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Mensurado S, Condeço C, Sánchez-Martínez D, Shirley S, Coelho RML, Tirado N, Vinyoles M, Blanco-Domínguez R, Barros L, Galvão B, Custódio N, Gomes da Silva M, Menéndez P, Silva-Santos B. CD155/PVR determines acute myeloid leukemia targeting by Delta One T cells. Blood 2024; 143:1488-1495. [PMID: 38437507 PMCID: PMC11033583 DOI: 10.1182/blood.2023022992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/19/2023] [Revised: 01/12/2024] [Accepted: 01/25/2024] [Indexed: 03/06/2024] Open
Abstract
ABSTRACT Relapsed or refractory acute myeloid leukemia (AML) remains a major therapeutic challenge. We have recently developed a Vδ1+ γδ T cell-based product for adoptive immunotherapy, named Delta One T (DOT) cells, and demonstrated their cytolytic capacity to eliminate AML cell lines and primary blasts in vitro and in vivo. However, the molecular mechanisms responsible for the broad DOT-cell recognition of AML cells remain poorly understood. Here, we dissected the role of natural killer (NK) cell receptor ligands in AML cell recognition by DOT cells. Screening of multiple AML cell lines highlighted a strong upregulation of the DNAM-1 ligands, CD155/pulmonary vascular resistance (PVR), CD112/nectin-2, as well as the NKp30 ligand, B7-H6, in contrast with NKG2D ligands. CRISPR-mediated ablation revealed key nonredundant and synergistic contributions of PVR and B7-H6 but not nectin-2 to DOT-cell targeting of AML cells. We further demonstrate that PVR and B7-H6 are critical for the formation of robust immunological synapses between AML and DOT cells. Importantly, PVR but not B7-H6 expression in primary AML samples predicted their elimination by DOT cells. These data provide new mechanistic insight into tumor targeting by DOT cells and suggest that assessing PVR expression levels may be highly relevant to DOT cell-based clinical trials.
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Affiliation(s)
- Sofia Mensurado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Carolina Condeço
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Diego Sánchez-Martínez
- Josep Carreras Leukaemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terapias Avanzadas, Instituto de Salud Carlos III, Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RD21/0017/0029), Madrid, Spain
- Aragon Health Research Institute, Centro de Investigación Biomédica en Red en Enfermedades Infecciosas, Instituto de Salud Carlos III, Zaragoza, Spain
- Aragon I+D Foundation, Zaragoza, Spain
| | - Sara Shirley
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Rui M. L. Coelho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Néstor Tirado
- Josep Carreras Leukaemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terapias Avanzadas, Instituto de Salud Carlos III, Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RD21/0017/0029), Madrid, Spain
| | - Meritxell Vinyoles
- Josep Carreras Leukaemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terapias Avanzadas, Instituto de Salud Carlos III, Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RD21/0017/0029), Madrid, Spain
| | - Rafael Blanco-Domínguez
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Leandro Barros
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Beatriz Galvão
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Noélia Custódio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | - Pablo Menéndez
- Josep Carreras Leukaemia Research Institute, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Red Española de Terapias Avanzadas, Instituto de Salud Carlos III, Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RD21/0017/0029), Madrid, Spain
- Centro de Investigación Biomédica en Red-Oncología, Instituto de Salud Carlos III, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Bruno Silva-Santos
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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Tammer L, Hameiri O, Keydar I, Roy VR, Ashkenazy-Titelman A, Custódio N, Sason I, Shayevitch R, Rodríguez-Vaello V, Rino J, Lev Maor G, Leader Y, Khair D, Aiden EL, Elkon R, Irimia M, Sharan R, Shav-Tal Y, Carmo-Fonseca M, Ast G. Gene architecture directs splicing outcome in separate nuclear spatial regions. Mol Cell 2022; 82:1021-1034.e8. [PMID: 35182478 DOI: 10.1016/j.molcel.2022.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 12/13/2022]
Abstract
How the splicing machinery defines exons or introns as the spliced unit has remained a puzzle for 30 years. Here, we demonstrate that peripheral and central regions of the nucleus harbor genes with two distinct exon-intron GC content architectures that differ in the splicing outcome. Genes with low GC content exons, flanked by long introns with lower GC content, are localized in the periphery, and the exons are defined as the spliced unit. Alternative splicing of these genes results in exon skipping. In contrast, the nuclear center contains genes with a high GC content in the exons and short flanking introns. Most splicing of these genes occurs via intron definition, and aberrant splicing leads to intron retention. We demonstrate that the nuclear periphery and center generate different environments for the regulation of alternative splicing and that two sets of splicing factors form discrete regulatory subnetworks for the two gene architectures. Our study connects 3D genome organization and splicing, thus demonstrating that exon and intron definition modes of splicing occur in different nuclear regions.
