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Rengifo Rojas C, Cercy J, Perillous S, Gonthier-Guéret C, Montibus B, Maupetit-Méhouas S, Espinadel A, Dupré M, Hong CC, Hata K, Nakabayashi K, Plagge A, Bouschet T, Arnaud P, Vaillant I, Court F. Biallelic non-productive enhancer-promoter interactions precede imprinted expression of Kcnk9 during mouse neural commitment. HGG Adv 2024; 5:100271. [PMID: 38297831 PMCID: PMC10869267 DOI: 10.1016/j.xhgg.2024.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
It is only partially understood how constitutive allelic methylation at imprinting control regions (ICRs) interacts with other regulation levels to drive timely parental allele-specific expression along large imprinted domains. The Peg13-Kcnk9 domain is an imprinted domain with important brain functions. To gain insights into its regulation during neural commitment, we performed an integrative analysis of its allele-specific epigenetic, transcriptomic, and cis-spatial organization using a mouse stem cell-based corticogenesis model that recapitulates the control of imprinted gene expression during neurodevelopment. We found that, despite an allelic higher-order chromatin structure associated with the paternally CTCF-bound Peg13 ICR, enhancer-Kcnk9 promoter contacts occurred on both alleles, although they were productive only on the maternal allele. This observation challenges the canonical model in which CTCF binding isolates the enhancer and its target gene on either side and suggests a more nuanced role for allelic CTCF binding at some ICRs.
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Affiliation(s)
- Cecilia Rengifo Rojas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jil Cercy
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sophie Perillous
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Céline Gonthier-Guéret
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bertille Montibus
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Stéphanie Maupetit-Méhouas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Astrid Espinadel
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Marylou Dupré
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan; Department of Human Molecular Genetics, Gunma University Graduate School of Medicine 3-39-22 Showa, Maebashi, Gunma 371-8511, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Antonius Plagge
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Philippe Arnaud
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Isabelle Vaillant
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Franck Court
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
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2
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Le Boiteux E, Court F, Guichet PO, Vaurs-Barrière C, Vaillant I, Chautard E, Verrelle P, Costa BM, Karayan-Tapon L, Fogli A, Arnaud P. Widespread overexpression from the four DNA hypermethylated HOX clusters in aggressive (IDHwt) glioma is associated with H3K27me3 depletion and alternative promoter usage. Mol Oncol 2021; 15:1995-2010. [PMID: 33720519 PMCID: PMC8334257 DOI: 10.1002/1878-0261.12944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 11/30/2020] [Revised: 02/17/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
In human, the 39 coding HOX genes and 18 referenced noncoding antisense transcripts are arranged in four genomic clusters named HOXA, B, C, and D. This highly conserved family belongs to the homeobox class of genes that encode transcription factors required for normal development. Therefore, HOX gene deregulation might contribute to the development of many cancer types. Here, we study HOX gene deregulation in adult glioma, a common type of primary brain tumor. We performed extensive molecular analysis of tumor samples, classified according to their isocitrate dehydrogenase (IDH1) gene mutation status, and of glioma stem cells. We found widespread expression of sense and antisense HOX transcripts only in aggressive (IDHwt) glioma samples, although the four HOX clusters displayed DNA hypermethylation. Integrative analysis of expression, DNA methylation, and histone modification signatures along the clusters revealed that HOX gene upregulation relies on canonical and alternative bivalent CpG island promoters that escape hypermethylation. H3K27me3 loss at these promoters emerges as the main cause of widespread HOX gene upregulation in IDHwt glioma cell lines and tumors. Our study provides the first comprehensive description of the epigenetic changes at HOX clusters and their contribution to the transcriptional changes observed in adult glioma. It also identified putative 'master' HOX proteins that might contribute to the tumorigenic potential of glioma stem cells.
