1
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Danckwardt S, Trégouët DA, Castoldi E. Post-transcriptional control of haemostatic genes: mechanisms and emerging therapeutic concepts in thrombo-inflammatory disorders. Cardiovasc Res 2023; 119:1624-1640. [PMID: 36943786 PMCID: PMC10325701 DOI: 10.1093/cvr/cvad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 03/23/2023] Open
Abstract
The haemostatic system is pivotal to maintaining vascular integrity. Multiple components involved in blood coagulation have central functions in inflammation and immunity. A derailed haemostasis is common in prevalent pathologies such as sepsis, cardiovascular disorders, and lately, COVID-19. Physiological mechanisms limit the deleterious consequences of a hyperactivated haemostatic system through adaptive changes in gene expression. While this is mainly regulated at the level of transcription, co- and posttranscriptional mechanisms are increasingly perceived as central hubs governing multiple facets of the haemostatic system. This layer of regulation modulates the biogenesis of haemostatic components, for example in situations of increased turnover and demand. However, they can also be 'hijacked' in disease processes, thereby perpetuating and even causally entertaining associated pathologies. This review summarizes examples and emerging concepts that illustrate the importance of posttranscriptional mechanisms in haemostatic control and crosstalk with the immune system. It also discusses how such regulatory principles can be used to usher in new therapeutic concepts to combat global medical threats such as sepsis or cardiovascular disorders.
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Affiliation(s)
- Sven Danckwardt
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre
Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- German Centre for Cardiovascular Research (DZHK),
Berlin, Germany
- Posttranscriptional Gene Regulation, University Medical Centre
Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University
Medical Centre Mainz, Langenbeckstr. 1, 55131
Mainz, Germany
- Center for Healthy Aging (CHA), Mainz,
Germany
| | - David-Alexandre Trégouët
- INSERM, Bordeaux Population Health Research Center, UMR 1219, Department of
Molecular Epidemiology of Vascular and Brain Disorders (ELEANOR), University of
Bordeaux, Bordeaux, France
| | - Elisabetta Castoldi
- Department of Biochemistry, Cardiovascular Research Institute Maastricht
(CARIM), Maastricht University, Universiteitsingel 50, 6229
ER Maastricht, The Netherlands
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2
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Interpreting neural networks for biological sequences by learning stochastic masks. NAT MACH INTELL 2022; 4:41-54. [DOI: 10.1038/s42256-021-00428-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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3
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Roos D, de Boer M. Mutations in cis that affect mRNA synthesis, processing and translation. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166166. [PMID: 33971252 DOI: 10.1016/j.bbadis.2021.166166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022]
Abstract
Genetic mutations that cause hereditary diseases usually affect the composition of the transcribed mRNA and its encoded protein, leading to instability of the mRNA and/or the protein. Sometimes, however, such mutations affect the synthesis, the processing or the translation of the mRNA, with similar disastrous effects. We here present an overview of mRNA synthesis, its posttranscriptional modification and its translation into protein. We then indicate which elements in these processes are known to be affected by pathogenic mutations, but we restrict our review to mutations in cis, in the DNA of the gene that encodes the affected protein. These mutations can be in enhancer or promoter regions of the gene, which act as binding sites for transcription factors involved in pre-mRNA synthesis. We also describe mutations in polyadenylation sequences and in splice site regions, exonic and intronic, involved in intron removal. Finally, we include mutations in the Kozak sequence in mRNA, which is involved in protein synthesis. We provide examples of genetic diseases caused by mutations in these DNA regions and refer to databases to help identify these regions. The over-all knowledge of mRNA synthesis, processing and translation is essential for improvement of the diagnosis of patients with genetic diseases.
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Affiliation(s)
- Dirk Roos
- Sanquin Blood Supply Organization, Dept. of Blood Cell Research, Landsteiner Laboratory, Amsterdam University Medical Centre, location AMC, University of Amsterdam, Amsterdam, the Netherlands.
| | - Martin de Boer
- Sanquin Blood Supply Organization, Dept. of Blood Cell Research, Landsteiner Laboratory, Amsterdam University Medical Centre, location AMC, University of Amsterdam, Amsterdam, the Netherlands
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4
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Abukhiran I, Jasser J, Bhagavathi S. Education Case: Hereditary Thrombophilia With Double Heterozygous Factor V Leiden and Factor II c.*97G>A Mutations. Acad Pathol 2021; 8:2374289521990788. [PMID: 33614922 PMCID: PMC7874341 DOI: 10.1177/2374289521990788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 12/07/2020] [Accepted: 12/30/2020] [Indexed: 11/15/2022] Open
Abstract
The following fictional case is intended as a learning tool within the Pathology Competencies for Medical Education (PCME), a set of national standards for teaching pathology. These are divided into three basic competencies: Disease Mechanisms and Processes, Organ System Pathology, and Diagnostic Medicine and Therapeutic Pathology. For additional information, and a full list of learning objectives for all three competencies, see http://journals.sagepub.com/doi/10.1177/2374289517715040.1.
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Affiliation(s)
- Ibrahim Abukhiran
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Judy Jasser
- Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA, USA
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5
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Abukhiran I, Jasser J, Bhagavathi S. Double-homozygosity for Factor V Leiden and Prothrombin c.*97G > A Mutation in a Young Female with Recurrent Fetal Losses and no Venous Thromboembolism. HUMAN PATHOLOGY: CASE REPORTS 2020. [DOI: 10.1016/j.ehpc.2020.200425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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6
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Pruner I, Farm M, Tomic B, Gvozdenov M, Kovac M, Miljic P, Soutari NMH, Antovic A, Radojkovic D, Antovic J, Djordjevic V. The Silence Speaks, but We Do Not Listen: Synonymous c.1824C>T Gene Variant in the Last Exon of the Prothrombin Gene as a New Prothrombotic Risk Factor. Clin Chem 2020; 66:379-389. [PMID: 32040579 DOI: 10.1093/clinchem/hvz015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/18/2019] [Indexed: 11/14/2022]
Abstract
BACKGROUND Thrombosis is a major global disease burden with almost 60% of cases related to underlying heredity and most cases still idiopathic. Synonymous single nucleotide polymorphisms (sSNPs) are considered silent and phenotypically neutral. Our previous study revealed a novel synonymous FII c.1824C>T variant as a potential risk factor for pregnancy loss, but it has not yet been associated with thrombotic diseases. METHODS To determine the frequency of the FII c.1824C>T variant we have sequenced patients' DNA. Prothrombin RNA expression was measured by quantitative PCR. Functional analyses included routine hemostasis tests, western blotting and ELISA to determine prothrombin levels in plasma, and global hemostasis assays for thrombin and fibrin generation in carriers of the FII c.1824C>T variant. Scanning electron microscopy was used to examine the structure of fibrin clots. RESULTS Frequency of the FII c.1824C>T variant was significantly increased in patients with venous thromboembolism and cerebrovascular insult. Examination in vitro demonstrated increased expression of prothrombin mRNA in FII c.1824T transfected cells. Our ex vivo study of FII c.1824C>T carriers showed that the presence of this variant was associated with hyperprothrombinemia, hypofibrinolysis, and formation of densely packed fibrin clots resistant to fibrinolysis. CONCLUSION Our data indicate that FII c.1824C>T, although a synonymous variant, leads to the development of a prothrombotic phenotype and could represent a new prothrombotic risk factor. As a silent variant, FII c.1824C>T would probably be overlooked during genetic screening, and our results show that it could not be detected in routine laboratory tests.
