1
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Andjus S, Szachnowski U, Vogt N, Gioftsidi S, Hatin I, Cornu D, Papadopoulos C, Lopes A, Namy O, Wery M, Morillon A. Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast. RNA 2024:rna.079903.123. [PMID: 38443115 DOI: 10.1261/rna.079903.123] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
Despite being predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn1-sensitive lncRNAs (XUTs) are targeted by the Nonsense-Mediated mRNA Decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are pervasively translated, which impacts their decay. We show that XUTs globally accumulate upon translation elongation inhibition, but not when initial ribosome loading is impaired. Ribo-Seq confirmed ribosomes binding to XUTs and identified actively translated 5'-proximal small ORFs. Mechanistically, the NMD-sensitivity of XUTs mainly depends on the 3'-untranslated region length. Finally, we show that the peptide resulting from the translation of an NMD-sensitive XUT reporter exists in NMD-competent cells. Our work highlights the role of translation in the post-transcriptional metabolism of XUTs. We propose that XUT-derived peptides could be exposed to the natural selection, while NMD restricts XUTs levels.
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Affiliation(s)
- Sara Andjus
- Institut Curie, PSL University, Sorbonne University
| | | | | | | | - Isabelle Hatin
- Institute for Integrative Biology of the Cell, Paris-Saclay University
| | - David Cornu
- Institute for Integrative Biology of the Cell, Paris-Saclay University
| | | | - Anne Lopes
- Institute for Integrative Biology of the Cell, Paris-Saclay University
| | - Olivier Namy
- Institute for Integrative Biology of the Cell, Paris-Saclay University
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2
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Papoutsoglou P, Pineau R, Leroux R, Louis C, L'Haridon A, Foretek D, Morillon A, Banales JM, Gilot D, Aubry M, Coulouarn C. TGFβ-induced long non-coding RNA LINC00313 activates Wnt signaling and promotes cholangiocarcinoma. EMBO Rep 2024; 25:1022-1054. [PMID: 38332153 PMCID: PMC10933437 DOI: 10.1038/s44319-024-00075-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
Cholangiocarcinoma is a devastating liver cancer characterized by high aggressiveness and therapy resistance, resulting in poor prognosis. Long non-coding RNAs and signals imposed by oncogenic pathways, such as transforming growth factor β (TGFβ), frequently contribute to cholangiocarcinogenesis. Here, we explore novel effectors of TGFβ signalling in cholangiocarcinoma. LINC00313 is identified as a novel TGFβ target gene. Gene expression and genome-wide chromatin accessibility profiling reveal that nuclear LINC00313 transcriptionally regulates genes involved in Wnt signalling, such as the transcriptional activator TCF7. LINC00313 gain-of-function enhances TCF/LEF-dependent transcription, promotes colony formation in vitro and accelerates tumour growth in vivo. Genes affected by LINC00313 over-expression in CCA tumours are associated with KRAS and TP53 mutations and reduce overall patient survival. Mechanistically, ACTL6A and BRG1, subunits of the SWI/SNF chromatin remodelling complex, interact with LINC00313 and affect TCF7 and SULF2 transcription. We propose a model whereby TGFβ induces LINC00313 in order to regulate the expression of hallmark Wnt pathway genes, in co-operation with SWI/SNF. By modulating key genes of the Wnt pathway, LINC00313 fine-tunes Wnt/TCF/LEF-dependent transcriptional responses and promotes cholangiocarcinogenesis.
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Grants
- Recurrent Funding Institut National de la Santé et de la Recherche Médicale (Inserm)
- Recurrent Funding,PhD felloship Université de Rennes 1 (University of Rennes 1)
- PhD fellowship Conseil Régional de Bretagne (Brittany Council)
- R22026NN,R21011NN Ligue Contre le Cancer (French League Against Cancer)
- R21043NN Fondation ARC pour la Recherche sur le Cancer (ARC)
- C18007NS,C20013NS,C20014NS INCa and ITMO Cancer AVIESAN (Alliance Nationale pour les Sciences de la Vie et de la Santé) dans le cadre du Plan cancer (Non-coding RNA in cancerology: fundamental to translational)
- R21095NN French Ministry of Health and the French National Cancer Institute, PRT-K20-136, CHU Rennes, CLCC Eugene Marquis, Rennes
- FIS PI18/01075,PI21/00922,CPII19/00008 Spanish Carlos III Health Institute (ISCIII) [(FIS PI18/01075, PI21/00922, and Miguel Servet Programme CPII19/00008) cofinanced by "Fondo Europeo de Desarrollo Regional" (FEDER)] and CIBERehd (ISCIII)
- HR17-00601 'la Caixa' Foundation ('la Caixa')
- EU/2019/AMMFt/001 AMMF-The Cholangiocarcinoma Charity
- 06119JB PSC Partners US and PSC Supports UK
- 825510/ESCALON European Union Horizon 2020 Research and Innovation Program
- EU TRANSCAN23-002-2023-129,INCa_18688 Institut National Du Cancer (INCa)
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Affiliation(s)
- Panagiotis Papoutsoglou
- Inserm, Univ Rennes, OSS (Oncogenesis, Stress, Signaling) laboratory, UMR_S 1242, Centre de Lutte contre le Cancer Eugène Marquis, F-35042, Rennes, France
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Raphaël Pineau
- Inserm, Univ Rennes, OSS (Oncogenesis, Stress, Signaling) laboratory, UMR_S 1242, Centre de Lutte contre le Cancer Eugène Marquis, F-35042, Rennes, France
| | - Raffaële Leroux
- Inserm, Univ Rennes, OSS (Oncogenesis, Stress, Signaling) laboratory, UMR_S 1242, Centre de Lutte contre le Cancer Eugène Marquis, F-35042, Rennes, France
| | - Corentin Louis
- Inserm, Univ Rennes, OSS (Oncogenesis, Stress, Signaling) laboratory, UMR_S 1242, Centre de Lutte contre le Cancer Eugène Marquis, F-35042, Rennes, France
| | - Anaïs L'Haridon
- Inserm, Univ Rennes, OSS (Oncogenesis, Stress, Signaling) laboratory, UMR_S 1242, Centre de Lutte contre le Cancer Eugène Marquis, F-35042, Rennes, France
| | - Dominika Foretek
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biogipuzkoa Health Research Institute, Donostia University Hospital, CIBERehd, Ikerbasque, San Sebastian, Spain
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - David Gilot
- Inserm, Univ Rennes, OSS (Oncogenesis, Stress, Signaling) laboratory, UMR_S 1242, Centre de Lutte contre le Cancer Eugène Marquis, F-35042, Rennes, France
- Mechanistic & Structural Biology, Discovery Sciences, R&D, AstraZeneca, SE-48183, Mölndal, Sweden
| | - Marc Aubry
- Inserm, Univ Rennes, OSS (Oncogenesis, Stress, Signaling) laboratory, UMR_S 1242, Centre de Lutte contre le Cancer Eugène Marquis, F-35042, Rennes, France
| | - Cédric Coulouarn
- Inserm, Univ Rennes, OSS (Oncogenesis, Stress, Signaling) laboratory, UMR_S 1242, Centre de Lutte contre le Cancer Eugène Marquis, F-35042, Rennes, France.
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3
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Bhargava A, Szachnowski U, Chazal M, Foretek D, Caval V, Aicher SM, Pipoli da Fonseca J, Jeannin P, Beauclair G, Monot M, Morillon A, Jouvenet N. Transcriptomic analysis of sorted lung cells revealed a proviral activity of the NF-κB pathway toward SARS-CoV-2. iScience 2023; 26:108449. [PMID: 38213785 PMCID: PMC10783605 DOI: 10.1016/j.isci.2023.108449] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/30/2023] [Accepted: 11/10/2023] [Indexed: 01/13/2024] Open
Abstract
Investigations of cellular responses to viral infection are commonly performed on mixed populations of infected and uninfected cells or using single-cell RNA sequencing, leading to inaccurate and low-resolution gene expression interpretations. Here, we performed deep polyA+ transcriptome analyses and novel RNA profiling of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected lung epithelial cells, sorted based on the expression of the viral spike (S) protein. Infection caused a massive reduction in mRNAs and long non-coding RNAs (lncRNAs), including transcripts coding for antiviral factors, such as interferons (IFNs). This absence of IFN signaling probably explained the poor transcriptomic response of bystander cells co-cultured with S+ ones. NF-κB pathway and the inflammatory response escaped the global shutoff in S+ cells. Functional investigations revealed the proviral function of the NF-κB pathway and the antiviral activity of CYLD, a negative regulator of the pathway. Thus, our transcriptomic analysis on sorted cells revealed additional genes that modulate SARS-CoV-2 replication in lung cells.
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Affiliation(s)
- Anvita Bhargava
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Ugo Szachnowski
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Maxime Chazal
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Dominika Foretek
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Vincent Caval
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | - Sophie-Marie Aicher
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
| | | | - Patricia Jeannin
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité Épidémiologie et Physiopathologie des Virus Oncogènes, 75015 Paris, France
| | - Guillaume Beauclair
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91190 Gif-sur-Yvette, France
| | - Marc Monot
- Institut Pasteur, Université de Paris, Biomics Platform, C2RT, 75015 Paris, France
| | - Antonin Morillon
- CNRS UMR3244, Sorbonne University, PSL University, Institut Curie, Centre de Recherche, 75005 Paris, France
| | - Nolwenn Jouvenet
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Virus sensing and signaling Unit, 75015 Paris, France
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4
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Wery M, Szachnowski U, Andjus S, de Andres-Pablo A, Morillon A. The RNA helicases Dbp2 and Mtr4 regulate the expression of Xrn1-sensitive long non-coding RNAs in yeast. Front RNA Res 2023; 1:1244554. [PMID: 37667796 PMCID: PMC7615016 DOI: 10.3389/frnar.2023.1244554] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
The expression of yeast long non-coding (lnc)RNAs is restricted by RNA surveillance machineries, including the cytoplasmic 5'-3' exonuclease Xrn1 which targets a conserved family of lncRNAs defined as XUTs, and that are mainly antisense to protein-coding genes. However, the co-factors involved in the degradation of these transcripts and the underlying molecular mechanisms remain largely unknown. Here, we show that two RNA helicases, Dbp2 and Mtr4, act as global regulators of XUTs expression. Using RNA-Seq, we found that most of them accumulate upon Dbp2 inactivation or Mtr4 depletion. Mutants of the cytoplasmic RNA helicases Ecm32, Ski2, Slh1, Dbp1, and Dhh1 did not recapitulate this global stabilization of XUTs, suggesting that XUTs decay is specifically controlled by Dbp2 and Mtr4. Notably, Dbp2 and Mtr4 affect XUTs independently of their configuration relative to their paired-sense mRNAs. Finally, we show that the effect of Dbp2 on XUTs depends on a cytoplasmic localization. Overall, our data indicate that Dbp2 and Mtr4 are global regulators of lncRNAs expression and contribute to shape the non-coding transcriptome together with RNA decay machineries.
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Affiliation(s)
- Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
| | - Ugo Szachnowski
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
| | - Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL
University, Sorbonne Université, CNRS UMR3244, Paris Cedex, France
| | - Alvaro de Andres-Pablo
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne
Université, CNRS UMR3244, Paris Cedex, France
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5
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Yague-Sanz C, Migeot V, Larochelle M, Bachand F, Wéry M, Morillon A, Hermand D. Chromatin remodeling by Pol II primes efficient Pol III transcription. Nat Commun 2023; 14:3587. [PMID: 37328480 PMCID: PMC10276017 DOI: 10.1038/s41467-023-39387-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 12/16/2022] [Accepted: 06/09/2023] [Indexed: 06/18/2023] Open
Abstract
The packaging of the genetic material into chromatin imposes the remodeling of this barrier to allow efficient transcription. RNA polymerase II activity is coupled with several histone modification complexes that enforce remodeling. How RNA polymerase III (Pol III) counteracts the inhibitory effect of chromatin is unknown. We report here a mechanism where RNA Polymerase II (Pol II) transcription is required to prime and maintain nucleosome depletion at Pol III loci and contributes to efficient Pol III recruitment upon re-initiation of growth from stationary phase in Fission yeast. The Pcr1 transcription factor participates in the recruitment of Pol II, which affects local histone occupancy through the associated SAGA complex and a Pol II phospho-S2 CTD / Mst2 pathway. These data expand the central role of Pol II in gene expression beyond mRNA synthesis.
