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Mofayezi A, Jadaliha M, Zangeneh FZ, Khoddami V. Poly(A) tale: From A to A; RNA polyadenylation in prokaryotes and eukaryotes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1837. [PMID: 38485452 DOI: 10.1002/wrna.1837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Most eukaryotic mRNAs and different non-coding RNAs undergo a form of 3' end processing known as polyadenylation. Polyadenylation machinery is present in almost all organisms except few species. In bacteria, the machinery has evolved from PNPase, which adds heteropolymeric tails, to a poly(A)-specific polymerase. Differently, a complex machinery for accurate polyadenylation and several non-canonical poly(A) polymerases are developed in eukaryotes. The role of poly(A) tail has also evolved from serving as a degradative signal to a stabilizing modification that also regulates translation. In this review, we discuss poly(A) tail emergence in prokaryotes and its development into a stable, yet dynamic feature at the 3' end of mRNAs in eukaryotes. We also describe how appearance of novel poly(A) polymerases gives cells flexibility to shape poly(A) tail. We explain how poly(A) tail dynamics help regulate cognate RNA metabolism in a context-dependent manner, such as during oocyte maturation. Finally, we describe specific mRNAs in metazoans that bear stem-loops instead of poly(A) tails. We conclude with how recent discoveries about poly(A) tail can be applied to mRNA technology. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Ahmadreza Mofayezi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
- ReNAP Therapeutics, Tehran, Iran
| | - Mahdieh Jadaliha
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | | | - Vahid Khoddami
- ReNAP Therapeutics, Tehran, Iran
- Pediatric Cell and Gene Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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2
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de Prisco N, Ford C, Elrod ND, Lee W, Tang LC, Huang KL, Lin A, Ji P, Jonnakuti VS, Boyle L, Cabaj M, Botta S, Õunap K, Reinson K, Wojcik MH, Rosenfeld JA, Bi W, Tveten K, Prescott T, Gerstner T, Schroeder A, Fong CT, George-Abraham JK, Buchanan CA, Hanson-Khan A, Bernstein JA, Nella AA, Chung WK, Brandt V, Jovanovic M, Targoff KL, Yalamanchili HK, Wagner EJ, Gennarino VA. Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites. SCIENCE ADVANCES 2023; 9:eade4814. [PMID: 36800428 PMCID: PMC9937581 DOI: 10.1126/sciadv.ade4814] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Alternative polyadenylation (APA) creates distinct transcripts from the same gene by cleaving the pre-mRNA at poly(A) sites that can lie within the 3' untranslated region (3'UTR), introns, or exons. Most studies focus on APA within the 3'UTR; however, here, we show that CPSF6 insufficiency alters protein levels and causes a developmental syndrome by deregulating APA throughout the transcript. In neonatal humans and zebrafish larvae, CPSF6 insufficiency shifts poly(A) site usage between the 3'UTR and internal sites in a pathway-specific manner. Genes associated with neuronal function undergo mostly intronic APA, reducing their expression, while genes associated with heart and skeletal function mostly undergo 3'UTR APA and are up-regulated. This suggests that, under healthy conditions, cells toggle between internal and 3'UTR APA to modulate protein expression.
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Affiliation(s)
- Nicola de Prisco
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Caitlin Ford
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Nathan D. Elrod
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA
| | - Lauren C. Tang
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kai-Lieh Huang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Ai Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, WC67+HC Dongcheng, Beijing, China
| | - Ping Ji
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Venkata S. Jonnakuti
- Department of Pediatrics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Lia Boyle
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Maximilian Cabaj
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Salvatore Botta
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Caserta, Italy
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Karit Reinson
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H. Wojcik
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Trine Prescott
- Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway
| | - Thorsten Gerstner
- Department of Child Neurology and Rehabilitation and Department of Pediatrics, Hospital of Southern Norway, Arendal, Norway
| | - Audrey Schroeder
- Division of Medical Genetics, University of Rochester Medical Center, Rochester, NY, USA
| | - Chin-To Fong
- Department of Pediatrics and of Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Jaya K. George-Abraham
- Dell Children’s Medical Group, Austin, TX, USA
- Department of Pediatrics, The University of Texas at Austin Dell Medical School, Austin, TX, USA
| | | | - Andrea Hanson-Khan
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Palo Alto, CA, USA
- Department of Genetics, Stanford School of Medicine, Palo Alto, CA, USA
| | - Jonathan A. Bernstein
- Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Palo Alto, CA, USA
| | - Aikaterini A. Nella
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Wendy K. Chung
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Vicky Brandt
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Kimara L. Targoff
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Hari Krishna Yalamanchili
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Eric J. Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Vincenzo A. Gennarino
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA
- Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY, USA
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3
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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4
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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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5
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Population-scale genetic control of alternative polyadenylation and its association with human diseases. QUANTITATIVE BIOLOGY 2021. [DOI: 10.15302/j-qb-021-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Wachs AS, Bohne J. Two sides of the same medal: Noncoding mutations reveal new pathological mechanisms and insights into the regulation of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1616. [PMID: 32633083 DOI: 10.1002/wrna.1616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/22/2022]
Abstract
Noncoding sequences constitute the major part of the human genome and also of pre-mRNAs. Single nucleotide variants in these regions are often overlooked, but may be responsible for much of the variation of phenotypes observed. Mutations in the noncoding part of pre-mRNAs often reveal new and meaningful insights into the regulation of cellular gene expression. Thus, the mechanistic analysis of the pathological mechanism of such mutations will both foster a deeper understanding of the disease and the underlying cellular pathways. Even synonymous mutations can cause diseases, since the primary mRNA sequence not only encodes amino acids, but also encrypts information on RNA-binding proteins and secondary structure. In fact, the RNA sequence directs assembly of a specific mRNP complex, which in turn dictates the fate of the mRNA or regulates its biogenesis. The accumulation of genomic sequence information is increasing at a rapid pace. However, much of the diversity uncovered may not explain the phenotype of a certain syndrome or disease. For this reason, we also emphasize the value of mechanistic studies on pathological mechanisms being complementary to genome-wide studies and bioinformatic approaches. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Amelie S Wachs
- Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Jens Bohne
- Institute of Virology, Hannover Medical School, Hanover, Germany
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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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Murphy MR, Kleiman FE. Connections between 3' end processing and DNA damage response: Ten years later. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1571. [PMID: 31657151 PMCID: PMC7295566 DOI: 10.1002/wrna.1571] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 12/23/2022]
Abstract
