1
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Chu C, Lin EW, Tran A, Jin H, Ho NI, Veit A, Cortes-Ciriano I, Burns KH, Ting DT, Park PJ. The landscape of human SVA retrotransposons. Nucleic Acids Res 2023; 51:11453-11465. [PMID: 37823611 PMCID: PMC10681720 DOI: 10.1093/nar/gkad821] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are evolutionarily young and still-active transposable elements (TEs) in the human genome. Several pathogenic SVA insertions have been identified that directly mutate host genes to cause neurodegenerative and other types of diseases. However, due to their sequence heterogeneity and complex structures as well as limitations in sequencing techniques and analysis, SVA insertions have been less well studied compared to other mobile element insertions. Here, we identified polymorphic SVA insertions from 3646 whole-genome sequencing (WGS) samples of >150 diverse populations and constructed a polymorphic SVA insertion reference catalog. Using 20 long-read samples, we also assembled reference and polymorphic SVA sequences and characterized the internal hexamer/variable-number-tandem-repeat (VNTR) expansions as well as differing SVA activity for SVA subfamilies and human populations. In addition, we developed a module to annotate both reference and polymorphic SVA copies. By characterizing the landscape of both reference and polymorphic SVA retrotransposons, our study enables more accurate genotyping of these elements and facilitate the discovery of pathogenic SVA insertions.
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Affiliation(s)
- Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Eric W Lin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Antuan Tran
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Hu Jin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Natalie I Ho
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - David T Ting
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
- Department of Medicine, Massachusetts General Hospital Harvard Medical School, Boston, MA 02114, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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2
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Vezain M, Thauvin-Robinet C, Vial Y, Coutant S, Drunat S, Urtizberea JA, Rolland A, Jacquin-Piques A, Fehrenbach S, Nicolas G, Lecoquierre F, Saugier-Veber P. Retrotransposon insertion as a novel mutational cause of spinal muscular atrophy. Hum Genet 2023; 142:125-138. [PMID: 36138164 DOI: 10.1007/s00439-022-02473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/15/2022] [Indexed: 01/18/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder resulting from biallelic alterations of the SMN1 gene: deletion, gene conversion or, in rare cases, intragenic variants. The disease severity is mainly influenced by the copy number of SMN2, a nearly identical gene, which produces only low amounts of full-length (FL) mRNA. Here we describe the first example of retrotransposon insertion as a pathogenic SMN1 mutational event. The 50-year-old patient is clinically affected by SMA type III with a diagnostic odyssey spanning nearly 30 years. Despite a mild disease course, he carries a single SMN2 copy. Using Exome Sequencing and Sanger sequencing, we characterized a SINE-VNTR-Alu (SVA) type F retrotransposon inserted in SMN1 intron 7. Using RT-PCR and RNASeq experiments on lymphoblastoid cell lines, we documented the dramatic decrease of FL transcript production in the patient compared to subjects with the same SMN1 and SMN2 copy number, thus validating the pathogenicity of this SVA insertion. We described the mutant FL-SMN1-SVA transcript characterized by exon extension and showed that it is subject to degradation by nonsense-mediated mRNA decay. The stability of the SMN-SVA protein may explain the mild course of the disease. This observation exemplifies the role of retrotransposons in human genetic disorders.
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Affiliation(s)
- Myriam Vezain
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Christel Thauvin-Robinet
- INSERM UMR1231 GAD-Génétique des Anomalies du Développement, Bourgogne Franche-Comté University, F-21000 , Dijon, France.,Genetics Center, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Yoann Vial
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, 48 boulevard Sérurier, 75019 , Paris, France
| | - Sophie Coutant
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Séverine Drunat
- INSERM UMR 1141, PROTECT, Paris University, F-75019, Paris, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, F-75019, Paris, France
| | - Jon Andoni Urtizberea
- Myology Institute, AP-HP Pitié-Salpêtrière University Hospital, F-75013, Paris, France
| | - Anne Rolland
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Pediatrics Department, Valence Hospital, 179 boulevard du Maréchal Juin, 26000, Valence, France
| | - Agnès Jacquin-Piques
- Department of Neurology, Clinical Neurophysiology, Competence Center of Neuromuscular Diseases, Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Séverine Fehrenbach
- Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Gaël Nicolas
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - François Lecoquierre
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France. .,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France. .,Laboratoire de Génétique Moléculaire, UFR-Santé, 22 boulevard Gambetta, 76183, Rouen, France.
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3
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Pfaff AL, Singleton LM, Kõks S. Mechanisms of disease-associated SINE-VNTR-Alus. Exp Biol Med (Maywood) 2022; 247:756-764. [PMID: 35387528 DOI: 10.1177/15353702221082612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
SINE-VNTR-Alus (SVAs) are the youngest retrotransposon family in the human genome. Their ongoing mobilization has generated genetic variation within the human population. At least 24 insertions to date, detailed in this review, have been associated with disease. The predominant mechanisms through which this occurs are alterations to normal splicing patterns, exonic insertions causing loss-of-function mutations, and large genomic deletions. Dissecting the functional impact of these SVAs and the mechanism through which they cause disease provides insight into the consequences of their presence in the genome and how these elements could influence phenotypes. Many of these disease-associated SVAs have been difficult to characterize and would not have been identified through routine analyses. However, the number identified has increased in recent years as DNA and RNA sequencing data became more widely available. Therefore, as the search for complex structural variation in disease continues, it is likely to yield further disease-causing SVA insertions.
