1
|
Di Vona C, Barba L, Ferrari R, de la Luna S. Loss of the DYRK1A Protein Kinase Results in the Reduction in Ribosomal Protein Gene Expression, Ribosome Mass and Reduced Translation. Biomolecules 2023; 14:31. [PMID: 38254631 PMCID: PMC10813206 DOI: 10.3390/biom14010031] [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: 11/17/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Ribosomal proteins (RPs) are evolutionary conserved proteins that are essential for protein translation. RP expression must be tightly regulated to ensure the appropriate assembly of ribosomes and to respond to the growth demands of cells. The elements regulating the transcription of RP genes (RPGs) have been characterized in yeast and Drosophila, yet how cells regulate the production of RPs in mammals is less well understood. Here, we show that a subset of RPG promoters is characterized by the presence of the palindromic TCTCGCGAGA motif and marked by the recruitment of the protein kinase DYRK1A. The presence of DYRK1A at these promoters is associated with the enhanced binding of the TATA-binding protein, TBP, and it is negatively correlated with the binding of the GABP transcription factor, establishing at least two clusters of RPGs that could be coordinately regulated. However, DYRK1A silencing leads to a global reduction in RPGs mRNAs, pointing at DYRK1A activities beyond those dependent on its chromatin association. Significantly, cells in which DYRK1A is depleted have reduced RP levels, fewer ribosomes, reduced global protein synthesis and a smaller size. We therefore propose a novel role for DYRK1A in coordinating the expression of genes encoding RPs, thereby controlling cell growth in mammals.
Collapse
Affiliation(s)
- Chiara Di Vona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Laura Barba
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 23/A, 43124 Parma, Italy;
| | - Susana de la Luna
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
2
|
Vezzoli M, de Llobet Cucalon LI, Di Vona C, Morselli M, Montanini B, de la Luna S, Teichmann M, Dieci G, Ferrari R. TFIIIC as a Potential Epigenetic Modulator of Histone Acetylation in Human Stem Cells. Int J Mol Sci 2023; 24:ijms24043624. [PMID: 36835038 PMCID: PMC9961906 DOI: 10.3390/ijms24043624] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Regulation of histone acetylation dictates patterns of gene expression and hence cell identity. Due to their clinical relevance in cancer biology, understanding how human embryonic stem cells (hESCs) regulate their genomic patterns of histone acetylation is critical, but it remains largely to be investigated. Here, we provide evidence that acetylation of histone H3 lysine-18 (H3K18ac) and lysine-27 (H3K27ac) is only partially established by p300 in stem cells, while it represents the main histone acetyltransferase (HAT) for these marks in somatic cells. Our analysis reveals that whereas p300 marginally associated with H3K18ac and H3K27ac in hESCs, it largely overlapped with these histone marks upon differentiation. Interestingly, we show that H3K18ac is found at "stemness" genes enriched in RNA polymerase III transcription factor C (TFIIIC) in hESCs, whilst lacking p300. Moreover, TFIIIC was also found in the vicinity of genes involved in neuronal biology, although devoid of H3K18ac. Our data suggest a more complex pattern of HATs responsible for histone acetylations in hESCs than previously considered, suggesting a putative role for H3K18ac and TFIIIC in regulating "stemness" genes as well as genes associated with neuronal differentiation of hESCs. The results break ground for possible new paradigms for genome acetylation in hESCs that could lead to new avenues for therapeutic intervention in cancer and developmental diseases.