Ten years ago we reviewed how the cellular DNA damage response (DDR) is controlled by changes in the functional and structural properties of nuclear proteins, resulting in a timely coordinated control of gene expression that allows DNA repair. Expression of genes that play a role in DDR is regulated not only at transcriptional level during mRNA biosynthesis but also by changing steady-state levels due to turnover of the transcripts. The 3' end processing machinery, which is important in the regulation of mRNA stability, is involved in these gene-specific responses to DNA damage. Here, we review the latest mechanistic connections described between 3' end processing and DDR, with a special emphasis on alternative polyadenylation, microRNA and RNA binding proteins-mediated deadenylation, and discuss the implications of deregulation of these steps in DDR and human disease. This article is categorized under: RNA Processing > 3' End Processing RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Michael Robert Murphy
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
| | - Frida Esther Kleiman
- Department of Chemistry, Hunter College and Biochemistry Program, The Graduate Center, City University of New York, New York, New York
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9
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Leung MKK, Delong A, Frey BJ. Inference of the human polyadenylation code. Bioinformatics 2019; 34:2889-2898. [PMID: 29648582 PMCID: PMC6129302 DOI: 10.1093/bioinformatics/bty211] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 04/09/2018] [Indexed: 01/02/2023] Open
Abstract
Motivation Processing of transcripts at the 3′-end involves cleavage at a polyadenylation site followed by the addition of a poly(A)-tail. By selecting which site is cleaved, the process of alternative polyadenylation enables genes to produce transcript isoforms with different 3′-ends. To facilitate the identification and treatment of disease-causing mutations that affect polyadenylation and to understand the sequence determinants underlying this regulatory process, a computational model that can accurately predict polyadenylation patterns from genomic features is desirable. Results Previous works have focused on identifying candidate polyadenylation sites and classifying tissue-specific sites. By training on how multiple sites in genes are competitively selected for polyadenylation from 3′-end sequencing data, we developed a deep learning model that can predict the tissue-specific strength of a polyadenylation site in the 3′ untranslated region of the human genome given only its genomic sequence. We demonstrate the model’s broad utility on multiple tasks, without any application-specific training. The model can be used to predict which polyadenylation site is more likely to be selected in genes with multiple sites. It can be used to scan the 3′ untranslated region to find candidate polyadenylation sites. It can be used to classify the pathogenicity of variants near annotated polyadenylation sites in ClinVar. It can also be used to anticipate the effect of antisense oligonucleotide experiments to redirect polyadenylation. We provide analysis on how different features affect the model’s predictive performance and a method to identify sensitive regions of the genome at the single-based resolution that can affect polyadenylation regulation. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Michael K K Leung
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada.,Deep Genomics, MaRS Centre, Toronto, Canada
| | - Andrew Delong
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada.,Deep Genomics, MaRS Centre, Toronto, Canada
| | - Brendan J Frey
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada.,Deep Genomics, MaRS Centre, Toronto, Canada.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
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10
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Abstract
Most human genes have multiple sites at which RNA 3' end cleavage and polyadenylation can occur, enabling the expression of distinct transcript isoforms under different conditions. Novel methods to sequence RNA 3' ends have generated comprehensive catalogues of polyadenylation (poly(A)) sites; their analysis using innovative computational methods has revealed how poly(A) site choice is regulated by core RNA 3' end processing factors, such as cleavage factor I and cleavage and polyadenylation specificity factor, as well as by other RNA-binding proteins, particularly splicing factors. Here, we review the experimental and computational methods that have enabled the global mapping of mRNA and of long non-coding RNA 3' ends, quantification of the resulting isoforms and the discovery of regulators of alternative cleavage and polyadenylation (APA). We highlight the different types of APA-derived isoforms and their functional differences, and illustrate how APA contributes to human diseases, including cancer and haematological, immunological and neurological diseases.
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11
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Behlmann AM, Goyal NA, Yang X, Chen PH, Ankala A. A Hemizygous Deletion Within the PGK1 Gene in Males with PGK1 Deficiency. JIMD Rep 2018; 45:105-110. [PMID: 30570712 PMCID: PMC6336546 DOI: 10.1007/8904_2018_147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/24/2018] [Accepted: 09/25/2018] [Indexed: 02/05/2023] Open
Abstract
Phosphoglycerate kinase-1 (PGK1) deficiency is a rare X-linked disorder caused by pathogenic variants in the PGK1 gene. Complete loss-of-function variants have not been reported in this gene, indicating that residual enzyme function is critical for viability in males. Therefore, copy number variants (CNVs) that include single exon or multiple exon deletions or duplications are generally not expected in individuals with PGK1 deficiency. Here we describe a 64-year-old male presenting with a family history (three additional affected males) and a personal history of childhood-onset metabolic myopathy that involves episodes of muscle pain, stiffness after activity, exercise intolerance, and myoglobinuria after exertion. Biochemical analysis on a muscle biopsy indicated significantly reduced activity (15% compared to normal) for phosphoglycerate kinase (PGK1), a glycolytic enzyme encoded by PGK1. A diagnosis of PGK1 deficiency was established by molecular analysis which detected an approximately 886 kb deletion involving the polyadenylation site in the 3'UTR of the PGK1 gene. RNA analysis showed significantly reduced PGK1 transcript levels (30% compared to normal). This is the first deletion reported in the PGK1 gene and is the first pathogenic variant involving the 3'UTR polyadenylation site of this gene. Our report emphasizes the role of 3'UTR variants in human disorders and underscores the need for exploring noncoding regions of disease-associated genes when seeking a molecular diagnosis.
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Affiliation(s)
- Andrea Medrano Behlmann
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Namita A. Goyal
- grid.266093.80000 0001 0668 7243Department of Neurology, University of California, Irvine, CA USA
| | - Xiaoyu Yang
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Ping H. Chen
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Arunkanth Ankala
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA ,EGL Genetic Diagnostics LLC, Tucker, GA USA
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12
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Zhang Q, Fan X, Xu M, Zhang Y, Xu H, Wen X, Zhou W. Hb H Disease Caused by Multiple Mutations in the Polyadenylation Signal Site and - - SEA/αα. Hemoglobin 2018; 41:189-192. [PMID: 28950779 DOI: 10.1080/03630269.2017.1366917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Thalassemia is the most common monogenic disease, with the highest incidence in Guangxi Zhuang Autonomous Region, People's Republic of China (PRC). The blood test result was not consistent with α-globin gene testing in one of the patients during daily screening. It was confirmed that there were multiple mutations at the α2-globin gene polyadenylation (polyA) signal site: HBA2: c.*64(T>C), HBA2: c.*68(A>C), HBA2: c.*71(G>A), HBA2: c.*74(C>A), HBA2: c.*82(G>A), HBA2: c.*92(A>G) and HBA2: c.*98(T>C) and compound - -SEA/αα by sequencing of the HBA1 and HBA2 genes of the proband and core family members. After that, we found a further two cases of unrelated patients with this type of mutation. The mutation is not an accidental phenomenon, and likely to occur with a considerable incidence in Guangxi Zhuang Autonomous Region, PRC. We analyzed the hematological manifestations of this type of thalassemia and showed that it was a Hb H (β4) disease caused by rare mutations. We suggest that it is essential to pay attention to this mutation during future clinical diagnoses and genetic counseling of patients.