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Affiliation(s)
- Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Lewis M Singleton
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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4
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Riba A, Fumagalli MR, Caselle M, Osella M. A Model-Driven Quantitative Analysis of Retrotransposon Distributions in the Human Genome. Genome Biol Evol 2021; 12:2045-2059. [PMID: 32986810 PMCID: PMC7750997 DOI: 10.1093/gbe/evaa201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2020] [Indexed: 12/21/2022] Open
Abstract
Retrotransposons, DNA sequences capable of creating copies of themselves, compose about half of the human genome and played a central role in the evolution of mammals. Their current position in the host genome is the result of the retrotranscription process and of the following host genome evolution. We apply a model from statistical physics to show that the genomic distribution of the two most populated classes of retrotransposons in human deviates from random placement, and that this deviation increases with time. The time dependence suggests a major role of the host genome dynamics in shaping the current retrotransposon distributions. Focusing on a neutral scenario, we show that a simple model based on random placement followed by genome expansion and sequence duplications can reproduce the empirical retrotransposon distributions, even though more complex and possibly selective mechanisms can have contributed. Besides the inherent interest in understanding the origin of current retrotransposon distributions, this work sets a general analytical framework to analyze quantitatively the effects of genome evolutionary dynamics on the distribution of genomic elements.
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Affiliation(s)
| | - Maria Rita Fumagalli
- Institute of Biophysics - CNR, National Research Council, Genova, Italy.,Department of Environmental Science and Policy, Center for Complexity and Biosystems, University of Milan, Milano, Italy
| | - Michele Caselle
- Department of Physics and INFN, University of Torino, Torino, Italy
| | - Matteo Osella
- Department of Physics and INFN, University of Torino, Torino, Italy
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5
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Sabatella M, Mantere T, Waanders E, Neveling K, Mensenkamp AR, van Dijk F, Hehir‐Kwa JY, Derks R, Kwint M, O'Gorman L, Tropa Martins M, Gidding CEM, Lequin MH, Küsters B, Wesseling P, Nelen M, Biegel JA, Hoischen A, Jongmans MC, Kuiper RP. Optical genome mapping identifies a germline retrotransposon insertion in SMARCB1 in two siblings with atypical teratoid rhabdoid tumors. J Pathol 2021; 255:202-211. [PMID: 34231212 PMCID: PMC8519051 DOI: 10.1002/path.5755] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/29/2022]
Abstract
In a subset of pediatric cancers, a germline cancer predisposition is highly suspected based on clinical and pathological findings, but genetic evidence is lacking, which hampers genetic counseling and predictive testing in the families involved. We describe a family with two siblings born from healthy parents who were both neonatally diagnosed with atypical teratoid rhabdoid tumor (ATRT). This rare and aggressive pediatric tumor is associated with biallelic inactivation of SMARCB1, and in 30% of the cases, a predisposing germline mutation is involved. Whereas the tumors of both siblings showed loss of expression of SMARCB1 and acquired homozygosity of the locus, whole exome and whole genome sequencing failed to identify germline or somatic SMARCB1 pathogenic mutations. We therefore hypothesized that the insertion of a pathogenic repeat‐rich structure might hamper its detection, and we performed optical genome mapping (OGM) as an alternative strategy to identify structural variation in this locus. Using this approach, an insertion of ~2.8 kb within intron 2 of SMARCB1 was detected. Long‐range PCR covering this region remained unsuccessful, but PacBio HiFi genome sequencing identified this insertion to be a SINE‐VNTR‐Alu, subfamily E (SVA‐E) retrotransposon element, which was present in a mosaic state in the mother. This SVA‐E insertion disrupts correct splicing of the gene, resulting in loss of a functional allele. This case demonstrates the power of OGM and long‐read sequencing to identify genomic variations in high‐risk cancer‐predisposing genes that are refractory to detection with standard techniques, thereby completing the clinical and molecular diagnosis of such complex cases and greatly improving counseling and surveillance of the families involved. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
| | - Tuomo Mantere
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit and Biocenter OuluUniversity of OuluOuluFinland
| | - Esmé Waanders
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Kornelia Neveling
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
| | - Arjen R Mensenkamp
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Freerk van Dijk
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
| | | | - Ronnie Derks
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Michael Kwint
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Luke O'Gorman
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | | | | | - Maarten H Lequin
- Department of RadiologyUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Benno Küsters
- Department of PathologyRadboud University Medical CenterNijmegenThe Netherlands
| | - Pieter Wesseling
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of PathologyAmsterdam University Medical Centers, Location VUmc and Brain Tumor Center AmsterdamAmsterdamThe Netherlands
| | - Marcel Nelen
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - Jacklyn A Biegel
- Department of Pathology and Laboratory MedicineChildren's Hospital, Los AngelesLos AngelesCAUSA
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Alexander Hoischen
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
- Radboud Institute of Molecular Life SciencesRadboud University Medical CenterNijmegenThe Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI)Radboud University Medical CenterNijmegenThe Netherlands
| | - Marjolijn C Jongmans
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of GeneticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Roland P Kuiper
- Princess Máxima Centre for Pediatric OncologyUtrechtThe Netherlands
- Department of Human GeneticsRadboud University Medical CenterNijmegenThe Netherlands
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6
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Disease onset in X-linked dystonia-parkinsonism correlates with expansion of a hexameric repeat within an SVA retrotransposon in TAF1. Proc Natl Acad Sci U S A 2017; 114:E11020-E11028. [PMID: 29229810 PMCID: PMC5754783 DOI: 10.1073/pnas.1712526114] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The genetic basis of X-Linked dystonia-parkinsonism (XDP) has been difficult to unravel, in part because all patients inherit the same haplotype of seven sequence variants, none of which has ever been identified in control individuals. This study revealed that one of the haplotype markers, a retrotransposon insertion within an intron of TAF1, has a variable number of hexameric repeats among affected individuals with an increase in repeat number strongly correlated with earlier age at disease onset. These data support a contributing role for this sequence in disease pathogenesis while further suggesting that XDP may be part of a growing list of neurodegenerative disorders associated with unstable repeat expansions. X-linked dystonia-parkinsonism (XDP) is a neurodegenerative disease associated with an antisense insertion of a SINE-VNTR-Alu (SVA)-type retrotransposon within an intron of TAF1. This unique insertion coincides with six additional noncoding sequence changes in TAF1, the gene that encodes TATA-binding protein–associated factor-1, which appear to be inherited together as an identical haplotype in all reported cases. Here we examined the sequence of this SVA in XDP patients (n = 140) and detected polymorphic variation in the length of a hexanucleotide repeat domain, (CCCTCT)n. The number of repeats in these cases ranged from 35 to 52 and showed a highly significant inverse correlation with age at disease onset. Because other SVAs exhibit intrinsic promoter activity that depends in part on the hexameric domain, we assayed the transcriptional regulatory effects of varying hexameric lengths found in the unique XDP SVA retrotransposon using luciferase reporter constructs. When inserted sense or antisense to the luciferase reading frame, the XDP variants repressed or enhanced transcription, respectively, to an extent that appeared to vary with length of the hexamer. Further in silico analysis of this SVA sequence revealed multiple motifs predicted to form G-quadruplexes, with the greatest potential detected for the hexameric repeat domain. These data directly link sequence variation within the XDP-specific SVA sequence to phenotypic variability in clinical disease manifestation and provide insight into potential mechanisms by which this intronic retroelement may induce transcriptional interference in TAF1 expression.