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Affiliation(s)
- Luna Tammer
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ofir Hameiri
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ifat Keydar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Vanessa Rachel Roy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Asaf Ashkenazy-Titelman
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Noélia Custódio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Itay Sason
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ronna Shayevitch
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Victoria Rodríguez-Vaello
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain, ICREA, Barcelona, Spain
| | - José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Galit Lev Maor
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Yodfat Leader
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Doha Khair
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain, ICREA, Barcelona, Spain
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel.
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3
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Custódio N, Savisaar R, Carvalho C, Bak-Gordon P, Ribeiro MI, Tavares J, Nunes PB, Peixoto A, Pinto C, Escudeiro C, Teixeira MR, Carmo-Fonseca M. Expression Profiling in Ovarian Cancer Reveals Coordinated Regulation of BRCA1/2 and Homologous Recombination Genes. Biomedicines 2022; 10:biomedicines10020199. [PMID: 35203410 PMCID: PMC8868827 DOI: 10.3390/biomedicines10020199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 11/16/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Predictive biomarkers are crucial in clarifying the best strategy to use poly(ADP-ribose) polymerase inhibitors (PARPi) for the greatest benefit to ovarian cancer patients. PARPi are specifically lethal to cancer cells that cannot repair DNA damage by homologous recombination (HR), and HR deficiency is frequently associated with BRCA1/2 mutations. Genetic tests for BRCA1/2 mutations are currently used in the clinic, but results can be inconclusive due to the high prevalence of rare DNA sequence variants of unknown significance. Most tests also fail to detect epigenetic modifications and mutations located deep within introns that may alter the mRNA. The aim of this study was to investigate whether quantitation of BRCA1/2 mRNAs in ovarian cancer can provide information beyond the DNA tests. Using the nCounter assay from NanoString Technologies, we analyzed RNA isolated from 38 ovarian cancer specimens and 11 normal fallopian tube samples. We found that BRCA1/2 expression was highly variable among tumors. We further observed that tumors with lower levels of BRCA1/2 mRNA showed downregulated expression of 12 additional HR genes. Analysis of 299 ovarian cancer samples from The Cancer Genome Atlas (TCGA) confirmed the coordinated expression of BRCA1/2 and HR genes. To facilitate the routine analysis of BRCA1/2 mRNA in the clinical setting, we developed a targeted droplet digital PCR approach that can be used with FFPE samples. In conclusion, this study underscores the potential clinical benefit of measuring mRNA levels in tumors when BRCA1/2 DNA tests are negative or inconclusive.
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Affiliation(s)
- Noélia Custódio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
- Correspondence: ; Tel.: +35-121-799-9411
| | - Rosina Savisaar
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Célia Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Pedro Bak-Gordon
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Maria I. Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Joana Tavares
- Serviço de Anatomia Patológica, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-028 Lisboa, Portugal;
| | - Paula B. Nunes
- Hospital CUF Descobertas, 1998-018 Lisboa, Portugal;
- Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana Peixoto
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Carla Pinto
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Carla Escudeiro
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Manuel R. Teixeira
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
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4
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Abstract
Transcription and splicing are fundamental steps in gene expression. These processes have been studied intensively over the past four decades, and very recent findings are challenging some of the formerly established ideas. In particular, splicing was shown to occur much faster than previously thought, with the first spliced products observed as soon as splice junctions emerge from RNA polymerase II (Pol II). Splicing was also found coupled to a specific phosphorylation pattern of Pol II carboxyl-terminal domain (CTD), suggesting a new layer of complexity in the CTD code. Moreover, phosphorylation of the CTD may be scarcer than expected, and other post-translational modifications of the CTD are emerging with unanticipated roles in gene expression regulation.