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Affiliation(s)
- Iva Pruner
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.,Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Maria Farm
- Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.,Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
| | - Branko Tomic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Maja Gvozdenov
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Mirjana Kovac
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Hemostasis Department, Blood Transfusion Institute of Serbia, Belgrade, Serbia
| | - Predrag Miljic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic of Hematology, University Clinical Center, Belgrade, Serbia
| | - Nida Mahmoud Hourani Soutari
- Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.,Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
| | - Aleksandra Antovic
- Department of Medicine, Unit of Rheumatology, Karolinska University Hospital, Stockholm, Sweden.,Academic Specialist Center, Center for Rheumatology, Stockholm Health Services, Stockholm, Sweden
| | - Dragica Radojkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Jovan Antovic
- Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.,Clinical Chemistry, Karolinska University Hospital, Stockholm, Sweden
| | - Valentina Djordjevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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7
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Nourse J, Spada S, Danckwardt S. Emerging Roles of RNA 3'-end Cleavage and Polyadenylation in Pathogenesis, Diagnosis and Therapy of Human Disorders. Biomolecules 2020; 10:biom10060915. [PMID: 32560344 PMCID: PMC7356254 DOI: 10.3390/biom10060915] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/10/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022] Open
Abstract
A crucial feature of gene expression involves RNA processing to produce 3′ ends through a process termed 3′ end cleavage and polyadenylation (CPA). This ensures the nascent RNA molecule can exit the nucleus and be translated to ultimately give rise to a protein which can execute a function. Further, alternative polyadenylation (APA) can produce distinct transcript isoforms, profoundly expanding the complexity of the transcriptome. CPA is carried out by multi-component protein complexes interacting with multiple RNA motifs and is tightly coupled to transcription, other steps of RNA processing, and even epigenetic modifications. CPA and APA contribute to the maintenance of a multitude of diverse physiological processes. It is therefore not surprising that disruptions of CPA and APA can lead to devastating disorders. Here, we review potential CPA and APA mechanisms involving both loss and gain of function that can have tremendous impacts on health and disease. Ultimately we highlight the emerging diagnostic and therapeutic potential CPA and APA offer.
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Affiliation(s)
- Jamie Nourse
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Stefano Spada
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Rhine-Main, Germany
- Correspondence:
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8
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Cell Cycle Kinase Polo Is Controlled by a Widespread 3' Untranslated Region Regulatory Sequence in Drosophila melanogaster. Mol Cell Biol 2019; 39:MCB.00581-18. [PMID: 31085682 DOI: 10.1128/mcb.00581-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 05/04/2019] [Indexed: 01/06/2023] Open
Abstract
Alternative polyadenylation generates transcriptomic diversity, although the physiological impact and regulatory mechanisms involved are still poorly understood. The cell cycle kinase Polo is controlled by alternative polyadenylation in the 3' untranslated region (3'UTR), with critical physiological consequences. Here, we characterized the molecular mechanisms required for polo alternative polyadenylation. We identified a conserved upstream sequence element (USE) close to the polo proximal poly(A) signal. Transgenic flies without this sequence show incorrect selection of polo poly(A) signals with consequent downregulation of Polo expression levels and insufficient/defective activation of Polo kinetochore targets Mps1 and Aurora B. Deletion of the USE results in abnormal mitoses in neuroblasts, revealing a role for this sequence in vivo We found that Hephaestus binds to the USE RNA and that hephaestus mutants display defects in polo alternative polyadenylation concomitant with a striking reduction in Polo protein levels, leading to mitotic errors and aneuploidy. Bioinformatic analyses show that the USE is preferentially localized upstream of noncanonical polyadenylation signals in Drosophila melanogaster genes. Taken together, our results revealed the molecular mechanisms involved in polo alternative polyadenylation, with remarkable physiological functions in Polo expression and activity at the kinetochores, and disclosed a new in vivo function for USEs in Drosophila melanogaster.
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9
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Bogard N, Linder J, Rosenberg AB, Seelig G. A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation. Cell 2019; 178:91-106.e23. [PMID: 31178116 PMCID: PMC6599575 DOI: 10.1016/j.cell.2019.04.046] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 03/18/2019] [Accepted: 04/29/2019] [Indexed: 12/22/2022]
Abstract
Alternative polyadenylation (APA) is a major driver of transcriptome diversity in human cells. Here, we use deep learning to predict APA from DNA sequence alone. We trained our model (APARENT, APA REgression NeT) on isoform expression data from over 3 million APA reporters. APARENT's predictions are highly accurate when tasked with inferring APA in synthetic and human 3'UTRs. Visualizing features learned across all network layers reveals that APARENT recognizes sequence motifs known to recruit APA regulators, discovers previously unknown sequence determinants of 3' end processing, and integrates these features into a comprehensive, interpretable, cis-regulatory code. We apply APARENT to forward engineer functional polyadenylation signals with precisely defined cleavage position and isoform usage and validate predictions experimentally. Finally, we use APARENT to quantify the impact of genetic variants on APA. Our approach detects pathogenic variants in a wide range of disease contexts, expanding our understanding of the genetic origins of disease.
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Affiliation(s)
- Nicholas Bogard
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Johannes Linder
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alexander B Rosenberg
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA.
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10
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Nourse J, Braun J, Lackner K, Hüttelmaier S, Danckwardt S. Large-scale identification of functional microRNA targeting reveals cooperative regulation of the hemostatic system. J Thromb Haemost 2018; 16:2233-2245. [PMID: 30207063 DOI: 10.1111/jth.14290] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Indexed: 12/22/2022]
Abstract
Essentials MicroRNAs (miRNAs) regulate the molecular networks controlling biological functions such as hemostasis. We utilized novel methods to analyze miRNA-mediated regulation of the hemostatic system. 52 specific miRNA interactions with 11 key hemostatic associated genes were identified. Functionality and drugability of miRNA-19b-3p against antithrombin were demonstrated in vivo. SUMMARY: Background microRNAs (miRNAs) confer robustness to complex molecular networks regulating biological functions. However, despite the involvement of miRNAs in almost all biological processes, and the importance of the hemostatic system for a multitude of actions in and beyond blood coagulation, the role of miRNAs in hemostasis is poorly defined. Objectives Here we comprehensively illuminate miRNA-mediated regulation of the hemostatic system in an unbiased manner. Methods In contrast to widely applied association studies, we used an integrative screening approach that combines functional aspects of miRNA silencing with biophysical miRNA interaction based on RNA pull-downs (miTRAP) coupled to next-generation sequencing. Results Examination of a panel of 27 hemostasis-associated gene 3'UTRs revealed the majority to possess substantial Dicer-dependent silencing capability, suggesting functional miRNA targeting. miTRAP revealed 150 specific miRNA interactions with 14 3'UTRs, of which 52, involving 40 miRNAs, were functionally confirmed. This includes cooperative miRNA regulation of key hemostatic genes comprising procoagulant (F7, F8, F11, FGA, FGG and KLKB1) and anticoagulant (SERPINA10, PROZ, SERPIND1 and SERPINC1) as well as fibrinolytic (PLG) components. Bioinformatic analysis of miRNA functionality reveals established and potential novel links between the hemostatic system and other pathologies, such as cancer, bone metabolism and renal function. Conclusions Our findings provide, along with an in-vivo proof of concept, deep insights into the network of miRNAs regulating the hemostatic system and present a foundation for biomarker discovery and novel targeted therapeutics for correction of de-regulated hemostasis and associated processes in the future. A repository of the miRNA targetome covering 14 hemostatic components is provided.
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Affiliation(s)
- J Nourse
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - J Braun
- Institute of Molecular Medicine, Martin Luther University Halle (Saale), Halle, Germany
| | - K Lackner
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - S Hüttelmaier
- Institute of Molecular Medicine, Martin Luther University Halle (Saale), Halle, Germany
| | - S Danckwardt
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Rhine-Main, University Medical Center, Mainz, Germany
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11
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Venous thromboembolism laboratory testing (factor V Leiden and
factor II c.*97G>A), 2018 update: a technical standard of the American College of
Medical Genetics and Genomics (ACMG). Genet Med 2018; 20:1489-1498. [DOI: 10.1038/s41436-018-0322-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 02/07/2023] Open
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12
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Targeting the Polyadenylation Signal of Pre-mRNA: A New Gene Silencing Approach for Facioscapulohumeral Dystrophy. Int J Mol Sci 2018; 19:ijms19051347. [PMID: 29751519 PMCID: PMC5983732 DOI: 10.3390/ijms19051347] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 02/07/2023] Open
Abstract
Facioscapulohumeral dystrophy (FSHD) is characterized by the contraction of the D4Z4 array located in the sub-telomeric region of the chromosome 4, leading to the aberrant expression of the DUX4 transcription factor and the mis-regulation of hundreds of genes. Several therapeutic strategies have been proposed among which the possibility to target the polyadenylation signal to silence the causative gene of the disease. Indeed, defects in mRNA polyadenylation leads to an alteration of the transcription termination, a disruption of mRNA transport from the nucleus to the cytoplasm decreasing the mRNA stability and translation efficiency. This review discusses the polyadenylation mechanisms, why alternative polyadenylation impacts gene expression, and how targeting polyadenylation signal may be a potential therapeutic approach for FSHD.