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Affiliation(s)
- Qiang Zhang
- a Department of Medical Genetics , School of Basic Medical Sciences, Southern Medical University , Guangzhou , Guangdong Province , People's Republic of China.,b Department of Genetic Metabolism , Prenatal Diagnostic Center, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region , Nanning , Guangxi Zhuang Autonomous Region , People's Republic of China
| | - Xin Fan
- b Department of Genetic Metabolism , Prenatal Diagnostic Center, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region , Nanning , Guangxi Zhuang Autonomous Region , People's Republic of China
| | - Mingli Xu
- a Department of Medical Genetics , School of Basic Medical Sciences, Southern Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Yijia Zhang
- a Department of Medical Genetics , School of Basic Medical Sciences, Southern Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Huiling Xu
- a Department of Medical Genetics , School of Basic Medical Sciences, Southern Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Xiaojun Wen
- a Department of Medical Genetics , School of Basic Medical Sciences, Southern Medical University , Guangzhou , Guangdong Province , People's Republic of China
| | - Wanjun Zhou
- a Department of Medical Genetics , School of Basic Medical Sciences, Southern Medical University , Guangzhou , Guangdong Province , People's Republic of China
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Steri M, Idda ML, Whalen MB, Orrù V. Genetic variants in mRNA untranslated regions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1474. [PMID: 29582564 DOI: 10.1002/wrna.1474] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/05/2018] [Accepted: 02/11/2018] [Indexed: 12/24/2022]
Abstract
Genome Wide Association Studies (GWAS) have mapped thousands of genetic variants associated with complex disease risk and regulating quantitative traits, thus exploiting an unprecedented high-resolution genetic characterization of the human genome. A small fraction (3.7%) of the identified associations is located in untranslated regions (UTRs), and the molecular mechanism has been elucidated for few of them. Genetic variations at UTRs may modify regulatory elements affecting the interaction of the UTRs with proteins and microRNAs. The overall functional consequences include modulation of messenger RNA (mRNA) transcription, secondary structure, stability, localization, translation, and access to regulators like microRNAs (miRNAs) and RNA-binding proteins (RBPs). Alterations of these regulatory mechanisms are known to modify molecular pathways and cellular processes, potentially leading to disease processes. Here, we analyze some examples of genetic risk variants mapping in the UTR regulatory elements. We describe a recently identified genetic variant localized in the 3'UTR of the TNFSF13B gene, associated with autoimmunity risk and responsible of an increased stability and translation of TNFSF13B mRNA. We discuss how the correct use and interpretation of public GWAS repositories could lead to a better understanding of etiopathogenetic mechanisms and the generation of robust biological hypothesis as starting point for further functional studies. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Evolution and Genomics > Computational Analyses of RNA RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - M Laura Idda
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institute of Health, Baltimore, Maryland
| | - Michael B Whalen
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Trento, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
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Wang Y, Xu Y, Yan W, Han P, Liu J, Gong J, Li D, Ding X, Wang H, Lin Z, Tian D, Liao J. CFIm25 inhibits hepatocellular carcinoma metastasis by suppressing the p38 and JNK/c-Jun signaling pathways. Oncotarget 2018; 9:11783-11793. [PMID: 29545935 PMCID: PMC5837768 DOI: 10.18632/oncotarget.24364] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 12/05/2017] [Indexed: 01/05/2023] Open
Abstract
Alternative polyadenylation (APA), a post-transcriptional modification, has been implicated in many diseases, but especially in tumor proliferation. CFIm25, the 25 kDa subunit of human cleavage factor Im (CFIm), is a key factor in APA. We show that CFIm25 expression is reduced in human hepatocellular carcinoma (HCC), and its expression correlates with metastasis. Kaplan-Meier analysis indicated that CFIm25 is related to overall survival in HCC. Moreover, CFIm25 expression is negatively related to the metastatic potential of HCC cell lines. CFIm25 knockdown promotes cell invasion and migration in vitro, while overexpression of CFIm25 inhibits cell invasion and migration in vitro and inhibits intrahepatic and lung metastasis in vivo. Additional studies showed that CFIm25 disrupts epithelial-mesenchymal transition by increasing E-cadherin, that it inhibits HCC cell migration and invasion by blocking the p38 and JNK/c-Jun signaling pathways, and that CFIm25 knockdown increases the transcriptional activity of activating protein-1 (AP-1). These findings indicate that therapy directed at increasing CFIm25 expression is a potential HCC treatment.
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Affiliation(s)
- Yunwu Wang
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Yu Xu
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Wei Yan
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Ping Han
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jingmei Liu
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jin Gong
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Dongxiao Li
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Xiangming Ding
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Han Wang
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Zhuoying Lin
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Dean Tian
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
| | - Jiazhi Liao
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
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Chang JW, Yeh HS, Yong J. Alternative Polyadenylation in Human Diseases. Endocrinol Metab (Seoul) 2017; 32:413-421. [PMID: 29271615 PMCID: PMC5744726 DOI: 10.3803/enm.2017.32.4.413] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 12/02/2022] Open
Abstract
Varying length of messenger RNA (mRNA) 3'-untranslated region is generated by alternating the usage of polyadenylation sites during pre-mRNA processing. It is prevalent through all eukaryotes and has emerged as a key mechanism for controlling gene expression. Alternative polyadenylation (APA) plays an important role for cell growth, proliferation, and differentiation. In this review, we discuss the functions of APA related with various physiological conditions including cellular metabolism, mRNA processing, and protein diversity in a variety of disease models. We also discuss the molecular mechanisms underlying APA regulation, such as variations in the concentration of mRNA processing factors and RNA-binding proteins, as well as global transcriptome changes under cellular signaling pathway.
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Affiliation(s)
- Jae Woong Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities College of Biological Sciences, Minneapolis, MN, USA
| | - Hsin Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities College of Biological Sciences, Minneapolis, MN, USA
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities College of Biological Sciences, Minneapolis, MN, USA.
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16
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Ghoti H, Fibach E, Rachmilewitz EA, Jeadi H, Filon D. New Insights on β-Thalassemia in the Palestinian Population of Gaza: High Frequency and Milder Phenotype Among Homozygous IVS-I-1 (HBB: c.92+1G>A) Patients with High Levels of Hb F. Hemoglobin 2017; 41:144-146. [PMID: 28670942 DOI: 10.1080/03630269.2017.1339611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
β-Thalassemia (β-thal) is a very common disease in the Palestinian population of the Gaza Strip. We studied their mutation frequency and clinical features. Thirteen different mutations were identified. The most common mutation was IVS-I-1 (G>A) (HBB: c.92+1G>A), which was prevalent in 31.5% of the thalassemia alleles studied. The IVS-I-110 (G>A) (HBB: c.93-21G>A) mutation was found in 25.0% of the alleles. Homozygotes for the IVS-I-1 mutation had higher mean hemoglobin (Hb) levels, required less blood transfusions, and lower transferrin saturation than the homozygotes for the IVS-I-110 mutation. This milder phenotype was, most likely, the result of the persistent production of Hb F; it was 9-fold higher in absolute terms (g/dL) and 7.7-fold higher in relative terms (percentage of total Hb). About half of our IVS-I-1 patients carried the XmnI polymorphism, which is known to be associated with elevated Hb F levels.
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Affiliation(s)
- Hussam Ghoti
- a Department of Hematology , Augusta Victoria Hospital , Jerusalem , Israel
| | - Eitan Fibach
- a Department of Hematology , Augusta Victoria Hospital , Jerusalem , Israel.,b Department of Hematology , Hadassah, Hebrew University Medical Center , Jerusalem , Israel
| | | | - Hisham Jeadi
- d Department of Hematology , European Hospital of Gaza , Gaza , Palestinian Territory
| | - Dvora Filon
- b Department of Hematology , Hadassah, Hebrew University Medical Center , Jerusalem , Israel
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17
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Vinciguerra M, Passarello C, Cassarà F, Leto F, Cannata M, Calvaruso G, Di Maggio R, Renda D, Maggio A, Giambona A. Co-heredity of silent CAP + 1570 T>C (HBB:c*96T>C) defect and severe β-thal mutation: a cause of mild β-thalassemia intermedia. Int J Lab Hematol 2015; 38:17-26. [PMID: 26418075 DOI: 10.1111/ijlh.12433] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/05/2015] [Indexed: 11/29/2022]
Abstract
INTRODUCTION During an intensive screening program aimed at identifying the healthy carriers of thalassemia and the couples at risk of bearing an affected fetus, a rare single nucleotide variation (SNV), CAP + 1570 T > C (HBB:c*96T > C), located 12 nucleotides upstream of the polyadenylation signal in 3'UTR of the beta globin gene was identified. It was previously reported as a β+ thalassemia mutation and later as a plain polymorphism. METHODS Genotype identification of globin gene mutations was carried out using sequencing analysis, GAP-PCR, and MLPA methods. RESULTS CAP + 1570 T > C (HBB:c*96T > C) was found in 39 heterozygotes, in one case in homozygous state and in thirteen cases of co-inheritance of this nucleotide substitution with other mutations in globin genes. Carriers of this mutation showed a 'silent' phenotype without appreciable microcytosis and hypochromia, so they cannot be differentiated from noncarrier individuals. Compound heterozygotes for this mutation and severe β-thal mutations showed a variable phenotype ranging from β-thal carrier to mild form of β-thalassemia intermedia, revealing new aspects and allowing to better understand the clinical implications of this nucleotide substitution that can be classified as a silent β-thalassemic defect. CONCLUSION Data reported in this study indicate the need of investigating partner of β-thalassemia carrier by complete sequencing analysis of β-globin gene and of providing an appropriate genetic counseling for couples at risk undergoing prenatal diagnosis.