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7
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Hancks DC, Kazazian HH. Roles for retrotransposon insertions in human disease. Mob DNA 2016; 7:9. [PMID: 27158268 PMCID: PMC4859970 DOI: 10.1186/s13100-016-0065-9] [Citation(s) in RCA: 421] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022] Open
Abstract
Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs. To date in humans, 124 LINE-1-mediated insertions which result in genetic diseases have been reported. Disease causing LINE-1 insertions have provided a wealth of insight and the foundation for valuable tools to study these genomic parasites. In this review, we provide an overview of LINE-1 biology followed by highlights from new reports of LINE-1-mediated genetic disease in humans.
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Affiliation(s)
- Dustin C. Hancks
- />Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Haig H. Kazazian
- />McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins School of Medicine, Baltimore, MD USA
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8
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Abstract
Transposable elements have had a profound impact on the structure and function of mammalian genomes. The retrotransposon Long INterspersed Element-1 (LINE-1 or L1), by virtue of its replicative mobilization mechanism, comprises ∼17% of the human genome. Although the vast majority of human LINE-1 sequences are inactive molecular fossils, an estimated 80-100 copies per individual retain the ability to mobilize by a process termed retrotransposition. Indeed, LINE-1 is the only active, autonomous retrotransposon in humans and its retrotransposition continues to generate both intra-individual and inter-individual genetic diversity. Here, we briefly review the types of transposable elements that reside in mammalian genomes. We will focus our discussion on LINE-1 retrotransposons and the non-autonomous Short INterspersed Elements (SINEs) that rely on the proteins encoded by LINE-1 for their mobilization. We review cases where LINE-1-mediated retrotransposition events have resulted in genetic disease and discuss how the characterization of these mutagenic insertions led to the identification of retrotransposition-competent LINE-1s in the human and mouse genomes. We then discuss how the integration of molecular genetic, biochemical, and modern genomic technologies have yielded insight into the mechanism of LINE-1 retrotransposition, the impact of LINE-1-mediated retrotransposition events on mammalian genomes, and the host cellular mechanisms that protect the genome from unabated LINE-1-mediated retrotransposition events. Throughout this review, we highlight unanswered questions in LINE-1 biology that provide exciting opportunities for future research. Clearly, much has been learned about LINE-1 and SINE biology since the publication of Mobile DNA II thirteen years ago. Future studies should continue to yield exciting discoveries about how these retrotransposons contribute to genetic diversity in mammalian genomes.
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9
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Retroelements in human disease. Gene 2013; 518:231-41. [PMID: 23333607 DOI: 10.1016/j.gene.2013.01.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/28/2012] [Accepted: 01/02/2013] [Indexed: 12/16/2022]
Abstract
Retroelements are an abundant class of noncoding DNAs present in about half of the human genome. Among them, L1, Alu and SVA are currently active. They "jump" by retrotransposition, shuffle genomic regions by 5' and 3' transduction, and promote or inhibit gene transcription by providing alternative promoters or generating antisense and/or regulatory noncoding RNAs. Recent data also suggest that retroelement insertions into exons and introns of genes induce different types of genetic disease, including cancer. Retroelements interfere with the expression of genes by inducing alternative splicing via exon skipping and exonization using cryptic splice sites, and by providing polyadenylation signals. Here we summarize our current understanding of the molecular mechanisms of retroelement-induced mutagenesis which causes fifty different types of human disease. We categorize these mutagenic effects according to eleven different mechanisms and show that most of them may be explained either by traditional exon definition or transcriptional interference, a previously unrecognized molecular mechanism. In summary, this review gives an overview of retroelement insertions in genes that cause significant changes in their transcription and cotranscriptional splicing and show a remarkable level of complexity.