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Affiliation(s)
- Elisa Le Boiteux
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Franck Court
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pierre-Olivier Guichet
- INSERM-U1084, Poitiers, France.,Poitiers University, France.,Department of Cancer Biology, Poitiers Hospital, France
| | | | - Isabelle Vaillant
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Emmanuel Chautard
- Pathology Department, Jean Perrin Center, Clermont-Ferrand, France.,INSERM, U1240 IMoST, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pierre Verrelle
- CIMB, INSERM U1196 CNRS UMR9187, Curie Institute, Orsay, France.,Radiotherapy Department, Curie Institute, Paris, France.,Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Lucie Karayan-Tapon
- INSERM-U1084, Poitiers, France.,Poitiers University, France.,Department of Cancer Biology, Poitiers Hospital, France
| | - Anne Fogli
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France.,Biochemistry and Molecular Biology Department, Clermont-Ferrand Hospital, France
| | - Philippe Arnaud
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
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3
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Montibus B, Cercy J, Bouschet T, Charras A, Maupetit-Méhouas S, Nury D, Gonthier-Guéret C, Chauveau S, Allegre N, Chariau C, Hong CC, Vaillant I, Marques CJ, Court F, Arnaud P. TET3 controls the expression of the H3K27me3 demethylase Kdm6b during neural commitment. Cell Mol Life Sci 2021; 78:757-768. [PMID: 32405722 PMCID: PMC9644380 DOI: 10.1007/s00018-020-03541-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 01/03/2023]
Abstract
The acquisition of cell identity is associated with developmentally regulated changes in the cellular histone methylation signatures. For instance, commitment to neural differentiation relies on the tightly controlled gain or loss of H3K27me3, a hallmark of polycomb-mediated transcriptional gene silencing, at specific gene sets. The KDM6B demethylase, which removes H3K27me3 marks at defined promoters and enhancers, is a key factor in neurogenesis. Therefore, to better understand the epigenetic regulation of neural fate acquisition, it is important to determine how Kdm6b expression is regulated. Here, we investigated the molecular mechanisms involved in the induction of Kdm6b expression upon neural commitment of mouse embryonic stem cells. We found that the increase in Kdm6b expression is linked to a rearrangement between two 3D configurations defined by the promoter contact with two different regions in the Kdm6b locus. This is associated with changes in 5-hydroxymethylcytosine (5hmC) levels at these two regions, and requires a functional ten-eleven-translocation (TET) 3 protein. Altogether, our data support a model whereby Kdm6b induction upon neural commitment relies on an intronic enhancer the activity of which is defined by its TET3-mediated 5-hmC level. This original observation reveals an unexpected interplay between the 5-hmC and H3K27me3 pathways during neural lineage commitment in mammals. It also questions to which extent KDM6B-mediated changes in H3K27me3 level account for the TET-mediated effects on gene expression.
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Affiliation(s)
- Bertille Montibus
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
- King's College, London, UK
| | - Jil Cercy
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle (IGF), University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Amandine Charras
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
- Department of Women's and Children's Health, Institute of Lifecourse and Medical Sciences, Liverpool University, Liverpool, UK
| | | | - David Nury
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | | | - Sabine Chauveau
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - Nicolas Allegre
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - Caroline Chariau
- Nantes Université, CHU Nantes, SFR Santé, FED4203, Inserm UMS 016, CNRS UMS 3556, 44000, Nantes, France
| | - Charles C Hong
- Vanderbilt University School of Medicine Nashville, Nashville, USA
| | - Isabelle Vaillant
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France
| | - C Joana Marques
- Life and Health Sciences Research Institute (ICVS), University of Minho, Campus de Gualtar, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
- Department of Genetics, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Franck Court
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France.
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, GReD, 63000, Clermont-Ferrand, France.
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4
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Bourguet P, de Bossoreille S, López-González L, Pouch-Pélissier MN, Gómez-Zambrano Á, Devert A, Pélissier T, Pogorelcnik R, Vaillant I, Mathieu O. A role for MED14 and UVH6 in heterochromatin transcription upon destabilization of silencing. Life Sci Alliance 2018; 1:e201800197. [PMID: 30574575 PMCID: PMC6291795 DOI: 10.26508/lsa.201800197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 09/19/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 01/11/2023] Open
Abstract
The TFIIH component UVH6 and the mediator subunit MED14 are differentially required for the release of heterochromatin silencing, and MED14 regulates non-CG DNA methylation in Arabidopsis. Constitutive heterochromatin is associated with repressive epigenetic modifications of histones and DNA which silence transcription. Yet, particular mutations or environmental changes can destabilize heterochromatin-associated silencing without noticeable changes in repressive epigenetic marks. Factors allowing transcription in this nonpermissive chromatin context remain poorly known. Here, we show that the transcription factor IIH component UVH6 and the mediator subunit MED14 are both required for heat stress–induced transcriptional changes and release of heterochromatin transcriptional silencing in Arabidopsis thaliana. We find that MED14, but not UVH6, is required for transcription when heterochromatin silencing is destabilized in the absence of stress through mutating the MOM1 silencing factor. In this case, our results raise the possibility that transcription dependency over MED14 might require intact patterns of repressive epigenetic marks. We also uncover that MED14 regulates DNA methylation in non-CG contexts at a subset of RNA-directed DNA methylation target loci. These findings provide insight into the control of heterochromatin transcription upon silencing destabilization and identify MED14 as a regulator of DNA methylation.
