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Abstract
The biological processes associated with the onset of schizophrenia remain largely unknown. Current hypotheses favor gene × environment interactions as supported by our recent report about DNA methylation changes during the onset of psychosis. Here, we conducted the first longitudinal transcriptomic analysis of blood samples from 31 at-risk individuals who later converted to psychosis and 63 at-risk individuals who did not. Individuals were followed for a maximum of 1 year. Blood samples were collected at baseline and at the end of follow-up and individuals served as their own controls. Differentially expressed genes between the 2 groups were identified using the RNA sequencing of an initial discovery subgroup (n = 15 individuals). The most promising results were replicated using high-throughput real-time qPCR in the whole cohort (n = 94 individuals). We identified longitudinal changes in 4 brain-expressed genes based on RNAseq analysis. One of these genes (CPT1A) was replicated in the whole cohort. The previously observed hypermethylation in NRP1 and GSTM5 during the onset of psychosis correlated with a decrease in corresponding gene expression. RNA sequencing also identified 2 co-expression networks that were impaired after conversion compared with baseline-the Wnt pathway including AKT1, CPT1A and semaphorins, and the Toll-like receptor pathway, related to innate immunity. This longitudinal study of transcriptomic changes in individuals with at-risk mental state revealed alterations during conversion to psychosis in pathways and genes relevant to schizophrenia. These results may be a first step toward better understanding psychosis onset. They may also help to identify new biomarkers and targets for disease-modifying therapeutic strategies.
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Affiliation(s)
- Boris Chaumette
- Universite Paris Descartes, Université Sorbonne Paris Cite, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, Paris, France,GDR3557-Institut de Psychiatrie, Paris, France,Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Oussama Kebir
- Universite Paris Descartes, Université Sorbonne Paris Cite, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, Paris, France,GDR3557-Institut de Psychiatrie, Paris, France,Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Juliette Pouch
- Plateforme qPCR-HD-GPC, Ecole Normale Supérieure, Fondation Pierre-Gilles de Gennes, PSL Research University, Paris, France
| | - Bertrand Ducos
- Plateforme qPCR-HD-GPC, Ecole Normale Supérieure, Fondation Pierre-Gilles de Gennes, PSL Research University, Paris, France,Laboratoire de Physique Statistique, Ecole normale Supérieure, PSL Research University, Université Paris-Diderot Sorbonne Paris-Cité, Sorbonne Universités Univ Paris, CNRS UMR, Paris, France
| | - Fekrije Selimi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR and INSERM U1050, Paris, France
| | - ICAAR study group
- Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Raphael Gaillard
- Universite Paris Descartes, Université Sorbonne Paris Cite, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, Paris, France,GDR3557-Institut de Psychiatrie, Paris, France,Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France
| | - Marie-Odile Krebs
- Universite Paris Descartes, Université Sorbonne Paris Cite, Paris, France,INSERM, Laboratoire de Physiopathologie des Maladies Psychiatriques, Centre de Psychiatrie et Neurosciences, Paris, France,GDR3557-Institut de Psychiatrie, Paris, France,Centre Hospitalier Sainte-Anne, Service Hospitalo-Universitaire, Paris, France,To whom correspondence should be addressed; Service Hospitalo-Universitaire, Centre Hospitalier Sainte Anne, 7 rue Cabanis, 75014 Paris, France; tel: +33 14 5658 646, fax: +33 14 5658 160, e-mail:
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van den Beek M, da Silva B, Pouch J, Ali Chaouche MEA, Carré C, Antoniewski C. Dual-layer transposon repression in heads of Drosophila melanogaster. RNA 2018; 24:1749-1760. [PMID: 30217866 PMCID: PMC6239173 DOI: 10.1261/rna.067173.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/05/2018] [Indexed: 05/11/2023]
Abstract
piRNA-mediated repression of transposable elements (TE) in the germline limits the accumulation of mutations caused by their transposition. It is not clear whether the piRNA pathway plays a role in adult, nongonadal tissues in Drosophila melanogaster. To address this question, we analyzed the small RNA content of adult Drosophila melanogaster heads. We found that the varying amount of piRNA-sized, ping-pong positive molecules in heads correlates with contamination by gonadal tissue during RNA extraction, suggesting that most of the piRNAs detected in heads originate from gonads. We next sequenced the heads of wild-type and piwi mutants to address whether piwi loss of function would affect the low amount of piRNA-sized, ping-pong negative molecules that are still detected in heads hand-checked to avoid gonadal contamination. We find that loss of piwi does not significantly affect these 24-28 nt RNAs. Instead, we observe increased siRNA levels against the majority of Drosophila TE families. To determine the effect of this siRNA level change on transposon expression, we sequenced the transcriptome of wild-type, piwi, dicer-2 and piwi, dicer-2 double-mutant heads. We find that RNA expression levels of the majority of TE in piwi or dicer-2 mutants remain unchanged and that TE transcripts increase only in piwi, dicer-2 double-mutants. These results lead us to suggest a dual-layer model for TE repression in adult somatic tissues. Piwi-mediated gene silencing established during embryogenesis constitutes the first layer of TE repression whereas Dicer-2-dependent siRNA-mediated silencing provides a backup mechanism to repress TEs that escape silencing by Piwi.