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10
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Pathogenic exon-trapping by SVA retrotransposon and rescue in Fukuyama muscular dystrophy. Nature 2011; 478:127-31. [PMID: 21979053 PMCID: PMC3412178 DOI: 10.1038/nature10456] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 08/12/2011] [Indexed: 12/23/2022]
Abstract
Fukuyama muscular dystrophy (FCMD; MIM253800), one of the most common autosomal recessive disorders in Japan, was the first human disease found to result from ancestral insertion of a SINE-VNTR-Alu (SVA) retrotransposon into a causative gene1-3. In FCMD, the SVA insertion occurs in the 3′-untranslated region (UTR) of the fukutin gene. The pathogenic mechanism for FCMD is unknown, and no effective clinical treatments exist. Here we show that aberrant mRNA splicing, induced by SVA exon-trapping, underlies the molecular pathogenesis of FCMD. Quantitative mRNA analysis pinpointed a region that was missing from transcripts in FCMD patients. This region spans part of the 3′ end of the fukutin coding region, proximal part of the 3′ UTR, and the SVA insertion. Correspondingly, fukutin mRNA transcripts in FCMD patients and SVA knock-in (KI) model mice were shorter than the expected length. Sequence analysis revealed an abnormal splicing event, provoked by a strong acceptor site in SVA and a rare alternative donor site in fukutin exon 10. The resulting product truncates the fukutin C-terminus and adds 129 amino acids encoded by the SVA. Introduction of antisense oligonucleotides (AONs) targeting the splice acceptor, the predicted exonic splicing enhancer, and the intronic splicing enhancer prevented pathogenic exon-trapping by SVA in FCMD patient cells and model mice, rescuing normal fukutin mRNA expression and protein production. AON treatment also restored fukutin functions, including O-glycosylation of α-dystroglycan (α-DG) and laminin binding by α-DG. Moreover, we observe exon-trapping in other SVA insertions associated with disease (hypercholesterolemia4, neutral lipid storage disease5) and human-specific SVA insertion in a novel gene. Thus, although splicing into SVA is known6-8, we have discovered in human disease a role for SVA-mediated exon-trapping and demonstrated the promise of splicing modulation therapy as the first radical clinical treatment for FCMD and other SVA-mediated diseases.
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11
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Hancks DC, Goodier JL, Mandal PK, Cheung LE, Kazazian HH. Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum Mol Genet 2011; 20:3386-400. [PMID: 21636526 DOI: 10.1093/hmg/ddr245] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human retrotransposons generate structural variation and genomic diversity through ongoing retrotransposition and non-allelic homologous recombination. Cell culture retrotransposition assays have provided great insight into the genomic impact of retrotransposons, in particular, LINE-1(L1) and Alu elements; however, no such assay exists for the youngest active human retrotransposon, SINE-VNTR-Alu (SVA). Here we report the development of an SVA cell culture retrotransposition assay. We marked several SVAs with either neomycin or EGFP retrotransposition indicator cassettes. Engineered SVAs retrotranspose using L1 proteins supplemented in trans in multiple cell lines, including U2OS osteosarcoma cells where SVA retrotransposition is equal to that of an engineered L1. Engineered SVAs retrotranspose at 1-54 times the frequency of a marked pseudogene in HeLa HA cells. Furthermore, our data suggest a variable requirement for L1 ORF1p for SVA retrotransposition. Recovered engineered SVA insertions display all the hallmarks of LINE-1 retrotransposition and some contain 5' and 3' transductions, which are common for genomic SVAs. Of particular interest is the fact that four out of five insertions recovered from one SVA are full-length, with the 5' end of these insertions beginning within 5 nt of the CMV promoter transcriptional start site. This assay demonstrates that SVA elements are indeed mobilized in trans by L1. Previously intractable questions regarding SVA biology can now be addressed.
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Affiliation(s)
- Dustin C Hancks
- Cell and Molecular Biology Graduate Group, The University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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12
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Iolascon A, King MJ, Robertson S, Avvisati RA, Vitiello F, Asci R, Scoppettuolo MN, Delaunay J. A genomic deletion causes truncation of α-spectrin and ellipto-poikilocytosis. Blood Cells Mol Dis 2011; 46:195-200. [PMID: 21212007 DOI: 10.1016/j.bcmd.2010.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 12/02/2010] [Indexed: 11/18/2022]
Abstract
We report on a truncated α-spectrin chain, spectrin(Exeter), associated with ellipto-poikilocytosis. Analysis of erythrocyte membranes of affected individuals revealed a truncated α-spectrin chain with normal amounts of spectrin dimer. In the proband and her father, one haploid set of α-spectrin cDNA lacked exons 11 and 12, leading to partial deletion of repeats α4 and α5 (83 amino acids) of the α-spectrin chain. In one allele of genomic DNA, a 3567bp deletion starting in intron 10 and ending in intron 12 of the SPTA1 gene was found. The common polymorphic SPTA1 α(LELY) allele was found in trans to the SPTA1αExeter allele in the proband. The proband had inherited the SPTA1Exeter allele from her father and the αLELY allele from her healthy, asymptomatic mother. This is the first report of an interstitial deletion in the SPTA1 gene associated with ellipto-poikilocytosis.
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Affiliation(s)
- A Iolascon
- CEINGE Biotecnologie Avanzate, Napoli, Italy.
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13
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Hancks DC, Kazazian H. SVA retrotransposons: Evolution and genetic instability. Semin Cancer Biol 2010; 20:234-45. [PMID: 20416380 PMCID: PMC2945828 DOI: 10.1016/j.semcancer.2010.04.001] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Revised: 04/01/2010] [Accepted: 04/14/2010] [Indexed: 01/21/2023]
Abstract
SINE-VNTR-Alus (SVA) are non-autonomous hominid specific retrotransposons that are associated with disease in humans. SVAs are evolutionarily young and presumably mobilized by the LINE-1 reverse transcriptase in trans. SVAs are currently active and may impact the host through a variety of mechanisms including insertional mutagenesis, exon shuffling, alternative splicing, and the generation of differentially methylated regions (DMR). Here we review SVA biology, including SVA insertions associated with known diseases. Further, we discuss a model describing the initial formation of SVA and the mechanisms by which SVA may impact the host.