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Affiliation(s)
- Pierre Bourguet
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Stève de Bossoreille
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Leticia López-González
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Marie-Noëlle Pouch-Pélissier
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ángeles Gómez-Zambrano
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Anthony Devert
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Thierry Pélissier
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Romain Pogorelcnik
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Isabelle Vaillant
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Olivier Mathieu
- Génétique Reproduction et Développement, Centre National de la Recherche Scientifique (CNRS), Inserm, Université Clermont Auvergne, Clermont-Ferrand, France
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5
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Côté J, Fortin MC, Auger P, Rouleau G, Dubois S, Boudreau N, Vaillant I, Gélinas-Lemay É. Web-Based Tailored Intervention to Support Optimal Medication Adherence Among Kidney Transplant Recipients: Pilot Parallel-Group Randomized Controlled Trial. JMIR Form Res 2018; 2:e14. [PMID: 30684400 PMCID: PMC6334708 DOI: 10.2196/formative.9707] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/16/2018] [Accepted: 06/18/2018] [Indexed: 12/05/2022] Open
Abstract
Background Optimal immunosuppressive medication adherence is essential to graft survival. Transplant-TAVIE is a Web-based tailored intervention developed to promote this adherence. Objective The objective of our study was to evaluate the Transplant-TAVIE intervention’s acceptability, feasibility, and preliminary efficacy. Methods In a pilot, parallel-group, randomized controlled trial, we randomly assigned a convenience sample of 70 kidney transplant patients on immunosuppressive medication either to an experimental group (Transplant-TAVIE) or to a control group (existing websites). Kidney transplant recipients had to be older than 18 years, be taking immunosuppressant medication, and have access to the internet to participate in this study. Transplant-TAVIE was composed of three interactive Web-based sessions hosted by a virtual nurse. We documented user appreciation of and exposure to the intervention. Furthermore, we assessed medication adherence, medication self-efficacy, intake-related skills, and medication side effects at baseline and 3 and 6 months later. Analyses of variance were used to assess intergroup differences over time. Results After baseline questionnaire completion, participants were randomly assigned either to Transplant-TAVIE (n=35) or to the websites (n=35) group. All participants had received their kidney graft <1 year to 32 years earlier (mean 6.8 years). Of the experimental group, 54% (19/35) completed the sessions of Transplant-TAVIE. Users found the intervention to be acceptable—33% were extremely satisfied (6/18), 39% were very satisfied (7/18), and 28% were satisfied (5/18). At baseline and over time, both experimental and control groups reported high medication adherence, high medication self-efficacy, and frequent use of skills related to medication intake. No intergroup differences emerged over time. Conclusions The results of this study support the feasibility and acceptability of Transplant-TAVIE. It could constitute an accessible adjunct in support of existing specialized services.