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13
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Neve J, Patel R, Wang Z, Louey A, Furger AM. Cleavage and polyadenylation: Ending the message expands gene regulation. RNA Biol 2017; 14:865-890. [PMID: 28453393 PMCID: PMC5546720 DOI: 10.1080/15476286.2017.1306171] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/02/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022] Open
Abstract
Cleavage and polyadenylation (pA) is a fundamental step that is required for the maturation of primary protein encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm. 3'end processing is dependent on the assembly of a multiprotein processing complex on the pA signals that reside in the pre-mRNAs. Most eukaryotic genes have multiple pA signals, resulting in alternative cleavage and polyadenylation (APA), a widespread phenomenon that is important to establish cell state and cell type specific transcriptomes. Here, we review how pA sites are recognized and comprehensively summarize how APA is regulated and creates mRNA isoform profiles that are characteristic for cell types, tissues, cellular states and disease.
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Affiliation(s)
- Jonathan Neve
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Radhika Patel
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Zhiqiao Wang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Alastair Louey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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14
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Ogorodnikov A, Kargapolova Y, Danckwardt S. Processing and transcriptome expansion at the mRNA 3' end in health and disease: finding the right end. Pflugers Arch 2016; 468:993-1012. [PMID: 27220521 PMCID: PMC4893057 DOI: 10.1007/s00424-016-1828-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 04/19/2016] [Indexed: 01/09/2023]
Abstract
The human transcriptome is highly dynamic, with each cell type, tissue, and organ system expressing an ensemble of transcript isoforms that give rise to considerable diversity. Apart from alternative splicing affecting the "body" of the transcripts, extensive transcriptome diversification occurs at the 3' end. Transcripts differing at the 3' end can have profound physiological effects by encoding proteins with distinct functions or regulatory properties or by affecting the mRNA fate via the inclusion or exclusion of regulatory elements (such as miRNA or protein binding sites). Importantly, the dynamic regulation at the 3' end is associated with various (patho)physiological processes, including the immune regulation but also tumorigenesis. Here, we recapitulate the mechanisms of constitutive mRNA 3' end processing and review the current understanding of the dynamically regulated diversity at the transcriptome 3' end. We illustrate the medical importance by presenting examples that are associated with perturbations of this process and indicate resulting implications for molecular diagnostics as well as potentially arising novel therapeutic strategies.
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Affiliation(s)
- Anton Ogorodnikov
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
| | - Yulia Kargapolova
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany.
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, Langenbeckstr 1, 55131, Mainz, Germany.
- German Center for Cardiovascular Research (DZHK), Langenbeckstr 1, 55131, Mainz, Germany.
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15
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Zhao LX, Liu B, Li CS. Progress in research into the genes associated with venous thromboembolism. World J Emerg Med 2015; 6:100-4. [PMID: 26056539 DOI: 10.5847/wjem.j.1920-8642.2015.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 04/06/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Venous thromboembolism (VTE), including both deep vein thrombosis (DVT) and pulmonary embolism (PE), is a common, lethal disorder that affects hospitalized and non-hospitalized patients. This study aimed to review the progress in the research into VTE. DATA SOURCES We reviewed the studies about VTE and verified different genetic polymoriphisms of VTE. RESULTS The pathogenesis of VTE involves hereditary and acquired factors. Many studies indicated that the disorder of coagulation and fibirnolytic system is of utmost importance to this disease. Genetic polymoriphism-related VTE demonstrated significant differences among geographies and ethnicities. CONCLUSION VTE has many risk factors, but genetic factors play an important role.
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Affiliation(s)
- Lian-Xing Zhao
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Bo Liu
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Chun-Sheng Li
- Department of Emergency Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
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Abstract
Thrombophilia is a multifactorial disorder that arises from the interaction of acquired and genetic risk factors. Despite the significant efforts made to understand the etiology of this disease, there are still a certain number of patients suffering from idiopathic thrombophilia. The aim of this study was to screen the 3′ end of the prothrombin (FII) gene, which is susceptible to gain-of-function mutations due to its non canonical architecture, in patients with idiopathic thrombophilia and to determine its eventual role in the pathogenesis of thrombophilia. This study was carried out in 100 patients with idiopathic thrombophilia and 100 healthy controls. DNA variants in the 715 bp long region of the 3′ end of the prothrombin gene were identified by sequencing. In our study, we detected two variants: A19911G and C20068T. The frequency of the A19911G gene variant was slightly increased in the group of patients compared to controls, however with no statistically significant difference compared to controls [odds ratio (OR) = 1.06; 95% confidence interval (95% CI) 0.53–2.13]. Heterozygous carriers of the FII C20068T gene variant were four times more frequent in patients (4.0%) than in controls (1.0%), but this difference did not reach statistical significance (OR = 4.12; 95% CI 0.45–37.57). Our findings suggest that variant A19911G is not a significant risk factor, while C20068T may represent a potential risk factor for idiopathic thrombophilia. To confirm our results, further studies should be conducted in a larger cohort of patients.
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17
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Djordjevic V, Pruner I, Tomic B, Nestorovic A, Gvozdenov M, Kovac M, Radojkovic D. The 3'end prothrombin gene variants in patients with different thrombotic events. Lab Med 2014; 45:309-14. [PMID: 25316662 DOI: 10.1309/lm8e84zslpdmwzcm] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
BACKGROUND Prothrombin (FII) A19911G and C20221T gene variants are associated with increased prothrombin levels and potentially represent thrombotic risk factors. OBJECTIVE To determine the frequency of A19911G and C20221T FII gene variants in patients with thrombotic disorders and in women who have experienced pregnancy loss (PL). METHODS We determined the frequency of these variants in 133 patients with deep venous thrombosis (DVT), 80 patients with isolated pulmonary embolism (PE), 101 patients with idiopathic PL, and 180 control individuals. RESULTS The FII A19911G variant was more prevalent in patients with DVT and with PL compared with controls; however, these differences were not statistically significant. The 19911GG genotype was associated with increased risk of PE (odds ratio, 1.91; 95% confidence interval, 1.04-3.51). We did not detect carriers of the FII C20221T gene variant in this study. CONCLUSIONS This is the first study, to our knowledge, that demonstrates the FII 19911GG genotype may represent a risk factor for isolated PE. Also, our results show that the FII C20221T is a rare variant in this population and therefore, routine thrombophilia screening should not include screening for this genotype.
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Affiliation(s)
| | - Iva Pruner
- Institute of Molecular Genetics and Genetic Engineeringand
| | - Branko Tomic
- Institute of Molecular Genetics and Genetic Engineeringand
| | | | - Maja Gvozdenov
- Institute of Molecular Genetics and Genetic Engineeringand
| | - Mirjana Kovac
- Faculty of Medicine, University of Belgrade, Serbia Blood Transfusion Institute of Serbia, Haemostasis Department, Belgrade, Serbia
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Laishram RS. Poly(A) polymerase (PAP) diversity in gene expression--star-PAP vs canonical PAP. FEBS Lett 2014; 588:2185-97. [PMID: 24873880 PMCID: PMC6309179 DOI: 10.1016/j.febslet.2014.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/02/2014] [Accepted: 05/15/2014] [Indexed: 01/09/2023]
Abstract
Almost all eukaryotic mRNAs acquire a poly(A) tail at the 3'-end by a concerted RNA processing event: cleavage and polyadenylation. The canonical PAP, PAPα, was considered the only nuclear PAP involved in general polyadenylation of mRNAs. A phosphoinositide-modulated nuclear PAP, Star-PAP, was then reported to regulate a select set of mRNAs in the cell. In addition, several non-canonical PAPs have been identified with diverse cellular functions. Further, canonical PAP itself exists in multiple isoforms thus illustrating the diversity of PAPs. In this review, we compare two nuclear PAPs, Star-PAP and PAPα with a general overview of PAP diversity in the cell. Emerging evidence suggests distinct niches of target pre-mRNAs for the two PAPs and that modulation of these PAPs regulates distinct cellular functions.
