV.BDD.EO]Life Sciences [q-bio]/Development Biology/Embryology and Organogenesis, embryonic structures, lcsh:Q, Research Article, Hagfish
Abstract

Whole genome duplications (WGDs) have been classically associated with the origin of evolutionary novelties and the so-called duplication-degeneration-complementation model describes the possible fates of genes after duplication. However, how sequence divergence effectively allows functional changes between gene duplicates is still unclear. In the vertebrate lineage, two rounds of WGDs took place, giving rise to paralogous gene copies observed for many gene families. For the retinoic acid receptors (RARs), for example, which are members of the nuclear hormone receptor (NR) superfamily, a unique ancestral gene has been duplicated resulting in three vertebrate paralogues: RAR alpha, RAR beta and RAR gamma. It has previously been shown that this single ancestral RAR was neofunctionalized to give rise to a larger substrate specificity range in the RARs of extant jawed vertebrates (also called gnathostomes). To understand RAR diversification, the members of the cyclostomes (lamprey and hagfish), jawless vertebrates representing the extant sister group of gnathostomes, provide an intermediate situation and thus allow the characterization of the evolutionary steps that shaped RAR ligand-binding properties following the WGDs. In this study, we assessed the ligand-binding specificity of cyclostome RARs and found that their ligand-binding pockets resemble those of gnathostome RAR alpha and RAR beta. In contrast, none of the cyclostome receptors studied showed any RAR gamma-like specificity. Together, our results suggest that cyclostome RARs cover only a portion of the specificity repertoire of the ancestral gnathostome RARs and indicate that the establishment of ligand-binding specificity was a stepwise event. This iterative process thus provides a rare example for the diversification of receptor-ligand interactions of NRs following WGDs.

Published
2016
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18. Marmoset Serotonin 5-HT 1A Receptor Mapping with a Biased Agonist PET Probe 18 F-F13714: Comparison with an Antagonist Tracer 18 F-MPPF in Awake and Anesthetized States

Author

Chiho Takeda, Kayo Onoe, Aya Mawatari, Hirotaka Onoe, Adrian Newman-Tancredi, Luc Zimmer, Hisashi Doi, Akihiro Kawasaki, Chihiro Yokoyama, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Neurolixis, Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL), Centre de recherche en neurosciences de Lyon - Lyon Neuroscience Research Center (CRNL), 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), Rayet, Béatrice, Centre de recherche en neurosciences de Lyon (CRNL), and 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)

Subjects
0301 basic medicine, Male, Fluorine Radioisotopes, Pyridines, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, [SDV]Life Sciences [q-bio], Caudate nucleus, Aminopyridines, Piperazines, chemistry.chemical_compound, 0302 clinical medicine, Piperidines, Callithrix jacchus, Pharmacology (medical), Tissue Distribution, Receptor, medicine.diagnostic_test, Brain, Callithrix, Molecular Imaging, [SDV] Life Sciences [q-bio], Psychiatry and Mental health, biased agonism, Positron emission tomography, Receptor, Serotonin, 5-HT1A, 5-HT1A receptor, MPPF, Protein Binding, Agonist, Consciousness, medicine.drug_class, Anesthesia, General, 5-hydroxytryptamine, 03 medical and health sciences, Predictive Value of Tests, medicine, Animals, Regular Research Article, Pharmacology, Binding potential, Serotonin 5-HT1 Receptor Agonists, F13714, 030104 developmental biology, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, chemistry, Positron-Emission Tomography, Serotonin, Radiopharmaceuticals, Neuroscience, 030217 neurology & neurosurgery
Abstract

Background In vivo mapping by positron emission tomography of the serotonin 1A receptors has been hindered by the lack of suitable agonist positron emission tomography probes. 18 F-labeled F13714 is a recently developed biased agonist positron emission tomography probe that preferentially targets subpopulations of serotonin 1A receptors in their " active state, " but its brain labeling pattern in nonhuman primate has not been described. In addition, a potential confound in the translatability of PET data between nonhuman animal and human arise from the use of anesthetics that may modify the binding profiles of target receptors. Methods Positron emission tomography scans were conducted in a cohort of common marmosets (n = 4) using the serotonin 1A receptor biased agonist radiotracer, 18 F-F13714, compared with a well-characterized 18 F-labeled antagonist radiotracer, 18 F-MPPF. Experiments on each animal were performed under both consciousness and isoflurane-anesthesia conditions. Results 18 F-F13714 binding distribution in marmosets by positron emission tomography differs markedly from that of the of the 18F-MPPF. Whereas 18F-MPPF showed highest binding in hippocampus and amygdala, 18F-F13714 showed highest labeling in other regions, including insular and cingulate cortex, thalamus, raphe, caudate nucleus, and putamen. The binding potential values of 18F-F13714 were about one-third of those observed with 18F-MPPF, with marked individual- and region-specific differences under isoflurane-anesthetized vs conscious conditions. Conclusions These findings highlight the importance of investigating the brain imaging of serotonin 1A receptors using agonist probes such as 18F-F13714, which may preferentially target subpopulations of serotonin 1A receptors in specific brain regions of nonhuman primate as a biased agonist.