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Affiliation(s)
- Carlo Yague-Sanz
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur, 5000, Belgium
| | - Valérie Migeot
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur, 5000, Belgium
| | - Marc Larochelle
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - François Bachand
- RNA Group, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, QC, J1E 4K8, Canada
| | - Maxime Wéry
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL Research University, Université Pierre et Marie Curie, CNRS UMR 3244, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL Research University, Université Pierre et Marie Curie, CNRS UMR 3244, Paris, France
| | - Damien Hermand
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur, 5000, Belgium.
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6
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Almeida A, Gabriel M, Firlej V, Martin‐Jaular L, Lejars M, Cipolla R, Petit F, Vogt N, San‐Roman M, Dingli F, Loew D, Destouches D, Vacherot F, de la Taille A, Théry C, Morillon A. Urinary extracellular vesicles contain mature transcriptome enriched in circular and long noncoding RNAs with functional significance in prostate cancer. J Extracell Vesicles 2022; 11:e12210. [PMID: 35527349 PMCID: PMC9081490 DOI: 10.1002/jev2.12210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/22/2022] [Accepted: 03/15/2022] [Indexed: 12/14/2022] Open
Abstract
Long noncoding (lnc)RNAs modulate gene expression alongside presenting unexpected source of neoantigens. Despite their immense interest, their ability to be transferred and control adjacent cells is unknown. Extracellular Vesicles (EVs) offer a protective environment for nucleic acids, with pro and antitumourigenic functions by controlling the immune response. In contrast to extracellular nonvesicular RNA, few studies have addressed the full RNA content within human fluids' EVs and have compared them with their tissue of origin. Here, we performed Total RNA-Sequencing on six Formalin-Fixed-Paraffin-Embedded (FFPE) prostate cancer (PCa) tumour tissues and their paired urinary (u)EVs to provide the first whole transcriptome comparison from the same patients. UEVs contain simplified transcriptome with intron-free cytoplasmic transcripts and enriched lnc/circular (circ)RNAs, strikingly common to an independent 20 patients' urinary cohort. Our full cellular and EVs transcriptome comparison within three PCa cell lines identified a set of overlapping 14 uEV-circRNAs characterized as essential for prostate cell proliferation in vitro and 28 uEV-lncRNAs belonging to the cancer-related lncRNA census (CLC2). In addition, we found 15 uEV-lncRNAs, predicted to encode 768 high-affinity neoantigens, and for which three of the encoded-ORF produced detectable unmodified peptides by mass spectrometry. Our dual analysis of EVs-lnc/circRNAs both in urines' and in vitro's EVs provides a fundamental resource for future uEV-lnc/circRNAs phenotypic characterization involved in PCa.
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Affiliation(s)
- Anna Almeida
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Departement de Recherche TranslationnellePSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Marc Gabriel
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Virginie Firlej
- AP‐HPHôpital H. MondorPlateforme de Ressources BiologiquesCréteilFrance
- Univ Paris Est CreteilUR TRePCaCréteilFrance
| | - Lorena Martin‐Jaular
- INSERM U932PSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Curie Core Tech Extracellular VesiclesInstitut Curie, Centre de RechercheParisFrance
| | - Matthieu Lejars
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Rocco Cipolla
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Floriane Petit
- Tumour BiologyINSERM U820, Sorbonne Université, PSL University, Institut CurieCentre de RechercheParisFrance
| | - Nicolas Vogt
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
| | - Mabel San‐Roman
- CNRS UMR3215, Sorbonne Université, PSL University, Institut CurieCentre de RechercheParisFrance
| | - Florent Dingli
- Laboratoire de Spectrométrie de Masse ProtéomiquePSL Research University, Institut Curie Centre de RechercheParisFrance
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse ProtéomiquePSL Research University, Institut Curie Centre de RechercheParisFrance
| | | | | | | | - Clotilde Théry
- INSERM U932PSL UniversityInstitut Curie, Centre de RechercheParisFrance
- Curie Core Tech Extracellular VesiclesInstitut Curie, Centre de RechercheParisFrance
| | - Antonin Morillon
- CNRS UMR3244Sorbonne UniversityPSL UniversityInstitut Curie, Centre de RechercheParisFrance
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7
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Finet O, Yague-Sanz C, Krüger LK, Tran P, Migeot V, Louski M, Nevers A, Rougemaille M, Sun J, Ernst FG, Wacheul L, Wery M, Morillon A, Dedon P, Lafontaine DL, Hermand D. Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation. Mol Cell 2022; 82:404-419.e9. [PMID: 34798057 PMCID: PMC8792297 DOI: 10.1016/j.molcel.2021.11.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/22/2023]
Abstract
The epitranscriptome has emerged as a new fundamental layer of control of gene expression. Nevertheless, the determination of the transcriptome-wide occupancy and function of RNA modifications remains challenging. Here we have developed Rho-seq, an integrated pipeline detecting a range of modifications through differential modification-dependent rhodamine labeling. Using Rho-seq, we confirm that the reduction of uridine to dihydrouridine (D) by the Dus reductase enzymes targets tRNAs in E. coli and fission yeast. We find that the D modification is also present on fission yeast mRNAs, particularly those encoding cytoskeleton-related proteins, which is supported by large-scale proteome analyses and ribosome profiling. We show that the α-tubulin encoding mRNA nda2 undergoes Dus3-dependent dihydrouridylation, which affects its translation. The absence of the modification on nda2 mRNA strongly impacts meiotic chromosome segregation, resulting in low gamete viability. Applying Rho-seq to human cells revealed that tubulin mRNA dihydrouridylation is evolutionarily conserved.
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Affiliation(s)
- Olivier Finet
- URPHYM-GEMO, The University of Namur, Namur 5000, Belgium,These authors contributed equally
| | - Carlo Yague-Sanz
- URPHYM-GEMO, The University of Namur, Namur 5000, Belgium,These authors contributed equally
| | | | - Phong Tran
- Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France
| | - Valérie Migeot
- URPHYM-GEMO, The University of Namur, Namur 5000, Belgium
| | - Max Louski
- URPHYM-GEMO, The University of Namur, Namur 5000, Belgium
| | - Alicia Nevers
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France,Present address: University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - Mathieu Rougemaille
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Jingjing Sun
- Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Felix G.M. Ernst
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles, Charleroi-Gosselies, Belgium
| | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles, Charleroi-Gosselies, Belgium
| | - Maxime Wery
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, Paris, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, Paris, France
| | - Peter Dedon
- Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
| | - Denis L.J. Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles, Charleroi-Gosselies, Belgium
| | - Damien Hermand
- URPHYM-GEMO, The University of Namur, Namur 5000, Belgium,Lead contact,Correspondence:
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8
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Andjus S, Morillon A, Wery M. From Yeast to Mammals, the Nonsense-Mediated mRNA Decay as a Master Regulator of Long Non-Coding RNAs Functional Trajectory. Noncoding RNA 2021; 7:ncrna7030044. [PMID: 34449682 PMCID: PMC8395947 DOI: 10.3390/ncrna7030044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 12/22/2022] Open
Abstract
The Nonsense-Mediated mRNA Decay (NMD) has been classically viewed as a translation-dependent RNA surveillance pathway degrading aberrant mRNAs containing premature stop codons. However, it is now clear that mRNA quality control represents only one face of the multiple functions of NMD. Indeed, NMD also regulates the physiological expression of normal mRNAs, and more surprisingly, of long non-coding (lnc)RNAs. Here, we review the different mechanisms of NMD activation in yeast and mammals, and we discuss the molecular bases of the NMD sensitivity of lncRNAs, considering the functional roles of NMD and of translation in the metabolism of these transcripts. In this regard, we describe several examples of functional micropeptides produced from lncRNAs. We propose that translation and NMD provide potent means to regulate the expression of lncRNAs, which might be critical for the cell to respond to environmental changes.
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Affiliation(s)
- Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL University, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France;
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France
- Correspondence: (A.M.); (M.W.)
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR3244, 26 Rue d’Ulm, CEDEX 05, F-75248 Paris, France
- Correspondence: (A.M.); (M.W.)
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9
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Prudent V, Demarre G, Vazeille E, Wery M, Quenech'Du N, Ravet A, Dauverd-Girault J, van Dijk E, Bringer MA, Descrimes M, Barnich N, Rimsky S, Morillon A, Espéli O. The Crohn's disease-related bacterial strain LF82 assembles biofilm-like communities to protect itself from phagolysosomal attack. Commun Biol 2021; 4:627. [PMID: 34035436 PMCID: PMC8149705 DOI: 10.1038/s42003-021-02161-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
Patients with Crohn's disease exhibit abnormal colonization of the intestine by adherent invasive E. coli (AIEC). They adhere to epithelial cells, colonize them and survive inside macrophages. It appeared recently that AIEC LF82 adaptation to phagolysosomal stress involves a long lag phase in which many LF82 cells become antibiotic tolerant. Later during infection, they proliferate in vacuoles and form colonies harboring dozens of LF82 bacteria. In the present work, we investigated the mechanism sustaining this phase of growth. We found that intracellular LF82 produced an extrabacterial matrix that acts as a biofilm and controls the formation of LF82 intracellular bacterial communities (IBCs) for several days post infection. We revealed the crucial role played by the pathogenicity island encoding the yersiniabactin iron capture system to form IBCs and for optimal LF82 survival. These results illustrate that AIECs use original strategies to establish their replicative niche within macrophages.
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Affiliation(s)
- Victoria Prudent
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Gaëlle Demarre
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Emilie Vazeille
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Nicole Quenech'Du
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Antinéa Ravet
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Julie Dauverd-Girault
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Erwin van Dijk
- Next-Generation Sequencing Service - I2BC, I2BC-CNRS, Gif-sur-Yvette, France
| | - Marie-Agnès Bringer
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Marc Descrimes
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Nicolas Barnich
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
| | - Sylvie Rimsky
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Olivier Espéli
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France.
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10
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Jarroux J, Foretek D, Bertrand C, Gabriel M, Szachnowski U, Saci Z, Guo S, Londoño-Vallejo A, Pinskaya M, Morillon A. HOTAIR lncRNA promotes epithelial-mesenchymal transition by redistributing LSD1 at regulatory chromatin regions. EMBO Rep 2021; 22:e50193. [PMID: 33960111 PMCID: PMC8366456 DOI: 10.15252/embr.202050193] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/02/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
Epithelial‐to‐mesenchymal transition (EMT) describes the loss of epithelial traits and gain of mesenchymal traits by normal cells during development and by neoplastic cells during cancer metastasis. The long noncoding RNA HOTAIR triggers EMT, in part by serving as a scaffold for PRC2 and thus promoting repressive histone H3K27 methylation. In addition to PRC2, HOTAIR interacts with the LSD1 lysine demethylase, an epigenetic regulator of cell fate during development and differentiation, but little is known about the role of LSD1 in HOTAIR function during EMT. Here, we show that HOTAIR requires its LSD1‐interacting domain, but not its PRC2‐interacting domain, to promote the migration of epithelial cells. This activity is suppressed by LSD1 overexpression. LSD1‐HOTAIR interactions induce partial reprogramming of the epithelial transcriptome altering LSD1 distribution at promoter and enhancer regions. Thus, we uncover an unexpected role of HOTAIR in EMT as an LSD1 decommissioning factor, counteracting its activity in the control of epithelial identity.