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Affiliation(s)
- Rakesh S Laishram
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India.
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19
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Jablonski J, Clementz M, Ryan K, Valente ST. Analysis of RNA processing reactions using cell free systems: 3' end cleavage of pre-mRNA substrates in vitro. J Vis Exp 2014. [PMID: 24835792 DOI: 10.3791/51309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The 3' end of mammalian mRNAs is not formed by abrupt termination of transcription by RNA polymerase II (RNPII). Instead, RNPII synthesizes precursor mRNA beyond the end of mature RNAs, and an active process of endonuclease activity is required at a specific site. Cleavage of the precursor RNA normally occurs 10-30 nt downstream from the consensus polyA site (AAUAAA) after the CA dinucleotides. Proteins from the cleavage complex, a multifactorial protein complex of approximately 800 kDa, accomplish this specific nuclease activity. Specific RNA sequences upstream and downstream of the polyA site control the recruitment of the cleavage complex. Immediately after cleavage, pre-mRNAs are polyadenylated by the polyA polymerase (PAP) to produce mature stable RNA messages. Processing of the 3' end of an RNA transcript may be studied using cellular nuclear extracts with specific radiolabeled RNA substrates. In sum, a long 32P-labeled uncleaved precursor RNA is incubated with nuclear extracts in vitro, and cleavage is assessed by gel electrophoresis and autoradiography. When proper cleavage occurs, a shorter 5' cleaved product is detected and quantified. Here, we describe the cleavage assay in detail using, as an example, the 3' end processing of HIV-1 mRNAs.
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Affiliation(s)
- Joseph Jablonski
- Department of Infectious Diseases, The Scripps Research Institute
| | - Mark Clementz
- Department of Infectious Diseases, The Scripps Research Institute
| | - Kevin Ryan
- Department of Chemistry, City College of New York
| | - Susana T Valente
- Department of Infectious Diseases, The Scripps Research Institute;
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20
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A meta-analysis of genome-wide association studies identifies ORM1 as a novel gene controlling thrombin generation potential. Blood 2014; 123:777-85. [DOI: 10.1182/blood-2013-10-529628] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Key PointsGenetic variations at the ORM1 locus and concentrations of the encoded protein associate with thrombin generation. These findings may guide the development of novel antithrombotic treatments.
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21
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Prasad MK, Bhalla K, Pan ZH, O’Connell JR, Weder AB, Chakravarti A, Tian B, Chang YPC. A polymorphic 3'UTR element in ATP1B1 regulates alternative polyadenylation and is associated with blood pressure. PLoS One 2013; 8:e76290. [PMID: 24098465 PMCID: PMC3788127 DOI: 10.1371/journal.pone.0076290] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/22/2013] [Indexed: 12/31/2022] Open
Abstract
Although variants in many genes have previously been shown to be associated with blood pressure (BP) levels, the molecular mechanism underlying these associations are mostly unknown. We identified a multi-allelic T-rich sequence (TRS) in the 3’UTR of ATP1B1 that varies in length and sequence composition (T22-27 and T12GT 3GT6). The 3’UTR of ATP1B1 contains 2 functional polyadenylation signals and the TRS is downstream of the proximal polyadenylation site (A2). Therefore, we hypothesized that alleles of this TRS might influence ATP1B1 expression by regulating alternative polyadenylation. In vitro, the T12GT 3GT6 allele increases polyadenylation at the A2 polyadenylation site as compared to the T23 allele. Consistent with our hypothesis, the relative abundance of the A2-polyadenylated ATP1B1 mRNA was higher in human kidneys with at least one copy of the T12GT 3GT6 allele than in those lacking this allele. The T12GT 3GT6 allele is also associated with higher systolic BP (beta = 3.3 mmHg, p = 0.014) and diastolic BP (beta = 2.4 mmHg, p = 0.003) in a European-American population. Therefore, we have identified a novel multi-allelic TRS in the 3’UTR of ATP1B1 that is associated with higher BP and may mediate its effect by regulating the polyadenylation of the ATP1B1 mRNA.
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Affiliation(s)
- Megana K. Prasad
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Kavita Bhalla
- Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Zhen Hua Pan
- Department of Biochemistry & Molecular Biology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey, United States of America
| | - Jeffrey R. O’Connell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Alan B. Weder
- Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, Michigan, United States of America
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Bin Tian
- Department of Biochemistry & Molecular Biology, University of Medicine and Dentistry of New Jersey, New Jersey Medical School, Newark, New Jersey, United States of America
| | - Yen-Pei C. Chang
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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22
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Pathologies at the nexus of blood coagulation and inflammation: thrombin in hemostasis, cancer, and beyond. J Mol Med (Berl) 2013; 91:1257-71. [PMID: 23955016 PMCID: PMC3825489 DOI: 10.1007/s00109-013-1074-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/24/2013] [Accepted: 07/29/2013] [Indexed: 02/06/2023]
Abstract
Thrombin is the protease involved in blood coagulation. Its deregulation can lead to hemostatic abnormalities, which range from subtle subclinical to serious life-threatening coagulopathies, i.e., during septicemia. Additionally, thrombin plays important roles in many (patho)physiological conditions that reach far beyond its well-established role in stemming blood loss and thrombosis, including embryonic development and angiogenesis but also extending to inflammatory processes, complement activation, and even tumor biology. In this review, we will address thrombin's broad roles in diverse (patho)physiological processes in an integrative way. We will also discuss thrombin as an emerging major target for novel therapies.
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23
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Rehfeld A, Plass M, Krogh A, Friis-Hansen L. Alterations in polyadenylation and its implications for endocrine disease. Front Endocrinol (Lausanne) 2013; 4:53. [PMID: 23658553 PMCID: PMC3647115 DOI: 10.3389/fendo.2013.00053] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/22/2013] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Polyadenylation is the process in which the pre-mRNA is cleaved at the poly(A) site and a poly(A) tail is added - a process necessary for normal mRNA formation. Genes with multiple poly(A) sites can undergo alternative polyadenylation (APA), producing distinct mRNA isoforms with different 3' untranslated regions (3' UTRs) and in some cases different coding regions. Two thirds of all human genes undergo APA. The efficiency of the polyadenylation process regulates gene expression and APA plays an important part in post-transcriptional regulation, as the 3' UTR contains various cis-elements associated with post-transcriptional regulation, such as target sites for micro-RNAs and RNA-binding proteins. Implications of alterations in polyadenylation for endocrine disease: Alterations in polyadenylation have been found to be causative of neonatal diabetes and IPEX (immune dysfunction, polyendocrinopathy, enteropathy, X-linked) and to be associated with type I and II diabetes, pre-eclampsia, fragile X-associated premature ovarian insufficiency, ectopic Cushing syndrome, and many cancer diseases, including several types of endocrine tumor diseases. PERSPECTIVES Recent developments in high-throughput sequencing have made it possible to characterize polyadenylation genome-wide. Antisense elements inhibiting or enhancing specific poly(A) site usage can induce desired alterations in polyadenylation, and thus hold the promise of new therapeutic approaches. SUMMARY This review gives a detailed description of alterations in polyadenylation in endocrine disease, an overview of the current literature on polyadenylation and summarizes the clinical implications of the current state of research in this field.