Collapse
Affiliation(s)
- Marco Vezzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | | | - Chiara Di Vona
- Genome Biology Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), 08003 Barcelona, Spain
| | - Marco Morselli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Barbara Montanini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Susana de la Luna
- Genome Biology Program, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) and Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Martin Teichmann
- Université de Bordeaux INSERM U1312 (Bordeaux Institute of Oncology) 146, rue Léo Saignat, 33076 Bordeaux, France
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Roberto Ferrari
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
- Correspondence:
| |
Collapse
|
3
|
Lara-Chica M, Correa-Sáez A, Jiménez-Izquierdo R, Garrido-Rodríguez M, Ponce FJ, Moreno R, Morrison K, Di Vona C, Arató K, Jiménez-Jiménez C, Morrugares R, Schmitz ML, de la Luna S, de la Vega L, Calzado MA. A novel CDC25A/DYRK2 regulatory switch modulates cell cycle and survival. Cell Death Differ 2022; 29:105-117. [PMID: 34363019 PMCID: PMC8738746 DOI: 10.1038/s41418-021-00845-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 02/09/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
The cell division cycle 25A (CDC25A) phosphatase is a key regulator of cell cycle progression that acts on the phosphorylation status of Cyclin-Cyclin-dependent kinase complexes, with an emergent role in the DNA damage response and cell survival control. The regulation of CDC25A activity and its protein level is essential to control the cell cycle and maintain genomic integrity. Here we describe a novel ubiquitin/proteasome-mediated pathway negatively regulating CDC25A stability, dependent on its phosphorylation by the serine/threonine kinase DYRK2. DYRK2 phosphorylates CDC25A on at least 7 residues, resulting in its degradation independent of the known CDC25A E3 ubiquitin ligases. CDC25A in turn is able to control the phosphorylation of DYRK2 at several residues outside from its activation loop, thus affecting DYRK2 localization and activity. An inverse correlation between DYRK2 and CDC25A protein amounts was observed during cell cycle progression and in response to DNA damage, with CDC25A accumulation responding to the manipulation of DYRK2 levels or activity in either physiological scenario. Functional data show that the pro-survival activity of CDC25A and the pro-apoptotic activity of DYRK2 could be partly explained by the mutual regulation between both proteins. Moreover, DYRK2 modulation of CDC25A expression and/or activity contributes to the DYRK2 role in cell cycle regulation. Altogether, we provide evidence suggesting that DYRK2 and CDC25A mutually control their activity and stability by a feedback regulatory loop, with a relevant effect on the genotoxic stress pathway, apoptosis, and cell cycle regulation.
Collapse
Affiliation(s)
- Maribel Lara-Chica
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Alejandro Correa-Sáez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Rafael Jiménez-Izquierdo
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Martín Garrido-Rodríguez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Francisco J Ponce
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Rita Moreno
- Division of Cellular Medicine, School of Medicine, University of Dundee, Scotland, UK
| | - Kimberley Morrison
- Division of Cellular Medicine, School of Medicine, University of Dundee, Scotland, UK
| | - Chiara Di Vona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Krisztina Arató
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Carla Jiménez-Jiménez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - Rosario Morrugares
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus-Liebig-University, Member of the German Center for Lung Research, Giessen, Germany
| | - Susana de la Luna
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Laureano de la Vega
- Division of Cellular Medicine, School of Medicine, University of Dundee, Scotland, UK
| | - Marco A Calzado
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain.
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Córdoba, Spain.
- Hospital Universitario Reina Sofía, Córdoba, Spain.
| |
Collapse
|
4
|
Ferrari R, de Llobet Cucalon LI, Di Vona C, Le Dilly F, Vidal E, Lioutas A, Oliete JQ, Jochem L, Cutts E, Dieci G, Vannini A, Teichmann M, de la Luna S, Beato M. TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation. Mol Cell 2020; 77:475-487.e11. [PMID: 31759822 PMCID: PMC7014570 DOI: 10.1016/j.molcel.2019.10.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/20/2019] [Accepted: 10/13/2019] [Indexed: 12/15/2022]
Abstract
How repetitive elements, epigenetic modifications, and architectural proteins interact ensuring proper genome expression remains poorly understood. Here, we report regulatory mechanisms unveiling a central role of Alu elements (AEs) and RNA polymerase III transcription factor C (TFIIIC) in structurally and functionally modulating the genome via chromatin looping and histone acetylation. Upon serum deprivation, a subset of AEs pre-marked by the activity-dependent neuroprotector homeobox Protein (ADNP) and located near cell-cycle genes recruits TFIIIC, which alters their chromatin accessibility by direct acetylation of histone H3 lysine-18 (H3K18). This facilitates the contacts of AEs with distant CTCF sites near promoter of other cell-cycle genes, which also become hyperacetylated at H3K18. These changes ensure basal transcription of cell-cycle genes and are critical for their re-activation upon serum re-exposure. Our study reveals how direct manipulation of the epigenetic state of AEs by a general transcription factor regulates 3D genome folding and expression.
