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Mikhaylova V, Rzepka M, Kawamura T, Xia Y, Chang PL, Zhou S, Paasch A, Pham L, Modi N, Yao L, Perez-Agustin A, Pagans S, Boles TC, Lei M, Wang Y, Garcia-Bassets I, Chen Z. Targeted phasing of 2-200 kilobase DNA fragments with a short-read sequencer and a single-tube linked-read library method. Sci Rep 2024; 14:7988. [PMID: 38580715 PMCID: PMC10997766 DOI: 10.1038/s41598-024-58733-0] [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: 08/15/2023] [Accepted: 04/02/2024] [Indexed: 04/07/2024] Open
Abstract
In the human genome, heterozygous sites refer to genomic positions with a different allele or nucleotide variant on the maternal and paternal chromosomes. Resolving these allelic differences by chromosomal copy, also known as phasing, is achievable on a short-read sequencer when using a library preparation method that captures long-range genomic information. TELL-Seq is a library preparation that captures long-range genomic information with the aid of molecular identifiers (barcodes). The same barcode is used to tag the reads derived from the same long DNA fragment within a range of up to 200 kilobases (kb), generating linked-reads. This strategy can be used to phase an entire genome. Here, we introduce a TELL-Seq protocol developed for targeted applications, enabling the phasing of enriched loci of varying sizes, purity levels, and heterozygosity. To validate this protocol, we phased 2-200 kb loci enriched with different methods: CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis for the longest fragments, CRISPR/Cas9-mediated protection from exonuclease digestion for mid-size fragments, and long PCR for the shortest fragments. All selected loci have known clinical relevance: BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA. Collectively, the analyses show that TELL-Seq can accurately phase 2-200 kb targets using a short-read sequencer.
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Affiliation(s)
| | - Madison Rzepka
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | | | - Yu Xia
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Peter L Chang
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | | | - Amber Paasch
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Long Pham
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Naisarg Modi
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA
| | - Likun Yao
- Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Adrian Perez-Agustin
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Sara Pagans
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | | | - Ming Lei
- Universal Sequencing Technology Corp., Canton, MA, 02021, USA
| | - Yong Wang
- Universal Sequencing Technology Corp., Canton, MA, 02021, USA
| | | | - Zhoutao Chen
- Universal Sequencing Technology Corp., Carlsbad, CA, 92011, USA.
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Mikhaylova V, Rzepka M, Kawamura T, Xia Y, Chang PL, Zhou S, Pham L, Modi N, Yao L, Perez-Agustin A, Pagans S, Boles TC, Lei M, Wang Y, Garcia-Bassets I, Chen Z. Targeted Phasing of 2-200 Kilobase DNA Fragments with a Short-Read Sequencer and a Single-Tube Linked-Read Library Method. bioRxiv 2023:2023.03.05.531179. [PMID: 36945366 PMCID: PMC10028795 DOI: 10.1101/2023.03.05.531179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
In the human genome, heterozygous sites are genomic positions with different alleles inherited from each parent. On average, there is a heterozygous site every 1-2 kilobases (kb). Resolving whether two alleles in neighboring heterozygous positions are physically linked-that is, phased-is possible with a short-read sequencer if the sequencing library captures long-range information. TELL-Seq is a library preparation method based on millions of barcoded micro-sized beads that enables instrument-free phasing of a whole human genome in a single PCR tube. TELL-Seq incorporates a unique molecular identifier (barcode) to the short reads generated from the same high-molecular-weight (HMW) DNA fragment (known as 'linked-reads'). However, genome-scale TELL-Seq is not cost-effective for applications focusing on a single locus or a few loci. Here, we present an optimized TELL-Seq protocol that enables the cost-effective phasing of enriched loci (targets) of varying sizes, purity levels, and heterozygosity. Targeted TELL-Seq maximizes linked-read efficiency and library yield while minimizing input requirements, fragment collisions on microbeads, and sequencing burden. To validate the targeted protocol, we phased seven 180-200 kb loci enriched by CRISPR/Cas9-mediated excision coupled with pulse-field electrophoresis, four 20 kb loci enriched by CRISPR/Cas9-mediated protection from exonuclease digestion, and six 2-13 kb loci amplified by PCR. The selected targets have clinical and research relevance (BRCA1, BRCA2, MLH1, MSH2, MSH6, APC, PMS2, SCN5A-SCN10A, and PKI3CA). These analyses reveal that targeted TELL-Seq provides a reliable way of phasing allelic variants within targets (2-200 kb in length) with the low cost and high accuracy of short-read sequencing.
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Affiliation(s)
| | - Madison Rzepka
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | | | - Yu Xia
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | - Peter L. Chang
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | | | - Long Pham
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | - Naisarg Modi
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
| | - Likun Yao
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093 USA
| | - Adrian Perez-Agustin
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Sara Pagans
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | | | - Ming Lei
- Universal Sequencing Technology Corp., Canton, MA 02021, USA
| | - Yong Wang
- Universal Sequencing Technology Corp., Canton, MA 02021, USA
| | | | - Zhoutao Chen
- Universal Sequencing Technology Corp., Carlsbad, CA 92011, USA
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Pinsach-Abuin M, del Olmo B, Pérez-Agustin A, Mates J, Allegue C, Iglesias A, Ma Q, Merkurjev D, Konovalov S, Zhang J, Sheikh F, Telenti A, Brugada J, Brugada R, Gymrek M, di Iulio J, Garcia-Bassets I, Pagans S. Analysis of Brugada syndrome loci reveals that fine-mapping clustered GWAS hits enhances the annotation of disease-relevant variants. Cell Rep Med 2021; 2:100250. [PMID: 33948580 PMCID: PMC8080235 DOI: 10.1016/j.xcrm.2021.100250] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 09/29/2020] [Revised: 01/07/2021] [Accepted: 03/23/2021] [Indexed: 11/30/2022]
Abstract
Genome-wide association studies (GWASs) are instrumental in identifying loci harboring common single-nucleotide variants (SNVs) that affect human traits and diseases. GWAS hits emerge in clusters, but the focus is often on the most significant hit in each trait- or disease-associated locus. The remaining hits represent SNVs in linkage disequilibrium (LD) and are considered redundant and thus frequently marginally reported or exploited. Here, we interrogate the value of integrating the full set of GWAS hits in a locus repeatedly associated with cardiac conduction traits and arrhythmia, SCN5A-SCN10A. Our analysis reveals 5 common 7-SNV haplotypes (Hap1-5) with 2 combinations associated with life-threatening arrhythmia-Brugada syndrome (the risk Hap1/1 and protective Hap2/3 genotypes). Hap1 and Hap2 share 3 SNVs; thus, this analysis suggests that assuming redundancy among clustered GWAS hits can lead to confounding disease-risk associations and supports the need to deconstruct GWAS data in the context of haplotype composition.