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Affiliation(s)
- Anders Rehfeld
- Genomic Medicine, Rigshospitalet, Copenhagen University HospitalCopenhagen, Denmark
| | - Mireya Plass
- Department of Biology, The Bioinformatics Centre, University of CopenhagenCopenhagen, Denmark
| | - Anders Krogh
- Department of Biology, The Bioinformatics Centre, University of CopenhagenCopenhagen, Denmark
| | - Lennart Friis-Hansen
- Genomic Medicine, Rigshospitalet, Copenhagen University HospitalCopenhagen, Denmark
- *Correspondence: Lennart Friis-Hansen, Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, 4113, Blegdamsvej 9, DK2100 Copenhagen, Denmark. e-mail:
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24
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Coagulation and the fibrin network in rheumatic disease: a role beyond haemostasis. Nat Rev Rheumatol 2012; 8:738-46. [PMID: 23147903 DOI: 10.1038/nrrheum.2012.184] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Activation of the immune system has been increasingly recognised to be associated with procoagulatory status in patients with inflammatory rheumatic disease. Changes in endothelial cell and platelet activation, blood flow, expression and activity of different coagulation factors, and impaired fibrinolysis serve as pathophysiological basis for enhanced risk of venous thromboembolism in inflammatory rheumatic diseases, such as rheumatoid arthritis (RA), connective tissue diseases and vasculitides. Recent studies identifying mechanisms for a functional role of coagulation factors beyond haemostasis have provided examples of interesting links between the coagulation system and innate immune activation. Furthermore, citrullinated fibrinogen is an important and early autoantigen in patients with RA carrying the HLA-DRβ1 shared epitope allele, which demonstrates an adaptive immune response to a coagulation factor in an inflammatory rheumatic disease. Additional studies have provided strong evidence that a multitude of different components of the haemostatic system (such as thrombin, fibrinogen, coagulation factor XIII and factors of the fibrinolytic system) are relevant mediators of inflammatory processes as well as of inflammatory control. Understanding the interactions between coagulation and the immune system in inflammatory rheumatic diseases will not only improve our knowledge of disease mechanisms, but could also permit the development of innovative therapeutic interventions.
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25
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Abstract
From the first genome wide association studies (GWAS) conducted on age-related macular degeneration back in 2005 until now, hundreds of studies have applied this strategy to identify novel genetic loci associated with hundreds of human diseases and related quantitative risk factors. While the GWAS revolution has just started to shift towards the next generation sequencing's burst, it is important to illustrate how the genetics research in venous thrombosis has benefit from the GWAS paradigm.
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26
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Ho ES, Gunderson SI. Long conserved fragments upstream of Mammalian polyadenylation sites. Genome Biol Evol 2011; 3:654-66. [PMID: 21705472 PMCID: PMC3157836 DOI: 10.1093/gbe/evr053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2011] [Indexed: 12/02/2022] Open
Abstract
Polyadenylation is a cotranscriptional nuclear RNA processing event involving endonucleolytic cleavage of the nascent, emerging pre-messenger RNA (pre-mRNA) from the RNA polymerase, immediately followed by the polymerization of adenine ribonucleotides, called the poly(A) tail, to the cleaved 3' end of the polyadenylation site (PAS). This apparently simple molecular processing step has been discovered to be connected to transcription and splicing therefore increasing its potential for regulation of gene expression. Here, through a bioinformatic analysis of cis-PAS-regulatory elements in mammals that includes taking advantage of multiple evolutionary time scales, we find unexpected selection pressure much further upstream, up to 200 nt, from the PAS than previously thought. Strikingly, close to 3,000 long (30-500 nt) noncoding conserved fragments (CFs) were discovered in the PAS flanking region of three remotely related mammalian species, human, mouse, and cow. When an even more remote transitional mammal, platypus, was included, still over a thousand CFs were found in the proximity of the PAS. Even though the biological function of these CFs remains unknown, their considerable sizes makes them unlikely to serve as protein recognition sites, which are typically ≤15 nt. By harnessing genome wide DNaseI hypersensitivity data, we have discovered that the presence of CFs correlates with chromatin accessibility. Our study is important in highlighting novel experimental targets, which may provide new understanding about the regulatory aspects of polyadenylation.
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Affiliation(s)
- Eric S. Ho
- Present address: Department of Molecular Genetics, Microbiology and Immunology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey
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27
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Danckwardt S, Gantzert AS, Macher-Goeppinger S, Probst HC, Gentzel M, Wilm M, Gröne HJ, Schirmacher P, Hentze MW, Kulozik AE. p38 MAPK controls prothrombin expression by regulated RNA 3' end processing. Mol Cell 2011; 41:298-310. [PMID: 21292162 DOI: 10.1016/j.molcel.2010.12.032] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 11/10/2010] [Accepted: 12/23/2010] [Indexed: 12/16/2022]
Abstract
Thrombin is a key protease involved in blood coagulation, complement activation, inflammation, angiogenesis, and tumor invasion. Although induced in many (patho-)physiological conditions, the underlying mechanisms controlling prothrombin expression remained enigmatic. We have now discovered that prothrombin expression is regulated by a posttranscriptional regulatory mechanism responding to stress and inflammation. This mechanism is triggered by external stimuli that activate p38 MAPK. In turn, p38 MAPK upmodulates canonical 3' end processing components and phosphorylates the RNA-binding proteins FBP2 and FBP3, which inhibit 3' end processing of mRNAs, such as prothrombin mRNA, that bear a defined upstream sequence element (USE) in their 3'UTRs. Upon phosphorylation, FBP2 and FBP3 dissociate from the USE, making it accessible to proteins that stimulate 3' end processing. We provide in vivo evidence suggesting the importance of this mechanism in inflammatory hypercoagulation and tumor invasion. Regulated 3' end processing thus emerges as a key mechanism of gene regulation with broad biological and medical implications.
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Affiliation(s)
- Sven Danckwardt
- Department of Pediatric Oncology, Hematology, and Immunology, University of Heidelberg, Heidelberg, Germany
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28
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Bertina RM, Vos HL. A Novel Genetic Risk Factor for Venous Thrombosis. Clin Chem 2011; 57:637-8. [DOI: 10.1373/clinchem.2010.158998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rogier M Bertina
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Thrombosis and Haemostasis, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans L Vos
- Einthoven Laboratory for Experimental Vascular Medicine, Department of Thrombosis and Haemostasis, Leiden University Medical Center, Leiden, the Netherlands
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29
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Liu X, Jiang Y, Russell JE. A potential regulatory role for mRNA secondary structures within the prothrombin 3'UTR. Thromb Res 2010; 126:130-6. [PMID: 20553951 DOI: 10.1016/j.thromres.2010.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 03/10/2010] [Accepted: 04/20/2010] [Indexed: 11/20/2022]
Abstract
The distal 3'UTR of prothrombin mRNA exhibits significant sequence heterogeneity reflecting an inexact 3'-cleavage/polyadenylation reaction. This same region encompasses a single-nucleotide polymorphism that enhances the normal post-transcriptional processing of nascent prothrombin transcripts. Both observations indicate the importance of 3'UTR structures to physiologically relevant properties of prothrombin mRNA. Using a HepG2-based model system, we mapped both the primary structures of reporter mRNAs containing the prothrombin 3'UTR, as well as the secondary structures of common, informative 3'UTR processing variants. A chromatographic method was subsequently employed to assess the effects of structural heterogeneities on the binding of candidate trans-acting regulatory factors. We observed that prothrombin 3'UTRs are constitutively polyadenylated at seven or more positions, and can fold into at least two distinct stem-loop conformations. These alternate structures expose/sequester a consensus binding site for hnRNP-I/PTB-1, a trans-acting factor with post-transcriptional regulatory properties. hnRNP-I/PTB-1 exhibits different affinities for the alternate 3'UTR secondary structures in vitro, predicting a corresponding regulatory role in vivo. These analyses demonstrate a critical link between the structure of the prothrombin 3'UTR and its normal function, providing a basis for further investigations into the molecular pathophysiology of naturally occurring polymorphisms within this region.