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Affiliation(s)
- Julien Jarroux
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Dominika Foretek
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Claire Bertrand
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Marc Gabriel
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Ugo Szachnowski
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Zohra Saci
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Shuling Guo
- Ionis Pharmaceuticals, Inc, Carlsbad, CA, USA
| | - Arturo Londoño-Vallejo
- Telomeres and Cancer, CNRS UMR3244, Sorbonne Université, PSL Université, Institut Curie, Centre de Recherche, Paris, France
| | - Marina Pinskaya
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
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11
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Forey R, Barthe A, Tittel-Elmer M, Wery M, Barrault MB, Ducrot C, Seeber A, Krietenstein N, Szachnowski U, Skrzypczak M, Ginalski K, Rowicka M, Cobb JA, Rando OJ, Soutourina J, Werner M, Dubrana K, Gasser SM, Morillon A, Pasero P, Lengronne A, Poli J. A Role for the Mre11-Rad50-Xrs2 Complex in Gene Expression and Chromosome Organization. Mol Cell 2020; 81:183-197.e6. [PMID: 33278361 DOI: 10.1016/j.molcel.2020.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/09/2023]
Abstract
Mre11-Rad50-Xrs2 (MRX) is a highly conserved complex with key roles in various aspects of DNA repair. Here, we report a new function for MRX in limiting transcription in budding yeast. We show that MRX interacts physically and colocalizes on chromatin with the transcriptional co-regulator Mediator. MRX restricts transcription of coding and noncoding DNA by a mechanism that does not require the nuclease activity of Mre11. MRX is required to tether transcriptionally active loci to the nuclear pore complex (NPC), and it also promotes large-scale gene-NPC interactions. Moreover, MRX-mediated chromatin anchoring to the NPC contributes to chromosome folding and helps to control gene expression. Together, these findings indicate that MRX has a role in transcription and chromosome organization that is distinct from its known function in DNA repair.
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Affiliation(s)
- Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France
| | - Mireille Tittel-Elmer
- Departments of Biochemistry and Molecular Biology and Oncology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Maxime Wery
- Institut Curie, PSL Research University, CNRS UMR 3244, ncRNA, Epigenetic and Genome Fluidity, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Marie-Bénédicte Barrault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Cécile Ducrot
- Institute of Molecular and Cellular Radiobiology, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA)/Direction de la Recherche Fondamentale (DRF), 92260 Fontenay-aux-Roses Cedex, France
| | - Andrew Seeber
- Center for Advanced Imaging, Harvard University, Cambridge, MA 02138, USA; University of Basel and Friedrich Miescher Institute for Biomedical Research, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Nils Krietenstein
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ugo Szachnowski
- Institut Curie, PSL Research University, CNRS UMR 3244, ncRNA, Epigenetic and Genome Fluidity, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Maga Rowicka
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA
| | - Jennifer A Cobb
- Departments of Biochemistry and Molecular Biology and Oncology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Michel Werner
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France
| | - Karine Dubrana
- Institute of Molecular and Cellular Radiobiology, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA)/Direction de la Recherche Fondamentale (DRF), 92260 Fontenay-aux-Roses Cedex, France
| | - Susan M Gasser
- University of Basel and Friedrich Miescher Institute for Biomedical Research, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Antonin Morillon
- Institut Curie, PSL Research University, CNRS UMR 3244, ncRNA, Epigenetic and Genome Fluidity, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris, France
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France.
| | - Jérôme Poli
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Equipe Labéllisée Ligue contre le Cancer, 34396 Montpellier, France; University of Basel and Friedrich Miescher Institute for Biomedical Research, Faculty of Natural Sciences, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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12
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Cassart C, Yague-Sanz C, Bauer F, Ponsard P, Stubbe FX, Migeot V, Wery M, Morillon A, Palladino F, Robert V, Hermand D. RNA polymerase II CTD S2P is dispensable for embryogenesis but mediates exit from developmental diapause in C. elegans. Sci Adv 2020; 6:6/50/eabc1450. [PMID: 33298437 PMCID: PMC7725455 DOI: 10.1126/sciadv.abc1450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/21/2020] [Indexed: 06/12/2023]
Abstract
Serine 2 phosphorylation (S2P) within the CTD of RNA polymerase II is considered a Cdk9/Cdk12-dependent mark required for 3'-end processing. However, the relevance of CTD S2P in metazoan development is unknown. We show that cdk-12 lesions or a full-length CTD S2A substitution results in an identical phenotype in Caenorhabditis elegans Embryogenesis occurs in the complete absence of S2P, but the hatched larvae arrest development, mimicking the diapause induced when hatching occurs in the absence of food. Genome-wide analyses indicate that when CTD S2P is inhibited, only a subset of growth-related genes is not properly expressed. These genes correspond to SL2 trans-spliced mRNAs located in position 2 and over within operons. We show that CDK-12 is required for maximal occupancy of cleavage stimulatory factor necessary for SL2 trans-splicing. We propose that CTD S2P functions as a gene-specific signaling mark ensuring the nutritional control of the C. elegans developmental program.
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Affiliation(s)
- C Cassart
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - C Yague-Sanz
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - F Bauer
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - P Ponsard
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - F X Stubbe
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - V Migeot
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium
| | - M Wery
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, Paris, France
| | - A Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, Paris, France
| | - F Palladino
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - V Robert
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - D Hermand
- URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium.
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13
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Yu YCY, Hui TZ, Kao TH, Liao HF, Yang CY, Hou CC, Hsieh HT, Chang JY, Tsai YT, Pinskaya M, Yang KC, Chen YR, Morillon A, Tsai MH, Lin SP. Transient DNMT3L Expression Reinforces Chromatin Surveillance to Halt Senescence Progression in Mouse Embryonic Fibroblast. Front Cell Dev Biol 2020; 8:103. [PMID: 32195249 PMCID: PMC7064442 DOI: 10.3389/fcell.2020.00103] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 11/09/2019] [Accepted: 02/07/2020] [Indexed: 01/10/2023] Open
Abstract
Global heterochromatin reduction, which is one of the hallmarks of senescent cells, is associated with reduced transposable element repression and increased risk of chromatin instability. To ensure genomic integrity, the irreparable cells in a population exit permanently from the cell cycle, and this process is termed "senescence." However, senescence only blocks the expansion of unwanted cells, and the aberrant chromatin of senescent cells remains unstable. Serendipitously, we found that the transient ectopic expression of a repressive epigenetic modulator, DNA methyltransferase 3-like (DNMT3L) was sufficient to delay the premature senescence progression of late-passage mouse embryonic fibroblasts (MEFs) associated with a tightened global chromatin structure. DNMT3L induces more repressive H3K9 methylation on endogenous retroviruses and downregulates the derepressed transposons in aging MEFs. In addition, we found that a pulse of ectopic DNMT3L resulted in the reestablishment of H3K27me3 on polycomb repressive complex 2 (PRC2)-target genes that were derepressed in old MEFs. We demonstrated that ectopic DNMT3L interacted with PRC2 in MEFs. Our data also suggested that ectopic DNMT3L might guide PRC2 to redress deregulated chromatin regions in cells undergoing senescence. This study might lead to an epigenetic reinforcement strategy for overcoming aging-associated epimutation and senescence.
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Affiliation(s)
- Yoyo Chih-Yun Yu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Tony Zk Hui
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Tzu-Hao Kao
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Hung-Fu Liao
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Chih-Yi Yang
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Chia-Chun Hou
- Center for Systems Biology, National Taiwan University, Taipei, Taiwan
| | - Hsin-Ting Hsieh
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Jen-Yun Chang
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Yi-Tzang Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Marina Pinskaya
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Kai-Chien Yang
- Graduate Institute and Department of Pharmacology, National Taiwan University School of Medicine, Taipei, Taiwan
| | - Yet-Ran Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, Paris, France
| | - Mong-Hsun Tsai
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Shau-Ping Lin
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.,Center for Systems Biology, National Taiwan University, Taipei, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.,Research Center for Developmental Biology and Regenerative Medicine, Taipei, Taiwan
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14
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Abstract
The subtelomeres, highly heterogeneous repeated sequences neighboring telomeres, are transcribed into coding and noncoding RNAs in a variety of organisms. Telomereproximal subtelomeric regions produce non-coding transcripts i.e., ARRET, αARRET, subTERRA, and TERRA, which function in telomere maintenance. The role and molecular mechanisms of the majority of subtelomeric transcripts remain unknown. This review depicts the current knowledge and puts into perspective the results obtained in different models from yeasts to humans.
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Affiliation(s)
- Marta Kwapisz
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248, Paris, France.
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15
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Courel M, Clément Y, Bossevain C, Foretek D, Vidal Cruchez O, Yi Z, Bénard M, Benassy MN, Kress M, Vindry C, Ernoult-Lange M, Antoniewski C, Morillon A, Brest P, Hubstenberger A, Roest Crollius H, Standart N, Weil D. GC content shapes mRNA storage and decay in human cells. eLife 2019; 8:49708. [PMID: 31855182 PMCID: PMC6944446 DOI: 10.7554/elife.49708] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [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: 06/26/2019] [Accepted: 12/18/2019] [Indexed: 02/07/2023] Open
Abstract
mRNA translation and decay appear often intimately linked although the rules of this interplay are poorly understood. In this study, we combined our recent P-body transcriptome with transcriptomes obtained following silencing of broadly acting mRNA decay and repression factors, and with available CLIP and related data. This revealed the central role of GC content in mRNA fate, in terms of P-body localization, mRNA translation and mRNA stability: P-bodies contain mostly AU-rich mRNAs, which have a particular codon usage associated with a low protein yield; AU-rich and GC-rich transcripts tend to follow distinct decay pathways; and the targets of sequence-specific RBPs and miRNAs are also biased in terms of GC content. Altogether, these results suggest an integrated view of post-transcriptional control in human cells where most translation regulation is dedicated to inefficiently translated AU-rich mRNAs, whereas control at the level of 5’ decay applies to optimally translated GC-rich mRNAs.
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Affiliation(s)
- Maïté Courel
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, Paris, France
| | - Yves Clément
- Ecole Normale Supérieure, Institut de Biologie de l'ENS, IBENS, Paris, France
| | - Clémentine Bossevain
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, Paris, France
| | - Dominika Foretek
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Sorbonne Université, Paris, France
| | | | - Zhou Yi
- Université Côte d'Azur, CNRS, INSERM, iBV, Nice, France
| | - Marianne Bénard
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, Paris, France
| | - Marie-Noëlle Benassy
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, Paris, France
| | - Michel Kress
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, Paris, France
| | - Caroline Vindry
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michèle Ernoult-Lange
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, Paris, France
| | - Christophe Antoniewski
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), ARTbio Bioinformatics Analysis Facility, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Sorbonne Université, Paris, France
| | - Patrick Brest
- Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU-OncoAge, Nice, France
| | | | | | - Nancy Standart
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Dominique Weil
- Sorbonne Université, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire de Biologie du Développement, Paris, France
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16
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Pinskaya M, Saci Z, Gallopin M, Gabriel M, Nguyen HT, Firlej V, Descrimes M, Rapinat A, Gentien D, Taille ADL, Londoño-Vallejo A, Allory Y, Gautheret D, Morillon A. Reference-free transcriptome exploration reveals novel RNAs for prostate cancer diagnosis. Life Sci Alliance 2019; 2:2/6/e201900449. [PMID: 31732695 PMCID: PMC6858606 DOI: 10.26508/lsa.201900449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 06/04/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 12/24/2022] Open
Abstract
The use of RNA-sequencing technologies held a promise of improved diagnostic tools based on comprehensive transcript sets. However, mining human transcriptome data for disease biomarkers in clinical specimens are restricted by the limited power of conventional reference-based protocols relying on unique and annotated transcripts. Here, we implemented a blind reference-free computational protocol, DE-kupl, to infer yet unreferenced RNA variations from total stranded RNA-sequencing datasets of tissue origin. As a bench test, this protocol was powered for detection of RNA subsequences embedded into putative long noncoding (lnc)RNAs expressed in prostate cancer. Through filtering of 1,179 candidates, we defined 21 lncRNAs that were further validated by NanoString for robust tumor-specific expression in 144 tissue specimens. Predictive modeling yielded a restricted probe panel enabling more than 90% of true-positive detections of cancer in an independent The Cancer Genome Atlas cohort. Remarkably, this clinical signature made of only nine unannotated lncRNAs largely outperformed PCA3, the only used prostate cancer lncRNA biomarker, in detection of high-risk tumors. This modular workflow is highly sensitive and can be applied to any pathology or clinical application.