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Affiliation(s)
- Mel·lina Pinsach-Abuin
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Bernat del Olmo
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Adrian Pérez-Agustin
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Jesus Mates
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Catarina Allegue
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Visiting Scholar Program, Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Anna Iglesias
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Qi Ma
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daria Merkurjev
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Statistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sergiy Konovalov
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jing Zhang
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Farah Sheikh
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Amalio Telenti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Josep Brugada
- Arrhythmia Unit, Hospital Clinic de Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Ramon Brugada
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
- Cardiology Service, Hospital Universitari Dr. Josep Trueta, Girona, Spain
| | - Melissa Gymrek
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Julia di Iulio
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ivan Garcia-Bassets
- Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sara Pagans
- Department of Medical Sciences, School of Medicine, Universitat de Girona, Girona, Spain
- Institut d’Investigació Biomèdica de Girona, Salt, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
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Carreras D, Martinez-Moreno R, Pinsach-Abuin M, Santafe MM, Gomà P, Brugada R, Scornik FS, Pérez GJ, Pagans S. Epigenetic Changes Governing Scn5a Expression in Denervated Skeletal Muscle. Int J Mol Sci 2021; 22:ijms22052755. [PMID: 33803193 PMCID: PMC7963191 DOI: 10.3390/ijms22052755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
The SCN5A gene encodes the α-subunit of the voltage-gated cardiac sodium channel (NaV1.5), a key player in cardiac action potential depolarization. Genetic variants in protein-coding regions of the human SCN5A have been largely associated with inherited cardiac arrhythmias. Increasing evidence also suggests that aberrant expression of the SCN5A gene could increase susceptibility to arrhythmogenic diseases, but the mechanisms governing SCN5A expression are not yet well understood. To gain insights into the molecular basis of SCN5A gene regulation, we used rat gastrocnemius muscle four days following denervation, a process well known to stimulate Scn5a expression. Our results show that denervation of rat skeletal muscle induces the expression of the adult cardiac Scn5a isoform. RNA-seq experiments reveal that denervation leads to significant changes in the transcriptome, with Scn5a amongst the fifty top upregulated genes. Consistent with this increase in expression, ChIP-qPCR assays show enrichment of H3K27ac and H3K4me3 and binding of the transcription factor Gata4 near the Scn5a promoter region. Also, Gata4 mRNA levels are significantly induced upon denervation. Genome-wide analysis of H3K27ac by ChIP-seq suggest that a super enhancer recently described to regulate Scn5a in cardiac tissue is activated in response to denervation. Altogether, our experiments reveal that similar mechanisms regulate the expression of Scn5a in denervated muscle and cardiac tissue, suggesting a conserved pathway for SCN5A expression among striated muscles.
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Affiliation(s)
- David Carreras
- Cardiovascular Genetics Center, Biomedical Research Institute of Girona, 17190 Salt, Spain; (D.C.); (R.M.-M.); (M.P.-A.); (P.G.); (R.B.)
- Department of Medical Sciences, Universitat de Girona, 17003 Girona, Spain
| | - Rebecca Martinez-Moreno
- Cardiovascular Genetics Center, Biomedical Research Institute of Girona, 17190 Salt, Spain; (D.C.); (R.M.-M.); (M.P.-A.); (P.G.); (R.B.)
- Department of Medical Sciences, Universitat de Girona, 17003 Girona, Spain
| | - Mel·lina Pinsach-Abuin
- Cardiovascular Genetics Center, Biomedical Research Institute of Girona, 17190 Salt, Spain; (D.C.); (R.M.-M.); (M.P.-A.); (P.G.); (R.B.)
- Department of Medical Sciences, Universitat de Girona, 17003 Girona, Spain
| | - Manel M. Santafe
- Unit of Histology and Neurobiology, Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Rovira i Virgili University, 43003 Reus, Spain;
| | - Pol Gomà
- Cardiovascular Genetics Center, Biomedical Research Institute of Girona, 17190 Salt, Spain; (D.C.); (R.M.-M.); (M.P.-A.); (P.G.); (R.B.)
- Department of Medical Sciences, Universitat de Girona, 17003 Girona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, Biomedical Research Institute of Girona, 17190 Salt, Spain; (D.C.); (R.M.-M.); (M.P.-A.); (P.G.); (R.B.)
- Department of Medical Sciences, Universitat de Girona, 17003 Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 21005 Madrid, Spain
- Hospital Josep Trueta, 17007 Girona, Spain
| | - Fabiana S. Scornik
- Cardiovascular Genetics Center, Biomedical Research Institute of Girona, 17190 Salt, Spain; (D.C.); (R.M.-M.); (M.P.-A.); (P.G.); (R.B.)
- Department of Medical Sciences, Universitat de Girona, 17003 Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 21005 Madrid, Spain
- Correspondence: (F.S.S.); (G.J.P.); (S.P.)
| | - Guillermo J. Pérez
- Cardiovascular Genetics Center, Biomedical Research Institute of Girona, 17190 Salt, Spain; (D.C.); (R.M.-M.); (M.P.-A.); (P.G.); (R.B.)
- Department of Medical Sciences, Universitat de Girona, 17003 Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 21005 Madrid, Spain
- Correspondence: (F.S.S.); (G.J.P.); (S.P.)
| | - Sara Pagans
- Cardiovascular Genetics Center, Biomedical Research Institute of Girona, 17190 Salt, Spain; (D.C.); (R.M.-M.); (M.P.-A.); (P.G.); (R.B.)
- Department of Medical Sciences, Universitat de Girona, 17003 Girona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 21005 Madrid, Spain
- Correspondence: (F.S.S.); (G.J.P.); (S.P.)
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5
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Pérez-Agustín A, Pinsach-Abuin M, Pagans S. Role of Non-Coding Variants in Brugada Syndrome. Int J Mol Sci 2020; 21:ijms21228556. [PMID: 33202810 PMCID: PMC7698069 DOI: 10.3390/ijms21228556] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022] Open
Abstract
Brugada syndrome (BrS) is an inherited electrical heart disease associated with a high risk of sudden cardiac death (SCD). The genetic characterization of BrS has always been challenging. Although several cardiac ion channel genes have been associated with BrS, SCN5A is the only gene that presents definitive evidence for causality to be used for clinical diagnosis of BrS. However, more than 65% of diagnosed cases cannot be explained by variants in SCN5A or other genes. Therefore, in an important number of BrS cases, the underlying mechanisms are still elusive. Common variants, mostly located in non-coding regions, have emerged as potential modulators of the disease by affecting different regulatory mechanisms, including transcription factors (TFs), three-dimensional organization of the genome, or non-coding RNAs (ncRNAs). These common variants have been hypothesized to modulate the interindividual susceptibility of the disease, which could explain incomplete penetrance of BrS observed within families. Altogether, the study of both common and rare variants in parallel is becoming increasingly important to better understand the genetic basis underlying BrS. In this review, we aim to describe the challenges of studying non-coding variants associated with disease, re-examine the studies that have linked non-coding variants with BrS, and provide further evidence for the relevance of regulatory elements in understanding this cardiac disorder.