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Affiliation(s)
- Xingge Liu
- Department of Medicine (Hematology-Oncology), University of Pennsylvania School of Medicine and The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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30
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Millevoi S, Vagner S. Molecular mechanisms of eukaryotic pre-mRNA 3' end processing regulation. Nucleic Acids Res 2009; 38:2757-74. [PMID: 20044349 PMCID: PMC2874999 DOI: 10.1093/nar/gkp1176] [Citation(s) in RCA: 291] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Messenger RNA (mRNA) 3′ end formation is a nuclear process through which all eukaryotic primary transcripts are endonucleolytically cleaved and most of them acquire a poly(A) tail. This process, which consists in the recognition of defined poly(A) signals of the pre-mRNAs by a large cleavage/polyadenylation machinery, plays a critical role in gene expression. Indeed, the poly(A) tail of a mature mRNA is essential for its functions, including stability, translocation to the cytoplasm and translation. In addition, this process serves as a bridge in the network connecting the different transcription, capping, splicing and export machineries. It also participates in the quantitative and qualitative regulation of gene expression in a variety of biological processes through the selection of single or alternative poly(A) signals in transcription units. A large number of protein factors associates with this machinery to regulate the efficiency and specificity of this process and to mediate its interaction with other nuclear events. Here, we review the eukaryotic 3′ end processing machineries as well as the comprehensive set of regulatory factors and discuss the different molecular mechanisms of 3′ end processing regulation by proposing several overlapping models of regulation.
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Affiliation(s)
- Stefania Millevoi
- Institut National de la Santé et de la Recherche Médicale U563, Toulouse, F-31000, France.
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31
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Shepherd AK, Singh R, Wesley CS. Notch mRNA expression in Drosophila embryos is negatively regulated at the level of mRNA 3' processing. PLoS One 2009; 4:e8063. [PMID: 19956683 PMCID: PMC2778129 DOI: 10.1371/journal.pone.0008063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2009] [Accepted: 10/30/2009] [Indexed: 12/24/2022] Open
Abstract
Notch receptor regulates differentiation of almost all tissues and organs during animal development. Many mechanisms function at the protein level to finely regulate Notch activity. Here we provide evidence for Notch regulation at an earlier step - mRNA 3′ processing. Processing at the Notch consensus polyadenylation site appears by default to be suppressed in Drosophila embryos. Interference with this suppression, by a mutation, results in increased levels of polyadenylated Notch mRNA, excess Notch signaling, and severe developmental defects. We propose that Notch mRNA 3′ processing is negatively regulated to limit the production of Notch protein and render it a controlling factor in the generation of Notch signaling.
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Affiliation(s)
- Andrew K. Shepherd
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Ravinder Singh
- Department of Molecular, Cell and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Cedric S. Wesley
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
- * E-mail:
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32
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Valente ST, Gilmartin GM, Venkatarama K, Arriagada G, Goff SP. HIV-1 mRNA 3' end processing is distinctively regulated by eIF3f, CDK11, and splice factor 9G8. Mol Cell 2009; 36:279-89. [PMID: 19854136 DOI: 10.1016/j.molcel.2009.10.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 06/01/2009] [Accepted: 10/06/2009] [Indexed: 01/30/2023]
Abstract
A genetic screen previously identified the N-terminal 91 amino acids of the eukaryotic initiation factor 3 subunit f (N91-eIF3f) as a potent inhibitor of HIV-1 replication. Overexpression of N91-eIF3f or full-length eIF3f reduced the level of HIV-1 mRNAs in the infected cell. Here we show that N91-eIF3f and eIF3f act by specifically blocking the 3' end processing of the HIV-1 pre-mRNA both in vivo and in vitro. Furthermore, the results suggest that eIF3f mediates this restriction of HIV-1 expression through the previously unsuspected involvement of a set of factors that includes eIF3f, the SR protein 9G8, and the cyclin-dependent kinase 11 (CDK11). eIF3f affects HIV-1 3' end processing by modulating the sequence-specific recognition of the HIV-1 pre-mRNA by 9G8.
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Affiliation(s)
- Susana T Valente
- Howard Hughes Medical Institute, College of Physicians and Surgeons, Columbia University, HHSC 1310c, 701 West 168th Street, New York, NY 10032, USA.
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33
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Leitner JM, Mannhalter C, Jilma B. Genetic variations and their influence on risk and treatment of venous thrombosis. Pharmacogenomics 2008; 9:423-37. [PMID: 18384256 DOI: 10.2217/14622416.9.4.423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Venous thrombosis (VT) is a highly prevalent disease. Risk factors can be genetic or acquired. The well-established genetic polymorphisms predisposing to thrombophilic disorders can be divided into rare 'loss-of-function mutations' in anticoagulant proteins and common 'gain-of-function mutations' in procoagulant proteins, which are weaker risk factors. In addition to functional polymorphisms, defects in common pathways affecting biosynthesis or clearance of plasma coagulation factors and their relations to VT risk have been detected. Recently, investigations regarding genetic variations and response to drug treatment, relevant for the pathogenesis as well as therapy of venous thromboembolism have been performed. The methodical advances in genetic research have led to the identification of a number of new variants with still unclear association to VT. This review aims to discuss the established genetic risk factors as well as some candidate predictors of VT. Further, the recent developments in pharmacogenomics are reviewed.
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Affiliation(s)
- Judith Maria Leitner
- Department of Clinical Pharmacology, Division for Hematology & Immunology, Medical University of Vienna, Währinger Gürtel 18-20, A-1090 Wien, Austria
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34
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3' end mRNA processing: molecular mechanisms and implications for health and disease. EMBO J 2008; 27:482-98. [PMID: 18256699 DOI: 10.1038/sj.emboj.7601932] [Citation(s) in RCA: 201] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 10/24/2007] [Indexed: 12/27/2022] Open
Abstract
Recent advances in the understanding of the molecular mechanism of mRNA 3' end processing have uncovered a previously unanticipated integrated network of transcriptional and RNA-processing mechanisms. A variety of human diseases impressively reflect the importance of the precision of the complex 3' end-processing machinery and gene specific deregulation of 3' end processing can result from mutations of RNA sequence elements that bind key specific processing factors. Interestingly, more general deregulation of 3' end processing can be caused either by mutations of these processing factors or by the disturbance of the well-coordinated equilibrium between these factors. From a medical perspective, both loss of function and gain of function can be functionally relevant, and an increasing number of different disease entities exemplifies that inappropriate 3' end formation of human mRNAs can have a tremendous impact on health and disease. Here, we review the mechanistic hallmarks of mRNA 3' end processing, highlight the medical relevance of deregulation of this important step of mRNA maturation and illustrate the implications for diagnostic and therapeutic strategies.
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35
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Sartini BL, Wang H, Wang W, Millette CF, Kilpatrick DL. Pre-Messenger RNA Cleavage Factor I (CFIm): Potential Role in Alternative Polyadenylation During Spermatogenesis1. Biol Reprod 2008; 78:472-82. [DOI: 10.1095/biolreprod.107.064774] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Uitte de Willige S, Rietveld IM, De Visser MCH, Vos HL, Bertina RM. Polymorphism 10034C>T is located in a region regulating polyadenylation of FGG transcripts and influences the fibrinogen gamma'/gammaA mRNA ratio. J Thromb Haemost 2007; 5:1243-9. [PMID: 17403086 DOI: 10.1111/j.1538-7836.2007.02566.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Fibrinogen gamma haplotype 2 (FGG-H2) is associated with reduced fibrinogen gamma' levels and fibrinogen gamma'/total fibrinogen ratios and with an increased deep-venous thrombosis (DVT) risk. Two FGG-H2 tagging single nucleotide polymorphisms (SNPs), 9615C>T and 10034C>T, are located in the region of alternative FGG pre-mRNA processing. 10034C>T is located in a GT-rich downstream sequence element (DSE) that comprises a putative cleavage stimulation factor (CstF) binding site. OBJECTIVES To investigate the functionality of SNPs 9615C>T and 10034C>T, and the importance of the DSE containing 10034C>T. METHODS Different minigene constructs containing FGG exon 9, intron 9, exon 10 and the 3' region were transiently transfected into HepG2 cells and quantitative real-time polymerase chain reaction was used to measure relative polyadenylation (pA) signal usage (pA1/pA2 ratio). RESULTS Compared with the reference construct CC (9615C-10034C; FGG-H1; pA1/pA2 ratio set at 100%), the pA1/pA2 ratio of construct TT (9615T-10034T; FGG-H2) was 1.4-fold decreased (71.5%, P = 0.015). The pA1/pA2 ratio of construct CT (9615C-10034T) was almost 1.2-fold decreased (85.3%, P = 0.001), whereas the pA1/pA2 ratio of construct TC (9615T-10034C) did not differ significantly from the reference construct (101.6%, P = 0.890). Functionality of the putative CstF binding site was confirmed using constructs in which this site was deleted or its sequence altered by point mutations. CONCLUSIONS SNP 10034C>T is located in a GT-rich DSE involved in regulating the usage of the pA2 signal of FGG, which may represent a CstF binding site. We propose that the 10034C>T change is the functional variation in FGG-H2 that is responsible for the reduction in the fibrinogen gamma'/total fibrinogen ratio and the increased DVT risk.