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Affiliation(s)
- Marina Pinskaya
- ncRNA, Epigenetic and Genome Fluidity, Université Paris Sciences & Lettres (PSL), Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut Curie, Research Center, Paris, France
| | - Zohra Saci
- ncRNA, Epigenetic and Genome Fluidity, Université Paris Sciences & Lettres (PSL), Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut Curie, Research Center, Paris, France
| | - Mélina Gallopin
- Institute for Integrative Biology of the Cell, Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette, France
| | - Marc Gabriel
- ncRNA, Epigenetic and Genome Fluidity, Université Paris Sciences & Lettres (PSL), Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut Curie, Research Center, Paris, France
| | - Ha Tn Nguyen
- Institute for Integrative Biology of the Cell, Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette, France.,Thuyloi University, Hanoi, Vietnam
| | - Virginie Firlej
- Université Paris-Est Créteil, Créteil, France.,Institut National de la Santé et de la Recherche Médicale, U955, Equipe 7, Créteil, France
| | - Marc Descrimes
- ncRNA, Epigenetic and Genome Fluidity, Université Paris Sciences & Lettres (PSL), Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut Curie, Research Center, Paris, France
| | - Audrey Rapinat
- Translational Research Department, Genomics Platform, Institut Curie, Université PSL, Paris, France
| | - David Gentien
- Translational Research Department, Genomics Platform, Institut Curie, Université PSL, Paris, France
| | - Alexandre de la Taille
- Université Paris-Est Créteil, Créteil, France.,Institut National de la Santé et de la Recherche Médicale, U955, Equipe 7, Créteil, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Henri Mondor, Département d'Urologie, Créteil, France
| | - Arturo Londoño-Vallejo
- Telomeres and Cancer, Université PSL, Sorbonne Université, CNRS, Institut Curie, Research Center, Paris, France
| | - Yves Allory
- Compartimentation et Dynamique Cellulaire, Université PSL, Sorbonne Université, CNRS, Institut Curie, Research Center, Paris, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, Commissariat à l'Energie Atomique, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif sur Yvette, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Université Paris Sciences & Lettres (PSL), Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut Curie, Research Center, Paris, France
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17
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Szachnowski U, Andjus S, Foretek D, Morillon A, Wery M. Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome. Life Sci Alliance 2019; 2:2/5/e201900407. [PMID: 31462400 PMCID: PMC6713810 DOI: 10.26508/lsa.201900407] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 04/26/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 12/19/2022] Open
Abstract
A genome-wide comparative analysis of “cryptic” aslncRNAs decay in RNAi-capable and RNAi-deficient budding yeasts suggests an evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome. Antisense long noncoding (aslnc)RNAs are extensively degraded by the nuclear exosome and the cytoplasmic exoribonuclease Xrn1 in the budding yeast Saccharomyces cerevisiae, lacking RNAi. Whether the ribonuclease III Dicer affects aslncRNAs in close RNAi-capable relatives remains unknown. Using genome-wide RNA profiling, here we show that aslncRNAs are primarily targeted by the exosome and Xrn1 in the RNAi-capable budding yeast Naumovozyma castellii, Dicer only affecting Xrn1-sensitive aslncRNAs levels in Xrn1-deficient cells. The dcr1 and xrn1 mutants display synergic growth defects, indicating that Dicer becomes critical in the absence of Xrn1. Small RNA sequencing showed that Dicer processes aslncRNAs into small RNAs, with a preference for Xrn1-sensitive aslncRNAs. Consistently, Dicer localizes into the cytoplasm. Finally, we observed an expansion of the exosome-sensitive antisense transcriptome in N. castellii compared with S. cerevisiae, suggesting that the presence of cytoplasmic RNAi has reinforced the nuclear RNA surveillance machinery to temper aslncRNAs expression. Our data provide fundamental insights into aslncRNAs metabolism and open perspectives into the possible evolutionary contribution of RNAi in shaping the aslncRNAs transcriptome.
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Affiliation(s)
- Ugo Szachnowski
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
| | - Sara Andjus
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
| | - Dominika Foretek
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne Université, CNRS UMR 3244, Paris, France
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18
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Abstract
Genetic, transcriptional, and post-transcriptional variations shape the transcriptome of individual cells, rendering establishing an exhaustive set of reference RNAs a complicated matter. Current reference transcriptomes, which are based on carefully curated transcripts, are lagging behind the extensive RNA variation revealed by massively parallel sequencing. Much may be missed by ignoring this unreferenced RNA diversity. There is plentiful evidence for non-reference transcripts with important phenotypic effects. Although reference transcriptomes are inestimable for gene expression analysis, they may turn limiting in important medical applications. We discuss computational strategies for retrieving hidden transcript diversity.
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Affiliation(s)
- Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, CNRS UMR 3244, Sorbonne Université, PSL University, Institut Curie, Centre de Recherche, 26 rue d'Ulm, 75248, Paris, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, Gif sur Yvette, France.
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19
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Xie B, Becker E, Stuparevic I, Wery M, Szachnowski U, Morillon A, Primig M. The anti-cancer drug 5-fluorouracil affects cell cycle regulators and potential regulatory long non-coding RNAs in yeast. RNA Biol 2019; 16:727-741. [PMID: 30760080 DOI: 10.1080/15476286.2019.1581596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
5-fluorouracil (5-FU) was isolated as an inhibitor of thymidylate synthase, which is important for DNA synthesis. The drug was later found to also affect the conserved 3'-5' exoribonuclease EXOSC10/Rrp6, a catalytic subunit of the RNA exosome that degrades and processes protein-coding and non-coding transcripts. Work on 5-FU's cytotoxicity has been focused on mRNAs and non-coding transcripts such as rRNAs, tRNAs and snoRNAs. However, the effect of 5-FU on long non-coding RNAs (lncRNAs), which include regulatory transcripts important for cell growth and differentiation, is poorly understood. RNA profiling of synchronized 5-FU treated yeast cells and protein assays reveal that the drug specifically inhibits a set of cell cycle regulated genes involved in mitotic division, by decreasing levels of the paralogous Swi5 and Ace2 transcriptional activators. We also observe widespread accumulation of different lncRNA types in treated cells, which are typically present at high levels in a strain lacking EXOSC10/Rrp6. 5-FU responsive lncRNAs include potential regulatory antisense transcripts that form double-stranded RNAs (dsRNAs) with overlapping sense mRNAs. Some of these transcripts encode proteins important for cell growth and division, such as the transcription factor Ace2, and the RNA exosome subunit EXOSC6/Mtr3. In addition to revealing a transcriptional effect of 5-FU action via DNA binding regulators involved in cell cycle progression, our results have implications for the function of putative regulatory lncRNAs in 5-FU mediated cytotoxicity. The data raise the intriguing possibility that the drug deregulates lncRNAs/dsRNAs involved in controlling eukaryotic cell division, thereby highlighting a new class of promising therapeutical targets.
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Affiliation(s)
- Bingning Xie
- a Univ Rennes , Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)- UMR_S 1085 , Rennes , France
| | - Emmanuelle Becker
- a Univ Rennes , Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)- UMR_S 1085 , Rennes , France.,b Univ Rennes , Inria, CNRS, IRISA F-35000 , Rennes , France
| | - Igor Stuparevic
- a Univ Rennes , Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)- UMR_S 1085 , Rennes , France
| | - Maxime Wery
- c ncRNA, Epigenetic and Genome Fluidity , Institut Curie, PSL UniversityCNRS UMR 3244, Université Pierre et Marie Curie , Paris , France
| | - Ugo Szachnowski
- c ncRNA, Epigenetic and Genome Fluidity , Institut Curie, PSL UniversityCNRS UMR 3244, Université Pierre et Marie Curie , Paris , France
| | - Antonin Morillon
- c ncRNA, Epigenetic and Genome Fluidity , Institut Curie, PSL UniversityCNRS UMR 3244, Université Pierre et Marie Curie , Paris , France
| | - Michael Primig
- a Univ Rennes , Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)- UMR_S 1085 , Rennes , France
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20
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Hocher A, Ruault M, Kaferle P, Descrimes M, Garnier M, Morillon A, Taddei A. Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions. Genome Res 2018; 28:1867-1881. [PMID: 30355601 PMCID: PMC6280759 DOI: 10.1101/gr.236554.118] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 03/06/2018] [Accepted: 10/20/2018] [Indexed: 01/20/2023]
Abstract
The eukaryotic genome is divided into chromosomal domains of heterochromatin and euchromatin. Transcriptionally silent heterochromatin is found at subtelomeric regions, leading to the telomeric position effect (TPE) in yeast, fly, and human. Heterochromatin generally initiates and spreads from defined loci, and diverse mechanisms prevent the ectopic spread of heterochromatin into euchromatin. Here, we overexpressed the silencing factor Sir3 at varying levels in yeast and found that Sir3 spreads into extended silent domains (ESDs), eventually reaching saturation at subtelomeres. We observed the spread of Sir3 into subtelomeric domains associated with specific histone marks in wild-type cells, and stopping at zones of histone mark transitions including H3K79 trimethylation levels. Our study shows that the conserved H3K79 methyltransferase Dot1 is essential in restricting Sir3 spread beyond ESDs, thus ensuring viability upon overexpression of Sir3. Last, our analyses of published data demonstrate how ESDs unveil uncharacterized discrete domains isolating structural and functional subtelomeric features from the rest of the genome. Our work offers a new approach on how to separate subtelomeres from the core chromosome.
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Affiliation(s)
- Antoine Hocher
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.,Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR3664, F-75005 Paris, France
| | - Myriam Ruault
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.,Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR3664, F-75005 Paris, France
| | - Petra Kaferle
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.,Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR3664, F-75005 Paris, France
| | - Marc Descrimes
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.,Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR3664, F-75005 Paris, France
| | - Mickaël Garnier
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.,Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR3664, F-75005 Paris, France
| | - Antonin Morillon
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.,Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR3664, F-75005 Paris, France
| | - Angela Taddei
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France.,Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR3664, F-75005 Paris, France
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21
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Watts BR, Wittmann S, Wery M, Gautier C, Kus K, Birot A, Heo DH, Kilchert C, Morillon A, Vasiljeva L. Histone deacetylation promotes transcriptional silencing at facultative heterochromatin. Nucleic Acids Res 2018; 46:5426-5440. [PMID: 29618061 PMCID: PMC6009587 DOI: 10.1093/nar/gky232] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 12/13/2017] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/25/2022] Open
Abstract
It is important to accurately regulate the expression of genes involved in development and environmental response. In the fission yeast Schizosaccharomyces pombe, meiotic genes are tightly repressed during vegetative growth. Despite being embedded in heterochromatin these genes are transcribed and believed to be repressed primarily at the level of RNA. However, the mechanism of facultative heterochromatin formation and the interplay with transcription regulation is not understood. We show genome-wide that HDAC-dependent histone deacetylation is a major determinant in transcriptional silencing of facultative heterochromatin domains. Indeed, mutation of class I/II HDACs leads to increased transcription of meiotic genes and accumulation of their mRNAs. Mechanistic dissection of the pho1 gene where, in response to phosphate, transient facultative heterochromatin is established by overlapping lncRNA transcription shows that the Clr3 HDAC contributes to silencing independently of SHREC, but in an lncRNA-dependent manner. We propose that HDACs promote facultative heterochromatin by establishing alternative transcriptional silencing.