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Affiliation(s)
- M Vinciguerra
- Department of Hematology for Rare Diseases of Blood and Blood-Forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Hemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
| | - C Passarello
- Department of Hematology for Rare Diseases of Blood and Blood-Forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Hemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
| | - F Cassarà
- Department of Hematology for Rare Diseases of Blood and Blood-Forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Hemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
| | - F Leto
- Department of Hematology for Rare Diseases of Blood and Blood-Forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Hemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
| | - M Cannata
- Department of Hematology for Rare Diseases of Blood and Blood-Forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Hemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
| | - G Calvaruso
- Department of Hematology for Rare Diseases of Blood and Blood-Forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Hemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
| | - R Di Maggio
- Department of Hematology for Rare Diseases of Blood and Blood-Forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Hemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
| | - D Renda
- Department of Hematology for Rare Diseases of Blood and Blood-Forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Hemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
| | - A Maggio
- Department of Hematology for Rare Diseases of Blood and Blood-Forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Hemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
| | - A Giambona
- Department of Hematology for Rare Diseases of Blood and Blood-Forming Organs, Regional Reference Laboratory for Screening and Prenatal Diagnosis of Hemoglobinopathies, Villa Sofia-Cervello Hospital, Palermo, Italy
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18
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Curinha A, Oliveira Braz S, Pereira-Castro I, Cruz A, Moreira A. Implications of polyadenylation in health and disease. Nucleus 2014; 5:508-19. [PMID: 25484187 DOI: 10.4161/nucl.36360] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Polyadenylation is the RNA processing step that completes the maturation of nearly all eukaryotic mRNAs. It is a two-step nuclear process that involves an endonucleolytic cleavage of the pre-mRNA at the 3'-end and the polymerization of a polyadenosine (polyA) tail, which is fundamental for mRNA stability, nuclear export and efficient translation during development. The core molecular machinery responsible for the definition of a polyA site includes several recognition, cleavage and polyadenylation factors that identify and act on a given polyA signal present in a pre-mRNA, usually an AAUAAA hexamer or similar sequence. This mechanism is tightly regulated by other cis-acting elements and trans-acting factors, and its misregulation can cause inefficient gene expression and may ultimately lead to disease. The majority of genes generate multiple mRNAs as a result of alternative polyadenylation in the 3'-untranslated region. The variable lengths of the 3' untranslated regions created by alternative polyadenylation are a recognizable target for differential regulation and clearly affect the fate of the transcript, ultimately modulating the expression of the gene. Over the past few years, several studies have highlighted the importance of polyadenylation and alternative polyadenylation in gene expression and their impact in a variety of physiological conditions, as well as in several illnesses. Abnormalities in the 3'-end processing mechanisms thus represent a common feature among many oncological, immunological, neurological and hematological disorders, but slight imbalances can lead to the natural establishment of a specific cellular state. This review addresses the key steps of polyadenylation and alternative polyadenylation in different cellular conditions and diseases focusing on the molecular effectors that ensure a faultless pre-mRNA 3' end formation.
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Key Words
- 3′ untranslated region
- 3′READS, 3′ Region Extraction and Deep Sequencing
- AD, Alzheimer disease
- APA, Alternative polyadenylation
- AREs, Au-rich elements
- BPV, bovine papilloma virus
- CAH, congenital adrenal hyperplasia
- CFIm25, Cleavage Factor Im 25 kDa
- COX-2, cyclooxygenase 2
- CPSF, Cleavage and Polyadenylation Specificity Factor
- CSTF2, cleavage stimulatory factor-64kDa
- DMKN, dermokine
- DSE, downstream sequence element
- ESC, embryonic stem cells
- FMR1, Fragil X mental retardation 1
- FOXP3, forkhead box P3
- FXPOI, fragile X-associated immature ovarian insufficiency
- FXS, Fragile X syndrome
- FXTAS, fragile X-associated tremor/ataxia syndrome
- HGRG-14, high-glucose-regulated gene
- IMP-1, Insulin-like growth factor 2 mRNA binding protein 1
- IPEX, immune dysfunction, polyendocrinopathy, enteropathy, X-linked
- LPS, lipopolysaccharide
- OPMD, oculopharyngeal muscular dystrophy
- PABPN1, poly(A) binding protein
- PAP, polyA polymerase
- PAS, polyA site
- PD, Parkinson disease
- PDXK, pyridoxal kinase
- PPIE, peptidylpropylisomerase E
- RBP, RNA-binding protein
- RNA Pol II, RNA polymerase II
- SLE, systemic lupus erythematosus
- SMA, Spinal Muscular Atrophy
- SMN, Survival Motor Neuron
- SNP, single nucleotide polymorphism
- StAR, steroigogenic acute regulatory
- TCF/LEF, T cell factor/lymphoid enhancer factor.
- TCF7L2, transcription factor 7-like 2
- TCR, T cell receptor
- TLI, tandem UTR length index
- TNF-α, tumor necrosis factor-α
- USE, upstream sequence element
- UTR, untranslated region
- WAS, Wiskott-Aldrich syndrome
- WASP, Wiskott-Aldrich syndrome protein
- aSyn, α-Synuclein
- aSynL, longest aSyn isoform
- alternative polyadenylation
- cell state
- disease
- gene expression
- miRNA, microRNA
- nuclear 1
- pA signal, polyA signal
- pA tail, polyA tail
- polyadenylation
- siRNAs, small interfering RNAs
- snRNPs, spliceosomal small nuclear ribonucleoproteins
- α-GalA, α-galactosidase A
- μ, IgM heavy-chain mRNA
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Affiliation(s)
- Ana Curinha
- a Gene Regulation Group; IBMC-Instituto de Biologia Molecular e Celular ; Universidade do Porto ; Porto , Portugal
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19
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Genome-wide search for exonic variants affecting translational efficiency. Nat Commun 2014; 4:2260. [PMID: 23900168 PMCID: PMC3749366 DOI: 10.1038/ncomms3260] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 07/05/2013] [Indexed: 01/10/2023] Open
Abstract
The search for expression quantitative trait loci (eQTL) has traditionally centered entirely on the process of transcription, whereas variants with effects on mRNA translation have not been systematically studied. Here we present a high throughput approach for measuring translational cis-regulation in the human genome. Using ribosomal association as proxy for translational efficiency of polymorphic mRNAs, we test the ratio of polysomal/nonpolysomal mRNA level as a quantitative trait for association with single-nucleotide polymorphisms on the same mRNA transcript. We identify one important ribosomal-distribution effect, from rs1131017 in the 5’UTR of RPS26 , that is in high linkage disequilibrium (LD) with the 12q13 locus for susceptibility to type 1 diabetes. The effect on translation is confirmed at the protein level by quantitative Western blots, both ex vivo and after in vitro translation. Our results are a proof-of-principle that allelic effects on translation can be detected at a transcriptome-wide scale.