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Affiliation(s)
- Dustin C. Hancks
- Department of Genetics, The University of Pennsylvania School of Medicine
| | - Haig Kazazian
- Department of Genetics, The University of Pennsylvania School of Medicine
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14
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Chen JM, Férec C, Cooper DN. LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease: mutation detection bias and multiple mechanisms of target gene disruption. J Biomed Biotechnol 2010; 2006:56182. [PMID: 16877817 PMCID: PMC1510945 DOI: 10.1155/jbb/2006/56182] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
LINE-1 (L1) elements are the most abundant autonomous non-LTR retrotransposons in the human genome. Having recently performed a meta-analysis of L1 endonuclease-mediated retrotranspositional events causing human genetic disease, we have extended this study by focusing on two key issues, namely, mutation detection bias and the multiplicity of mechanisms of target gene disruption. Our analysis suggests that whereas an ascertainment bias may have generally militated against the detection of autosomal L1-mediated insertions, autosomal L1 direct insertions could have been disproportionately overlooked owing to their unusually large size. Our analysis has also indicated that the mechanisms underlying the functional disruption of target genes by L1-mediated retrotranspositional events are likely to be dependent on several different factors such as the type of insertion (L1 direct, L1 trans-driven Alu, or SVA), the precise locations of the inserted sequences within the target gene regions, the length of the inserted sequences, and possibly also their orientation.
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Affiliation(s)
- Jian-Min Chen
- INSERM U613, Génétique
Moléculaire et Génétique Épidémiologique,
29220 Brest, France
- Faculté de Médecine de Brest
et des Sciences de la Santé, Université de Bretagne Occidentale, 29238
Brest, France
- Etablissement Français du Sang-Bretagne,
35000 Rennes, France
- *Jian-Min Chen:
| | - Claude Férec
- INSERM U613, Génétique
Moléculaire et Génétique Épidémiologique,
29220 Brest, France
- Faculté de Médecine de Brest
et des Sciences de la Santé, Université de Bretagne Occidentale, 29238
Brest, France
- Etablissement Français du Sang-Bretagne,
35000 Rennes, France
- Hôpital Morvan, CHRU Brest, Laboratoire de
Génétique Moléculaire et d'Histocompatibilité, 29200 Brest, France
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine,
Cardiff University, Heath Park Campus, Cardiff CF14 4XN, UK
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15
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Polymorphic SVA retrotransposons at four loci and their association with classical HLA class I alleles in Japanese, Caucasians and African Americans. Immunogenetics 2010; 62:211-30. [PMID: 20174920 DOI: 10.1007/s00251-010-0427-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 02/01/2010] [Indexed: 01/07/2023]
Abstract
Polymorphic insertion frequencies of the retrotransposons known as the "SVA" elements were investigated at four loci in the MHC class I genomic region to determine their allele and haplotype frequencies and associations with the HLA-A, -B or -C genes for 100 Japanese, 100 African Americans, 174 Australian Caucasians and 66 reference cell lines obtained from different ethnic groups. The SVA insertions representing different subfamily members varied in frequency between none for SVA-HF in Japanese and 65% for SVA-HB in Caucasians or African Americans with significant differences in frequencies between the three populations at least at three loci. The SVA loci were in Hardy-Weinberg equilibrium except for the SVA-HA locus which deviated significantly in African Americans and Caucasians possibly because of a genomic deletion of this locus in individuals with the HLA-A*24 allele. Strong linkage disequilibria and high percentage associations between the human leucocyte antigen (HLA) class I gene alleles and some of the SVA insertions were detected in all three populations in spite of significant frequency differences for the SVA and HLA class I alleles between the three populations. The highest percentage associations (>86%) were between SVA-HB and HLA-B*08, -B*27, -B*37 to -B*41, -B*52 and -B*53; SVA-HC and HLA-B*07; SVA-HA and HLA-A*03, -A*11 and -A*30; and SVA-HF and HLA-A*03 and HLA-B*47. From pairwise associations in the three populations and the homozygous cell line results, it was possible to deduce the SVA and HLA class I allelic combinations (haplotypes), population differences and the identity by descent of several common HLA-A allelic lineages.
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16
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Goodier JL, Mandal PK, Zhang L, Kazazian HH. Discrete subcellular partitioning of human retrotransposon RNAs despite a common mechanism of genome insertion. Hum Mol Genet 2010; 19:1712-25. [PMID: 20147320 DOI: 10.1093/hmg/ddq048] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Despite the immense significance retrotransposons have had for genome evolution much about their biology is unknown, including the processes of forming their ribonucleoprotein (RNP) particles and transporting them about the cell. Suppression of retrotransposon expression, together with the presence of retrotransposon sequence within numerous mRNAs, makes tracking endogenous L1 RNP particles in cells problematic. We overcame these difficulties by assaying in living and fixed cells tagged-RNPs generated from constructs expressing retrotransposition-competent L1s. In this way, we demonstrate for the first time the subcellular colocalization of L1 RNA and proteins ORF1p and ORF2p, and show their targeting together to cytoplasmic foci. Foci are often associated with markers of cytoplasmic stress granules. Furthermore, mutation analyses reveal that ORF1p can direct L1 RNP distribution within the cell. We also assayed RNA localization of the non-autonomous retrotransposons Alu and SVA. Despite a requirement for the L1 integration machinery, each manifests unique features of subcellular RNA distribution. In nuclei Alu RNA forms small round foci partially associated with marker proteins for coiled bodies, suborganelles involved in the processing of non-coding RNAs. SVA RNA patterning is distinctive, being cytoplasmic but without prominent foci and concentrated in large nuclear aggregates that often ring nucleoli. Such variability predicts significant differences in the life cycles of these elements.