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Affiliation(s)
- Beth R Watts
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Sina Wittmann
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Maxime Wery
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Camille Gautier
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Krzysztof Kus
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Adrien Birot
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Dong-Hyuk Heo
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Cornelia Kilchert
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Institut für Biochemie, Heinrich-Buff-Ring 17, 35392 Gießen, Germany
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Lidia Vasiljeva
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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22
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Chang KW, Tseng YT, Chen YC, Yu CY, Liao HF, Chen YC, Tu YFE, Wu SC, Liu IH, Pinskaya M, Morillon A, Pain B, Lin SP. Correction to: Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development. BMC Genomics 2018; 19:480. [PMID: 29921224 PMCID: PMC6006743 DOI: 10.1186/s12864-018-4863-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 11/19/2022] Open
Affiliation(s)
- Kai-Wei Chang
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.,Present Address: Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Yen-Tzu Tseng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Chen Chen
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan.,Univ Lyon, Université Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Chih-Yun Yu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Hung-Fu Liao
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Chun Chen
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Yu-Fan Evan Tu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Shinn-Chih Wu
- Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - I-Hsuan Liu
- Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Marina Pinskaya
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University, Université Pierre et Marie Curie, F-75005, Paris, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University, Université Pierre et Marie Curie, F-75005, Paris, France
| | - Bertrand Pain
- Univ Lyon, Université Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Shau-Ping Lin
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan. .,Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan. .,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 106, Taiwan. .,Agricultural Biotechnology Research Centre, Academia Sinica, Taipei, 106, Taiwan. .,Center for Systems Biology, National Taiwan University, Taipei, 106, Taiwan.
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23
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Santos-Rosa H, Schneider R, Bernstein BE, Karabetsou N, Morillon A, Weise C, Schreiber SL, Mellor J, Kouzarides T. Methylation of Histone H3 K4 Mediates Association of the Isw1p ATPase with Chromatin. Mol Cell 2018; 70:983. [PMID: 29883612 DOI: 10.1016/j.molcel.2018.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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24
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Chang KW, Tseng YT, Chen YC, Yu CY, Liao HF, Chen YC, Tu YFE, Wu SC, Liu IH, Pinskaya M, Morillon A, Pain B, Lin SP. Stage-dependent piRNAs in chicken implicated roles in modulating male germ cell development. BMC Genomics 2018; 19:425. [PMID: 29859049 PMCID: PMC5984780 DOI: 10.1186/s12864-018-4820-9] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023] Open
Abstract
Background The PIWI/piRNA pathway is a conserved machinery important for germ cell development and fertility. This piRNA-guided molecular machinery is best known for repressing derepressed transposable elements (TE) during epigenomic reprogramming. The extent to which piRNAs are involved in modulating transcripts beyond TEs still need to be clarified, and it may be a stage-dependent event. We chose chicken germline as a study model because of the significantly lower TE complexity in the chicken genome compared to mammalian species. Results We generated high-confidence piRNA candidates in various stages across chicken germline development by 3′-end-methylation-enriched small RNA sequencing and in-house bioinformatics analysis. We observed a significant developmental stage-dependent loss of TE association and a shifting of the ping-pong cycle signatures. Moreover, the stage-dependent reciprocal abundance of LINE retrotransposons, CR1-C, and its associated piRNAs implicated the developmental stage-dependent role of piRNA machinery. The stage dependency of piRNA expression and its potential functions can be better addressed by analyzing the piRNA precursors/clusters. Interestingly, the new piRNA clusters identified from embryonic chicken testes revealed evolutionary conservation between chickens and mammals, which was previously thought to not exist. Conclusions In this report, we provided an original chicken RNA resource and proposed an analytical methodology that can be used to investigate stage-dependent changes in piRNA compositions and their potential roles in TE regulation and beyond, and also revealed possible conserved functions of piRNAs in developing germ cells. Electronic supplementary material The online version of this article (10.1186/s12864-018-4820-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kai-Wei Chang
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan.,Present Address: Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Yen-Tzu Tseng
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Chen Chen
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan.,Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan.,Univ Lyon, Université Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Chih-Yun Yu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Hung-Fu Liao
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Yi-Chun Chen
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Yu-Fan Evan Tu
- Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan
| | - Shinn-Chih Wu
- Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - I-Hsuan Liu
- Department of Animal Science and Technology, National Taiwan University, Taipei, 106, Taiwan
| | - Marina Pinskaya
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University, Université Pierre et Marie Curie, F-75005, Paris, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University, Université Pierre et Marie Curie, F-75005, Paris, France
| | - Bertrand Pain
- Univ Lyon, Université Lyon 1, INSERM, INRA, Stem Cell and Brain Research Institute, U1208, USC1361, F-69500, Bron, France
| | - Shau-Ping Lin
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, 106, Taiwan. .,Institute of Biotechnology, National Taiwan University, Taipei, 106, Taiwan. .,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 106, Taiwan. .,Agricultural Biotechnology Research Centre, Academia Sinica, Taipei, 106, Taiwan. .,Center for Systems Biology, National Taiwan University, Taipei, 106, Taiwan.
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25
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Wery M, Gautier C, Descrimes M, Yoda M, Vennin-Rendos H, Migeot V, Gautheret D, Hermand D, Morillon A. Native elongating transcript sequencing reveals global anti-correlation between sense and antisense nascent transcription in fission yeast. RNA 2018; 24:196-208. [PMID: 29114019 PMCID: PMC5769747 DOI: 10.1261/rna.063446.117] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 08/10/2017] [Accepted: 11/03/2017] [Indexed: 05/07/2023]
Abstract
Antisense transcription can regulate sense gene expression. However, previous annotations of antisense transcription units have been based on detection of mature antisense long noncoding (aslnc)RNAs by RNA-seq and/or microarrays, only giving a partial view of the antisense transcription landscape and incomplete molecular bases for antisense-mediated regulation. Here, we used native elongating transcript sequencing to map genome-wide nascent antisense transcription in fission yeast. Strikingly, antisense transcription was detected for most protein-coding genes, correlating with low sense transcription, especially when overlapping the mRNA start site. RNA profiling revealed that the resulting aslncRNAs mainly correspond to cryptic Xrn1/Exo2-sensitive transcripts (XUTs). ChIP-seq analyses showed that antisense (as)XUT's expression is associated with specific histone modification patterns. Finally, we showed that asXUTs are controlled by the histone chaperone Spt6 and respond to meiosis induction, in both cases anti-correlating with levels of the paired-sense mRNAs, supporting physiological significance to antisense-mediated gene attenuation. Our work highlights that antisense transcription is much more extended than anticipated and might constitute an additional nonpromoter determinant of gene regulation complexity.
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Affiliation(s)
- Maxime Wery
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Camille Gautier
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Marc Descrimes
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Mayuko Yoda
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Hervé Vennin-Rendos
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
| | - Valérie Migeot
- URPHYM, Namur Research College (NARC), University of Namur, Namur 5000, Belgium
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, CNRS, CEA, Université Paris Sud, 91405, Orsay Cedex, France
| | - Damien Hermand
- URPHYM, Namur Research College (NARC), University of Namur, Namur 5000, Belgium
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, France
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26
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Alculumbre SG, Saint-André V, Di Domizio J, Vargas P, Sirven P, Bost P, Maurin M, Maiuri P, Wery M, Roman MS, Savey L, Touzot M, Terrier B, Saadoun D, Conrad C, Gilliet M, Morillon A, Soumelis V. Diversification of human plasmacytoid predendritic cells in response to a single stimulus. Nat Immunol 2017; 19:63-75. [PMID: 29203862 DOI: 10.1038/s41590-017-0012-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022]
Abstract
Innate immune cells adjust to microbial and inflammatory stimuli through a process termed environmental plasticity, which links a given individual stimulus to a unique activated state. Here, we report that activation of human plasmacytoid predendritic cells (pDCs) with a single microbial or cytokine stimulus triggers cell diversification into three stable subpopulations (P1-P3). P1-pDCs (PD-L1+CD80-) displayed a plasmacytoid morphology and specialization for type I interferon production. P3-pDCs (PD-L1-CD80+) adopted a dendritic morphology and adaptive immune functions. P2-pDCs (PD-L1+CD80+) displayed both innate and adaptive functions. Each subpopulation expressed a specific coding- and long-noncoding-RNA signature and was stable after secondary stimulation. P1-pDCs were detected in samples from patients with lupus or psoriasis. pDC diversification was independent of cell divisions or preexisting heterogeneity within steady-state pDCs but was controlled by a TNF autocrine and/or paracrine communication loop. Our findings reveal a novel mechanism for diversity and division of labor in innate immune cells.
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Affiliation(s)
- Solana G Alculumbre
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France.,INSERM U932, Immunity and Cancer, Paris, France
| | - Violaine Saint-André
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France.,CNRS UMR 3244, ncRNA, Epigenetic, and Genome Fluidity, Université Pierre et Marie Curie, Paris, France
| | - Jeremy Di Domizio
- Department of Dermatology, University Hospital CHUV, Lausanne, Switzerland
| | - Pablo Vargas
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France.,CNRS UMR144, Paris, France
| | - Philemon Sirven
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France.,INSERM U932, Immunity and Cancer, Paris, France
| | - Pierre Bost
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France.,INSERM U932, Immunity and Cancer, Paris, France.,Department of Biology, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Mathieu Maurin
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France.,INSERM U932, Immunity and Cancer, Paris, France
| | - Paolo Maiuri
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France.,IFOM Foundation, Institute FIRC of Molecular Oncology, Milan, Italy
| | - Maxime Wery
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France.,CNRS UMR 3244, ncRNA, Epigenetic, and Genome Fluidity, Université Pierre et Marie Curie, Paris, France
| | - Mabel San Roman
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France.,INSERM U932, Immunity and Cancer, Paris, France
| | - Léa Savey
- UMR7211 and Inflammation-Immunopathology-Biotherapy Departement (DHU i2B), Sorbonne Universités, UPMC Université de Paris, Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe Hospitalier Pitié Salpétrière, Department of Internal Medicine and Clinical Immunology, National Reference Center for Autoimmune and Systemic Diseases, Paris, France
| | | | - Benjamin Terrier
- Department of Internal Medicine, National Referral Center for Rare Autoimmune and Systemic Diseases, Cochin Hospital, AP-HP, Université Paris Descartes, Paris, France
| | - David Saadoun
- UMR7211 and Inflammation-Immunopathology-Biotherapy Departement (DHU i2B), Sorbonne Universités, UPMC Université de Paris, Paris, France.,Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe Hospitalier Pitié Salpétrière, Department of Internal Medicine and Clinical Immunology, National Reference Center for Autoimmune and Systemic Diseases, Paris, France
| | - Curdin Conrad
- Department of Dermatology, University Hospital CHUV, Lausanne, Switzerland
| | - Michel Gilliet
- Department of Dermatology, University Hospital CHUV, Lausanne, Switzerland
| | - Antonin Morillon
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France.,CNRS UMR 3244, ncRNA, Epigenetic, and Genome Fluidity, Université Pierre et Marie Curie, Paris, France
| | - Vassili Soumelis
- Institut Curie, Centre de Recherche, PSL Research University, Paris, France. .,INSERM U932, Immunity and Cancer, Paris, France. .,CIC IGR-Curie 1428, Paris, France.
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Abstract
The RNA World Hypothesis suggests that prebiotic life revolved around RNA instead of DNA and proteins. Although modern cells have changed significantly in 4 billion years, RNA has maintained its central role in cell biology. Since the discovery of DNA at the end of the nineteenth century, RNA has been extensively studied. Many discoveries such as housekeeping RNAs (rRNA, tRNA, etc.) supported the messenger RNA model that is the pillar of the central dogma of molecular biology, which was first devised in the late 1950s. Thirty years later, the first regulatory non-coding RNAs (ncRNAs) were initially identified in bacteria and then in most eukaryotic organisms. A few long ncRNAs (lncRNAs) such as H19 and Xist were characterized in the pre-genomic era but remained exceptions until the early 2000s. Indeed, when the sequence of the human genome was published in 2001, studies showed that only about 1.2% encodes proteins, the rest being deemed "non-coding." It was later shown that the genome is pervasively transcribed into many ncRNAs, but their functionality remained controversial. Since then, regulatory lncRNAs have been characterized in many species and were shown to be involved in processes such as development and pathologies, revealing a new layer of regulation in eukaryotic cells. This newly found focus on lncRNAs, together with the advent of high-throughput sequencing, was accompanied by the rapid discovery of many novel transcripts which were further characterized and classified according to specific transcript traits.In this review, we will discuss the many discoveries that led to the study of lncRNAs, from Friedrich Miescher's "nuclein" in 1869 to the elucidation of the human genome and transcriptome in the early 2000s. We will then focus on the biological relevance during lncRNA evolution and describe their basic features as genes and transcripts. Finally, we will present a non-exhaustive catalogue of lncRNA classes, thus illustrating the vast complexity of eukaryotic transcriptomes.