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Al-Rasadi K, Al-Waili K, Al-Zidi WAM, Al-Abri AR, Al-Hinai AT, Al-Sabti HA, Al-Tobi S, Al-Zakwani I, Al-Zadjali F, Al-Hashmi K, Banerjee Y. Low-density lipoprotein receptor gene mutation analysis and structure-function correlation in an Omani arab family with familial hypercholesterolemia. Angiology 2013; 65:911-8. [PMID: 24249837 DOI: 10.1177/0003319713510059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Familial hypercholesterolemia (FH) is an autosomal dominant disorder typified by elevated low-density lipoprotein cholesterol (LDL-C) levels caused by mutations in the LDL receptor (LDLR), apolipoprotein B (ApoB), or proprotein convertase subtilisin/kexin type 9 (PCSK9) genes. Previously, we reported a novel mutation in the exon-3 of LDLR gene, observed in a 9-year-old Omani Arab female. Here, we investigated the mode of inheritance of this mutation and confirmed that FH in this family is due to mutation only in the LDLR and not PCSK9 and ApoB genes. Further, the effect of the mutation has been appraised in silico on the tertiary structure of LDLR. A model of the mutant LDLR has been constructed using the coordinates of the wild-type LDLR extracellular domain. Based on the model, we present a mechanistic justification behind the observed detrimental effect of the mutation on LDL-C levels.
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Affiliation(s)
- Khalid Al-Rasadi
- Department of Clinical Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman Familial Hypercholesterolemia Study Group, Oman Society of Lipid and Atherosclerosis (OSLA), Sultan Qaboos University, Muscat, Oman
| | - Khalid Al-Waili
- Department of Clinical Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman Familial Hypercholesterolemia Study Group, Oman Society of Lipid and Atherosclerosis (OSLA), Sultan Qaboos University, Muscat, Oman
| | - Ward Al-Muna Al-Zidi
- Department of Clinical Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Abdul Rahim Al-Abri
- Department of Clinical Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman Familial Hypercholesterolemia Study Group, Oman Society of Lipid and Atherosclerosis (OSLA), Sultan Qaboos University, Muscat, Oman
| | - Ali T Al-Hinai
- Department of Medicine, College of Medicine & Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Hilal Ali Al-Sabti
- Department of Surgery, Cardiothoracic Surgery Division, Sultan Qaboos University Hospital, Muscat, Oman
| | - Sheikha Al-Tobi
- Department of Clinical Biochemistry, Medical Laboratory Science program, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ibrahim Al-Zakwani
- Department of Pharmacology & Clinical Pharmacy, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Fahad Al-Zadjali
- Department of Clinical Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Khamis Al-Hashmi
- Department of Physiology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Yajnavalka Banerjee
- Department of Clinical Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman Familial Hypercholesterolemia Study Group, Oman Society of Lipid and Atherosclerosis (OSLA), Sultan Qaboos University, Muscat, Oman
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Abstract
The β-thalassemias are characterized by a quantitative deficiency of β-globin chains underlaid by a striking heterogeneity of molecular defects. Although most of the molecular lesions involve the structural β gene directly, some down-regulate the gene through distal cis effects, and rare trans-acting mutations have also been identified. Most β-thalassemias are inherited in a Mendelian recessive fashion but there is a subgroup of β-thalassemia alleles that behave as dominant negatives. Unraveling the molecular basis of β-thalassemia has provided a paradigm for understanding of much of human genetics.
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Affiliation(s)
- Swee Lay Thein
- Department of Haematological Medicine, King's College London School of Medicine/King's College Hospital NHS Foundation Trust, London SE5 9NU, United Kingdom.
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22
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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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23
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Brown FC, Scott N, Rank G, Collinge JE, Vadolas J, Vickaryous N, Whitelaw N, Whitelaw E, Kile BT, Jane SM, Curtis DJ. ENU mutagenesis identifies the first mouse mutants reproducing human β-thalassemia at the genomic level. Blood Cells Mol Dis 2012; 50:86-92. [PMID: 23040355 DOI: 10.1016/j.bcmd.2012.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 09/11/2012] [Indexed: 12/24/2022]
Abstract
Forward genetic screens have been performed in many species to identify phenotypes in specific organ systems. We have undertaken a large-scale N-ethyl-N-nitrosourea (ENU) mutagenesis screen to identify dominant mutations that perturb erythropoiesis in mice. Mutant mice that displayed an erythrocyte mean cell volume (MCV) greater than three standard deviations from the population mean were identified. Two of these lines, RBC13 and RBC14, displayed a hypochromic, microcytic anemia, accompanied by a marked reticulocytosis, splenomegaly and diminished red cell survival. Timed pregnancies from heterozygous intercrosses revealed that a quarter of the embryos displayed severe anemia and did not survive beyond embryonic day (E) 18.5, consistent with homozygous β-thalassemia. Genetic complementation studies with a β-thalassemia mouse line reproduced the embryonic lethality in compound heterozygotes and a genomic custom capture array and massively parallel sequencing of the β-globin locus identified the causative mutations. The RBC13 line displayed a nonsense mutation at codon 40 in exon 2 of the β-major gene, invoking parallels with the common β(0)39 thalassemia mutation seen in humans. The RBC14 line exhibited a mutation at the polyadenylation signal of the β-major gene, exactly replicating a human β-thalassemia mutation. The RBC13 and RBC14 lines are the first β-thalassemia mouse models that reproduce human β-thalassemia at the genomic level, and as such highlight the power of ENU mutagenesis screens in generating mouse models of human disease.
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Affiliation(s)
- Fiona C Brown
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC 3004, Australia
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24
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Lopes-Marques M, Pereira-Castro I, Amorim A, Azevedo L. Characterization of the human ornithine transcarbamylase 3' untranslated regulatory region. DNA Cell Biol 2011; 31:427-33. [PMID: 22054066 DOI: 10.1089/dna.2011.1391] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutations in the untranslated regulatory regions of genes may result in abnormal gene expression or transcriptional regulation. In this study, we characterize the ornithine transcarbamylase (OTC) mRNA isoforms of the X-linked OTC gene involved in the urea formation in the liver. Our data revealed that two major transcripts (OTC-t1 and OTC-t2) are more highly expressed than any of the other isoforms in all the tissues analyzed, though a longer transcript (OTC-t3) was also isolated and characterized from the brain sample. The OTC-t2 sequence fully matches the OTC mRNA reference sequence (NM_000531.5). All three isoforms use a canonical AAUAAA hexamer that is predicted to fold into a hairpin secondary structure which might be exposed to the cleavage and polyadenylation specificity factor. In addition, we observed that the OTC-t1 and OTC-t2 transcripts display heterogeneity at the cleavage sites in a tissue-dependent manner. Taken together, our data demonstrate that several mRNA isoforms are transcribed from the OTC gene, thereby indicating a wide degree of variability in post-transcriptional regulation.