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Affiliation(s)
- Marius van den Beek
- Drosophila Genetics and Epigenetics; Sorbonne Université, CNRS, Biologie du développement - Institut de Biologie Paris Seine, 75005 Paris, France
| | - Bruno da Silva
- Drosophila Genetics and Epigenetics; Sorbonne Université, CNRS, Biologie du développement - Institut de Biologie Paris Seine, 75005 Paris, France
| | - Juliette Pouch
- Genomic facility, Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Mohammed El Amine Ali Chaouche
- Genomic facility, Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Clément Carré
- Drosophila Genetics and Epigenetics; Sorbonne Université, CNRS, Biologie du développement - Institut de Biologie Paris Seine, 75005 Paris, France
| | - Christophe Antoniewski
- Drosophila Genetics and Epigenetics; Sorbonne Université, CNRS, Biologie du développement - Institut de Biologie Paris Seine, 75005 Paris, France
- ARTbio Bioinformatics Analysis Facility, Sorbonne Université, CNRS, Institut de Biologie Paris Seine, 75005 Paris, France
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Dardalhon-Cuménal D, Deraze J, Dupont CA, Ribeiro V, Coléno-Costes A, Pouch J, Le Crom S, Thomassin H, Debat V, Randsholt NB, Peronnet F. Cyclin G and the Polycomb Repressive complexes PRC1 and PR-DUB cooperate for developmental stability. PLoS Genet 2018; 14:e1007498. [PMID: 29995890 PMCID: PMC6065198 DOI: 10.1371/journal.pgen.1007498] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 07/27/2018] [Accepted: 06/19/2018] [Indexed: 12/16/2022] Open
Abstract
In Drosophila, ubiquitous expression of a short Cyclin G isoform generates extreme developmental noise estimated by fluctuating asymmetry (FA), providing a model to tackle developmental stability. This transcriptional cyclin interacts with chromatin regulators of the Enhancer of Trithorax and Polycomb (ETP) and Polycomb families. This led us to investigate the importance of these interactions in developmental stability. Deregulation of Cyclin G highlights an organ intrinsic control of developmental noise, linked to the ETP-interacting domain, and enhanced by mutations in genes encoding members of the Polycomb Repressive complexes PRC1 and PR-DUB. Deep-sequencing of wing imaginal discs deregulating CycG reveals that high developmental noise correlates with up-regulation of genes involved in translation and down-regulation of genes involved in energy production. Most Cyclin G direct transcriptional targets are also direct targets of PRC1 and RNAPolII in the developing wing. Altogether, our results suggest that Cyclin G, PRC1 and PR-DUB cooperate for developmental stability.