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Affiliation(s)
- Julien Jarroux
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France.
| | - Marina Pinskaya
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, PSL Research University and Université Pierre et Marie Curie, Paris, France
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28
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de Andres-Pablo A, Morillon A, Wery M. LncRNAs, lost in translation or licence to regulate? Curr Genet 2016; 63:29-33. [DOI: 10.1007/s00294-016-0615-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 11/28/2022]
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29
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Meseure D, Vacher S, Lallemand F, Alsibai KD, Hatem R, Chemlali W, Nicolas A, De Koning L, Pasmant E, Callens C, Lidereau R, Morillon A, Bieche I. Prognostic value of a newly identified MALAT1 alternatively spliced transcript in breast cancer. Br J Cancer 2016; 114:1395-404. [PMID: 27172249 PMCID: PMC4984455 DOI: 10.1038/bjc.2016.123] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [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: 11/20/2015] [Revised: 02/16/2016] [Accepted: 03/31/2016] [Indexed: 12/22/2022] Open
Abstract
Background: Epigenetic deregulation is considered as a new hallmark of cancer. The long non-coding RNA MALAT1 has been implicated in several cancers; however, its role in breast cancer is still little known. Methods: We used RT–PCR, in situ hybridisation, and RPPA methods to quantify (i) the full-length (FL) and an alternatively spliced variant (Δsv) of MALAT1, and (ii) a panel of transcripts and proteins involved in MALAT1 pathways, in a large series of breast tumours from patients with known clinical/pathological status and long-term outcome. Results: MALAT1 was overexpressed in 14% (63/446) of the breast tumours. MALAT1-overexpressed tumour epithelial cells showed marked diffuse nuclear signals and numerous huge nuclear speckles. Screening of the dbEST database led to the identification of Δsv-MALAT1, a major alternatively spliced MALAT1 transcript, with a very different expression pattern compared with FL-MALAT1. This alternative Δsv-MALAT1 transcript was mainly underexpressed (18.8%) in our breast tumour series. Multivariate analysis showed that alternative Δsv-MALAT1 transcript is an independent prognostic factor. Δsv-MALAT1 expression was associated with alterations of the pre-mRNAs alternative splicing machinery, and of the Drosha-DGCR8 complex required for non-coding RNA biogenesis. Alternative Δsv-MALAT1 transcript expression was associated to YAP protein status and with an activation of the PI3K-AKT pathway. Conclusions: Our results reveal a complex expression pattern of various MALAT1 transcript variants in breast tumours, and suggest that this pattern of expressions should be taken into account to evaluate MALAT1 as predictive biomarker and therapeutic target.
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Affiliation(s)
- Didier Meseure
- Department of Genetics, Unit of Pharmacogenetics, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France.,Department of Pathology, Platform of Investigative Pathology, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - Sophie Vacher
- Department of Genetics, Unit of Pharmacogenetics, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - François Lallemand
- Department of Genetics, Unit of Pharmacogenetics, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - Kinan Drak Alsibai
- Department of Pathology, Platform of Investigative Pathology, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - Rana Hatem
- Department of Genetics, Unit of Pharmacogenetics, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - Walid Chemlali
- Department of Genetics, Unit of Pharmacogenetics, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - Andre Nicolas
- Department of Pathology, Platform of Investigative Pathology, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - Leanne De Koning
- Department of Translational Research, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - Eric Pasmant
- EA7331, Faculty of Pharmaceutical and Biological Sciences, Paris Descartes University, Sorbonne Paris Cité, Paris Cedex F-75006, France
| | - Celine Callens
- Department of Genetics, Unit of Pharmacogenetics, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - Rosette Lidereau
- Department of Genetics, Unit of Pharmacogenetics, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - Antonin Morillon
- CNRS UMR 3244, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France
| | - Ivan Bieche
- Department of Genetics, Unit of Pharmacogenetics, Institut Curie, 26 rue d'Ulm, Paris Cedex F-75248, France.,EA7331, Faculty of Pharmaceutical and Biological Sciences, Paris Descartes University, Sorbonne Paris Cité, Paris Cedex F-75006, France
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30
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Wery M, Descrimes M, Vogt N, Dallongeville AS, Gautheret D, Morillon A. Nonsense-Mediated Decay Restricts LncRNA Levels in Yeast Unless Blocked by Double-Stranded RNA Structure. Mol Cell 2016; 61:379-392. [PMID: 26805575 PMCID: PMC4747904 DOI: 10.1016/j.molcel.2015.12.020] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [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: 06/12/2015] [Revised: 10/23/2015] [Accepted: 12/14/2015] [Indexed: 12/16/2022]
Abstract
Antisense long non-coding (aslnc)RNAs represent a substantial part of eukaryotic transcriptomes that are, in yeast, controlled by the Xrn1 exonuclease. Nonsense-Mediated Decay (NMD) destabilizes the Xrn1-sensitive aslncRNAs (XUT), but what determines their sensitivity remains unclear. We report that 3′ single-stranded (3′-ss) extension mediates XUTs degradation by NMD, assisted by the Mtr4 and Dbp2 helicases. Single-gene investigation, genome-wide RNA analyses, and double-stranded (ds)RNA mapping revealed that 3′-ss extensions discriminate the NMD-targeted XUTs from stable lncRNAs. Ribosome profiling showed that XUT are translated, locking them for NMD activity. Interestingly, mutants of the Mtr4 and Dbp2 helicases accumulated XUTs, suggesting that dsRNA unwinding is a critical step for degradation. Indeed, expression of anticomplementary transcripts protects cryptic intergenic lncRNAs from NMD. Our results indicate that aslncRNAs form dsRNA that are only translated and targeted to NMD if dissociated by Mtr4 and Dbp2. We propose that NMD buffers genome expression by discarding pervasive regulatory transcripts. Xrn1-sensitive Unstable Transcripts (XUTs) are 3′-extended isoforms of stable lncRNAs Nonsense-Mediated Decay preferentially targets long XUTs with single-stranded 3′ end Antisense XUTs form double-stranded RNA in vivo Formation of double-stranded RNA protects XUTs from Nonsense-Mediated Decay
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Affiliation(s)
- Maxime Wery
- ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Marc Descrimes
- ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Nicolas Vogt
- ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Anne-Sophie Dallongeville
- ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, CNRS, CEA, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
| | - Antonin Morillon
- ncRNA, Epigenetic, and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France.
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31
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Descrimes M, Ben Zouari Y, Wery M, Legendre R, Gautheret D, Morillon A. VING: a software for visualization of deep sequencing signals. BMC Res Notes 2015; 8:419. [PMID: 26346985 PMCID: PMC4562374 DOI: 10.1186/s13104-015-1404-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 04/01/2015] [Accepted: 08/31/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next generation sequencing (NGS) data treatment often requires mapping sequenced reads onto a reference genome for further analysis. Mapped data are commonly visualized using genome browsers. However, such software are not suited for a publication-ready and versatile representation of NGS data coverage, especially when multiple experiments are simultaneously treated. RESULTS We developed 'VING', a stand-alone R script that takes as input NGS mapping files and genome annotations to produce accurate snapshots of the NGS coverage signal for any specified genomic region. VING offers multiple viewing options, including strand-specific views and a special heatmap mode for representing multiple experiments in a single figure. CONCLUSIONS VING produces high-quality figures for NGS data representation in a genome region of interest. It is available at http://vm-gb.curie.fr/ving/. We also developed a Galaxy wrapper, available in the Galaxy tool shed with installation and usage instructions.
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Affiliation(s)
- Marc Descrimes
- ncRNA, Epigenetics and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248, Paris Cedex 05, France.
| | - Yousra Ben Zouari
- ncRNA, Epigenetics and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248, Paris Cedex 05, France.
| | - Maxime Wery
- ncRNA, Epigenetics and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248, Paris Cedex 05, France.
| | - Rachel Legendre
- Institute for Integrative Biology of the Cell, CNRS, CEA, Université Paris Sud, Bâtiment 400, 91405, Orsay Cedex, France.
| | - Daniel Gautheret
- Institute for Integrative Biology of the Cell, CNRS, CEA, Université Paris Sud, Bâtiment 400, 91405, Orsay Cedex, France.
| | - Antonin Morillon
- ncRNA, Epigenetics and Genome Fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248, Paris Cedex 05, France.
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32
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Manfrini N, Clerici M, Wery M, Colombo CV, Descrimes M, Morillon A, d'Adda di Fagagna F, Longhese MP. Resection is responsible for loss of transcription around a double-strand break in Saccharomyces cerevisiae. eLife 2015; 4. [PMID: 26231041 PMCID: PMC4541074 DOI: 10.7554/elife.08942] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 05/22/2015] [Accepted: 07/30/2015] [Indexed: 11/13/2022] Open
Abstract
Emerging evidence indicate that the mammalian checkpoint kinase ATM induces transcriptional silencing in cis to DNA double-strand breaks (DSBs) through a poorly understood mechanism. Here we show that in Saccharomyces cerevisiae a single DSB causes transcriptional inhibition of proximal genes independently of Tel1/ATM and Mec1/ATR. Since the DSB ends undergo nucleolytic degradation (resection) of their 5'-ending strands, we investigated the contribution of resection in this DSB-induced transcriptional inhibition. We discovered that resection-defective mutants fail to stop transcription around a DSB, and the extent of this failure correlates with the severity of the resection defect. Furthermore, Rad9 and generation of γH2A reduce this DSB-induced transcriptional inhibition by counteracting DSB resection. Therefore, the conversion of the DSB ends from double-stranded to single-stranded DNA, which is necessary to initiate DSB repair by homologous recombination, is responsible for loss of transcription around a DSB in S. cerevisiae.
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Affiliation(s)
- Nicola Manfrini
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maxime Wery
- Institut Curie, Dynamics of Genetic Information: Fundamental Basis and Cancer, Université Pierre et Marie Curie, Paris, France
| | | | - Marc Descrimes
- Institut Curie, Dynamics of Genetic Information: Fundamental Basis and Cancer, Université Pierre et Marie Curie, Paris, France
| | - Antonin Morillon
- Institut Curie, Dynamics of Genetic Information: Fundamental Basis and Cancer, Université Pierre et Marie Curie, Paris, France
| | | | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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33
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Liao HF, Mo CF, Wu SC, Cheng DH, Yu CY, Chang KW, Kao TH, Lu CW, Pinskaya M, Morillon A, Lin SS, Cheng WTK, Bourc'his D, Bestor T, Sung LY, Lin SP. Dnmt3l-knockout donor cells improve somatic cell nuclear transfer reprogramming efficiency. Reproduction 2015; 150:245-56. [PMID: 26159833 DOI: 10.1530/rep-15-0031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 07/09/2015] [Indexed: 12/18/2022]
Abstract
Nuclear transfer (NT) is a technique used to investigate the development and reprogramming potential of a single cell. DNA methyltransferase-3-like, which has been characterized as a repressive transcriptional regulator, is expressed in naturally fertilized egg and morula/blastocyst at pre-implantation stages. In this study, we demonstrate that the use of Dnmt3l-knockout (Dnmt3l-KO) donor cells in combination with Trichostatin A treatment improved the developmental efficiency and quality of the cloned embryos. Compared with the WT group, Dnmt3l-KO donor cell-derived cloned embryos exhibited increased cell numbers as well as restricted OCT4 expression in the inner cell mass (ICM) and silencing of transposable elements at the blastocyst stage. In addition, our results indicate that zygotic Dnmt3l is dispensable for cloned embryo development at pre-implantation stages. In Dnmt3l-KO mouse embryonic fibroblasts, we observed reduced nuclear localization of HDAC1, increased levels of the active histone mark H3K27ac and decreased accumulation of the repressive histone marks H3K27me3 and H3K9me3, suggesting that Dnmt3l-KO donor cells may offer a more permissive epigenetic state that is beneficial for NT reprogramming.