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Affiliation(s)
- S Uitte de Willige
- Department of Hematology, Hemostasis and Thrombosis Research Center, Leiden University Medical Center, Leiden, The Netherlands
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Abstract
High plasma levels of several coagulation factors have been described to be associated with an increased risk of venous thrombosis. However, the mechanisms underlying these associations, as well as those involved in the regulation of plasma levels of coagulation factors, are mostly unknown. Whether these factors should be included in the workup of patients with venous thrombosis remains to be determined. In this review, we discuss the present knowledge on the effects of plasma levels of coagulation factors on the development of venous thrombosis. Furthermore, we review recent findings and ideas on the mechanisms through which elevated plasma coagulation factor levels may influence thrombosis. Finally, we enter into the matter of the possible determinants of elevated plasma levels of coagulation factors.
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Affiliation(s)
- A Yaël Nossent
- Hemostasis and Thrombosis Research Center, Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
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Castoldi E, Simioni P, Tormene D, Thomassen MCLGD, Spiezia L, Gavasso S, Rosing J. Differential effects of high prothrombin levels on thrombin generation depending on the cause of the hyperprothrombinemia. J Thromb Haemost 2007; 5:971-9. [PMID: 17461930 DOI: 10.1111/j.1538-7836.2007.02448.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Hyperprothrombinemia, resulting from the prothrombin G20210A mutation or other causes, is associated with activated protein C (APC) resistance and increased thrombosis risk. When high prothrombin levels are a result of increased hepatic biosynthesis, these effects may be counteracted by concomitantly increased levels of the anticoagulant factors (particularly protein S). Differently, in prothrombin G20210A carriers only prothrombin levels are elevated. OBJECTIVE To investigate whether prothrombin G20210A carriers have a more severe hypercoagulable state than non-carriers with comparable prothrombin levels. PATIENTS/METHODS Coagulation factor levels, thrombin generation (Calibrated Automated Thrombogram in the presence and absence of APC) and APC resistance were measured in normal (n = 132), heterozygous (n = 167) and homozygous (n = 3) individuals. RESULTS Prothrombin levels, thrombin generation and APC resistance were higher in carriers of the prothrombin G20210A mutation (especially those who had experienced venous thrombosis) than in non-carriers, whereas protein S and antithrombin levels were similar among genotype groups. Because individuals with high prothrombin levels in the absence of the prothrombin G20210A mutation tend to have all liver-synthesized factors elevated, carriers of the mutation had lower protein S and antithrombin levels than non-carriers with equally high prothrombin levels. Accordingly, they also generated more thrombin and showed a tendency toward higher APC resistance. Analogous effects, but less pronounced, were observed in homozygotes for the prothrombin A19911G polymorphism, which also upregulates prothrombin levels. CONCLUSIONS Individuals with hyperprothrombinemia as a result of prothrombin gene mutations generate more thrombin and tend to be more APC-resistant than individuals with comparable prothrombin levels because of other causes.
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Affiliation(s)
- E Castoldi
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands.
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Flaujac C, Conard J, Horellou MH, Le Flem L, Samama MM. Atypical mutations of the prothrombin gene at positions 20,209 and 20,218, and a novel mutation at position 20,219. Report on 10 patients. J Thromb Haemost 2007; 5:1064-8. [PMID: 17461935 DOI: 10.1111/j.1538-7836.2007.02478.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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40
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Danckwardt S, Kaufmann I, Gentzel M, Foerstner KU, Gantzert AS, Gehring NH, Neu-Yilik G, Bork P, Keller W, Wilm M, Hentze MW, Kulozik AE. Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals. EMBO J 2007; 26:2658-69. [PMID: 17464285 PMCID: PMC1888663 DOI: 10.1038/sj.emboj.7601699] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Accepted: 04/02/2007] [Indexed: 12/26/2022] Open
Abstract
The prothrombin (F2) 3' end formation signal is highly susceptible to thrombophilia-associated gain-of-function mutations. In its unusual architecture, the F2 3' UTR contains an upstream sequence element (USE) that compensates for weak activities of the non-canonical cleavage site and the downstream U-rich element. Here, we address the mechanism of USE function. We show that the F2 USE contains a highly conserved nonameric core sequence, which promotes 3' end formation in a position- and sequence-dependent manner. We identify proteins that specifically interact with the USE, and demonstrate their function as trans-acting factors that promote 3' end formation. Interestingly, these include the splicing factors U2AF35, U2AF65 and hnRNPI. We show that these splicing factors not only modulate 3' end formation via the USEs contained in the F2 and the complement C2 mRNAs, but also in the biocomputationally identified BCL2L2, IVNS and ACTR mRNAs, suggesting a broader functional role. These data uncover a novel mechanism that functionally links the splicing and 3' end formation machineries of multiple cellular mRNAs in an USE-dependent manner.
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Affiliation(s)
- Sven Danckwardt
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
| | | | - Marc Gentzel
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Anne-Susan Gantzert
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
| | - Niels H Gehring
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
| | - Gabriele Neu-Yilik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Matthias Wilm
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthias W Hentze
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
- European Molecular Biology Laboratory, Meyerhof str. 1, 69117 Heidelberg, Germany. Tel.: +49 6221 387501; Fax: +49 6221 387518; E-mail:
| | - Andreas E Kulozik
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 156, 69120 Heidelberg, Germany. Tel.: +49 6221 564555; Fax: +49 6221 564559; E-mail:
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Schambach A, Galla M, Maetzig T, Loew R, Baum C. Improving transcriptional termination of self-inactivating gamma-retroviral and lentiviral vectors. Mol Ther 2007; 15:1167-73. [PMID: 17406345 DOI: 10.1038/sj.mt.6300152] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Adverse events relating to insertional mutagenesis have reinforced the interest in self-inactivating (SIN) gamma-retroviral and lentiviral vectors without enhancer-promoter sequences in the U3 region of the long terminal repeats. However, SIN vectors suffer from leaky transcriptional termination, increasing the probability of read-through into cellular genes. To improve 3' end processing, we incorporated seven upstream polyadenylation enhancer elements (or upstream sequence elements, USEs) derived from viral or cellular genes into the 3' U3 region of gamma-retroviral and lentiviral SIN vectors. A 100-base-pair sequence representing a recombinant direct repeat of the USE derived from simian virus 40 (2xSV USE) gave the best results, improving both titer and gene expression. In both gamma-retroviral and lentiviral SIN vectors, the 2xSV USE partially substituted for effects provided by the much larger post-transcriptional regulatory element derived from woodchuck hepatitis virus (wPRE). By northern blot and reporter assays, we found that the 2xSV USE greatly improved proper messenger RNA (mRNA) processing at the retroviral termination signal. Importantly, the 2xSV USE was superior to the wPRE in suppressing transcriptional read-through, improving not only vector efficiency but potentially also biosafety.