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Affiliation(s)
- Monica Lopes-Marques
- Population Genetics Group, IPATIMUP-Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
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Ahmed F, Benedito VA, Zhao PX. Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives. FRONTIERS IN PLANT SCIENCE 2011; 2:84. [PMID: 22639614 PMCID: PMC3355573 DOI: 10.3389/fpls.2011.00084] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 11/03/2011] [Indexed: 05/03/2023]
Abstract
Eukaryotic messenger RNA (mRNA) contains not only protein-coding regions but also a plethora of functional cis-elements that influence or coordinate a number of regulatory aspects of gene expression, such as mRNA stability, splicing forms, and translation rates. Understanding the rules that apply to each of these element types (e.g., whether the element is defined by primary or higher-order structure) allows for the discovery of novel mechanisms of gene expression as well as the design of transcripts with controlled expression. Bioinformatics plays a major role in creating databases and finding non-evident patterns governing each type of eukaryotic functional element. Much of what we currently know about mRNA regulatory elements in eukaryotes is derived from microorganism and animal systems, with the particularities of plant systems lagging behind. In this review, we provide a general introduction to the most well-known eukaryotic mRNA regulatory motifs (splicing regulatory elements, internal ribosome entry sites, iron-responsive elements, AU-rich elements, zipcodes, and polyadenylation signals) and describe available bioinformatics resources (databases and analysis tools) to analyze eukaryotic transcripts in search of functional elements, focusing on recent trends in bioinformatics methods and tool development. We also discuss future directions in the development of better computational tools based upon current knowledge of these functional elements. Improved computational tools would advance our understanding of the processes underlying gene regulations. We encourage plant bioinformaticians to turn their attention to this subject to help identify novel mechanisms of gene expression regulation using RNA motifs that have potentially evolved or diverged in plant species.
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Affiliation(s)
- Firoz Ahmed
- Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble FoundationArdmore, OK, USA
| | - Vagner A. Benedito
- Genetics and Developmental Biology, Plant and Soil Sciences Division, West Virginia UniversityMorgantown, WV, USA
| | - Patrick Xuechun Zhao
- Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble FoundationArdmore, OK, USA
- *Correspondence: Patrick Xuechun Zhao, Bioinformatics Laboratory, Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA e-mail:
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Impact of copy number of distinct SV40PolyA segments on expression of a GFP reporter gene. SCIENCE CHINA-LIFE SCIENCES 2010; 53:606-12. [PMID: 20596944 DOI: 10.1007/s11427-010-0110-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2009] [Accepted: 09/08/2009] [Indexed: 10/19/2022]
Abstract
The presence of Alu repeats downregulates the expression of the green fluorescent protein (GFP) gene. We found that SV40PolyA (PolyA, 240 bp), in either orientation, eliminated the inhibition of GFP gene expression induced by Alu repeats when it was placed between the GFP gene and the Alu repeats. In this study, 4 different segments (each 60 bp) were amplified from antisense PolyA (PolyAas) by PCR, and inserted upstream of Alu14 in pAlu14 plasmid (14 Alu repeats inserted downstream of the GFP gene in vector pEGFP-C1 in a head-tail tandem manner). Segments 1F1R (the first 60 bp segment at the 5' end of PolyAas) and 4F4R (the fourth 60 bp segment from the 5' end of PolyAas) did not activate GFP gene expression, whereas 2F2R and 3F3R (the middle two segments) did (as detected by Northern blot analysis and fluorescent microscopy). Different copy numbers of 2F2R and 3F3R segments, in a head and tail tandem manner, were inserted downstream of the GFP gene in pAlu14. p2F2R*4-Alu28, p3F3R*4-Alu18 and p3F3R*4-Alu28 were used as length controls to verify that the decrease in the expression of GFP was not due to the increased length of the inserted segment in the expression vectors. We found that 2 and 4 copies of 2F2R or 3F3R activated the GFP gene more strongly than one copy of them. However, more than 8 copies of 2F2R or 3F3R reduced the activation of the GFP gene. We concluded that SV40PolyAas contained at least two gene-activating elements (2F2R and 3F3R) and 2-4 copies of 2F2R or 3F3R were optimal for the expression of the GFP gene.
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Jacquette A, Le Roux G, Lacombe C, Goossens M, Pissard S. Compound Heterozygosity for Two New Mutations in the β‐Globin Gene [Codon 9 (+ TA) and Polyadenylation Site (AATAAA→AAAAAA)] Leads to Thalassemia Intermedia in a Tunisian Patient. Hemoglobin 2009; 28:243-8. [PMID: 15481893 DOI: 10.1081/hem-120040304] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
More than 200 mutations that are associated with beta-thalassemia (thal) have been found. In most cases, studies to detect a mutation in a patient is made easier because of the existence of geographical sets of mutations that allow the use of a dedicated mutation detection kit. We describe here a patient who originated from Tunisia, in whom we found two as yet unreported mutations, showing that even in a well-studied population a full gene study might be needed to characterize mutation(s).
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Affiliation(s)
- Aurelia Jacquette
- Laboratoire de Biochimie et de Génétique, Hôpital Henri Mondor, Créteil, France
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28
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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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29
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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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30
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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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31
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Danckwardt S, Gehring NH, Neu-Yilik G, Hundsdoerfer P, Pforsich M, Frede U, Hentze MW, Kulozik AE. The prothrombin 3'end formation signal reveals a unique architecture that is sensitive to thrombophilic gain-of-function mutations. Blood 2004; 104:428-35. [PMID: 15059842 DOI: 10.1182/blood-2003-08-2894] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The functional analysis of the common prothrombin 20210 G>A(F2 20210(*)A) mutation has recently revealed gain of function of 3'end processing as a novel genetic mechanism predisposing to human disease. We now show that the physiologic G at the cleavage site at position 20210 is the functionally least efficient nucleotide to support 3'end processing but has evolved to be physiologically optimal. Furthermore, the F2 3'end processing signal is characterized by a weak downstream cleavage stimulating factor (CstF) binding site with a low uridine density, and the functional efficiency of F2 3'end processing can be enhanced by the introduction of additional uridine residues. The recently identified thrombosis-related mutation (F2 20221(*)T) within the CstF binding site up-regulates F2 3'end processing and prothrombin biosynthesis in vivo. F2 20221(*)T thus represents the first example of a likely pathologically relevant mutation of the putative CstF binding site in the 3'flanking sequence of a human gene. Finally, we show that the low-efficiency F2 cleavage and CstF binding sites are balanced by a stimulatory upstream uridine-rich element in the 3'UTR. The architecture of the F2 3'end processing signal is thus characterized by a delicate balance of positive and negative signals. This balance appears to be highly susceptible to being disturbed by clinically relevant gain-of-function mutations.
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Affiliation(s)
- Sven Danckwardt
- Molecular Medicine Partnership Unit, Im Neuenheimer Feld 153, 69120 Heidelberg, Germany
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32
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Yasuda M, Shabbeer J, Osawa M, Desnick RJ. Fabry disease: novel alpha-galactosidase A 3'-terminal mutations result in multiple transcripts due to aberrant 3'-end formation. Am J Hum Genet 2003; 73:162-73. [PMID: 12796853 PMCID: PMC1180577 DOI: 10.1086/376608] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2003] [Accepted: 04/29/2003] [Indexed: 01/26/2023] Open
Abstract
Mutations in the gene that encodes the lysosomal exoglycohydrolase, alpha-galactosidase A (alpha-GalA), cause Fabry disease, an X-linked recessive inborn error of glycosphingolipid catabolism. Human alpha-GalA is one of the rare mammalian genes that has its polyadenylation signal in the coding sequence and lacks a 3' untranslated region (UTR). We identified two novel frameshift mutations, 1277delAA (del2) and 1284delACTT (del4), in unrelated men with classical Fabry disease. Both mutations occurred in the 3' terminus of the coding region and obliterated the termination codon, and del2 also altered the polyadenylation signal. To characterize these mutations, 3' rapid amplification of cDNA ends (RACE) and polymerase chain reactions (PCR) were performed, and the amplicons were subcloned and sequenced. Both mutations generated multiple transcripts with various lengths of 3' terminal sequences, some elongating approximately 1 kb. Mutant transcripts were classified as follows: type I transcripts had terminal in-frame thymidines that created termination codons when polyadenylated, type II had downstream termination codons within the elongated alpha-GalA sequence, and type III, the most abundant, lacked termination codons at their 3' ends. To determine if the type III transcripts were degraded by the recently described cytosolic messenger RNA degradation pathway for messages lacking termination codons, northern blot analysis was performed. However, the finding of similar levels of nuclear and cytoplasmic alpha-GalA mRNA in normal and patient lymphoblasts suggested that mRNA degradation did not result from either mutation. Expression of representative transcript types revealed differences in intracellular localization and/or protein stability and catalytic activity, with most mutant proteins being nonfunctional. Characterization of these 3' mutations identified a novel molecular mechanism causing classical Fabry disease.