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Affiliation(s)
- Hung-Fu Liao
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Chu-Fan Mo
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Shinn-Chih Wu
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Dai-Han Cheng
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Chih-Yun Yu
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Kai-Wei Chang
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Tzu-Hao Kao
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Chia-Wei Lu
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Marina Pinskaya
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Antonin Morillon
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Shih-Shun Lin
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, T
| | - Winston T K Cheng
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Déborah Bourc'his
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Timothy Bestor
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Li-Ying Sung
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan
| | - Shau-Ping Lin
- Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, Taichung 407, TaiwanINSERM U934/CNRS UMR3215Institut Curie, 75005 Paris, FranceDepartment of Genetics and DevelopmentCollege of Physicians and Surgeons of Columbia University, New York, New York 10032, USAAgricultural Biotechnology Research CenterAcademia Sinica, Taipei 115, TaiwanCenter for Systems BiologyResearch Center for Developmental Biology and Regenerative MedicineNational Taiwan University, Taipei 106, Taiwan Institute of BiotechnologyDepartment of Animal Science and TechnologyGenome and Systems Biology Degree ProgramNational Taiwan University, Taipei 106, TaiwanGenome and Systems Biology Degree ProgramAcademia Sinica, Taipei, TaiwanInstitut CurieCNRS UMR3244, Université Pierre et Marie Curie, 75248 Paris Cedex 05, FranceDepartment of Animal Science and BiotechnologyTunghai University, T
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Kwapisz M, Ruault M, van Dijk E, Gourvennec S, Descrimes M, Taddei A, Morillon A. Expression of Subtelomeric lncRNAs Links Telomeres Dynamics to RNA Decay in S. cerevisiae. Noncoding RNA 2015; 1:94-126. [PMID: 29861418 PMCID: PMC5932542 DOI: 10.3390/ncrna1020094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 04/20/2015] [Revised: 06/17/2015] [Accepted: 06/17/2015] [Indexed: 11/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to regulate gene expression, chromatin domains and chromosome stability in eukaryotic cells. Recent observations have reported the existence of telomeric repeats containing long ncRNAs – TERRA in mammalian and yeast cells. However, their functions remain poorly characterized. Here, we report the existence in S. cerevisiae of several lncRNAs within Y′ subtelomeric regions. We have called them subTERRA. These belong to Cryptic Unstable Transcripts (CUTs) and Xrn1p-sensitive Unstable Transcripts (XUTs) family. subTERRA transcription, carried out mainly by RNAPII, is initiated within the subtelomeric Y’ element and occurs in both directions, towards telomeres as well as centromeres. We show that subTERRA are distinct from TERRA and are mainly degraded by the general cytoplasmic and nuclear 5′- and 3′- RNA decay pathways in a transcription-dependent manner. subTERRA accumulates preferentially during the G1/S transition and in C-terminal rap1 mutant but independently of Rap1p function in silencing. The accumulation of subTERRA in RNA decay mutants coincides with telomere misregulation: shortening of telomeres, loss of telomeric clustering in mitotic cells and changes in silencing of subtelomeric regions. Our data suggest that subtelomeric RNAs expression links telomere maintenance to RNA degradation pathways.
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Affiliation(s)
- Marta Kwapisz
- ncRNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mail: (M.D.)
- Authors to whom correspondence should be addressed; E-Mails: (M.K.); (A.M.); Tel.: +33-561-335-824 (M.K.); +33-(0)-156-246-515 (A.M.); Fax: +33-524-335-886 (M.K.); +33-(0)-156-246-674 (A.M.)
| | - Myriam Ruault
- Nuclear Dynamics, Institut Curie, PSL Research University, CNRS UMR3664, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mails: (M.R.); (A.T.)
| | - Erwin van Dijk
- ncRNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mail: (M.D.)
| | - Stephanie Gourvennec
- ncRNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mail: (M.D.)
| | - Marc Descrimes
- ncRNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mail: (M.D.)
| | - Angela Taddei
- Nuclear Dynamics, Institut Curie, PSL Research University, CNRS UMR3664, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mails: (M.R.); (A.T.)
| | - Antonin Morillon
- ncRNA, epigenetics and genome fluidity, Institut Curie, PSL Research University, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d’Ulm, 75248 Paris Cedex 05, France; E-Mail: (M.D.)
- Authors to whom correspondence should be addressed; E-Mails: (M.K.); (A.M.); Tel.: +33-561-335-824 (M.K.); +33-(0)-156-246-515 (A.M.); Fax: +33-524-335-886 (M.K.); +33-(0)-156-246-674 (A.M.)
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Manfrini N, Trovesi C, Wery M, Martina M, Cesena D, Descrimes M, Morillon A, d'Adda di Fagagna F, Longhese MP. RNA-processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. EMBO Rep 2014; 16:221-31. [PMID: 25527408 DOI: 10.15252/embr.201439458] [Citation(s) in RCA: 27] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA-processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. The lack of Xrn1 inhibits ssDNA generation at the DSB by preventing the loading of the MRX complex. By contrast, DSB resection is not affected in the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by homologous recombination (HR), suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Noteworthy, deep transcriptome analyses do not identify common misregulated gene expression that could explain the observed phenotypes. Our results provide a novel link between RNA processing and genome stability.
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Affiliation(s)
- Nicola Manfrini
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Camilla Trovesi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maxime Wery
- Institut Curie, CNRS UMR3244 Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Marina Martina
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Daniele Cesena
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Marc Descrimes
- Institut Curie, CNRS UMR3244 Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Antonin Morillon
- Institut Curie, CNRS UMR3244 Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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Pinskaya M, Ghavi-Helm Y, Mariotte-Labarre S, Morillon A, Soutourina J, Werner M. PHD and TFIIS-Like domains of the Bye1 transcription factor determine its multivalent genomic distribution. PLoS One 2014; 9:e102464. [PMID: 25029256 PMCID: PMC4100922 DOI: 10.1371/journal.pone.0102464] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/19/2014] [Indexed: 11/18/2022] Open
Abstract
The BYpass of Ess1 (Bye1) protein is a putative S. cerevisiae transcription factor homologous to the human cancer-associated PHF3/DIDO family of proteins. Bye1 contains a Plant Homeodomain (PHD) and a TFIIS-like domain. The Bye1 PHD finger interacts with tri-methylated lysine 4 of histone H3 (H3K4me3) while the TFIIS-like domain binds to RNA polymerase (Pol) II. Here, we investigated the contribution of these structural features to Bye1 recruitment to chromatin as well as its function in transcriptional regulation. Genome-wide analysis of Bye1 distribution revealed at least two distinct modes of association with actively transcribed genes: within the core of Pol II- and Pol III-transcribed genes concomitant with the presence of the TFIIS transcription factor and, additionally, with promoters of a subset of Pol II-transcribed genes. Specific loss of H3K4me3 abolishes Bye1 association to gene promoters, but doesn't affect its binding within gene bodies. Genetic interactions suggested an essential role of Bye1 in cell fitness under stress conditions compensating the absence of TFIIS. Furthermore, BYE1 deletion resulted in the attenuation of GAL genes expression upon galactose-mediated induction indicating its positive role in transcription regulation. Together, these findings point to a bimodal role of Bye1 in regulation of Pol II transcription. It is recruited via its PHD domain to H3K4 tri-methylated promoters at early steps of transcription. Once Pol II is engaged into elongation, Bye1 binds directly to the transcriptional machinery, modulating its progression along the gene.
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Affiliation(s)
- Marina Pinskaya
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
- * E-mail: (MW); (MP)
| | - Yad Ghavi-Helm
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Sylvie Mariotte-Labarre
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Antonin Morillon
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, Paris, France
| | - Julie Soutourina
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
| | - Michel Werner
- iBiTec-S CEA, FRE3377, Gif-sur-Yvette, France
- CNRS, FRE3377, Gif-sur-Yvette, France
- Université Paris-Sud, FRE3377, Gif-sur-Yvette, France
- * E-mail: (MW); (MP)
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Wery M, Descrimes M, Thermes C, Gautheret D, Morillon A. Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq. Methods 2013; 63:25-31. [PMID: 23523657 DOI: 10.1016/j.ymeth.2013.03.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/28/2013] [Accepted: 03/12/2013] [Indexed: 11/26/2022] Open
Abstract
Whole transcriptome RNA-Seq has emerged as a powerful tool in transcriptomics, enabling genome-wide quantitative analysis of gene expression and qualitative identification of novel coding or non-coding RNA species through transcriptome reassembly. Common protocols for preparation of RNA-Seq libraries include an RNA fragmentation step for which several RNA sizing techniques are commercially available. To date, there is no global information about their putative bias on transcriptome analysis. Here we compared the effects of RNase III- and zinc-mediated RNA fragmentation on transcript expression measurement and transcriptome reassembly in the budding yeast Saccharomyces cerevisiae. We observed that RNA cleavage by RNase III is heterogeneous along transcripts with a striking decrease of autocorrelation between adjacent nucleotides along the transcriptome. This had little impact on mRNA expression measurement, but specific classes of transcripts such as abundant non-coding RNAs were underrepresented in the libraries constructed using RNase III. Furthermore, zinc-mediated fragmentation allows proper reassembly of more transcripts, with more precise 5' and 3' ends. Together, our results show that transcriptome reassembly from RNA-Seq data is very sensitive to the RNA fragmentation technique, and that zinc-mediated fragmentation provides more robust and accurate transcript identification than cleavage by RNase III.
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Affiliation(s)
- Maxime Wery
- ncRNA, epigenetic and genome fluidity, Institut Curie, Centre de Recherche, CNRS UMR 3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
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Abstract
Pervasive transcription is now accepted to be a general feature of eukaryotic genomes, generating short and long non-coding RNAs (ncRNAs). Growing number of examples have shown that regulatory ncRNAs can control gene expression and chromatin domain formation. In this review, we discuss recent reports that show that Saccharomyces cerevisiae's genome also supports pervasive transcription, which is strongly controlled by RNA decay pathways and nucleosome positioning. We therefore propose that S. cerevisiae is an excellent model for studying large ncRNAs, which has already provided important examples of antisense-mediated transcriptional silencing.
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Affiliation(s)
- Mathieu Tisseur
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
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van Dijk EL, Chen CL, d'Aubenton-Carafa Y, Gourvennec S, Kwapisz M, Roche V, Bertrand C, Silvain M, Legoix-Né P, Loeillet S, Nicolas A, Thermes C, Morillon A. XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature 2011; 475:114-7. [PMID: 21697827 DOI: 10.1038/nature10118] [Citation(s) in RCA: 268] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 04/14/2011] [Indexed: 01/13/2023]
Abstract
Non-coding (nc)RNAs are key players in numerous biological processes such as gene regulation, chromatin domain formation and genome stability. Large ncRNAs interact with histone modifiers and are involved in cancer development, X-chromosome inactivation and autosomal gene imprinting. However, despite recent evidence showing that pervasive transcription is more widespread than previously thought, only a few examples mediating gene regulation in eukaryotes have been described. In Saccharomyces cerevisiae, the bona-fide regulatory ncRNAs are destabilized by the Xrn1 5'-3' RNA exonuclease (also known as Kem1), but the genome-wide characterization of the entire regulatory ncRNA family remains elusive. Here, using strand-specific RNA sequencing (RNA-seq), we identify a novel class of 1,658 Xrn1-sensitive unstable transcripts (XUTs) in which 66% are antisense to open reading frames. These transcripts are polyadenylated and RNA polymerase II (RNAPII)-dependent. The majority of XUTs strongly accumulate in lithium-containing media, indicating that they might have a role in adaptive responses to changes in growth conditions. Notably, RNAPII chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) analysis of Xrn1-deficient strains revealed a significant decrease of RNAPII occupancy over 273 genes with antisense XUTs. These genes show an unusual bias for H3K4me3 marks and require the Set1 histone H3 lysine 4 methyl-transferase for silencing. Furthermore, abolishing H3K4me3 triggers the silencing of other genes with antisense XUTs, supporting a model in which H3K4me3 antagonizes antisense ncRNA repressive activity. Our results demonstrate that antisense ncRNA-mediated regulation is a general regulatory pathway for gene expression in S. cerevisiae.