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Affiliation(s)
- John L Goodier
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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17
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Schneider AM, Duffield AS, Symer DE, Burns KH. Roles of retrotransposons in benign and malignant hematologic disease. CELLSCIENCE 2009; 6:121-145. [PMID: 20200603 PMCID: PMC2830787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nearly half of our genomes are repetitive sequences derived from retrotransposons. These repeats have accumulated by a 'copy-and-paste' mechanism whereby: (i.) a genomic template sequence is transcribed to RNA, (ii.) the RNA is reverse-transcribed, and (iii.) the DNA copy is inserted at a new location in the host genome. As we remain susceptible to new retrotransposition events, many of these insertions are highly polymorphic. Transposons are of interest since insertions into both coding and non-coding gene regions have been associated with a wide variety of functional sequelae and because transposable elements can be involved in genomic rearrangements in transformed cells. In this review, we highlight how expression of retrotransposons, de novo and polymorphic transposon insertions, and genomic rearrangements that these repeats potentiate contribute to both benign and neoplastic hematopoietic diseases.
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Affiliation(s)
- Anna M Schneider
- Dept. of Molecular Biology & Genetics, Johns Hopkins University School of Medicine
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18
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Hancks DC, Ewing AD, Chen JE, Tokunaga K, Kazazian HH. Exon-trapping mediated by the human retrotransposon SVA. Genome Res 2009; 19:1983-91. [PMID: 19635844 DOI: 10.1101/gr.093153.109] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Although most human retrotransposons are inactive, both inactive and active retrotransposons drive genome evolution and may influence transcription through various mechanisms. In humans, three retrotransposon families are still active, but one of these, SVA, remains mysterious. Here we report the identification of a new subfamily of SVA, which apparently formed after an alternative splicing event where the first exon of the MAST2 gene spliced into an intronic SVA and subsequently retrotransposed. Additional examples of SVA retrotransposing upstream exons due to splicing into SVA were also identified in other primate genomes. After molecular and computational experiments, we found a number of functional 3' splice sites within many different transcribed SVAs across the human and chimpanzee genomes. Using a minigene splicing construct containing an SVA, we observed splicing in cell culture, along with SVA exonization events that introduced premature termination codons (PTCs). These data imply that an SVA residing within an intron in the same orientation as the gene may alter normal gene transcription either by gene-trapping or by introducing PTCs through exonization, possibly creating differences within and across species.
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Affiliation(s)
- Dustin C Hancks
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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19
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Takasu M, Hayashi R, Maruya E, Ota M, Imura K, Kougo K, Kobayashi C, Saji H, Ishikawa Y, Asai T, Tokunaga K. Deletion of entire HLA-A gene accompanied by an insertion of a retrotransposon. ACTA ACUST UNITED AC 2007; 70:144-50. [PMID: 17610419 DOI: 10.1111/j.1399-0039.2007.00870.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Unusual HLA-A'null' alleles because of an entire gene deletion were found in three apparently unrelated Japanese families with leukemia patients. Inclusion of the entire HLA-A gene in the deletion was confirmed by polymerase chain reaction direct sequencing of the surrounding regions of HLA-A. Further localization of the breakpoints of the HLA-A deletion at the centromeric and telomeric sides was performed, and these families were shown to possess the identical deletion. We then determined the genomic sequence of the HLA-A-deleted haplotype. Surprisingly, the haplotype turned out to carry an insertion of an SVA (SINE-VNTR-Alu) retrotransposon of 2 kb as well as the 14 kb deletion that included the entire HLA-A gene.
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Affiliation(s)
- M Takasu
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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20
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Mills RE, Bennett EA, Iskow RC, Devine SE. Which transposable elements are active in the human genome? Trends Genet 2007; 23:183-91. [PMID: 17331616 DOI: 10.1016/j.tig.2007.02.006] [Citation(s) in RCA: 327] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 01/15/2007] [Accepted: 02/12/2007] [Indexed: 01/20/2023]
Abstract
Although a large proportion (44%) of the human genome is occupied by transposons and transposon-like repetitive elements, only a small proportion (<0.05%) of these elements remain active today. Recent evidence indicates that approximately 35-40 subfamilies of Alu, L1 and SVA elements (and possibly HERV-K elements) remain actively mobile in the human genome. These active transposons are of great interest because they continue to produce genetic diversity in human populations and also cause human diseases by integrating into genes. In this review, we examine these active human transposons and explore mechanistic factors that influence their mobilization.
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Affiliation(s)
- Ryan E Mills
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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21
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Chen JM, Stenson PD, Cooper DN, Férec C. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 2005; 117:411-27. [PMID: 15983781 DOI: 10.1007/s00439-005-1321-0] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Accepted: 04/04/2005] [Indexed: 10/25/2022]
Abstract
Diverse long interspersed element-1 (LINE-1 or L1)-dependent mutational mechanisms have been extensively studied with respect to L1 and Alu elements engineered for retrotransposition in cultured cells and/or in genome-wide analyses. To what extent the in vitro studies can be held to accurately reflect in vivo events in the human genome, however, remains to be clarified. We have attempted to address this question by means of a systematic analysis of recent L1-mediated retrotranspositional events that have caused human genetic disease, with a view to providing a more complete picture of how L1-mediated retrotransposition impacts upon the architecture of the human genome. A total of 48 such mutations were identified, including those described as L1-mediated retrotransposons, as well as insertions reported to contain a poly(A) tail: 26 were L1 trans-driven Alu insertions, 15 were direct L1 insertions, four were L1 trans-driven SVA insertions, and three were associated with simple poly(A) insertions. The systematic study of these lesions, when combined with previous in vitro and genome-wide analyses, has strengthened several important conclusions regarding L1-mediated retrotransposition in humans: (a) approximately 25% of L1 insertions are associated with the 3' transduction of adjacent genomic sequences, (b) approximately 25% of the new L1 inserts are full-length, (c) poly(A) tail length correlates inversely with the age of the element, and (d) the length of target site duplication in vivo is rarely longer than 20 bp. Our analysis also suggests that some 10% of L1-mediated retrotranspositional events are associated with significant genomic deletions in humans. Finally, the identification of independent retrotranspositional events that have integrated at the same genomic locations provides new insight into the L1-mediated insertional process in humans.