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Affiliation(s)
- José Côté
- Research Chair in Innovative Nursing Practices, Montreal, QC, Canada.,Faculty of Nursing, Université de Montréal, Montreal, QC, Canada.,Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Marie-Chantal Fortin
- Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada.,Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Patricia Auger
- Research Chair in Innovative Nursing Practices, Montreal, QC, Canada.,Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Geneviève Rouleau
- Research Chair in Innovative Nursing Practices, Montreal, QC, Canada.,Research Centre of the Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Sylvie Dubois
- Faculty of Nursing, Université de Montréal, Montreal, QC, Canada
| | - Nathalie Boudreau
- Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Isabelle Vaillant
- Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
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6
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Layat E, Cotterell S, Vaillant I, Yukawa Y, Tutois S, Tourmente S. Transcript levels, alternative splicing and proteolytic cleavage of TFIIIA control 5S rRNA accumulation during Arabidopsis thaliana development. Plant J 2012; 71:35-44. [PMID: 22353599 DOI: 10.1111/j.1365-313x.2012.04948.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Ribosome biogenesis is critical for eukaryotic cells and requires coordinated synthesis of the protein and rRNA moieties of the ribosome, which are therefore highly regulated. 5S ribosomal RNA, an essential component of the large ribosomal subunit, is transcribed by RNA polymerase III and specifically requires transcription factor IIIA (TFIIIA). To obtain insight into the regulation of 5S rRNA transcription, we have investigated the expression of 5S rRNA and the exon-skipped (ES) and exon-including (EI) TFIIIA transcripts, two transcript isoforms that result from alternative splicing of the TFIIIA gene, and TFIIIA protein amounts with respect to requirements for 5S rRNA during development. We show that 5S rRNA quantities are regulated through distinct but complementary mechanisms operating through transcriptional and post-transcriptional control of TFIIIA transcripts as well as at the post-translational level through proteolytic cleavage of the TFIIIA protein. During the reproductive phase, high expression of the TFIIIA gene together with low proteolytic cleavage contributes to accumulation of functional, full-length TFIIIA protein, and results in 5S rRNA accumulation in the seed. In contrast, just after germination, the levels of TFIIIA-encoding transcripts are low and stable. Full-length TFIIIA protein is undetectable, and the level of 5S rRNA stored in the embryo progressively decreases. After day 4, in correlation with the reorganization of 5S rDNA chromatin to a mature state, full-length TFIIIA protein with transcriptional activity accumulates and permits de novo transcription of 5S rRNA.
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Affiliation(s)
- Elodie Layat
- CNRS, UMR 6293 GReD, Clermont Université, INSERM U1103, 24 Avenue des Landais, BP 80026, 63171 Aubière Cedex, France
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7
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Vaillant I, Tutois S, Jasencakova Z, Douet J, Schubert I, Tourmente S. Hypomethylation and hypermethylation of the tandem repetitive 5S rRNA genes in Arabidopsis. Plant J 2008; 54:299-309. [PMID: 18208523 DOI: 10.1111/j.1365-313x.2008.03413.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
5S ribosomal DNA (5S rDNA) is organized in tandem repeats on chromosomes 3, 4 and 5 in Arabidopsis thaliana. One part of the 5S rDNA is located within the heterochromatic chromocenters, and the other fraction forms loops with euchromatic features that emanate from the chromocenters. We investigated whether the A. thaliana heterochromatin, and particularly the 5S rDNA, is modified when changing the culture conditions (cultivation in growth chamber versus greenhouse). Nuclei from challenged tissues displayed larger total, as well as 5S rDNA, heterochromatic fractions, and the DNA methyltransferase mutants met1 and cmt3 had different impacts in Arabidopsis. The enlarged fraction of heterochromatic 5S rDNA was observed, together with the reversal of the silencing of some 5S rRNA genes known as minor genes. We observed hypermethylation at CATG sites, and a concomitant DNA hypomethylation at CG/CXG sites in 5S rDNA. Our results show that the asymmetrical hypermethylation is correlated with the ageing of the plants, whereas hypomethylation results from the growth chamber/culture conditions. In spite of severely reduced DNA methylation, the met1 mutant revealed no increase in minor 5S rRNA transcripts in these conditions. The increasing proportion of cytosines in asymmetrical contexts during transition from the euchromatic to the heterochromatic state in the 5S rDNA array suggests that 5S rDNA units are differently affected by the (hypo and hyper)methylation patterns along the 5S rDNA locus. This might explain the different behaviour of 5S rDNA subpopulations inside a 5S array in terms of chromatin compaction and expression, i.e. some 5S rRNA genes would become derepressed, whereas others would join the heterochromatic fraction.