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Affiliation(s)
- Adrian Pérez-Agustín
- Department of Medical Sciences, School of Medicine, University of Girona, 17003 Girona, Spain;
- Biomedical Research Institute of Girona, 17190 Salt, Spain;
| | | | - Sara Pagans
- Department of Medical Sciences, School of Medicine, University of Girona, 17003 Girona, Spain;
- Biomedical Research Institute of Girona, 17190 Salt, Spain;
- Correspondence:
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6
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Boehm D, Jeng M, Camus G, Gramatica A, Schwarzer R, Johnson JR, Hull PA, Montano M, Sakane N, Pagans S, Godin R, Deeks SG, Krogan NJ, Greene WC, Ott M. SMYD2-Mediated Histone Methylation Contributes to HIV-1 Latency. Cell Host Microbe 2017; 21:569-579.e6. [PMID: 28494238 DOI: 10.1016/j.chom.2017.04.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 03/07/2017] [Accepted: 04/24/2017] [Indexed: 12/28/2022]
Abstract
Transcriptional latency of HIV is a last barrier to viral eradication. Chromatin-remodeling complexes and post-translational histone modifications likely play key roles in HIV-1 reactivation, but the underlying mechanisms are incompletely understood. We performed an RNAi-based screen of human lysine methyltransferases and identified the SET and MYND domain-containing protein 2 (SMYD2) as an enzyme that regulates HIV-1 latency. Knockdown of SMYD2 or its pharmacological inhibition reactivated latent HIV-1 in T cell lines and in primary CD4+ T cells. SMYD2 associated with latent HIV-1 promoter chromatin, which was enriched in monomethylated lysine 20 at histone H4 (H4K20me1), a mark lost in cells lacking SMYD2. Further, we find that lethal 3 malignant brain tumor 1 (L3MBTL1), a reader protein with chromatin-compacting properties that recognizes H4K20me1, was recruited to the latent HIV-1 promoter in a SMYD2-dependent manner. We propose that a SMYD2-H4K20me1-L3MBTL1 axis contributes to HIV-1 latency and can be targeted with small-molecule SMYD2 inhibitors.
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Affiliation(s)
- Daniela Boehm
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark Jeng
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gregory Camus
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrea Gramatica
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Roland Schwarzer
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey R Johnson
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Philip A Hull
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mauricio Montano
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Naoki Sakane
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Pharmaceutical Frontier Research Laboratory, JT, 1-13-2 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Sara Pagans
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Warner C Greene
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Melanie Ott
- Gladstone Institute for Virology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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7
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Onwuli DO, Yañez-Bisbe L, Pinsach-Abuin ML, Tarradas A, Brugada R, Greenman J, Pagans S, Beltran-Alvarez P. Do sodium channel proteolytic fragments regulate sodium channel expression? Channels (Austin) 2017; 11:476-481. [PMID: 28718687 DOI: 10.1080/19336950.2017.1355663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 01/19/2023] Open
Abstract
The cardiac voltage-gated sodium channel (gene: SCN5A, protein: NaV1.5) is responsible for the sodium current that initiates the cardiomyocyte action potential. Research into the mechanisms of SCN5A gene expression has gained momentum over the last few years. We have recently described the transcriptional regulation of SCN5A by GATA4 transcription factor. In this addendum to our study, we report our observations that 1) the linker between domains I and II (LDI-DII) of NaV1.5 contains a nuclear localization signal (residues 474-481) that is necessary to localize LDI-DII into the nucleus, and 2) nuclear LDI-DII activates the SCN5A promoter in gene reporter assays using cardiac-like H9c2 cells. Given that voltage-gated sodium channels are known targets of proteases such as calpain, we speculate that NaV1.5 degradation is signaled to the cell transcriptional machinery via nuclear localization of LDI-DII and subsequent stimulation of the SCN5A promoter.
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Affiliation(s)
- Donatus O Onwuli
- a Biomedical Sciences , School of Life Sciences, University of Hull , Kingston upon Hull , UK
| | - Laia Yañez-Bisbe
- b Cardiovascular Genetics Center , Institut d'Investigació Biomèdica de Girona (IDIBGI), University of Girona , Girona , Spain
| | - Mel Lina Pinsach-Abuin
- b Cardiovascular Genetics Center , Institut d'Investigació Biomèdica de Girona (IDIBGI), University of Girona , Girona , Spain.,c Medical Science Department , School of Medicine, University of Girona , Girona , Spain.,d Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV) , Instituto de Salud Carlos III , Madrid , Spain
| | - Anna Tarradas
- b Cardiovascular Genetics Center , Institut d'Investigació Biomèdica de Girona (IDIBGI), University of Girona , Girona , Spain.,c Medical Science Department , School of Medicine, University of Girona , Girona , Spain.,d Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV) , Instituto de Salud Carlos III , Madrid , Spain
| | - Ramon Brugada
- b Cardiovascular Genetics Center , Institut d'Investigació Biomèdica de Girona (IDIBGI), University of Girona , Girona , Spain.,c Medical Science Department , School of Medicine, University of Girona , Girona , Spain.,d Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV) , Instituto de Salud Carlos III , Madrid , Spain.,e Cardiology Service , Hospital Josep Trueta , Girona , Spain
| | - John Greenman
- a Biomedical Sciences , School of Life Sciences, University of Hull , Kingston upon Hull , UK
| | - Sara Pagans
- b Cardiovascular Genetics Center , Institut d'Investigació Biomèdica de Girona (IDIBGI), University of Girona , Girona , Spain.,c Medical Science Department , School of Medicine, University of Girona , Girona , Spain.,d Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV) , Instituto de Salud Carlos III , Madrid , Spain
| | - Pedro Beltran-Alvarez
- a Biomedical Sciences , School of Life Sciences, University of Hull , Kingston upon Hull , UK
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8
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Affiliation(s)
- S. Pagans
- Medical Sciences Department; University of Girona Medical School; Girona Spain
- Girona Biomedical Research Institute; Salt Spain
- Biomedical Research Networking Center on Cardiovascular Diseases (CIBERCV); Madrid Spain
| | - M. Vergés
- Medical Sciences Department; University of Girona Medical School; Girona Spain
- Girona Biomedical Research Institute; Salt Spain
- Biomedical Research Networking Center on Cardiovascular Diseases (CIBERCV); Madrid Spain
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9
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Tarradas A, Pinsach-Abuin ML, Mackintosh C, Llorà-Batlle O, Pérez-Serra A, Batlle M, Pérez-Villa F, Zimmer T, Garcia-Bassets I, Brugada R, Beltran-Alvarez P, Pagans S. Transcriptional regulation of the sodium channel gene (SCN5A) by GATA4 in human heart. J Mol Cell Cardiol 2016; 102:74-82. [PMID: 27894866 DOI: 10.1016/j.yjmcc.2016.10.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 10/07/2016] [Accepted: 10/24/2016] [Indexed: 01/12/2023]
Abstract
Aberrant expression of the sodium channel gene (SCN5A) has been proposed to disrupt cardiac action potential and cause human cardiac arrhythmias, but the mechanisms of SCN5A gene regulation and dysregulation still remain largely unexplored. To gain insight into the transcriptional regulatory networks of SCN5A, we surveyed the promoter and first intronic regions of the SCN5A gene, predicting the presence of several binding sites for GATA transcription factors (TFs). Consistent with this prediction, chromatin immunoprecipitation (ChIP) and sequential ChIP (Re-ChIP) assays show co-occupancy of cardiac GATA TFs GATA4 and GATA5 on promoter and intron 1 SCN5A regions in fresh-frozen human left ventricle samples. Gene reporter experiments show GATA4 and GATA5 synergism in the activation of the SCN5A promoter, and its dependence on predicted GATA binding sites. GATA4 and GATA6 mRNAs are robustly expressed in fresh-frozen human left ventricle samples as measured by highly sensitive droplet digital PCR (ddPCR). GATA5 mRNA is marginally but still clearly detected in the same samples. Importantly, GATA4 mRNA levels are strongly and positively correlated with SCN5A transcript levels in the human heart. Together, our findings uncover a novel mechanism of GATA TFs in the regulation of the SCN5A gene in human heart tissue. Our studies suggest that GATA5 but especially GATA4 are main contributors to SCN5A gene expression, thus providing a new paradigm of SCN5A expression regulation that may shed new light into the understanding of cardiac disease.