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Affiliation(s)
- Jian-Min Chen
- INSERM U613-Génétique Moléculaire et Génétique Epidémiologique, Etablissement Français du Sang-Bretagne, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, 29220, France.
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22
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Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. Natural genetic variation caused by transposable elements in humans. Genetics 2005; 168:933-51. [PMID: 15514065 PMCID: PMC1448813 DOI: 10.1534/genetics.104.031757] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transposons and transposon-like repetitive elements collectively occupy 44% of the human genome sequence. In an effort to measure the levels of genetic variation that are caused by human transposons, we have developed a new method to broadly detect transposon insertion polymorphisms of all kinds in humans. We began by identifying 606,093 insertion and deletion (indel) polymorphisms in the genomes of diverse humans. We then screened these polymorphisms to detect indels that were caused by de novo transposon insertions. Our method was highly efficient and led to the identification of 605 nonredundant transposon insertion polymorphisms in 36 diverse humans. We estimate that this represents 25-35% of approximately 2075 common transposon polymorphisms in human populations. Because we identified all transposon insertion polymorphisms with a single method, we could evaluate the relative levels of variation that were caused by each transposon class. The average human in our study was estimated to harbor 1283 Alu insertion polymorphisms, 180 L1 polymorphisms, 56 SVA polymorphisms, and 17 polymorphisms related to other forms of mobilized DNA. Overall, our study provides significant steps toward (i) measuring the genetic variation that is caused by transposon insertions in humans and (ii) identifying the transposon copies that produce this variation.
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Affiliation(s)
- E Andrew Bennett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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23
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Abstract
Hereditary elliptocytosis (HE) is a common disorder of erythrocyte shape, occurring especially in individuals of African and Mediterranean ancestry, presumably because elliptocytes confer some resistance to malaria. The principle lesion in HE is mechanical weakness or fragility of the erythrocyte membrane skeleton due to defects in alpha-spectrin, beta-spectrin, or protein 4.1. Numerous mutations have been described in the genes encoding these proteins, including point mutations, gene deletions and insertions, and mRNA processing defects. Several mutations have been identified in a number of individuals on the same genetic background, suggesting a "founder effect." The majority of HE patients are asymptomatic, but some may experience hemolytic anemia, splenomegaly, and intermittent jaundice.
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Affiliation(s)
- Patrick G Gallagher
- Department of Pediatrics, Yale University School of Medicine, 333 Cedar Street, PO Box 208064, New Haven, CT 06520-8064, USA
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24
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Ostertag EM, Goodier JL, Zhang Y, Kazazian HH. SVA elements are nonautonomous retrotransposons that cause disease in humans. Am J Hum Genet 2003; 73:1444-51. [PMID: 14628287 PMCID: PMC1180407 DOI: 10.1086/380207] [Citation(s) in RCA: 253] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Accepted: 09/24/2003] [Indexed: 11/04/2022] Open
Abstract
L1 elements are the only active autonomous retrotransposons in the human genome. The nonautonomous Alu elements, as well as processed pseudogenes, are retrotransposed by the L1 retrotransposition proteins working in trans. Here, we describe another repetitive sequence in the human genome, the SVA element. Our analysis reveals that SVA elements are currently active in the human genome. SVA elements, like Alus and L1s, occasionally insert into genes and cause disease. Furthermore, SVA elements are probably mobilized in trans by active L1 elements.
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Affiliation(s)
- Eric M Ostertag
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6145, USA
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25
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Wandersee NJ, Birkenmeier CS, Bodine DM, Mohandas N, Barker JE. Mutations in the murine erythroid alpha-spectrin gene alter spectrin mRNA and protein levels and spectrin incorporation into the red blood cell membrane skeleton. Blood 2003; 101:325-30. [PMID: 12393645 DOI: 10.1182/blood-2002-01-0113] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tetramers of alpha- and beta-spectrin heterodimers, linked by intermediary proteins to transmembrane proteins, stabilize the red blood cell cytoskeleton. Deficiencies of either alpha- or beta-spectrin can result in severe hereditary spherocytosis (HS) or hereditary elliptocytosis (HE) in mice and humans. Four mouse mutations, sph, sph(Dem), sph(2BC), and sph(J), affect the erythroid alpha-spectrin gene, Spna1, on chromosome 1 and cause severe HS and HE. Here we describe the molecular alterations in alpha-spectrin and their consequences in sph(2BC)/sph(2BC) and sph(J)/sph(J) erythrocytes. A splicing mutation, sph(2BC) initiates the skipping of exon 41 and premature protein termination before the site required for dimerization of alpha-spectrin with beta-spectrin. A nonsense mutation in exon 52, sph(J) eliminates the COOH-terminal 13 amino acids. Both defects result in instability of the red cell membrane and loss of membrane surface area. In sph(2BC)/sph(2BC), barely perceptible levels of messenger RNA and consequent decreased synthesis of alpha-spectrin protein are primarily responsible for the resultant hemolysis. By contrast, sph(J)/sph(J) mice synthesize the truncated alpha-spectrin in which the 13-terminal amino acids are deleted at higher levels than normal, but they cannot retain this mutant protein in the cytoskeleton. The sph(J) deletion is near the 4.1/actin-binding region at the junctional complex providing new evidence that this 13-amino acid segment at the COOH-terminus of alpha-spectrin is crucial to the stability of the junctional complex.