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Affiliation(s)
- Noélia Custódio
- a Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
| | - Maria Carmo-Fonseca
- a Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
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5
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Vaz-Drago R, Pinheiro MT, Martins S, Enguita FJ, Carmo-Fonseca M, Custódio N. Transcription-coupled RNA surveillance in human genetic diseases caused by splice site mutations. Hum Mol Genet 2015; 24:2784-95. [PMID: 25652404 DOI: 10.1093/hmg/ddv039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 01/31/2015] [Indexed: 12/15/2022] Open
Abstract
Current estimates indicate that approximately one-third of all disease-causing mutations are expected to disrupt splicing. Abnormal splicing often leads to disruption of the reading frame with introduction of a premature termination codon (PTC) that targets the mRNA for degradation in the cytoplasm by nonsense mediated decay (NMD). In addition to NMD there are RNA surveillance mechanisms that act in the nucleus while transcripts are still associated with the chromatin template. However, the significance of nuclear RNA quality control in the context of human genetic diseases is unknown. Here we used patient-derived lymphoblastoid cell lines as disease models to address how biogenesis of mRNAs is affected by splice site mutations. We observed that most of the mutations analyzed introduce PTCs and trigger mRNA degradation in the cytoplasm. However, for some mutant transcripts, RNA levels associated with chromatin were found down-regulated. Quantification of nascent transcripts further revealed that a subset of genes containing splicing mutations (SM) have reduced transcriptional activity. Following treatment with the translation inhibitor cycloheximide the cytoplasmic levels of mutant RNAs increased, while the levels of chromatin-associated transcripts remained unaltered. These results suggest that transcription-coupled surveillance mechanisms operate independently from NMD to reduce cellular levels of abnormal RNAs caused by SM.
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Affiliation(s)
- Rita Vaz-Drago
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Marco T Pinheiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Noélia Custódio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
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6
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de Almeida SF, García-Sacristán A, Custódio N, Carmo-Fonseca M. A link between nuclear RNA surveillance, the human exosome and RNA polymerase II transcriptional termination. Nucleic Acids Res 2010; 38:8015-26. [PMID: 20699273 PMCID: PMC3001075 DOI: 10.1093/nar/gkq703] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In eukaryotes, the production of mature messenger RNA that exits the nucleus to be translated into protein in the cytoplasm requires precise and extensive modification of the nascent transcript. Any failure that compromises the integrity of an mRNA may cause its retention in the nucleus and trigger its degradation. Multiple studies indicate that mRNAs with processing defects accumulate in nuclear foci or ‘dots’ located near the site of transcription, but how exactly are defective RNAs recognized and tethered is still unknown. Here, we present evidence suggesting that unprocessed β-globin transcripts render RNA polymerase II (Pol II) incompetent for termination and that this quality control process requires the integrity of the nuclear exosome. Our results show that unprocessed pre-mRNAs remain tethered to the DNA template in association with Pol II, in an Rrp6-dependent manner. This reveals an unprecedented link between nuclear RNA surveillance, the exosome and Pol II transcriptional termination.
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Affiliation(s)
- Sérgio F de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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7
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Custódio N, Vivo M, Antoniou M, Carmo-Fonseca M. Splicing- and cleavage-independent requirement of RNA polymerase II CTD for mRNA release from the transcription site. ACTA ACUST UNITED AC 2007; 179:199-207. [PMID: 17938247 PMCID: PMC2064756 DOI: 10.1083/jcb.200612109] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Eukaryotic cells have a surveillance mechanism that identifies aberrantly processed pre-mRNAs and prevents their flow to the cytoplasm by tethering them near the site of transcription. Here we provide evidence that mRNA release from the transcription site requires the heptad repeat structure of the C-terminal domain (CTD) of RNA polymerase II. The mammalian CTD, which is essential for normal co-transcriptional maturation of mRNA precursors, comprises 52 heptad repeats. We show that a truncated CTD containing 31 repeats (heptads 1–23, 36–38, and 48–52) is sufficient to support transcription, splicing, cleavage, and polyadenylation. Yet, the resulting mRNAs are mostly retained in the vicinity of the gene after transcriptional shutoff. The retained mRNAs maintain the ability to recruit components of the exon junction complex and the nuclear exosome subunit Rrp6p, suggesting that binding of these proteins is not sufficient for RNA release. We propose that the missing heptads in the truncated CTD mutant are required for binding of proteins implicated in a final co-transcriptional maturation of spliced and 3′ end cleaved and polyadenylated mRNAs into export-competent ribonucleoprotein particles.