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Affiliation(s)
- Anna Tarradas
- Medical Sciences Department, School of Medicine, University of Girona, 17071 Girona, Spain; Institut d'Investigació Biomèdica de Girona, 17190 Salt, Spain
| | - Mel Lina Pinsach-Abuin
- Medical Sciences Department, School of Medicine, University of Girona, 17071 Girona, Spain; Institut d'Investigació Biomèdica de Girona, 17190 Salt, Spain; School of Medicine, University of California San Diego, La Jolla, CA 92093-0648, USA
| | - Carlos Mackintosh
- School of Medicine, University of California San Diego, La Jolla, CA 92093-0648, USA
| | - Oriol Llorà-Batlle
- Medical Sciences Department, School of Medicine, University of Girona, 17071 Girona, Spain; Institut d'Investigació Biomèdica de Girona, 17190 Salt, Spain
| | - Alexandra Pérez-Serra
- Medical Sciences Department, School of Medicine, University of Girona, 17071 Girona, Spain; Institut d'Investigació Biomèdica de Girona, 17190 Salt, Spain
| | - Montserrat Batlle
- Thorax Institute, Cardiology Department, Hospital Clínic, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer, 08036 Barcelona, Spain
| | - Félix Pérez-Villa
- Thorax Institute, Cardiology Department, Hospital Clínic, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer, 08036 Barcelona, Spain
| | - Thomas Zimmer
- Institute for Physiology II, University Hospital, 07743 Jena, Germany
| | - Ivan Garcia-Bassets
- School of Medicine, University of California San Diego, La Jolla, CA 92093-0648, USA
| | - Ramon Brugada
- Medical Sciences Department, School of Medicine, University of Girona, 17071 Girona, Spain; Institut d'Investigació Biomèdica de Girona, 17190 Salt, Spain; Hospital Universitari Dr. Josep Trueta, 17001 Girona, Spain
| | - Pedro Beltran-Alvarez
- Medical Sciences Department, School of Medicine, University of Girona, 17071 Girona, Spain; Institut d'Investigació Biomèdica de Girona, 17190 Salt, Spain; School of Biological, Biomedical, and Environmental Sciences, University of Hull, HU6 7RX, Hull, UK.
| | - Sara Pagans
- Medical Sciences Department, School of Medicine, University of Girona, 17071 Girona, Spain; Institut d'Investigació Biomèdica de Girona, 17190 Salt, Spain.
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10
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Mademont-Soler I, Pinsach-Abuin M, Riuró H, Mates J, Pérez-Serra A, Coll M, Porres JM, del Olmo B, Iglesias A, Selga E, Picó F, Pagans S, Ferrer-Costa C, Sarquella-Brugada G, Arbelo E, Cesar S, Brugada J, Campuzano Ó, Brugada R. Large Genomic Imbalances in Brugada Syndrome. PLoS One 2016; 11:e0163514. [PMID: 27684715 PMCID: PMC5042553 DOI: 10.1371/journal.pone.0163514] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/09/2016] [Indexed: 01/01/2023] Open
Abstract
Purpose Brugada syndrome (BrS) is a form of cardiac arrhythmia which may lead to sudden cardiac death. The recommended genetic testing (direct sequencing of SCN5A) uncovers disease-causing SNVs and/or indels in ~20% of cases. Limited information exists about the frequency of copy number variants (CNVs) in SCN5A in BrS patients, and the role of CNVs in BrS-minor genes is a completely unexplored field. Methods 220 BrS patients with negative genetic results were studied to detect CNVs in SCN5A. 63 cases were also screened for CNVs in BrS-minor genes. Studies were performed by Multiplex ligation-dependent probe amplification or Next-Generation Sequencing (NGS). Results The detection rate for CNVs in SCN5A was 0.45% (1/220). The detected imbalance consisted of a duplication from exon 15 to exon 28, and could potentially explain the BrS phenotype. No CNVs were found in BrS-minor genes. Conclusion CNVs in current BrS-related genes are uncommon among BrS patients. However, as these rearrangements may underlie a portion of cases and they undergo unnoticed by traditional sequencing, an appealing alternative to conventional studies in these patients could be targeted NGS, including in a single experiment the study of SNVs, indels and CNVs in all the known BrS-related genes.