Collapse
Affiliation(s)
- Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Lara Isabel de Llobet Cucalon
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Chiara Di Vona
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - François Le Dilly
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Vidal
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Antonios Lioutas
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Javier Quilez Oliete
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Laura Jochem
- The Institute of Cancer Research (ICR), London, UK
| | - Erin Cutts
- The Institute of Cancer Research (ICR), London, UK
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alessandro Vannini
- The Institute of Cancer Research (ICR), London, UK; Human Technopole. Via Cristina Belgioioso, 171, 20157 Milano MI, Italy
| | - Martin Teichmann
- Université de Bordeaux, INSERM U1212 CNRS UMR 5320 146, Bordeaux, France
| | - Susana de la Luna
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
5
|
Roewenstrunk J, Di Vona C, Chen J, Borras E, Dong C, Arató K, Sabidó E, Huen MSY, de la Luna S. A comprehensive proteomics-based interaction screen that links DYRK1A to RNF169 and to the DNA damage response. Sci Rep 2019; 9:6014. [PMID: 30979931 PMCID: PMC6461666 DOI: 10.1038/s41598-019-42445-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 01/23/2019] [Accepted: 03/29/2019] [Indexed: 12/15/2022] Open
Abstract
Dysregulation of the DYRK1A protein kinase has been associated with human disease. On the one hand, its overexpression in trisomy 21 has been linked to certain pathological traits of Down syndrome, while on the other, inactivating mutations in just one allele are responsible for a distinct yet rare clinical syndrome, DYRK1A haploinsufficiency. Moreover, altered expression of this kinase may also provoke other human pathologies, including cancer and diabetes. Although a few DYRK1A substrates have been described, its upstream regulators and downstream targets are still poorly understood, an information that could shed light on the functions of DYRK1A in the cell. Here, we carried out a proteomic screen using antibody-based affinity purification coupled to mass spectrometry to identify proteins that directly or indirectly bind to endogenous DYRK1A. We show that the use of a cell line not expressing DYRK1A, generated by CRISPR/Cas9 technology, was needed in order to discriminate between true positives and non-specific interactions. Most of the proteins identified in the screen are novel candidate DYRK1A interactors linked to a variety of activities in the cell. The in-depth characterization of DYRK1A's functional interaction with one of them, the E3 ubiquitin ligase RNF169, revealed a role for this kinase in the DNA damage response. We found that RNF169 is a DYRK1A substrate and we identified several of its phosphorylation sites. In particular, one of these sites appears to modify the ability of RNF169 to displace 53BP1 from sites of DNA damage. Indeed, DYRK1A depletion increases cell sensitivity to ionizing irradiation. Therefore, our unbiased proteomic screen has revealed a novel activity of DYRK1A, expanding the complex role of this kinase in controlling cell homeostasis.
Collapse
Affiliation(s)
- Julia Roewenstrunk
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Chiara Di Vona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Jie Chen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, S.A.R., Hong Kong, China
| | - Eva Borras
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Chao Dong
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, S.A.R., Hong Kong, China
| | - Krisztina Arató
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Michael S Y Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, S.A.R., Hong Kong, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, S.A.R., Hong Kong, China
| | - Susana de la Luna
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain.
| |
Collapse
|
6
|
Sharma P, Lioutas A, Fernandez-Fuentes N, Quilez J, Carbonell-Caballero J, Wright RHG, Di Vona C, Le Dily F, Schüller R, Eick D, Oliva B, Beato M. Arginine Citrullination at the C-Terminal Domain Controls RNA Polymerase II Transcription. Mol Cell 2018; 73:84-96.e7. [PMID: 30472187 DOI: 10.1016/j.molcel.2018.10.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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: 05/22/2018] [Revised: 08/31/2018] [Accepted: 10/09/2018] [Indexed: 12/21/2022]
Abstract
The post-translational modification of key residues at the C-terminal domain of RNA polymerase II (RNAP2-CTD) coordinates transcription, splicing, and RNA processing by modulating its capacity to act as a landing platform for a variety of protein complexes. Here, we identify a new modification at the CTD, the deimination of arginine and its conversion to citrulline by peptidyl arginine deiminase 2 (PADI2), an enzyme that has been associated with several diseases, including cancer. We show that, among PADI family members, only PADI2 citrullinates R1810 (Cit1810) at repeat 31 of the CTD. Depletion of PADI2 or loss of R1810 results in accumulation of RNAP2 at transcription start sites, reduced gene expression, and inhibition of cell proliferation. Cit1810 is needed for interaction with the P-TEFb (positive transcription elongation factor b) kinase complex and for its recruitment to chromatin. In this way, CTD-Cit1810 favors RNAP2 pause release and efficient transcription in breast cancer cells.