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Affiliation(s)
- E L van Dijk
- Centre de Génétique Moléculaire (CNRS UPR 3404), avenue de la Terrasse, 91198 Gif sur Yvette, France
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Cosnier B, Kwapisz M, Hatin I, Namy O, Denmat SHL, Morillon A, Rousset JP, Fabret C. A viable hypomorphic allele of the essential IMP3 gene reveals novel protein functions in Saccharomyces cerevisiae. PLoS One 2011; 6:e19500. [PMID: 21559332 PMCID: PMC3084874 DOI: 10.1371/journal.pone.0019500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 04/06/2011] [Indexed: 12/31/2022] Open
Abstract
In Saccharomyces cerevisiae, the essential IMP3 gene encodes a component of the SSU processome, a large ribonucleoprotein complex required for processing of small ribosomal subunit RNA precursors. Mutation of the IMP3 termination codon to a sense codon resulted in a viable mutant allele producing a C-terminal elongated form of the Imp3 protein. A strain expressing the mutant allele displayed ribosome biogenesis defects equivalent to IMP3 depletion. This hypomorphic allele represented a unique opportunity to investigate and better understand the Imp3p functions. We demonstrated that the +1 frameshifting was increased in the mutant strain. Further characterizations revealed involvement of the Imp3 protein in DNA repair and telomere length control, pointing to a functional relationship between both pathways and ribosome biogenesis.
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Affiliation(s)
- Bruno Cosnier
- IGM, CNRS, UMR 8621, Orsay, France
- Université Paris-Sud, Orsay, France
| | | | - Isabelle Hatin
- IGM, CNRS, UMR 8621, Orsay, France
- Université Paris-Sud, Orsay, France
| | - Olivier Namy
- IGM, CNRS, UMR 8621, Orsay, France
- Université Paris-Sud, Orsay, France
| | | | | | | | - Céline Fabret
- IGM, CNRS, UMR 8621, Orsay, France
- Université Pierre et Marie Curie, Paris, France
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Abstract
RNAs have been traditionally viewed as intermediates between DNA and proteins. However, there is a growing body of literature indicating that noncoding RNAs (ncRNAs) are key players for gene regulation, genome stability, and chromatin modification. In addition to the well-known small interfering RNAs and microRNAs acting in transcriptional and posttranscriptional gene silencing, recent advances in the field of transcriptome exploration have revealed novel sets of new small and large ncRNAs. Many of them appear to be conserved across mammals, and abnormal expression of several ncRNAs has been linked to a wide variety of human diseases, such as cancer. Here, we review the different classes of ncRNAs identified to date, in yeast and mammals, and we discuss the mechanisms by which they affect gene regulation.
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Affiliation(s)
- Maxime Wery
- Institut Curie, Centre de Recherche, Paris, France
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Pinskaya M, Gourvennec S, Morillon A. H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation. EMBO J 2009; 28:1697-707. [PMID: 19407817 DOI: 10.1038/emboj.2009.108] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 03/26/2009] [Indexed: 12/23/2022] Open
Abstract
Set1-dependent H3K4 di- and tri-methylation (H3K4me2/3) have been associated with active transcription. Recent data indicate that the H3K4me2/3 also plays a poorly characterized RNA-dependent repressive role. Here, we show that GAL1 promoter is attenuated by the H3K4me2/3 deposited by cryptic transcription. The H3K4me2/3 delay the recruitment of RNA polymerase II (RNAPII) and TBP on GAL1 promoter. Inactivation of RNA decay components revealed the existence of the RNAPII-dependent unstable RNAs, initiating upstream of GAL1 (GAL1ucut). GAL1ucut RNAs are synthesized in glucose and require the Reb1 transcription factor. Consistent with a regulatory function of the cryptic transcription, Reb1 depletion leads to a decrease of H3K4me3 on GAL10-GAL1 locus in glucose and to an acceleration of GAL1 induction. A candidate approach shows that the RPD3 histone deacetylase attenuates GAL1 induction and is tethered at the GAL10-GAL1 locus by H3K4me2/3 upon repression. Strikingly, Set1-dependent Rpd3 recruitment represses also the usage of a hidden promoter within SUC2, suggesting a general function for H3K4me2/3 in promoter fidelity. Our data support a model wherein certain promoters are embedded in a repressive chromatin controlled by cryptic transcription.
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Affiliation(s)
- Marina Pinskaya
- Centre de Génétique Moléculaire CNRS, Université Pierre et Marie Curie, Gif sur Yvette, France
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45
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Berretta J, Pinskaya M, Morillon A. A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae. Genes Dev 2008; 22:615-26. [PMID: 18316478 DOI: 10.1101/gad.458008] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Cryptic unstable transcripts (CUTs) are synthesized from intra- and intergenic regions in Saccharomyces cerevisiae and are rapidly degraded by RNA surveillance pathways, but their function(s) remain(s) elusive. Here, we show that an antisense TY1 CUT, starting within the Ty1 retrotransposon and encompassing the promoter 5' long terminal repeat (LTR), mediates RNA-dependent gene silencing and represses Ty1 mobility. We show that the Ty1 regulatory RNA is synthesized by RNA polymerase II, polyadenylated, and destabilized by the cytoplasmic 5' RNA degradation pathway. Moreover, the Ty1 regulatory RNA represses Ty1 transcription and transposition in trans by acting on the de novo transcribed TY1 RNA. Consistent with a transcriptional regulation mechanism, we show that RNA polymerase II occupancy is reduced on the Ty1 chromatin upon silencing, although TBP binding remains unchanged. Furthermore, the Ty1 silencing is partially mediated by histone deacetylation and requires Set1-dependent histone methylation, pointing out an analogy with heterochromatin gene silencing. Our results show the first example of an RNA-dependent gene trans-silencing mediated by epigenetic marks in S. cerevisiae.
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Affiliation(s)
- Julia Berretta
- Centre de Genetique Moleculaire-Centre National de la Recherche Scientifique (CGM-CNRS), 91198 Gif/Yvette, France
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46
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Abstract
Chromatin modifications play a crucial role in regulating DNA metabolism. Chromatin structures can be remodeled by covalently modifying histones, by shifting nucleosomes along the DNA, and by changing the histone composition of nucleosomes. Lately, nucleosome displacement has been extensively described within transcribed genes and DNA breaks. This review focuses on recently published work that describes the relationships between histone modification/exchange and nucleosome displacement.
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Affiliation(s)
- Antonin Morillon
- CNRS CGM, 1, avenue de la terrasse, 91198 Gif/Yvette cedex, France.
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Todeschini AL, Morillon A, Springer M, Lesage P. Severe adenine starvation activates Ty1 transcription and retrotransposition in Saccharomyces cerevisiae. Mol Cell Biol 2005; 25:7459-72. [PMID: 16107695 PMCID: PMC1190277 DOI: 10.1128/mcb.25.17.7459-7472.2005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [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: 01/08/2023] Open
Abstract
Ty1 retrotransposons of the yeast Saccharomyces cerevisiae are activated by different kinds of stress. Here we show that Ty1 transcription is stimulated under severe adenine starvation conditions. The Bas1 transcriptional activator, responsible for the induction of genes of the de novo AMP biosynthesis pathway (ADE) in the absence of adenine, is not involved in this response. Activation occurs mainly on Ty1 elements, whose expression is normally repressed by chromatin and is suppressed in a hta1-htb1Delta mutant that alters chromatin structure. Activation is also abolished in a snf2Delta mutant. Several regions of the Ty1 promoter are necessary to achieve full activation, suggesting that full integrity of the promoter sequences might be important for activation. Together, these observations are consistent with a model in which the activation mechanism involves chromatin remodeling at Ty1 promoters. The consequence of Ty1 transcriptional activation in response to adenine starvation is an increase in Ty1 cDNA levels and a relief of Ty1 dormancy. The retrotransposition of four native Ty1 elements increases in proportion to their increase in transcription. Implications for the regulation of Ty1 mobility by changes in Ty1 mRNA levels are discussed.
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48
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Morillon A, Karabetsou N, Nair A, Mellor J. Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. Mol Cell 2005; 18:723-34. [PMID: 15949446 DOI: 10.1016/j.molcel.2005.05.009] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2005] [Revised: 04/01/2005] [Accepted: 05/09/2005] [Indexed: 11/21/2022]
Abstract
Covalent modifications to histones are key epigenetic marks that control gene transcription. Multiple lysine residues on histone H3 are methylated (me), but their functions are unclear. Here, we demonstrate two phases of combinatorial and dynamic H3 methylation during induction of transcription at MET16 in yeast. K4me3 with K36me2/3 define a postinitiation regulatory phase and precede the appearance of K4me2 with K79me2 at the onset of transcript elongation. The Isw1 ATPase delays the release of initiated RNA polymerase II (RNAPII) into elongation to facilitate chromatin modifications. The Spp1 subunit of complex associated with Set1 (COMPASS) and Set2, determining K4me3 and K36me2/3, respectively, are required for transient NuA4-dependent H4K8ac. This releases RNAPII from Isw1 control and promotes controlled transcription elongation and termination. We propose that newly initiated RNAPII is under epigenetic control.
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Affiliation(s)
- Antonin Morillon
- Department of Biochemistry, Division of Molecular Genetics, Oxford, United Kingdom
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O'Sullivan JM, Tan-Wong SM, Morillon A, Lee B, Coles J, Mellor J, Proudfoot NJ. Gene loops juxtapose promoters and terminators in yeast. Nat Genet 2004; 36:1014-8. [PMID: 15314641 DOI: 10.1038/ng1411] [Citation(s) in RCA: 281] [Impact Index Per Article: 14.1] [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: 05/28/2004] [Accepted: 07/14/2004] [Indexed: 11/08/2022]
Abstract
Mechanistic analysis of transcriptional initiation and termination by RNA polymerase II (PolII) indicates that some factors are common to both processes. Here we show that two long genes of Saccharomyces cerevisiae, FMP27 and SEN1, exist in a looped conformation, effectively bringing together their promoter and terminator regions. We also show that PolII is located at both ends of FMP27 when this gene is transcribed from a GAL1 promoter under induced and noninduced conditions. Under these conditions, the C-terminal domain of the large subunit of PolII is phosphorylated at Ser5. Notably, inactivation of Kin28p causes a loss of both Ser5 phosphorylation and the loop conformation. These data suggest that gene loops are involved in the early stages of transcriptional activation. They also predict a previously unknown structural dimension to gene regulation, in which both ends of the transcription unit are defined before and during the transcription cycle.
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Affiliation(s)
- Justin M O'Sullivan
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, UK
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50
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Abstract
The imitation switch (ISWI) class of chromatin remodeling ATPase is ubiquitous in eukaryotes. It is becoming clear that these enzymes exist as part of larger complexes and the nature of the associated proteins dictate the function associated with a complex both in biochemical assays and in the cell. Much progress has been made in understanding these relationships in the budding yeast Saccharomyces cerevisiae, containing two ATPases, Isw1p and Isw2p. This has been aided by the ease of genetic manipulation, by a number of systematic screens designed to specifically detect ISWI function and by the plethora of data generated from a number of global screens for function. At present, many functions for yeast Isw1p and Isw2p are related to effects on RNA levels and are associated with the controlled repression of gene expression that crudely fall into three types: displacement of the basal transcription machinery to repress or silence transcription of genes (Isw2 complex and Isw1/Ioc3 complex); control of the activation of expression leading to coordination of transcription elongation; and efficient termination of transcription (Isw1/Ioc4/Ioc2 complex). The latter two functions are regulated by specific phosphorylation of residues within the carboxy terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAPII). Other functions may relate to the ability of ISWI complex to displace transcription factors or enzymes from the template. Other ISWI-containing complexes that have yet to be characterized indicate that much remains to be learnt about yeast ISWI itself and importantly, how the various forms cooperate with different classes of chromatin remodeling ATPase, complexes containing histone acetylases, deacetylases, methylases and both DNA and RNA polymerases.
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Affiliation(s)
- Jane Mellor
- Department of Biochemistry, Microbiology Unit, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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