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Affiliation(s)
- Noélia Custódio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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8
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García-Sacristán A, Carvalho C, Custódio N, Carmo-Fonseca M. Quality control of aberrant β-globin transcripts. Blood Cells Mol Dis 2007. [DOI: 10.1016/j.bcmd.2006.10.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Custódio N, Antoniou M, Carmo-Fonseca M. Abundance of the largest subunit of RNA polymerase II in the nucleus is regulated by nucleo-cytoplasmic shuttling. Exp Cell Res 2006; 312:2557-67. [PMID: 16765347 DOI: 10.1016/j.yexcr.2006.04.018] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Revised: 04/15/2006] [Accepted: 04/19/2006] [Indexed: 12/15/2022]
Abstract
Eukaryotic RNA polymerase II is a complex enzyme composed of 12 distinct subunits that is present in cells in low abundance. Transcription of mRNA by RNA polymerase II involves a phosphorylation/dephosphorylation cycle of the carboxyl-terminal domain (CTD) of the enzyme's largest subunit. We have generated stable murine cell lines expressing an alpha-amanitin-resistant form of the largest subunit of RNA polymerase II (RNA Pol II LS). These cells maintained transcriptional activity in the presence of alpha-amanitin, indicating that the exogenous protein was functional. We observed that over-expressed RNA Pol II LS was predominantly hypophosphorylated, soluble and accumulated in the cytoplasm in a CRM1-dependent manner. Our results further showed that the transcriptionally active form of RNA Pol II LS containing phosphoserine in position 2 of the CTD repeats was restricted to the nucleus and its levels remained remarkably constant. We propose that nucleo-cytoplasmic shuttling of RNA Pol II LS may provide a mechanism to control the pool of RNA polymerase subunits that is accessible for assembly of a functional enzyme in the nucleus.
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Affiliation(s)
- Noélia Custódio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
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10
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Custódio N, Carvalho C, Condado I, Antoniou M, Blencowe BJ, Carmo-Fonseca M. In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei. RNA 2004; 10:622-33. [PMID: 15037772 PMCID: PMC1370553 DOI: 10.1261/rna.5258504] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Studies over the past years indicate that there is extensive coupling between nuclear export of mRNA and pre-mRNA processing. Here, we visualized the distribution of exon junction complex (EJC) proteins and RNA export factors relative to sites of abundant pre-mRNA synthesis in the nucleus. We analyzed both HeLa cells infected with adenovirus and murine erythroleukemia (MEL) cells stably transfected with the human beta-globin gene. Using in situ hybridization and confocal microscopy, we observe accumulation of EJC proteins (REF/Aly, Y14, SRm160, UAP56, RNPS1, and Magoh) and core spliceosome components (U snRNPs) at sites of transcription. This suggests that EJC proteins bind stably to pre-mRNA cotranscriptionally. No concentration of the export factors NXF1/TAP, p15, and Dbp5 was detected on nascent transcripts, arguing that in mammalian cells these proteins bind the mRNA shortly before or after release from the sites of transcription. These results also suggest that binding of EJC proteins to the mRNA is not sufficient to recruit TAP-p15, consistent with recent findings showing that the EJC does not play a crucial role in mRNA export. Contrasting to the results obtained in MEL cells expressing normal human beta-globin transcripts, mutant pre-mRNAs defective in splicing and 3'end processing do not colocalize with SRm160, REF, UAP56, or Sm proteins. This shows that the accumulation of EJC proteins at transcription sites requires efficient processing of the nascent pre-mRNAs, arguing that transcription per se is not sufficient for the stable assembly of the EJC.
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Affiliation(s)
- Noélia Custódio
- Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, Lisbon 1649-028, Portugal
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11
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Abstract
Proteins are responsible for most cellular and extra-cellular functions. If altered, proteins can loose their normal activity and/or gain new properties. Either way the consequences may be deleterious for the cell and lead to disease at the organism level. Not surprisingly, eukaryotes have evolved mechanisms to recognize abnormal messenger RNAs and prevent them from producing faulty proteins. Protein-encoding genes are transcribed in the nucleus by RNA polymerase II as precursor RNAs that undergo extensive processing before being translocated to the cytoplasm for translation by the ribosomes. This spatial and temporal separation between RNA and protein synthesis offers an immense opportunity for control and regulation. Here we review recent studies that are beginning to unravel how the coupling between transcription, processing and transport of mRNAs contributes to control the quality of gene expression in the nucleus.