Published
2016
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19. The Lasting Influences of Early Food-Related Variety Experience: A Longitudinal Study of Vegetable Acceptance from 5 Months to 6 Years in Two Populations

Author

Sylvie Issanchou, Peter D. Leathwood, Benoist Schaal, Andrea Maier-Nöth, Nestlé Research Center, RIKEN Center for Life Science Technologies, Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Nestle Nutrition, Centre des Sciences du Goût et de l'Alimentation [Dijon] (CSGA), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), and Centre National de la Recherche Scientifique (CNRS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)

Subjects
Questionnaires, Male, 0301 basic medicine, Longitudinal study, Physiology, Maternal Health, [ SDV.AEN ] Life Sciences [q-bio]/Food and Nutrition, Emotions, school-aged children, Psychological intervention, Breastfeeding, lcsh:Medicine, Pediatrics, Families, Eating, Vegetables, Medicine and Health Sciences, Medicine, Longitudinal Studies, lcsh:Science, Child, enfant, Children, Breast Milk, preferences, 2. Zero hunger, Multidisciplinary, infants, Follow up studies, Agriculture, [ SDV.SPEE ] Life Sciences [q-bio]/Santé publique et épidémiologie, Plants, Body Fluids, Breast Feeding, Milk, Research Design, repeated exposure, Child, Preschool, Alimentation et Nutrition, Female, Anatomy, Research Article, Adult, life, Adolescent, Crops, Context (language use), Weaning, Research and Analysis Methods, Food Preferences, 03 medical and health sciences, preschool-children, increase, Environmental health, Food and Nutrition, ENFANTS, LEGUMES, ACCEPTATION, APPRECIATION, CONSOMMATION, ALLAITEMENT, VARIETE, Humans, patterns, childhood, analyse sensorielle, Survey Research, 030109 nutrition & dietetics, business.industry, lcsh:R, Organisms, Biology and Life Sciences, Infant, légume, Biotechnology, Age Groups, People and Places, Women's Health, lcsh:Q, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Population Groupings, Neonatology, flavor-flavor, Physiological Processes, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Breast feeding, Crop Science, Follow-Up Studies
Abstract

International audience; Children's vegetable consumption falls below current recommendations, highlighting the need to identify strategies that can successfully promote better acceptance of vegetables. Recently, experimental studies have reported promising interventions that increase acceptance of vegetables. The first, offering infants a high variety of vegetables at weaning, increased acceptance of new foods, including vegetables. The second, offering an initially disliked vegetable at 8 subsequent meals markedly increased acceptance for that vegetable. So far, these effects have been shown to persist for at least several weeks. We now present follow-up data at 15 months, 3 and 6 years obtained through questionnaire (15 mo, 3y) and experimental (6y) approaches. At 15 months, participants who had been breast-fed were reported as eating and liking more vegetables than those who had been formula-fed. The initially disliked vegetable that became accepted after repeated exposure was still liked and eaten by 79% of the children. At 3 years, the initially disliked vegetable was still liked and eaten by 73% of the children. At 6 years, observations in an experimental setting showed that children who had been breast-fed and children who had experienced high vegetable variety at the start of weaning ate more of new vegetables and liked them more. They were also more willing to taste vegetables than formula-fed children or the no or low variety groups. The initially disliked vegetable was still liked by 57% of children. This follow-up study suggests that experience with chemosensory variety in the context of breastfeeding or at the onset of complementary feeding can influence chemosensory preferences for vegetables into childhood.