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Affiliation(s)
| | | | - Helena Riuró
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Jesus Mates
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | | | - Mònica Coll
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | | | - Bernat del Olmo
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Anna Iglesias
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Elisabet Selga
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Ferran Picó
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
| | - Sara Pagans
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | | | | | - Elena Arbelo
- Arrhythmia Unit, Hospital Clinic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Sergi Cesar
- Arrhythmia Unit, Hospital Clinic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Josep Brugada
- Arrhythmia Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
- Arrhythmia Unit, Hospital Clinic de Barcelona, University of Barcelona, Barcelona, Spain
| | - Óscar Campuzano
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, University of Girona-IDIBGI, Girona, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Cardiovascular Genetics Unit, Hospital Josep Trueta, Girona, Spain
- * E-mail:
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11
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Ali I, Ramage H, Boehm D, Dirk LMA, Sakane N, Hanada K, Pagans S, Kaehlcke K, Aull K, Weinberger L, Trievel R, Schnoelzer M, Kamada M, Houtz R, Ott M. The HIV-1 Tat Protein Is Monomethylated at Lysine 71 by the Lysine Methyltransferase KMT7. J Biol Chem 2016; 291:16240-8. [PMID: 27235396 DOI: 10.1074/jbc.m116.735415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 04/27/2016] [Indexed: 11/06/2022] Open
Abstract
The HIV-1 transactivator protein Tat is a critical regulator of HIV transcription primarily enabling efficient elongation of viral transcripts. Its interactions with RNA and various host factors are regulated by ordered, transient post-translational modifications. Here, we report a novel Tat modification, monomethylation at lysine 71 (K71). We found that Lys-71 monomethylation (K71me) is catalyzed by KMT7, a methyltransferase that also targets lysine 51 (K51) in Tat. Using mass spectrometry, in vitro enzymology, and modification-specific antibodies, we found that KMT7 monomethylates both Lys-71 and Lys-51 in Tat. K71me is important for full Tat transactivation, as KMT7 knockdown impaired the transcriptional activity of wild type (WT) Tat but not a Tat K71R mutant. These findings underscore the role of KMT7 as an important monomethyltransferase regulating HIV transcription through Tat.
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Affiliation(s)
- Ibraheem Ali
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Departments of Medicine and
| | - Holly Ramage
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Daniela Boehm
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Lynnette M A Dirk
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40508
| | - Naoki Sakane
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Pharmaceutical Frontier Research Laboratory, JT Inc., Yokohama 236-0004, Japan
| | - Kazuki Hanada
- Pharmaceutical Frontier Research Laboratory, JT Inc., Yokohama 236-0004, Japan
| | - Sara Pagans
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Katrin Kaehlcke
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158
| | - Katherine Aull
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158
| | - Leor Weinberger
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94158
| | - Raymond Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, and
| | | | - Masafumi Kamada
- Pharmaceutical Frontier Research Laboratory, JT Inc., Yokohama 236-0004, Japan
| | - Robert Houtz
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40508
| | - Melanie Ott
- From the Gladstone Institute of Virology and Immunology, San Francisco, California 94158, Departments of Medicine and
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12
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Peeters U, Scornik F, Riuró H, Pérez G, Komurcu-Bayrak E, Van Malderen S, Pappaert G, Tarradas A, Pagans S, Daneels D, Breckpot K, Brugada P, Bonduelle M, Brugada R, Van Dooren S. Contribution of Cardiac Sodium Channel β-Subunit Variants to Brugada Syndrome. Circ J 2015; 79:2118-29. [PMID: 26179811 DOI: 10.1253/circj.cj-15-0164] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Brugada syndrome (BrS) is an inheritable cardiac disease associated with syncope, malignant ventricular arrhythmias and sudden cardiac death. The largest proportion of mutations in BrS is found in the SCN5A gene encoding the α-subunit of cardiac sodium channels (Nav1.5). Causal SCN5A mutations are present in 18-30% of BrS patients. The additional genetic diagnostic yield of variants in cardiac sodium channel β-subunits in BrS patients was explored and functional studies on 3 novel candidate variants were performed. METHODS AND RESULTS TheSCN1B-SCN4B genes were screened, which encode the 5 sodium channel β-subunits, in a SCN5A negative BrS population (n=74). Five novel variants were detected; in silico pathogenicity prediction classified 4 variants as possibly disease causing. Three variants were selected for functional study. These variants caused only limited alterations of Nav1.5 function. Next generation sequencing of a panel of 88 arrhythmia genes could not identify other major causal mutations. CONCLUSIONS It was hypothesized that the studied variants are not the primary cause of BrS in these patients. However, because small functional effects of these β-subunit variants can be discriminated, they might contribute to the BrS phenotype and be considered a risk factor. The existence of these risk factors can give an explanation to the reduced penetrance and variable expressivity seen in this syndrome. We therefore recommend including the SCN1-4B genes in a next generation sequencing-based gene panel.
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Affiliation(s)
- Uschi Peeters
- Centre for Medical Genetics, Reproduction and Genetics; Reproduction, Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel)
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13
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Selga E, Campuzano O, Pinsach-Abuin M, Pérez-Serra A, Mademont-Soler I, Riuró H, Picó F, Coll M, Iglesias A, Pagans S, Sarquella-Brugada G, Berne P, Benito B, Brugada J, Porres JM, López Zea M, Castro-Urda V, Fernández-Lozano I, Brugada R. Comprehensive Genetic Characterization of a Spanish Brugada Syndrome Cohort. PLoS One 2015; 10:e0132888. [PMID: 26173111 PMCID: PMC4501715 DOI: 10.1371/journal.pone.0132888] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/22/2015] [Indexed: 12/12/2022] Open
Abstract
Background Brugada syndrome (BrS) is a rare genetic cardiac arrhythmia that can lead to sudden cardiac death in patients with a structurally normal heart. Genetic variations in SCN5A can be identified in approximately 20-25% of BrS cases. The aim of our work was to determine the spectrum and prevalence of genetic variations in a Spanish cohort diagnosed with BrS. Methodology/Principal Findings We directly sequenced fourteen genes reported to be associated with BrS in 55 unrelated patients clinically diagnosed. Our genetic screening allowed the identification of 61 genetic variants. Of them, 20 potentially pathogenic variations were found in 18 of the 55 patients (32.7% of the patients, 83.3% males). Nineteen of them were located in SCN5A, and had either been previously reported as pathogenic variations or had a potentially pathogenic effect. Regarding the sequencing of the minority genes, we discovered a potentially pathogenic variation in SCN2B that was described to alter sodium current, and one nonsense variant of unknown significance in RANGRF. In addition, we also identified 40 single nucleotide variations which were either synonymous variants (four of them had not been reported yet) or common genetic variants. We next performed MLPA analysis of SCN5A for the 37 patients without an identified genetic variation, and no major rearrangements were detected. Additionally, we show that being at the 30-50 years range or exhibiting symptoms are factors for an increased potentially pathogenic variation discovery yield. Conclusions In summary, the present study is the first comprehensive genetic evaluation of 14 BrS-susceptibility genes and MLPA of SCN5A in a Spanish BrS cohort. The mean pathogenic variation discovery yield is higher than that described for other European BrS cohorts (32.7% vs 20-25%, respectively), and is even higher for patients in the 30-50 years age range.