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Affiliation(s)
- N Custódio
- Institute of Histology and Embryology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
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12
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Mühlemann O, Mock-Casagrande CS, Wang J, Li S, Custódio N, Carmo-Fonseca M, Wilkinson MF, Moore MJ. Precursor RNAs harboring nonsense codons accumulate near the site of transcription. Mol Cell 2001; 8:33-43. [PMID: 11511358 DOI: 10.1016/s1097-2765(01)00288-x] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [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] [Indexed: 11/28/2022]
Abstract
Messenger RNAs containing premature termination codons (PTCs) are selectively eliminated by nonsense-mediated mRNA decay (NMD). Paradoxically, although cytoplasmic ribosomes are the only known species capable of PTC recognition, in mammals many PTC-containing mRNAs are apparently eliminated prior to release from the nucleus. To determine whether PTCs can influence events within the nucleus proper, we studied the immunoglobulin (Ig)-mu and T cell receptor (TCR)-beta genes using fluorescent in situ hybridization (FISH). Alleles containing PTCs, but not those containing a missense mutation or a frameshift followed by frame-correcting mutations, exhibited elevated levels of pre-mRNA, which accumulated at or near the site of transcription. Our data indicate that mRNA reading frame can influence events at or near the site of gene transcription.
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Affiliation(s)
- O Mühlemann
- Howard Hughes Medical Institute, W.M. Keck Center for Cellular Visualization, Department of Biochemistry, Brandeis University, Waltham, MA 02454, USA
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Abstract
Within the nucleus, protein-encoding genes are transcribed into messenger RNA by RNA polymerase II. Messenger RNAs migrate to the cytoplasm, but before reaching their final destination the primary transcripts must undergo a series of modifications that include 5'-capping, splicing, and 3'-cleavage/polyadenylation. Errors in these processing events can originate aberrant products that, if translated, would produce abnormal proteins. Therefore, it is not surprising that eukaryotes have evolved a surveillance mechanism that recognizes and rapidly degrades aberrant mRNAs. Recent experiments provide exciting insights into how proper mRNAs are distinguished and selected for export. Transcription by RNA polymerase II is directly coupled to pre-mRNA processing, and the mechanism that targets the processing machinery to the polymerase complex suggests a model for co-transcriptional proofreading. Furthermore, there is evidence that at least some mRNAs move randomly throughout the nucleus, presumably by free diffusion. In this light, retention of aberrant mRNAs by the transcription/processing machinery is crucial to prevent their diffusion to the nuclear pores and eventual translocation to the cytoplasm.
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Affiliation(s)
- M Carmo-Fonseca
- Institute of Histology and Embryology, Faculty of Medicine, University of Lisbon, Portugal
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Custódio N, Carmo-Fonseca M, Geraghty F, Pereira HS, Grosveld F, Antoniou M. Inefficient processing impairs release of RNA from the site of transcription. EMBO J 1999; 18:2855-66. [PMID: 10329631 PMCID: PMC1171366 DOI: 10.1093/emboj/18.10.2855] [Citation(s) in RCA: 171] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We describe here for the first time the site of retention within the nucleus of pre-mRNA processing mutants unable to be exported to the cytoplasm. Fluorescence in situ hybridization was used to detect transcripts from human beta-globin genes that are either normal or defective in splicing or 3' end formation. Nuclear transcripts of both wild-type and mutant RNAs are detected only as intranuclear foci that colocalize with the template gene locus. The kinetics of transcript release from the site of transcription was assessed by treatment of cells with the transcriptional inhibitors actinomycin D, alpha-amanitin and DRB. These drugs induce the rapid disappearance of nuclear foci corresponding to wild-type human beta-globin RNA. In contrast, pre-mRNA mutants defective in either splicing or 3' end formation and which fail to be transported to the cytoplasm, are retained at the site of transcription. Therefore, 3' end processing and splicing appear to be rate limiting for release of mRNA from the site of transcription.
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Affiliation(s)
- N Custódio
- Institute of Histology and Embryology, Faculty of Medicine, University of Lisbon, 1699 Lisbon codex, Portugal
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15
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Abstract
At present several lines of evidence indicate that the nucleus is functionally compartmentalized into discrete structures with defined properties. For instance, it is well established that the molecular machines involved in replication, transcription, and RNA processing assemble into morphological entities but it remains unclear whether these correspond to autonomous "organelles" or rather represent temporary accumulations of either active factors recruited onto DNA templates or inactive factors stored in the vicinity of genes. According to the latter view, the spatial distribution of genes during interphase should play a major role in the subnuclear organization of nonchromatin components such as replication, transcription, and processing factors, and in this article we discuss current ideas on the functional compartmentalization of chromosomes and genes within the nucleus.
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Affiliation(s)
- M Carmo-Fonseca
- Institute of Histology and Embryology, University of Lisbon, Lisboa Codex, 1699, Portugal.
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