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Affiliation(s)
- Axel Schambach
- 1Department of Experimental Hematology, Hannover Medical School, Hannover, Germany
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DANCKWARDT S, HARTMANN K, KATZ B, BEN-TAL O, KULOZIK AE. More on: functional analysis of two prothrombin 3'-UTR variants: the C20209T variant, mainly found among African-Americans, and the C20209A variant. J Thromb Haemost 2006. [DOI: 10.1111/j.1538-7836.2006.02126.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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van der Putten HHAGM, Spaargaren-van Riel CC, Bertina RM, Vos HL. Functional analysis of two prothrombin 3'-untranslated region variants: the C20209T variant, mainly found among African-Americans, and the C20209A variant. J Thromb Haemost 2006; 4:2285-7; author reply 2288-9. [PMID: 16796711 DOI: 10.1111/j.1538-7836.2006.02102.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kunz JB, Neu-Yilik G, Hentze MW, Kulozik AE, Gehring NH. Functions of hUpf3a and hUpf3b in nonsense-mediated mRNA decay and translation. RNA (NEW YORK, N.Y.) 2006; 12:1015-22. [PMID: 16601204 PMCID: PMC1464862 DOI: 10.1261/rna.12506] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The exon-junction complex (EJC) components hUpf3a and hUpf3b serve a dual function: They promote nonsense-mediated mRNA decay (NMD), and they also regulate translation efficiency. Whether these two functions are interdependent or independent of each other is unknown. We characterized the function of the hUpf3 proteins in a lambdaN/boxB-based tethering system. Despite the high degree of sequence similarity between hUpf3b and hUpf3a, hUpf3a is much less active than hUpf3b to induce NMD and to stimulate translation. We show that induction of NMD by hUpf3 proteins requires interaction with Y14, Magoh, BTZ, and eIF4AIII. The protein region that mediates this interaction and discriminates between hUpf3a and hUpf3b in NMD function is located in the C-terminal domain and fully contained within a small sequence that is highly conserved in Upf3b but not Upf3a proteins. Stimulation of translation is independent of this interaction and is determined by other regions of the hUpf3 protein, indicating the presence of different downstream pathways of hUpf3 proteins either in NMD or in translation.
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Affiliation(s)
- Joachim B Kunz
- Department for Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
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45
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Danckwardt S, Hartmann K, Katz B, Hentze MW, Levy Y, Eichele R, Deutsch V, Kulozik AE, Ben-Tal O. The prothrombin 20209 C-->T mutation in Jewish-Moroccan Caucasians: molecular analysis of gain-of-function of 3' end processing. J Thromb Haemost 2006; 4:1078-85. [PMID: 16689762 DOI: 10.1111/j.1538-7836.2006.01885.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Mutations of the 3' end mRNA-processing signal of the prothrombin (F2) gene have been reported to cause elevated F2 plasma concentrations, thrombosis, and complications of pregnancy. Whereas the common F2 20210*A mutation is almost exclusively found in Caucasians, the F2 20209*T mutation has been reported in Afro-Americans and Afro-Caribbeans only. PATIENTS AND METHODS Using LightCycler technology, three unrelated Jewish-Moroccan patients tested for obstetric complications were found to be carriers of the F2 20209*T allele. A detailed molecular analysis was performed to identify the functional impact of this mutation. RESULTS We report three unrelated women of Jewish-Moroccan origin with a F2 20209*T mutation and fetal loss or infertility. The functional analysis revealed that the F2 20209*T mutation stimulates 3' end processing and up-regulates prothrombin protein expression as assessed by a highly sensitive luminescence-based reporter system. CONCLUSIONS This is the first report of 20209*T in Caucasians, and functional analysis demonstrates that F2 20209*T falls into a general category of mutations of the F2 gene, which may possibly contribute to thrombophilia and complications of pregnancy by interfering with a tightly balanced architecture of non-canonical F2 3' end formation signals.
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Affiliation(s)
- S Danckwardt
- Departments of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
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46
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Chen JM, Férec C, Cooper DN. A systematic analysis of disease-associated variants in the 3' regulatory regions of human protein-coding genes I: general principles and overview. Hum Genet 2006; 120:1-21. [PMID: 16645853 DOI: 10.1007/s00439-006-0180-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 03/26/2006] [Indexed: 10/24/2022]
Abstract
The 3' regulatory regions (3' RRs) of human genes play an important role in regulating mRNA 3' end formation, stability/degradation, nuclear export, subcellular localization and translation and are consequently rich in regulatory elements. Although 3' RRs contain only approximately 0.2% of known disease-associated mutations, this is likely to represent a rather conservative estimate of their actual prevalence. In an attempt to catalogue 3' RR-mediated disease and also to gain a greater understanding of the functional role of regulatory elements within 3' RRs, we have performed a systematic analysis of disease-associated 3' RR variants; 121 3' RR variants in 94 human genes were collated. These included 17 mutations in the upstream core polyadenylation signal sequence (UCPAS), 81 in the upstream sequence (USS) between the translational termination codon and the UCPAS, 6 in the left arm of the 'spacer' sequence (LAS) between the UCPAS and the pre-mRNA cleavage site (CS), 3 in the right arm of the 'spacer' sequence (RAS) or downstream core polyadenylation signal sequence (DCPAS) and 7 in the downstream sequence (DSS) of the 3'-flanking region, with 7 further mutations being treated as isolated examples. All the UCPAS mutations and the rather unusual cases of the DMPK, SCA8, FCMD and GLA mutations exert a significant effect on the mRNA phenotype and are usually associated with monogenic disease. By contrast, most of the remaining variants are polymorphisms that exert a comparatively minor influence on mRNA expression, but which may nevertheless predispose to or otherwise modify complex clinical phenotypes. Considerable efforts have been made to validate/elucidate the mechanisms through which the 3' untranslated region (3' UTR) variants affect gene expression. It is hoped that the integrative approach employed here in the study of naturally occurring variants of actual or potential pathological significance will serve to complement ongoing efforts to identify all functional regulatory elements in the human genome.
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Danckwardt S, Hartmann K, Gehring NH, Hentze MW, Kulozik AE. 3' end processing of the prothrombin mRNA in thrombophilia. Acta Haematol 2006; 115:192-7. [PMID: 16549895 DOI: 10.1159/000090934] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Clinical and genetic studies have led to the discovery of specific genotypes that predispose to thromboembolism in adults and children. The exploration of the underlying pathologies has revealed a broad variety of affected molecular mechanisms. Most recently, the functional analysis of the prothrombin (F2) 20210*A variant revealed increased efficiency of 3' end processing as a novel genetic mechanism predisposing to human disease. Here, we review the 3' end processing of the human F2 mRNA and demonstrate how clinically relevant mutations in the F2 gene contribute to thrombophilia by interfering with a tightly balanced architecture of noncanonical 3' end formation signals.
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Affiliation(s)
- Sven Danckwardt
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
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48
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Wylenzek C, Trübenbach J, Gohl P, Wildhardt G, Alkins S, Fausett MB, Decker J, Steinberger D. Mutation screening for the prothrombin variant G20210A by melting point analysis with the Light Cycler system: atypical results, detection of the variant C20209T and possible clinical implications. ACTA ACUST UNITED AC 2005; 27:343-6. [PMID: 16178919 DOI: 10.1111/j.1365-2257.2005.00720.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In the differential diagnosis of thrombophilic disorders genotyping of prothrombin and factor V are nowadays performed as a routine analysis. In the following we describe the unusual results of the mutation screening using melting point analysis for two patients and the consecutive detection of the mutation C20209T by sequencing the corresponding gene fragments. The molecular result is discussed with special respect to the medical history, ethnic background and clinical findings of both patients.
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49
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Lyon E. Discovering Rare Variants by Use of Melting Temperature Shifts Seen in Melting Curve Analysis. Clin Chem 2005; 51:1331-2. [PMID: 16040838 DOI: 10.1373/clinchem.2005.051177] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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50
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Ceelie H, Spaargaren-Van Riel CC, Lyon E, Bertina RM, Vos HL. Functional analysis of two polymorphisms in the 3'-UTR of the human prothrombin gene. J Thromb Haemost 2005; 3:806-8. [PMID: 15842380 DOI: 10.1111/j.1538-7836.2005.01241.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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