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Affiliation(s)
- Elisabet Selga
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
| | - Oscar Campuzano
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
| | - Mel·lina Pinsach-Abuin
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
| | - Alexandra Pérez-Serra
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
| | - Irene Mademont-Soler
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
| | - Helena Riuró
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
| | - Ferran Picó
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
| | - Mònica Coll
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
| | - Anna Iglesias
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
| | - Sara Pagans
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
| | - Georgia Sarquella-Brugada
- Paediatric Arrhythmia Unit, Cardiology Department, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Paola Berne
- Arrhythmia Unit, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Begoña Benito
- Arrhythmia Unit, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - Josep Brugada
- Arrhythmia Unit, Hospital Clínic of Barcelona, University of Barcelona, Barcelona, Spain
| | - José M. Porres
- Arrhythmia Unit, Hospital Universitario Donostia, San Sebastian, Spain
| | | | | | | | - Ramon Brugada
- Cardiovascular Genetics Centre, Institut d’Investigació Biomèdica de Girona (IDIBGi), Girona, Spain and Medical School, Universitat de Girona (UdG), Girona, Spain
- Hospital Josep Trueta, Girona, Spain
- * E-mail:
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Beltran-Alvarez P, Feixas F, Osuna S, Díaz-Hernández R, Brugada R, Pagans S. Interplay between R513 methylation and S516 phosphorylation of the cardiac voltage-gated sodium channel. Amino Acids 2014; 47:429-34. [PMID: 25501501 DOI: 10.1007/s00726-014-1890-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 12/04/2014] [Indexed: 10/24/2022]
Abstract
Arginine methylation is a novel post-translational modification within the voltage-gated ion channel superfamily, including the cardiac sodium channel, NaV1.5. We show that NaV1.5 R513 methylation decreases S516 phosphorylation rate by 4 orders of magnitude, the first evidence of protein kinase A inhibition by arginine methylation. Reciprocally, S516 phosphorylation blocks R513 methylation. NaV1.5 p.G514C, associated to cardiac conduction disease, abrogates R513 methylation, while leaving S516 phosphorylation rate unchanged. This is the first report of methylation-phosphorylation cross-talk of a cardiac ion channel.
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Affiliation(s)
- Pedro Beltran-Alvarez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona Dr. Josep Trueta, University of Girona, 17003, Girona, Spain,
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15
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Beltran-Alvarez P, Tarradas A, Chiva C, Pérez-Serra A, Batlle M, Pérez-Villa F, Schulte U, Sabidó E, Brugada R, Pagans S. Identification of N-terminal protein acetylation and arginine methylation of the voltage-gated sodium channel in end-stage heart failure human heart. J Mol Cell Cardiol 2014; 76:126-9. [PMID: 25172307 DOI: 10.1016/j.yjmcc.2014.08.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/25/2014] [Accepted: 08/15/2014] [Indexed: 11/30/2022]
Abstract
The α subunit of the cardiac voltage-gated sodium channel, NaV1.5, provides the rapid sodium inward current that initiates cardiomyocyte action potentials. Here, we analyzed for the first time the post-translational modifications of NaV1.5 purified from end-stage heart failure human cardiac tissue. We identified R526 methylation as the major post-translational modification of any NaV1.5 arginine or lysine residue. Unexpectedly, we found that the N terminus of NaV1.5 was: 1) devoid of the initiation methionine, and 2) acetylated at the resulting initial alanine residue. This is the first evidence for N-terminal acetylation in any member of the voltage-gated ion channel superfamily. Our results open the door to explore NaV1.5 N-terminal acetylation and arginine methylation levels as drivers or markers of end-stage heart failure.
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Affiliation(s)
- Pedro Beltran-Alvarez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, 17003 Girona, Spain.
| | - Anna Tarradas
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, 17003 Girona, Spain; Department of Medical Sciences, School of Medicine, University of Girona, 17003 Girona, Spain
| | - Cristina Chiva
- Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Alexandra Pérez-Serra
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, 17003 Girona, Spain; Department of Medical Sciences, School of Medicine, University of Girona, 17003 Girona, Spain
| | - Montserrat Batlle
- Thorax Institute, Cardiology Department, Hospital Clínic, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer, 08036 Barcelona, Spain
| | - Félix Pérez-Villa
- Thorax Institute, Cardiology Department, Hospital Clínic, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer, 08036 Barcelona, Spain
| | - Uwe Schulte
- Logopharm GmbH, 79232 March-Buchheim, Germany
| | - Eduard Sabidó
- Proteomics Unit, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Ramon Brugada
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, 17003 Girona, Spain; Department of Medical Sciences, School of Medicine, University of Girona, 17003 Girona, Spain.
| | - Sara Pagans
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, 17003 Girona, Spain; Department of Medical Sciences, School of Medicine, University of Girona, 17003 Girona, Spain.
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Tarradas A, Pinsach-Abuin M, Llora O, Beltran-Alvarez P, Brugada R, Pagans S. P579Novel insights into the regulatory mechanisms of scn5a expression. Cardiovasc Res 2014. [DOI: 10.1093/cvr/cvu098.11] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Alcalde M, Campuzano O, Beltran-Alvarez P, Pagans S, Verges M, Brugada R. P389Role of truncated plakophilin-2 in arrhythmogenic right ventricular cardiomyopathy. Cardiovasc Res 2014. [DOI: 10.1093/cvr/cvu091.71] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Riuró H, Beltran-Alvarez P, Tarradas A, Selga E, Campuzano O, Vergés M, Pagans S, Iglesias A, Brugada J, Brugada P, Vázquez FM, Pérez GJ, Scornik FS, Brugada R. A missense mutation in the sodium channel β2 subunit reveals SCN2B as a new candidate gene for Brugada syndrome. Hum Mutat 2013; 34:961-6. [PMID: 23559163 DOI: 10.1002/humu.22328] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/21/2013] [Indexed: 11/09/2022]
Abstract
Brugada Syndrome (BrS) is a familial disease associated with sudden cardiac death. A 20%-25% of BrS patients carry genetic defects that cause loss-of-function of the voltage-gated cardiac sodium channel. Thus, 70%-75% of patients remain without a genetic diagnosis. In this work, we identified a novel missense mutation (p.Asp211Gly) in the sodium β2 subunit encoded by SCN2B, in a woman diagnosed with BrS. We studied the sodium current (INa ) from cells coexpressing Nav 1.5 and wild-type (β2WT) or mutant (β2D211G) β2 subunits. Our electrophysiological analysis showed a 39.4% reduction in INa density when Nav 1.5 was coexpressed with the β2D211G. Single channel analysis showed that the mutation did not affect the Nav 1.5 unitary channel conductance. Instead, protein membrane detection experiments suggested that β2D211G decreases Nav 1.5 cell surface expression. The effect of the mutant β2 subunit on the INa strongly suggests that SCN2B is a new candidate gene associated with BrS.