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Affiliation(s)
- Delphine Dardalhon-Cuménal
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Jérôme Deraze
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Camille A. Dupont
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Valérie Ribeiro
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Anne Coléno-Costes
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Juliette Pouch
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale
supérieure, CNRS, INSERM, PSL Université Paris Paris, France
| | - Stéphane Le Crom
- Institut de biologie de l’Ecole normale supérieure (IBENS), Ecole normale
supérieure, CNRS, INSERM, PSL Université Paris Paris, France
- Sorbonne Université, Univ Antilles, Univ Nice Sophia Antipolis, CNRS,
Evolution Paris Seine—Institut de Biologie Paris Seine (EPS - IBPS), Paris,
France
| | - Hélène Thomassin
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Vincent Debat
- Institut de Systematique, Evolution, Biodiversité ISYEB UMR 7205, MNHN,
CNRS, Sorbonne Université, EPHE, Muséum national d'Histoire naturelle, Sorbonne
Universités, Paris, France
| | - Neel B. Randsholt
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
| | - Frédérique Peronnet
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS),
Institut de Biologie Paris-Seine (IBPS), Laboratory of Developmental Biology
(LBD), Paris, France
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Michel L, Reygagne P, Benech P, Jean-Louis F, Scalvino S, Ly Ka So S, Hamidou Z, Bianovici S, Pouch J, Ducos B, Bonnet M, Bensussan A, Patatian A, Lati E, Wdzieczak-Bakala J, Choulot JC, Loing E, Hocquaux M. Study of gene expression alteration in male androgenetic alopecia: evidence of predominant molecular signalling pathways. Br J Dermatol 2017; 177:1322-1336. [PMID: 28403520 DOI: 10.1111/bjd.15577] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND Male androgenetic alopecia (AGA) is the most common form of hair loss in men. It is characterized by a distinct pattern of progressive hair loss starting from the frontal area and the vertex of the scalp. Although several genetic risk loci have been identified, relevant genes for AGA remain to be defined. OBJECTIVES To identify biomarkers associated with AGA. METHODS Molecular biomarkers associated with premature AGA were identified through gene expression analysis using cDNA generated from scalp vertex biopsies of hairless or bald men with premature AGA, and healthy volunteers. RESULTS This monocentric study reveals that genes encoding mast cell granule enzymes, inflammatory mediators and immunoglobulin-associated immune mediators were significantly overexpressed in AGA. In contrast, underexpressed genes appear to be associated with the Wnt/β-catenin and bone morphogenic protein/transforming growth factor-β signalling pathways. Although involvement of these pathways in hair follicle regeneration is well described, functional interpretation of the transcriptomic data highlights different events that account for their inhibition. In particular, one of these events depends on the dysregulated expression of proopiomelanocortin, as confirmed by polymerase chain reaction and immunohistochemistry. In addition, lower expression of CYP27B1 in patients with AGA supports the notion that changes in vitamin D metabolism contributes to hair loss. CONCLUSIONS This study provides compelling evidence for distinct molecular events contributing to alopecia that may pave the way for new therapeutic approaches.
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Affiliation(s)
- L Michel
- Inserm UMR976, Skin Research Institute, F-75475, Paris, France.,University Paris Diderot, Sorbonne Paris-Cité, Hôpital Saint-Louis, F-75475, Paris, France
| | - P Reygagne
- Centre Sabouraud, F-75475, Paris, France
| | - P Benech
- NICN UMR 7259 CNRS Faculté de Médecine, 13344, Marseille, France.,GENEX, 91160, Longjumeau, France
| | - F Jean-Louis
- Inserm UMR976, Skin Research Institute, F-75475, Paris, France.,University Paris Diderot, Sorbonne Paris-Cité, Hôpital Saint-Louis, F-75475, Paris, France
| | - S Scalvino
- Laboratoire BIO-EC, 91160, Longjumeau, France
| | - S Ly Ka So
- Inserm UMR976, Skin Research Institute, F-75475, Paris, France
| | - Z Hamidou
- Centre Sabouraud, F-75475, Paris, France
| | | | - J Pouch
- Plateforme de qPCR à Haut Débit Genomic Paris Centre, IBENS, 75005, Paris, France
| | - B Ducos
- Plateforme de qPCR à Haut Débit Genomic Paris Centre, IBENS, 75005, Paris, France.,Laboratoire de Physique Statistique, École Normale Supérieure, PSL Research University, University Paris Diderot, Sorbonne Paris-Cité, CNRS, 75005, Paris, France
| | - M Bonnet
- Inserm UMR976, Skin Research Institute, F-75475, Paris, France
| | - A Bensussan
- Inserm UMR976, Skin Research Institute, F-75475, Paris, France.,University Paris Diderot, Sorbonne Paris-Cité, Hôpital Saint-Louis, F-75475, Paris, France
| | | | - E Lati
- GENEX, 91160, Longjumeau, France.,Laboratoire BIO-EC, 91160, Longjumeau, France
| | | | | | - E Loing
- IEB-Lucas Meyer Cosmetics, 31520, Ramonville, France
| | - M Hocquaux
- IEB-Lucas Meyer Cosmetics, 31520, Ramonville, France