Collapse
Affiliation(s)
- Priyanka Sharma
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Antonios Lioutas
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Narcis Fernandez-Fuentes
- IBERS, Institute of Biological, Environmental and Rural Science, Aberystwyth University, Aberystwyth SY23 3EB, UK
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - José Carbonell-Caballero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Roni H G Wright
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Chiara Di Vona
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Roland Schüller
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Dirk Eick
- Department of Molecular Epigenetics, Helmholtz Center Munich, Center of Integrated Protein Science, Munich, Germany
| | - Baldomero Oliva
- Universitat Pompeu Fabra (UPF), Barcelona, Spain; Structural Bioinformatics Laboratory (GRIB-IMIM), Department of Experimental and Health Sciences, Barcelona 08003, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
| |
Collapse
|
7
|
Rozen EJ, Roewenstrunk J, Barallobre MJ, Di Vona C, Jung C, Figueiredo AF, Luna J, Fillat C, Arbonés ML, Graupera M, Valverde MA, de la Luna S. DYRK1A Kinase Positively Regulates Angiogenic Responses in Endothelial Cells. Cell Rep 2018; 23:1867-1878. [PMID: 29742440 DOI: 10.1016/j.celrep.2018.04.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 07/24/2017] [Revised: 12/18/2017] [Accepted: 03/31/2018] [Indexed: 11/23/2022] Open
Abstract
Angiogenesis is a highly regulated process essential for organ development and maintenance, and its deregulation contributes to inflammation, cardiac disorders, and cancer. The Ca2+/nuclear factor of activated T cells (NFAT) signaling pathway is central to endothelial cell angiogenic responses, and it is activated by stimuli like vascular endothelial growth factor (VEGF) A. NFAT phosphorylation by dual-specificity tyrosine phosphorylation-regulated kinases (DYRKs) is thought to be an inactivating event. Contrary to expectations, we show that the DYRK family member DYRK1A positively regulates VEGF-dependent NFAT transcriptional responses in primary endothelial cells. DYRK1A silencing reduces intracellular Ca2+ influx in response to VEGF, which dampens NFAT activation. The effect is exerted at the level of VEGFR2 accumulation leading to impairment in PLCγ1 activation. Notably, Dyrk1a heterozygous mice show defects in developmental retinal vascularization. Our data establish a regulatory circuit, DYRK1A/ Ca2+/NFAT, to fine-tune endothelial cell proliferation and angiogenesis.
Collapse
Affiliation(s)
- Esteban J Rozen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Spain
| | - Julia Roewenstrunk
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Spain
| | - María José Barallobre
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Spain; Institut de Biologia Molecular de Barcelona (IBMB), 08028 Barcelona, Spain
| | - Chiara Di Vona
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Spain
| | - Carole Jung
- Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Ana F Figueiredo
- Vascular Signaling Laboratory, ProCURE and Oncobell Programs, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jeroni Luna
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Spain; Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Cristina Fillat
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Spain; Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Maria L Arbonés
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Spain; Institut de Biologia Molecular de Barcelona (IBMB), 08028 Barcelona, Spain
| | - Mariona Graupera
- Vascular Signaling Laboratory, ProCURE and Oncobell Programs, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), 08907 L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Spain
| | - Miguel A Valverde
- Laboratory of Molecular Physiology, Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Susana de la Luna
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
| |
Collapse
|
8
|
Di Vona C, Bezdan D, Islam ABMMK, Salichs E, López-Bigas N, Ossowski S, de la Luna S. Chromatin-wide profiling of DYRK1A reveals a role as a gene-specific RNA polymerase II CTD kinase. Mol Cell 2015; 57:506-20. [PMID: 25620562 DOI: 10.1016/j.molcel.2014.12.026] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [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: 07/14/2014] [Revised: 11/03/2014] [Accepted: 12/16/2014] [Indexed: 02/07/2023]
Abstract
DYRK1A is a dosage-sensitive protein kinase that fulfills key roles during development and in tissue homeostasis, and its dysregulation results in human pathologies. DYRK1A is present in both the nucleus and cytoplasm of mammalian cells, although its nuclear function remains unclear. Genome-wide analysis of DYRK1A-associated loci reveals that the kinase is recruited preferentially to promoters of genes actively transcribed by RNA polymerase II (RNAPII), which are functionally associated with translation, RNA processing, and cell cycle. DYRK1A-bound promoter sequences are highly enriched in a conserved palindromic motif, which is necessary to drive DYRK1A-dependent transcriptional activation. DYRK1A phosphorylates the C-terminal domain (CTD) of RNAPII at Ser2 and Ser5. Depletion of DYRK1A results in reduced association of RNAPII at the target promoters as well as hypophosphorylation of the RNAPII CTD along the target gene bodies. These results are consistent with DYRK1A being a transcriptional regulator by acting as a CTD kinase.
Collapse
Affiliation(s)
- Chiara Di Vona
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), Spain
| | - Daniela Bezdan
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Abul B M M K Islam
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Eulàlia Salichs
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), Spain
| | - Nuria López-Bigas
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Stephan Ossowski
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Susana de la Luna
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain; Centre for Biomedical Network Research on Rare Diseases (CIBERER), Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
| |
Collapse
|