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Affiliation(s)
- Helena Riuró
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Girona, Spain
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Sakane N, Kwon HS, Pagans S, Kaehlcke K, Mizusawa Y, Kamada M, Lassen KG, Chan J, Greene WC, Schnoelzer M, Ott M. Activation of HIV transcription by the viral Tat protein requires a demethylation step mediated by lysine-specific demethylase 1 (LSD1/KDM1). PLoS Pathog 2011; 7:e1002184. [PMID: 21876670 PMCID: PMC3158049 DOI: 10.1371/journal.ppat.1002184] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [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: 01/11/2011] [Accepted: 06/14/2011] [Indexed: 12/11/2022] Open
Abstract
The essential transactivator function of the HIV Tat protein is regulated by multiple posttranslational modifications. Although individual modifications are well characterized, their crosstalk and dynamics of occurrence during the HIV transcription cycle remain unclear.We examine interactions between two critical modifications within the RNA-binding domain of Tat: monomethylation of lysine 51 (K51) mediated by Set7/9/KMT7, an early event in the Tat transactivation cycle that strengthens the interaction of Tat with TAR RNA, and acetylation of lysine 50 (K50) mediated by p300/KAT3B, a later process that dissociates the complex formed by Tat, TAR RNA and the cyclin T1 subunit of the positive transcription elongation factor b (P-TEFb). We find K51 monomethylation inhibited in synthetic Tat peptides carrying an acetyl group at K50 while acetylation can occur in methylated peptides, albeit at a reduced rate. To examine whether Tat is subject to sequential monomethylation and acetylation in cells, we performed mass spectrometry on immunoprecipitated Tat proteins and generated new modification-specific Tat antibodies against monomethylated/acetylated Tat. No bimodified Tat protein was detected in cells pointing to a demethylation step during the Tat transactivation cycle. We identify lysine-specific demethylase 1 (LSD1/KDM1) as a Tat K51-specific demethylase, which is required for the activation of HIV transcription in latently infected T cells. LSD1/KDM1 and its cofactor CoREST associates with the HIV promoter in vivo and activate Tat transcriptional activity in a K51-dependent manner. In addition, small hairpin RNAs directed against LSD1/KDM1 or inhibition of its activity with the monoamine oxidase inhibitor phenelzine suppresses the activation of HIV transcription in latently infected T cells.Our data support the model that a LSD1/KDM1/CoREST complex, normally known as a transcriptional suppressor, acts as a novel activator of HIV transcription through demethylation of K51 in Tat. Small molecule inhibitors of LSD1/KDM1 show therapeutic promise by enforcing HIV latency in infected T cells.
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Affiliation(s)
- Naoki Sakane
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
- Pharmaceutical Frontier Research Laboratory, Yokohama, Japan
| | - Hye-Sook Kwon
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Sara Pagans
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Katrin Kaehlcke
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | | | - Masafumi Kamada
- Pharmaceutical Frontier Research Laboratory, Yokohama, Japan
| | - Kara G. Lassen
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Jonathan Chan
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Warner C. Greene
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, United States of America
- Department of Microbiology and Immunology, University of California, San Francisco, United States of America
| | - Martina Schnoelzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, United States of America
- * E-mail:
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20
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Abstract
The α subunit of the cardiac sodium channel (Na(v)1.5) is an essential protein in the initial depolarization phase of the cardiomyocyte action potential. Post-translational modifications such as phosphorylation are known to regulate Na(v)1.5 function. Here, we used a proteomic approach for the study of the post-translational modifications of Na(v)1.5 using tsA201 cells as a model system. We generated a stable cell line expressing Na(v)1.5, purified the sodium channel, and analyzed Na(v)1.5 by MALDI-TOF and LC-MS/MS. We report the identification of arginine methylation as a novel post-translational modification of Na(v)1.5. R513, R526, and R680, located in the linker between domains I and II in Na(v)1.5, were found in mono- or dimethylated states. The functional relevance of arginine methylation in Na(v)1.5 is underscored by the fact that R526H and R680H are known Na(v)1.5 mutations causing Brugada and long QT type 3 syndromes, respectively. Our work describes for the first time arginine methylation in the voltage-gated ion channel superfamily.
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Affiliation(s)
- Pedro Beltran-Alvarez
- Cardiovascular Genetics Center, Institut d'Investigació Biomèdica de Girona, Hospital Dr. Josep Trueta, Girona, Spain
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21
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Pagans S, Pedal A, North BJ, Kaehlcke K, Marshall BL, Dorr A, Hetzer-Egger C, Henklein P, Frye R, McBurney MW, Hruby H, Jung M, Verdin E, Ott M. SIRT1 regulates HIV transcription via Tat deacetylation. PLoS Biol 2005; 3:e41. [PMID: 15719057 PMCID: PMC546329 DOI: 10.1371/journal.pbio.0030041] [Citation(s) in RCA: 263] [Impact Index Per Article: 13.8] [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: 07/22/2004] [Accepted: 12/01/2004] [Indexed: 12/11/2022] Open
Abstract
The human immunodeficiency virus (HIV) Tat protein is acetylated by the transcriptional coactivator p300, a necessary step in Tat-mediated transactivation. We report here that Tat is deacetylated by human sirtuin 1 (SIRT1), a nicotinamide adenine dinucleotide-dependent class III protein deacetylase in vitro and in vivo. Tat and SIRT1 coimmunoprecipitate and synergistically activate the HIV promoter. Conversely, knockdown of SIRT1 via small interfering RNAs or treatment with a novel small molecule inhibitor of the SIRT1 deacetylase activity inhibit Tat-mediated transactivation of the HIV long terminal repeat. Tat transactivation is defective in SIRT1-null mouse embryonic fibroblasts and can be rescued by expression of SIRT1. These results support a model in which cycles of Tat acetylation and deacetylation regulate HIV transcription. SIRT1 recycles Tat to its unacetylated form and acts as a transcriptional coactivator during Tat transactivation. Cycles of Tat acetylation and deacetylation, mediated by human sirtuin 1 (SIRT1), regulate HIV transcription suggesting that SIRT1 could be a therapeutic target
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Affiliation(s)
- Sara Pagans
- 1Gladstone Institute of Virology and Immunology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
| | - Angelika Pedal
- 1Gladstone Institute of Virology and Immunology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
| | - Brian J North
- 1Gladstone Institute of Virology and Immunology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
| | - Katrin Kaehlcke
- 1Gladstone Institute of Virology and Immunology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
| | - Brett L Marshall
- 1Gladstone Institute of Virology and Immunology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
| | - Alexander Dorr
- 2Applied Tumorvirology, Deutsches KrebsforschungszentrumHeidelbergGermany
| | | | - Peter Henklein
- 3Institute of Biochemistry, Humboldt UniversityBerlinGermany
| | - Roy Frye
- 4Department of Pathology, University of PittsburghPittsburgh, PennsylvaniaUnited States of America
| | | | - Henning Hruby
- 6Department of Pharmaceutical Sciences, Albert-Ludwigs-UniversityFreiburgGermany
| | - Manfred Jung
- 6Department of Pharmaceutical Sciences, Albert-Ludwigs-UniversityFreiburgGermany
| | - Eric Verdin
- 1Gladstone Institute of Virology and Immunology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
| | - Melanie Ott
- 1Gladstone Institute of Virology and Immunology, University of CaliforniaSan Francisco, CaliforniaUnited States of America
- 2Applied Tumorvirology, Deutsches KrebsforschungszentrumHeidelbergGermany
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Pagans S, Piñeyro D, Kosoy A, Bernués J, Azorín F. Repression by TTK69 of GAGA-mediated activation occurs in the absence of TTK69 binding to DNA and solely requires the contribution of the POZ/BTB domain of TTK69. J Biol Chem 2003; 279:9725-32. [PMID: 14701830 DOI: 10.1074/jbc.m313200200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [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: 11/06/2022] Open
Abstract
tramtrack 69 (TTK69) is known to repress GAGA-mediated activation of the eve promoter in S2 cells. Here, we show that repression by TTK69 occurs in the absence of bona fide TTK69-binding sites on the template, indicating that it does not require the binding of TTK69 to DNA. Consistent with this interpretation, the POZ/BTB domain of TTK69, which does not bind DNA, is sufficient for repression. Moreover, a fusion protein in which the POZ/BTB domain of GAGA is replaced by that of TTK69 is not capable of activating the eve promoter but efficiently represses GAGA-dependent activation. Repression involves GAGA-TTK69 interaction because TTK69 is not capable of repressing basal transcription. Most probably, GAGA-TTK69 interaction occurs at the promoter because GAGA.TTK69 complexes are fully competent in binding DNA in vitro. Our results also show that repression by TTK69 of GAGA-dependent activation of the eve promoter is not mediated by any of the co-repressors known to interact with TTK69 (dMi2 or C-terminal binding protein) or by trichostatin A-sensitive histone deacetylases. Altogether, these observations strongly suggest that the binding of TTK69 prevents the interaction of GAGA with the transcription machinery and, therefore, compromises its activation potential.