Published
2016
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20. High-resolution NMR-based metabolic detection of microgram biopsies using a 1 mm HRμMAS probe

Author

Takahiro Nemoto, Anne-Karine Bouzier-Sore, Alan Wong, Yusuke Nishiyama, Yuki Endo, JEOL, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Centre de résonance magnétique des systèmes biologiques (CRMSB), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Structure et Dynamique par Résonance Magnétique (LCF) (LSDRM), Nanosciences et Innovation pour les Matériaux, la Biomédecine et l'Energie (ex SIS2M) (NIMBE UMR 3685), Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut Rayonnement Matière de Saclay (IRAMIS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), We would like to thank the French National ResearchAgency for financial support under ANR-12-JSV5-0005 (ANR33HRMACSZ) andJEOL RESONANCE Inc. AKBS is supported by ANR-10-LABX-57 (TRAIL), ANR-12-JSV5-0005,HRMACS,Développement et exploration de nouveaux micro-détecteurs RMN tournants pour des analyses métabolomiques de biopsies de petite masse(2012), ANR-10-LABX-0057,TRAIL,Translational Research and Advanced Imaging Laboratory(2010), Centre National de la Recherche Scientifique (CNRS)-Université de Bordeaux (UB), Solid State NMR Group, University of Warwick, University of Warwick [Coventry], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Institut Rayonnement Matière de Saclay (IRAMIS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)

Subjects
High resolution nmr, Magnetic Resonance Spectroscopy, Microgram, Biopsy, [SDV]Life Sciences [q-bio], 01 natural sciences, Biochemistry, Analytical Chemistry, 03 medical and health sciences, Nuclear magnetic resonance, Metabolomics, Electrochemistry, Environmental Chemistry, Spectroscopy, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Chemistry, 010401 analytical chemistry, Brain, Nuclear magnetic resonance spectroscopy, [CHIM.MATE]Chemical Sciences/Material chemistry, 0104 chemical sciences, Molecular Probes, Proton NMR, Molecular probe
Abstract

International audience; A prototype 1 mm High-Resolution micro-Magic Angle Spinning (HRμMAS) probe is described. High quality 1 H NMR spectra were obtained from 490 μg of heterogeneous biospecimens, offering a rich-metabolite profiling. The results demonstrate the potential of HRμMAS as a new NMR analytical tool in metabolomics. Today 1 H HRMAS (High-Resolution Magic-Angle Spinning) NMR (Nuclear Magnetic Resonance) spectroscopy finds great success in laboratory studies of the metabolome in heterogeneous biospecimens such as human and animal biopsies, 1–3 intact cells 4 and whole organisms, 5,6 owing to the nearly non-destructive nature of the technique and the straightforward data acquisition. 7 However, since NMR spectroscopy is an inherently insensitive analytical technique, HRMAS relies on a large sample mass, typically 10–20 mg per NMR data. For this reason, 1 H HRMAS analysis can be a real challenge (or even impossible) when samples – such as cells, organisms and tissue biopsies – are scarce. Moreover, analysis of 10–20 mg of heterogeneous specimens may prevent the investigation of a specific cell. In contrast, the high degree of homogeneity inside a microscopic specimen can offer a more direct NMR spectral analysis and enable a straightforward metabolic evaluation. The immediate advantages of small sample mass (i.e. microgram) analyses are: (1) they simplify the sample preparations such as cultivation and extraction; and (2) offer precise specimen-specific analyses for exploring the invisible phenotypes. The most cost-effective approach to microscopic NMR detection is the use of a miniature detection coil (μcoil). With this technique, the coil is in close proximity to the microscopic sample optimizing the filling-factor (the ratio of the sample volume to the coil detection volume). 8 Fabricating a μcoil for HRMAS analyses is no easy task, especially without sacrificing detection sensitivity and spectral resolution. 9 The commercial μMAS systems currently available (i.e. 0.7 mm Bruker MAS and 0.75 mm JEOL MAS) are designed for solid materials but do not offer adequate spectral resolution (0.002 ppm) for metabolic investigations. Today, the only approach to μMAS for metabolome analyses is the use of an inductively coupled High-Resolution Magic-Angle Coil Spinning (HRMACS) μcoil. 10 The HRMACS technique uses a secondary tuned circuit (i.e. μcoil-resonator), designed to fit inside a standard 4 mm MAS rotor, to convert the standard large volume MAS system into a high-resolution capable μMAS probe. 11,12 The use of HRMACS has shown

Published
2015
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21. Quality assessment of predicted protein models using energies calculated by the fragment molecular orbital method

Author

Kam Yj Zhang, Shinichiro Nakamura, Hiroya Nakata, Koji Ogata, David Simoncini, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RIKEN Cluster for Science, Technology and Innovation Hub (RCSTI), Tokyo Institute of Technology [Tokyo] (TITECH), Japanese Society for the Promotion of Science Fellow, JSPS - KAKENHI Grant Number 262235, Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), and Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRAE)