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Affiliation(s)
- Isabelle Vaillant
- Unité Mixte de Recherche CNRS 6247 GReD, INSERM, Université Blaise Pascal, 24 Avenue des Landais, 63177 Aubière Cedex, France
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8
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Vaillant I, Paszkowski J. Role of histone and DNA methylation in gene regulation. Curr Opin Plant Biol 2007; 10:528-33. [PMID: 17692561 DOI: 10.1016/j.pbi.2007.06.008] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 06/17/2007] [Indexed: 05/16/2023]
Abstract
Transcription is known to be regulated by given chromatin states, distinguished as transcriptionally active euchromatin and silent heterochromatin. In plants, silencing in heterochromatin is associated with hypermethylation of DNA and specific covalent modifications of histone H3. Several lines of evidence have suggested that maintenance of DNA methylation patterns at CG sequences is responsible for the formation of stable and thus heritable activity states termed epialleles. By contrast, histone modification and DNA methylation outside CGs confer the flexibility of transcriptional regulation necessary for plant development and adaptive responses to the environment. Recent studies have refined our understanding of the biological significance of and the molecular mechanisms involved in the interplay between DNA and histone H3 methylation.
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Affiliation(s)
- Isabelle Vaillant
- Laboratory of Plant Genetics, University of Geneva, Sciences III, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
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9
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Abstract
The Arabidopsis thaliana genome comprises around 1,000 copies of 5S rRNA genes encoding both major and minor 5S rRNAs. In mature wild-type leaves, the minor 5S rRNA genes are silent. Using different mutants of DNA methyltransferases (met1, cmt3 and met1 cmt3), components of the RNAi pathway (ago4) or post-translational histone modifier (hda6/sil1), we show that the corresponding proteins are needed to maintain proper methylation patterns at heterochromatic 5S rDNA repeats. Using reverse transcription-PCR and cytological analyses, we report that a decrease of 5S rDNA methylation at CG or CNG sites in these mutants leads to the release of 5S rRNA gene silencing which occurred without detectable changes of the 5S rDNA chromatin structure. In spite of severely reduced DNA methylation, the met1 cmt3 double mutant revealed no increase in minor 5S rRNA transcripts. Furthermore, the release of silencing of minor 5S rDNAs can be achieved without increased formation of euchromatic loops by 5S rDNA, and is independent from the global heterochromatin content. Additionally, fluorescence in situ hybridization with centromeric 180 bp repeats confirmed that these highly repetitive sequences, in spite of their elevated transcriptional activity in the DNA methyltransferase mutants (met1, cmt3 and met1 cmt3), remain within chromocenters of the mutant nuclei.
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Affiliation(s)
- Isabelle Vaillant
- Unité Mixte de Recherche CNRS 6547 BIOMOVE, Université Blaise Pascal, 24 Avenue des Landais, F-63177 Aubière Cedex, France
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10
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Vaillant I, Schubert I, Tourmente S, Mathieu O. MOM1 mediates DNA-methylation-independent silencing of repetitive sequences in Arabidopsis. EMBO Rep 2006; 7:1273-8. [PMID: 17082821 PMCID: PMC1794702 DOI: 10.1038/sj.embor.7400791] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2006] [Revised: 07/13/2006] [Accepted: 07/21/2006] [Indexed: 12/21/2022] Open
Abstract
The heterochromatic regions around centromeres of animal and plant chromosomes are composed of tandem repetitive sequences, interspersed with transposons and transposon derivatives. These sequences are largely transcriptionally silent and highly methylated, and are associated with specifically modified histones. Although embedded in heterochromatin, Arabidopsis 5S ribosomal RNA genes are among the most highly transcribed genes. However, some 5S genes are silenced, and we show here that this silencing can be suppressed by a reduction in CG methylation. Importantly, we show that mutation of MORPHEUS' MOLECULE 1 (MOM1) releases 5S repeat silencing independently of chromatin properties, as illustrated by the absence of detectable alteration of DNA and histone H3 methylation patterns. MOM1 also prevents transcription of 180-bp satellite repeats and 106B dispersed repeats but not of transposons. Our results provide evidence that transcription of densely methylated and highly repetitive heterochromatic sequences is controlled by two distinct epigenetic silencing pathways, one dependent on and the other independent of DNA methylation.