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Affiliation(s)
- Sara Pagans
- Department de Biologia Molecular i Cellular, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Jordi Girona Salgado, 18-26, 08034 Barcelona, Spain
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Abstract
GAGA factor is involved in many nuclear transactions, notably in transcription as an activator in Drosophila. The genomic region corresponding to the Trl promoter has been obtained, and a minimal version of a fully active Trl promoter has been defined using transient transfection assays in S2 cells. DNase I footprinting analysis has shown that this region contains multiple GAGA binding sites, suggesting a potential regulatory role of GAGA on its own promoter. The study shows that GAGA down-regulates Trl expression. The repression does not depend on the GAGA isoform, but binding to DNA is absolutely required. A fragment of the Trl promoter can mediate repression to a heterologous promoter only upon GAGA overexpression in transiently transfected S2 cells. Chromatin immunoprecipitation analysis of S2 cells confirmed that GAGA factors are bound to the Trl promoter over a region of 1.4 kbp. Using a double-stranded RNA interference approach, we show that endogenous GAGA factors limit Trl expression in S2 cells. Our results open the possibility of observing similar GAGA repressive effects on other promoters.
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Affiliation(s)
- Ana Kosoy
- Departament de Biologia Molecular i Cel.lular, Institut de Biologia Molecular de Barcelona, Consell Superior d'Investigacions Cientifiques, Jordi Girona, 18-26, Spain
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Pagans S, Ortiz-Lombardía M, Espinás ML, Bernués J, Azorín F. The Drosophila transcription factor tramtrack (TTK) interacts with Trithorax-like (GAGA) and represses GAGA-mediated activation. Nucleic Acids Res 2002; 30:4406-13. [PMID: 12384587 PMCID: PMC137134 DOI: 10.1093/nar/gkf570] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this study, we report the interaction of the Drosophila transcription factors Trithorax-like (GAGA) and tramtrack (TTK). This interaction is documented both in vitro, through GST pull-down assays, as well as in vivo, in yeast and Schneider S2 cells. GAGA and TTK share in common the presence of an N-terminal POZ/BTB domain that was found to be necessary and sufficient for GAGA-TTK interaction. Structural models that could account for this interaction are discussed. GAGA is known to activate the expression of many genes in Drosophila. On the other hand, TTK was proposed to act as a maternally provided repressor of several pair-rule genes, such as even-skipped (eve). As with many Drosophila genes, eve contains at its promoter region binding sites for GAGA and TTK. Here, in transient expression experiments, we showed that GAGA activates transcription from the eve stripe 2 promoter element and that TTK inhibits this GAGA-dependent activation. Repression by TTK of the eve promoter requires its activation by GAGA and depends on the presence of the POZ/BTB domains of TTK and GAGA. These results indicate that GAGA-TTK interaction contributes to the regulation of gene expression in Drosophila.
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Affiliation(s)
- Sara Pagans
- Departament de Biologia Molecular i Cel.lular, Institut de Biologia Molecular de Barcelona, CSIC, Jordi Girona Salgado, 18-26, 08034 Barcelona, Spain
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25
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García-Bassets I, Ortiz-Lombardía M, Pagans S, Romero A, Canals F, Avil s FX, Azorín F. The identification of nuclear proteins that bind the homopyrimidine strand of d(GA.TC)n DNA sequences, but not the homopurine strand. Nucleic Acids Res 1999; 27:3267-75. [PMID: 10454633 PMCID: PMC148559 DOI: 10.1093/nar/27.16.3267] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [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: 11/15/2022] Open
Abstract
Alternating d(GA.TC)(n)DNA sequences, which are abundant in eukaryotic genomes, can form altered DNA structures. Depending on the environmental conditions, the formation of (GA.GA) hairpins or [C+T(GA.TC)] and [GA(GA.TC)] intramolecular triplexes was observed in vitro. In vivo, the formation of these non-B-DNA structures would likely require the contribution of specific stabilizing factors. Here, we show that Friend's nuclear extracts are rich in proteins which bind the pyrimidine d(TC)(n)strand but not the purine d(GA)n strand (NOGA proteins). Upon chromatographic fractionation, four major proteins were detected (NOGA1-4) that have been purified and characterized. Purified NOGAs bind single-stranded d(TC)n with high affinity and specificity, showing no significant affinity for either d(GA)n or d(GA.TC)nDNA sequences. We also show that NOGA1, -2 and -3, which constitute the three most abundant and specific NOGA proteins, correspond to the single-stranded nucleic acid binding proteins hnRNP-L, -K and -I, respectively. These results are discussed in the context of the possible contribution of the NOGA proteins to the stabilization of the (GA.GA) and [GA(GA.TC)] conformers of the d(GA.TC)n DNA sequences.
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Affiliation(s)
- I García-Bassets
- Departament de Biologia Molecular i Cel.lular, Institut de Biologia Molecular de Barcelona, CID-CSIC, Jordi Girona Salgado 18-26, 08034 Barcelona, Spain
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