Subjects
Models, Molecular, Pair interaction energy, Structure prediction Quality assessment, 010402 general chemistry, Model selection, 01 natural sciences, Measure (mathematics), Structural Biology, Computational chemistry, 0103 physical sciences, Drug Discovery, [INFO]Computer Science [cs], Statistical physics, Quantitative Biology::Biomolecules, 010304 chemical physics, Chemistry, Organic Chemistry, Proteins, Function (mathematics), Protein structure prediction, 0104 chemical sciences, Computer Science Applications, Structural biology, Thermodynamics, Molecular Medicine, GAMESS, Fragment molecular orbital, Energy (signal processing)
Abstract

International audience; Protein structure prediction directly from sequences is a very challenging problem in computational biology. One of the most successful approaches employs stochastic conformational sampling to search an empirically derived energy function landscape for the global energy minimum state. Due to the errors in the empirically derived energy function, the lowest energy conformation may not be the best model. We have evaluated the use of energy calculated by the fragment molecular orbital method (FMO energy) to assess the quality of predicted models and its ability to identify the best model among an ensemble of predicted models. The fragment molecular orbital method implemented in GAMESS was used to calculate the FMO energy of predicted models. When tested on eight protein targets, we found that the model ranking based on FMO energies is better than that based on empirically derived energies when there is sufficient diversity among these models. This model diversity can be estimated prior to the FMO energy calculations. Our result demonstrates that the FMO energy calculated by the fragment molecular orbital method is a practical and promising measure for the assessment of protein model quality and the selection of the best protein model among many generated.

Published
2015
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22. The Reality of Pervasive Transcription

Author

Felix Schlesinger, Joel Rozowsky, Claes Wahlestedt, Peter F. Stadler, Marcel E. Dinger, Paulo P. Amaral, John L. Rinn, Michael B. Clark, Ryan J. Taft, Mark Gerstein, Chris P. Ponting, John S. Mattick, Kevin V. Morris, Yoshihide Hayashizaki, Piero Carninci, Thomas R. Gingeras, Antonin Morillon, Department of Computer Science, Southern Connecticut State University, Universitat Pompeu Fabra [Barcelona] (UPF), Institute for Molecular Bioscience, University of Queensland [Brisbane], MRC Functional Genomics Unit, University of Oxford [Oxford], Carl-Maria-von-Weber-Gesamtausgabe, Universität Paderborn (UPB), Dynamique de l'information génétique : bases fondamentales et cancer (DIG CANCER), Centre National de la Recherche Scientifique (CNRS)-Institut Curie [Paris]-Sorbonne Université (SU), Boise State University, Cold Spring Harbor Laboratory, RIKEN Center for Life Science Technologies (RIKEN CLST), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), and Publica

Subjects
Epigenomics, DNA, Complementary, Transcription, Genetic, QH301-705.5, [SDV]Life Sciences [q-bio], Biology, ENCODE, Genome, General Biochemistry, Genetics and Molecular Biology, Deep sequencing, 03 medical and health sciences, 0302 clinical medicine, Transcription (biology), Databases, Genetic, Animals, Humans, Genetics and Genomics/Genomics, Biology (General), Gene, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, 030304 developmental biology, Expressed Sequence Tags, Mammals, Genetics, 0303 health sciences, Tiling array, General Immunology and Microbiology, Sequence Analysis, RNA, General Neuroscience, Intron, Genetics and Genomics/Bioinformatics, Evolutionary biology, Perspective, Genetics and Genomics/Gene Discovery, Artifacts, General Agricultural and Biological Sciences, 030217 neurology & neurosurgery
Abstract

Current estimates indicate that only about 1.2% of the mammalian genome codes for amino acids in proteins. However, mounting evidence over the past decade has suggested that the vast majority of the genome is transcribed, well beyond the boundaries of known genes, a phenomenon known as pervasive transcription [1]. Challenging this view, an article published in PLoS Biology by van Bakel et al. concluded that “the genome is not as pervasively transcribed as previously reported” [2] and that the majority of the detected low-level transcription is due to technical artefacts and/or background biological noise. These conclusions attracted considerable publicity [3]–[6]. Here, we present an evaluation of the analysis and conclusions of van Bakel et al. compared to those of others and show that (1) the existence of pervasive transcription is supported by multiple independent techniques; (2) re-analysis of the van Bakel et al. tiling arrays shows that their results are atypical compared to those of ENCODE and lack independent validation; and (3) the RNA sequencing dataset used by van Bakel et al. suffered from insufficient sequencing depth and poor transcript assembly, compromising their ability to detect the less abundant transcripts outside of protein-coding genes. We conclude that the totality of the evidence strongly supports pervasive transcription of mammalian genomes, although the biological significance of many novel coding and noncoding transcripts remains to be explored.

Published
2011
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