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Diodato A, Ruinart de Brimont M, Yim YS, Derian N, Perrin S, Pouch J, Klatzmann D, Garel S, Choi GB, Fleischmann A. Molecular signatures of neural connectivity in the olfactory cortex. Nat Commun 2016; 7:12238. [PMID: 27426965 PMCID: PMC4960301 DOI: 10.1038/ncomms12238] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 06/14/2016] [Indexed: 01/01/2023] Open
Abstract
The ability to target subclasses of neurons with defined connectivity is crucial for uncovering neural circuit functions. The olfactory (piriform) cortex is thought to generate odour percepts and memories, and odour information encoded in piriform is routed to target brain areas involved in multimodal sensory integration, cognition and motor control. However, it remains unknown if piriform outputs are spatially organized, and if distinct output channels are delineated by different gene expression patterns. Here we identify genes selectively expressed in different layers of the piriform cortex. Neural tracing experiments reveal that these layer-specific piriform genes mark different subclasses of neurons, which project to distinct target areas. Interestingly, these molecular signatures of connectivity are maintained in reeler mutant mice, in which neural positioning is scrambled. These results reveal that a predictive link between a neuron's molecular identity and connectivity in this cortical circuit is determined independent of its spatial position. The piriform cortex projects to multiple brain regions involved in diverse aspects of olfactory behavior but information about the organization of these outputs is lacking. Here the authors show that piriform neurons exhibit layer specific gene expression patterns that also define distinct projection targets.
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Affiliation(s)
- Assunta Diodato
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, and CNRS, UMR 7241 and INSERM U1050, F-75005 Paris, France
| | - Marion Ruinart de Brimont
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, and CNRS, UMR 7241 and INSERM U1050, F-75005 Paris, France
| | - Yeong Shin Yim
- Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nicolas Derian
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U959, Immunology-Immunopathology-Immunotherapy (I3), and AP-HP, Clinical Investigation Center in Biotherapy, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Sandrine Perrin
- École Normale Supérieure, Institut de Biologie de l'ENS, Plateforme Génomique, and INSERM U1024, CNRS UMR 8197, F-75005 Paris, France
| | - Juliette Pouch
- École Normale Supérieure, Institut de Biologie de l'ENS, Plateforme Génomique, and INSERM U1024, CNRS UMR 8197, F-75005 Paris, France
| | - David Klatzmann
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U959, Immunology-Immunopathology-Immunotherapy (I3), and AP-HP, Clinical Investigation Center in Biotherapy, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Sonia Garel
- École Normale Supérieure, Institut de Biologie de l'ENS, and INSERM U1024, CNRS UMR 8197, F-75005 Paris, France
| | - Gloria B Choi
- Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Alexander Fleischmann
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, and CNRS, UMR 7241 and INSERM U1050, F-75005 Paris, France
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Merhej J, Thiebaut A, Blugeon C, Pouch J, Ali Chaouche MEA, Camadro JM, Le Crom S, Lelandais G, Devaux F. A Network of Paralogous Stress Response Transcription Factors in the Human Pathogen Candida glabrata. Front Microbiol 2016; 7:645. [PMID: 27242683 PMCID: PMC4860858 DOI: 10.3389/fmicb.2016.00645] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Accepted: 04/18/2016] [Indexed: 01/15/2023] Open
Abstract
The yeast Candida glabrata has become the second cause of systemic candidemia in humans. However, relatively few genome-wide studies have been conducted in this organism and our knowledge of its transcriptional regulatory network is quite limited. In the present work, we combined genome-wide chromatin immunoprecipitation (ChIP-seq), transcriptome analyses, and DNA binding motif predictions to describe the regulatory interactions of the seven Yap (Yeast AP1) transcription factors of C. glabrata. We described a transcriptional network containing 255 regulatory interactions and 309 potential target genes. We predicted with high confidence the preferred DNA binding sites for 5 of the 7 CgYaps and showed a strong conservation of the Yap DNA binding properties between S. cerevisiae and C. glabrata. We provided reliable functional annotation for 3 of the 7 Yaps and identified for Yap1 and Yap5 a core regulon which is conserved in S. cerevisiae, C. glabrata, and C. albicans. We uncovered new roles for CgYap7 in the regulation of iron-sulfur cluster biogenesis, for CgYap1 in the regulation of heme biosynthesis and for CgYap5 in the repression of GRX4 in response to iron starvation. These transcription factors define an interconnected transcriptional network at the cross-roads between redox homeostasis, oxygen consumption, and iron metabolism.