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Affiliation(s)
- Makiko Yasuda
- Department of Human Genetics, Mount Sinai School of Medicine, New York; and Department of Pediatrics, Tokyo Women’s Medical University, Tokyo
| | - Junaid Shabbeer
- Department of Human Genetics, Mount Sinai School of Medicine, New York; and Department of Pediatrics, Tokyo Women’s Medical University, Tokyo
| | - Makiko Osawa
- Department of Human Genetics, Mount Sinai School of Medicine, New York; and Department of Pediatrics, Tokyo Women’s Medical University, Tokyo
| | - Robert J. Desnick
- Department of Human Genetics, Mount Sinai School of Medicine, New York; and Department of Pediatrics, Tokyo Women’s Medical University, Tokyo
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Sgourou A, Papachatzopoulou A, Psiouri L, Antoniou M, Zoumbos N, Gibbs R, Athanassiadou A. The beta-globin C-->G mutation at 6 bp 3' to the termination codon causes beta-thalassaemia by decreasing the mRNA level. Br J Haematol 2002; 118:671-6. [PMID: 12139763 DOI: 10.1046/j.1365-2141.2002.03627.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have studied the expression of the silent beta-thalassaemia term+6 (C-->G) mutation, at nucleotide 6 after the stop codon within the human beta-globin 3' untranslated regions (3'UTR), by stable transfection in murine erythroleukaemia (MEL) cells. Steady state mRNA levels from transfected MEL cells containing the term+6 mutant allele were reduced by 52-60%, compared with those obtained from the normal beta-globin gene, in both total and cytoplasmic RNA fractions, showing that the mutation itself is responsible for the similar data obtained from patients. Upon analysis of nuclear RNA, the term+6 mutation was found to also lower the ratio of cleaved/uncleaved transcripts by 22-30%, thus revealing that it interferes with correct 3'-end formation of beta-globin mRNA. The term+6 mutation lies within a polypyrimidine track, similar to that in the beta-intervening sequence II (beta-IVSII), which is known to be an important contributor to the promotion of premRNA 3'-end formation. We propose that the two polypyrimidine tracks flanking the translated region of exon III of the human beta-globin gene may co-operate during beta-globin mRNA biogenesis.
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Affiliation(s)
- Argyro Sgourou
- Laboratory of Biology, Faculty of Medicine, University of Patras, Patras, Rion, 261-10 Greece
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34
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Ma SK, Lee ACW, Chan AYY, Chan LC. A novel AATAAACATAAA mutation at the polyadenylation site of the beta-globin gene. Br J Haematol 2001. [DOI: 10.1046/j.1365-2141.2001.115_1cr-3.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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Ma SK, Lee ACW, Chan AYY, Chan LC. A novel
A
ATAAA→
C
ATAAA mutation at the polyadenylation site of the β-globin gene. Br J Haematol 2001. [DOI: 10.1046/j.1365-2141.2001.0115_1cr-3.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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36
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Abstract
Schizophrenia is a devastating psychiatric disorder with a high prevalence worldwide. There is therefore a need for animal models allowing the development of new therapeutic interventions and reliable diagnostic tests. In the temporal domain, cannabinoid receptor gene (CB1) knockout mice exhibit behavioural alterations, which parallel symptoms in schizophrenia, cannabis intoxication and dopamine D2 activation. While a specific nucleotide homology between CB1 and D2 accounts for the pathophysiology, pre-inserted spirochaetal DNA on the polyadenylation signal of CB1 reveals the aetiology of schizophrenia. If, in analogy to thalassaemia, mutations occur within this 3' regulatory domain, the genetic expression of CB1 is disrupted and sequential information lost in time. CB1, previously unrecognized as a candidate gene, thus unifies the different aspects of schizophrenic psychosis: cannabis-induced model psychosis, disrupted information processing, spatio-temporal distortions and other psychotic symptoms, disturbed neuronal migration, schizophrenic brain disorder, familial transmission, and prenatal infection by Borrelia burgdorferi.
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Affiliation(s)
- M Fritzsche
- Praxis für Innere Medizin, Adliswil, Switzerland.
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37
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Abstract
The study of the beta globin gene has provided great insights into the mechanisms of gene regulation and expression. In this review, we consider the normal regulation and expression of the beta globin gene and illustrate how the various steps may be affected, providing a basis for understanding the molecular pathophysiology of beta thalassemia. Mutations causing beta thalassemia can be classified as beta0 or B+ according to whether they abolish or reduce the production of beta globin chains. The vast majority of beta thalassemia is caused by point mutations, mostly single base substitutions, within the gene or its immediate flanking sequences. Rarely, beta thalassemia is caused by major deletions of the beta globin cluster. All these mutations behave as alleles of the beta locus but in several families the beta thalassemia phenotype segregates independently of the beta globin complex, and are likely to be caused by mutations in trans-acting regulatory factors.
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Affiliation(s)
- P J Ho
- Institute of Haematology, Royal Prince Alfred Hospital, Camperdown, NSW Australia
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38
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Das B, Guo Z, Russo P, Chartrand P, Sherman F. The role of nuclear cap binding protein Cbc1p of yeast in mRNA termination and degradation. Mol Cell Biol 2000; 20:2827-38. [PMID: 10733586 PMCID: PMC85501 DOI: 10.1128/mcb.20.8.2827-2838.2000] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The cyc1-512 mutation in Saccharomyces cerevisiae causes a 90% reduction in the level of iso-1-cytochrome c because of the lack of a proper 3'-end-forming signal, resulting in low levels of eight aberrantly long cyc1-512 mRNAs which differ in length at their 3' termini. cyc1-512 can be suppressed by deletion of either of the nonessential genes CBC1 and CBC2, which encode the CBP80 and CBP20 subunits of the nuclear cap binding complex, respectively, or by deletion of the nonessential gene UPF1, which encodes a major component of the mRNA surveillance complex. The upf1-Delta deletion suppressed the cyc1-512 defect by diminishing degradation of the longer subset of cyc1-512 mRNAs, suggesting that downstream elements or structures occurred in the extended 3' region, similar to the downstream elements exposed by transcripts bearing premature nonsense mutations. On the other hand, suppression of cyc1-512 defects by cbc1-Delta occurred by two different mechanisms. The levels of the shorter cyc1-512 transcripts were enhanced in the cbc1-Delta mutants by promoting 3'-end formation at otherwise-weak sites, whereas the levels of the longer cyc1-512 transcripts, as well as of all mRNAs, were slightly enhanced by diminishing degradation. Furthermore, cbc1-Delta greatly suppressed the degradation of mRNAs and other phenotypes of a rat7-1 strain which is defective in mRNA export. We suggest that Cbc1p defines a novel degradation pathway that acts on mRNAs partially retained in nuclei.