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Affiliation(s)
- Isabelle Vaillant
- UMR CNRS 6547, BIOMOVE, Université Blaise Pascal, 24 Avenue des Landais, 63177 Aubière Cedex, France
| | - Ingo Schubert
- Department of Cytogenetics, Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Gatersleben, Germany
| | - Sylvette Tourmente
- UMR CNRS 6547, BIOMOVE, Université Blaise Pascal, 24 Avenue des Landais, 63177 Aubière Cedex, France
| | - Olivier Mathieu
- UMR CNRS 6547, BIOMOVE, Université Blaise Pascal, 24 Avenue des Landais, 63177 Aubière Cedex, France
- Tel: +33 4 73 40 77 31; Fax: +33 4 73 40 77 77; E-mail:
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Mathieu O, Jasencakova Z, Vaillant I, Gendrel AV, Colot V, Schubert I, Tourmente S. Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis. Plant Cell 2003; 15:2929-39. [PMID: 14630972 PMCID: PMC282831 DOI: 10.1105/tpc.017467] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Accepted: 09/26/2003] [Indexed: 05/20/2023]
Abstract
In the Arabidopsis accession Columbia, 5S rDNA is located in the pericentromeric heterochromatin of chromosomes 3, 4, and 5. Both a major and some minor 5S rRNA species are expressed from chromosomes 4 and 5, whereas the genes on chromosome 3 are not transcribed. Here, we show that 5S rDNA methylation is reduced in 2-day-old seedlings versus 4-day-old or older aerial plant tissues, and the minor 5S rRNA species are expressed most abundantly at this stage. Similarly, when 5S rDNA is demethylated by 5-azacytidine treatment or via the decrease in DNA methylation1 (ddm1) mutation, the expression of minor 5S rRNA species is increased. We also show that in leaf nuclei of mature wild-type plants, the transcribed fraction of 5S rDNA forms loops that emanate from chromocenters. These loops, which are enlarged in nuclei of mature ddm1 plants, are enriched for histone H3 acetylated at Lys-9 and methylated at Lys-4 compared with the heterochromatic chromocenters. Up to 4 days after germination, heterochromatin is not fully developed: the 5S rDNA resides in prechromocenters, does not form conspicuous loops, and shows the lowest transcription level. Our results indicate that the expression and chromatin organization of 5S rRNA genes change during heterochromatin establishment.
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Affiliation(s)
- Olivier Mathieu
- Unité Mixte de Recherche Centre National de la Recherche Scientifique, 6547 BIOMOVE, Université Blaise Pascal, 63177 Aubière Cedex, France
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Mathieu O, Yukawa Y, Prieto JL, Vaillant I, Sugiura M, Tourmente S. Identification and characterization of transcription factor IIIA and ribosomal protein L5 from Arabidopsis thaliana. Nucleic Acids Res 2003; 31:2424-33. [PMID: 12711688 PMCID: PMC154221 DOI: 10.1093/nar/gkg335] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Thus far, no transcription factor IIIA (TFIIIA) from higher plants has been cloned and characterized. We have cloned and characterized TFIIIA and ribosomal protein L5 from Arabidopsis thaliana. Primary sequence comparison revealed a high divergence of AtTFIIIA and a relatively high conservation of AtL5 when compared with other organisms. The AtTFIIIA cDNA encodes a protein with nine Cys(2)-His(2)-type zinc fingers, a 23 amino acid spacer between fingers 1 and 2, a 66 amino acid spacer between fingers 4 and 5, and a 50 amino acid non-finger C-terminal tail. Aside from the amino acids required for proper zinc finger folding, AtTFIIIA is highly divergent from other known TFIIIAs. AtTFIIIA can bind 5S rDNA, as well as 5S rRNA, and efficiently stimulates the transcription of an Arabidopsis 5S rRNA gene in vitro. AtL5 identity was confirmed by demonstrating that this protein binds to 5S rRNA but not to 5S rDNA. Protoplast transient expression assays with green fluorescent protein fusion proteins revealed that AtTFIIIA is absent from the cytoplasm and concentrated at several nuclear foci including the nucleolus. AtL5 protein accumulates in the nucleus, especially in the nucleolus, and is also present in the cytoplasm.
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Affiliation(s)
- Olivier Mathieu
- UMR CNRS 6547 BIOMOVE, Université Blaise Pascal, 24 Avenue des Landais, 63177 Aubière Cedex, France
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