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Affiliation(s)
- Jawad Merhej
- Laboratoire de Biologie Computationnelle et Quantitative, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7238, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
| | - Antonin Thiebaut
- Laboratoire de Biologie Computationnelle et Quantitative, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7238, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
| | - Corinne Blugeon
- École Normale Supérieure, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Plateforme Génomique Paris, France
| | - Juliette Pouch
- École Normale Supérieure, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Plateforme Génomique Paris, France
| | - Mohammed El Amine Ali Chaouche
- École Normale Supérieure, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Institut de Biologie de l'École Normale Supérieure, Plateforme Génomique Paris, France
| | - Jean-Michel Camadro
- Centre National de la Recherche Scientifique, UMR 7592, Institut Jacques Monod, Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - Stéphane Le Crom
- Évolution, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7138, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
| | - Gaëlle Lelandais
- Centre National de la Recherche Scientifique, UMR 7592, Institut Jacques Monod, Université Paris Diderot, Sorbonne Paris Cité Paris, France
| | - Frédéric Devaux
- Laboratoire de Biologie Computationnelle et Quantitative, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, UMR 7238, Sorbonne Universités, Université Pierre et Marie Curie Paris, France
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Carradec Q, Götz U, Arnaiz O, Pouch J, Simon M, Meyer E, Marker S. Primary and secondary siRNA synthesis triggered by RNAs from food bacteria in the ciliate Paramecium tetraurelia. Nucleic Acids Res 2015; 43:1818-33. [PMID: 25593325 PMCID: PMC4330347 DOI: 10.1093/nar/gku1331] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In various organisms, an efficient RNAi response can be triggered by feeding cells with bacteria producing double-stranded RNA (dsRNA) against an endogenous gene. However, the detailed mechanisms and natural functions of this pathway are not well understood in most cases. Here, we studied siRNA biogenesis from exogenous RNA and its genetic overlap with endogenous RNAi in the ciliate Paramecium tetraurelia by high-throughput sequencing. Using wild-type and mutant strains deficient for dsRNA feeding we found that high levels of primary siRNAs of both strands are processed from the ingested dsRNA trigger by the Dicer Dcr1, the RNA-dependent RNA polymerases Rdr1 and Rdr2 and other factors. We further show that this induces the synthesis of secondary siRNAs spreading along the entire endogenous mRNA, demonstrating the occurrence of both 3′-to-5′ and 5′-to-3′ transitivity for the first time in the SAR clade of eukaryotes (Stramenopiles, Alveolates, Rhizaria). Secondary siRNAs depend on Rdr2 and show a strong antisense bias; they are produced at much lower levels than primary siRNAs and hardly contribute to RNAi efficiency. We further provide evidence that the Paramecium RNAi machinery also processes single-stranded RNAs from its bacterial food, broadening the possible natural functions of exogenously induced RNAi in this organism.
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Affiliation(s)
- Quentin Carradec
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France UPMC, IFD, Sorbonne Universités, 4 place Jussieu, 75252 Paris cedex 05, France
| | - Ulrike Götz
- Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
| | - Olivier Arnaiz
- Centre de Génétique Moléculaire, CNRS UPR3404, 91198 Gif-sur-Yvette cedex, France
| | - Juliette Pouch
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France
| | - Martin Simon
- Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
| | - Eric Meyer
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France
| | - Simone Marker
- Institut de Biologie de l'ENS, IBENS, Ecole Normale Supérieure, Inserm, U1024, CNRS, UMR 8197, 75005 Paris, France Zentrum für Human- und Molekularbiologie, Molekulare Zelldynamik, Universität des Saarlandes, Campus A2 4, 66123 Saarbrücken, Germany
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Vague J, Boyer J, Nicolino J, Mattei A, Luciani J, Arnaud A, Pouch J, Valette A. [Klinefelter's disease in monozygotic twins]. Ann Endocrinol (Paris) 1968; 29:709-29. [PMID: 5737690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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