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Affiliation(s)
- B Das
- Department of Biochemistry and Biophysics, University of Rochester Medical School, Rochester, New York 14642, USA
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39
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van Solinge WW, Lind B, van Wijk R, Hart HC, Kraaijenhagen RJ. Clinical expression of a rare beta-globin gene mutation co-inherited with haemoglobin E-disease. EUROPEAN JOURNAL OF CLINICAL CHEMISTRY AND CLINICAL BIOCHEMISTRY : JOURNAL OF THE FORUM OF EUROPEAN CLINICAL CHEMISTRY SOCIETIES 1996; 34:949-54. [PMID: 8986398 DOI: 10.1515/cclm.1996.34.12.949] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A single nucleotide substitution and the effect on the phenotype in an Indonesian family with beta-thalassaemia, HbE-trait and HbE-beta-thalassaemia is described. In the proposita (female, age 20 (Hb 7.4 mmol/l; MCV 72 fl; MCH 1.45 fmol; HbA2 3.5%; HbF 2.4%)). An A/G mutation in the RNA cleavage and polyadenylation sequence was detected (AATAAA/AATAGA). Her sister (Hb 8.2 mmol/l; MCV 77 fl; MCH 1.60 fmol; HbA2/HbE 32.4%), carried a different mutation in the beta-globin gene (codon 25; G129/A), and consequently had HbE-trait. Their mother had a haemoglobin concentration of 6.4 mmol/l (MCV 56 fl; MCH 1.20 fmol; HbA2/HbE 55.8%). She was compound heterozygous for the mutation in the poly A-signal and HbE-trait. Using restriction enzyme analysis and linkage studies, we subsequently identified six family members with HbE-beta-thalassaemia, five with beta-thalassaemia and six with HbE-trait. Two individuals were unaffected. The mutation in the polyadenylation sequence causes a mild form of beta (+)-thalassaemia. The MCV and MCH in individuals with both beta-thalassaemia and HbE-trait were significantly lower, yet on average they were only slightly more anaemic than those carrying only the thalassaemic gene.
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Affiliation(s)
- W W van Solinge
- Klinisch Laboratorium, Ziekenhuis Eemland, Amersfoort, Nederland
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40
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Batista FD, Efremov DG, Tkach T, Burrone OR. Characterization of the human immunoglobulin epsilon mRNAs and their polyadenylation sites. Nucleic Acids Res 1995; 23:4805-11. [PMID: 8532522 PMCID: PMC307468 DOI: 10.1093/nar/23.23.4805] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Several IgE heavy (H) chain transcripts are produced by alternative splicing between constant region (CH3 and CH4) and membrane (M1 and M2) exons and by differential cleavage-polyadenylation at poly(A) sites downstream of the CH4 and M2 exons. We have now characterized the poly(A) signal of the epsilon transcripts that contain membrane exon sequences (epsilon CH4-M1'-M2, epsilon CH4-M1-M2, epsilon CH4-M2' and epsilon CH4-M2") and have determined the complete sequence of the M2 exon and 1.4 kb of downstream genomic DNA. The membrane locus poly(A) site was identified by RACE-PCR analysis of epsilon transcripts obtained from IgE-producing myeloma cells and normal peripheral blood lymphocytes (PBL). All membrane exon transcripts were found to be polyadenylated following a CA dinucleotide located 1046 nt from the beginning of the M2 exon. An AGTAAA hexamer, located 13 nt upstream from the site of cleavage and polyadenylation, was the only poly(A) signal sequence present in the 1.4 kb of genomic DNA downstream of the M2 exon. A (G+T)-rich region, which is also conserved in most poly(A) signals, was present 50 nt downstream of the AGTAAA hexamer. Northern blot analysis confirmed that this poly(A) site is used by the membrane exon epsilon mRNAs expressed by the U266 myeloma. The four membrane exon transcripts were detected in different relative amounts in PBL and IgE-producing myeloma cells, which could reflect different epsilon mRNA splicing patterns during B-cell differentiation.
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Affiliation(s)
- F D Batista
- International Centre for Genetic Engineering and Biotechnology, Area Science Park, Trieste, Italy
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41
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Guo Z, Russo P, Yun DF, Butler JS, Sherman F. Redundant 3' end-forming signals for the yeast CYC1 mRNA. Proc Natl Acad Sci U S A 1995; 92:4211-4. [PMID: 7753784 PMCID: PMC41913 DOI: 10.1073/pnas.92.10.4211] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The cyc1-512 mutation is a 38-bp deletion in the 3' untranslated region of the CYC1 gene, which encodes iso-1-cytochrome c in Saccharomyces cerevisiae. This deletion caused a 90% reduction in the levels of the CYC1 mRNA and protein because of the absence of the normal 3' end-forming signal. Although the 3' end-forming signal was not defined by previous analyses, we report that concomitant alteration by base-pair substitution of three 3' end-forming signals within and adjacent to the 38-bp region produced the same phenotype as the cyc1-512 mutation. Furthermore, these signals appear to be related to the previously identified 3' end-forming signal TATATA. A computer analysis revealed that TATATA and related sequences were present in the majority of 3' untranslated regions of yeast genes. Although TATATA may be the strongest and most frequently used signal in yeast genes, the CYC1+ gene concomitantly employed the weaker signals TT-TATA, TATGTT, and TATTTA, resulting in a strong signal.
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Affiliation(s)
- Z Guo
- Department of Biochemistry, University of Rochester School of Medicine and Dentistry, NY 14642, USA
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Kimberland ML, Boehm CD, Kazazian HH. Two novel beta-thalassemia alleles: poly A signal (AATAAA-->AAAA) and -92 C-->T. Hum Mutat 1995; 5:275-6. [PMID: 7599641 DOI: 10.1002/humu.1380050315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- M L Kimberland
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Filon D, Oron V, Shawa R, Elborno E, Najjar K, Tulchinsky T, Rachmilewitz E, Rund D, Oppenheim A. Spectrum of beta-thalassemia mutations in the Gaza area. Hum Mutat 1995; 5:351-3. [PMID: 7627194 DOI: 10.1002/humu.1380050416] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- D Filon
- Department of Hematology, Hebrew University-Hadassah Medical School, Jerusalem, Israel
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44
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Abstract
mRNAs that contain premature stop codons are unstable in most eukaryotes, but the mechanism of their degradation is largely unknown. We demonstrate that functions of the six C. elegans smg genes are necessary for rapid turnover of nonsense mutant mRNAs of the unc-54 myosin heavy chain gene. Nonsense alleles of unc-54 express mRNAs that are unstable in smg(+) genetic backgrounds but have normal or near normal stability in smg(-) backgrounds. smg mutations also stabilize mRNA of unc-54(r293), a small deletion that removes the unc-54 polyadenylation site and expresses an aberrant mRNA. Most unc-54 nonsense mutations are recessive in both smg(+) and smg(-) genetic backgrounds. However, four specific alleles are recessive when smg(+) and dominant when smg(-). These smg-dependent dominant alleles express nonsense mutant polypeptides that disrupt thick filament and/or sarcomere assembly. All four alleles are predicted to express nonsense fragment polypeptides that contain most of the myosin globular head domain without an attached rod segment. By degrading messages that contain premature stop codons, the smg genes eliminate mRNAs that encode potentially toxic protein fragments. We propose that this system of mRNA turnover protects cells from their own errors of transcription, mRNA processing, or mRNA transport.
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Affiliation(s)
- R Pulak
- Department of Genetics, University of Wisconsin, Madison 53706
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45
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Abstract
Gene mutations affecting mRNA processing and translation are not common causes of human genetic disease. Their analysis has nevertheless provided important insights into the basic biochemical mechanisms underlying mRNA transcription and translation.
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Affiliation(s)
- D N Cooper
- Charter Molecular Genetics Laboratory, Thrombosis Research Institute, London, U.K
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