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26
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Abstract
L1 retrotransposons comprise 17% of the human genome. Although most L1s are inactive, some elements remain capable of retrotransposition. L1 elements have a long evolutionary history dating to the beginnings of eukaryotic existence. Although many aspects of their retrotransposition mechanism remain poorly understood, they likely integrate into genomic DNA by a process called target primed reverse transcription. L1s have shaped mammalian genomes through a number of mechanisms. First, they have greatly expanded the genome both by their own retrotransposition and by providing the machinery necessary for the retrotransposition of other mobile elements, such as Alus. Second, they have shuffled non-L1 sequence throughout the genome by a process termed transduction. Third, they have affected gene expression by a number of mechanisms. For instance, they occasionally insert into genes and cause disease both in humans and in mice. L1 elements have proven useful as phylogenetic markers and may find other practical applications in gene discovery following insertional mutagenesis in mice and in the delivery of therapeutic genes.
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Affiliation(s)
- E M Ostertag
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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27
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Wandersee NJ, Roesch AN, Hamblen NR, de Moes J, van der Valk MA, Bronson RT, Gimm JA, Mohandas N, Demant P, Barker JE. Defective spectrin integrity and neonatal thrombosis in the first mouse model for severe hereditary elliptocytosis. Blood 2001; 97:543-50. [PMID: 11154235 DOI: 10.1182/blood.v97.2.543] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations affecting the conversion of spectrin dimers to tetramers result in hereditary elliptocytosis (HE), whereas a deficiency of human erythroid alpha- or beta-spectrin results in hereditary spherocytosis (HS). All spontaneous mutant mice with cytoskeletal deficiencies of spectrin reported to date have HS. Here, the first spontaneous mouse mutant, sph(Dem)/ sph(Dem), with severe HE is described. The sph(Dem) mutation is the insertion of an intracisternal A particle element in intron 10 of the erythroid alpha-spectrin gene. This causes exon skipping, the in-frame deletion of 46 amino acids from repeat 5 of alpha-spectrin and alters spectrin dimer/tetramer stability and osmotic fragility. The disease is more severe in sph(Dem)/sph(Dem) neonates than in alpha-spectrin-deficient mice with HS. Thrombosis and infarction are not, as in the HS mice, limited to adults but occur soon after birth. Genetic background differences that exist between HE and HS mice are suspect, along with red blood cell morphology differences, as modifiers of thrombosis timing. sph(Dem)/sph(Dem) mice provide a unique model for analyzing spectrin dimer- to-tetramer conversion and identifying factors that influence thrombosis.
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28
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Abstract
The recent discovery of the specific molecular defects in many patients with hereditary spherocytosis and hereditary elliptocytosis/pyropoikilocytosis partially clarifies the molecular pathology of these diseases. HE and HPP are caused by defects in the horizontal interactions that hold the membrane skeleton together, particularly the critical spectrin self-association reaction. Single gene defects cause red cells to elongate as they circulate, by a unknown mechanism, and are clinically harmless. The combination of two defective genes or one severe alpha spectrin defect and a thalassaemia-like defect in the opposite allele (alphaLELY) results in fragile cells that fragment into bizarre shapes in the circulation, with haemolysis and sometimes life-threatening anaemia. A few of the alpha spectrin defects are common, suggesting they provide an advantage against malaria or some other threat. HS, in contrast, is nearly always caused by family-specific private mutations. These involve the five proteins that link the membrane skeleton to the overlying lipid bilayer: alpha and beta spectrin, ankyrin, band 3 and protein 4.2. Somehow, perhaps through loss of the anchorage band 3 provides its lipid neighbours (Peters et al, 1996), microvesiculation of the membrane surface ensues, leading to spherocytosis, splenic sequestration and haemolysis. Future research will need to focus on how each type of defect causes its associated disease, how the spleen aggravates membrane skeleton defects (a process termed 'conditioning'), how defective red, cells are recognized and removed in the spleen, and why patients with similar or even identical defects can have different clinical severity. Emphasis also needs to be given to improving diagnostic tests, particularly for HS, and exploring new options for therapy, like partial splenectomy, which can ameliorate symptoms while better protecting patients from bacterial sepsis and red cell parasites, and perhaps from atherosclerosis (Robinette & Franmeni, 1977) and venous thrombosis (Stewart et al, 1996).
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Affiliation(s)
- W T Tse
- Division of Hematology/Oncology, Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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29
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Xie H, Brines ML, de Lanerolle NC. Transcripts of the transposon mariner are present in epileptic brain. Epilepsy Res 1998; 32:140-53. [PMID: 9761316 DOI: 10.1016/s0920-1211(98)00047-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mobile genetic elements termed transposons have been increasingly implicated in human disease. The small transposon mariner is widespread within non-vertebrate genomes and causes mutation by replication, excision, and insertion of itself without an RNA intermediate. We find that human DNA contains about 60 copies of this gene. Mariner transcripts are abundant in RNA prepared from sclerotic epileptic hippocampi. In contrast, typically no mariner-specific RNA is detected in non-sclerotic hippocampi from other epileptic patients or from autopsies. A complete but non-functional copy was obtained using rapid amplification of cDNA ends (RACE). This human mariner transcript is approximately 45% homologous to a functional counterpart active in Drosophila, with a coding region of 1035 bases flanked by 32 base inverted terminal repeats. The differential expression of mariner transcripts within sclerotic hippocampi suggests the probable activity of an autonomous element which by mutating critical genes could establish an epileptogenic substrate in the hippocampus.
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Affiliation(s)
- H Xie
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06520-8039, USA
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30
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Spectrin St Claude, a Splicing Mutation of the Human α-Spectrin Gene Associated With Severe Poikilocytic Anemia. Blood 1997. [DOI: 10.1182/blood.v89.12.4584] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractAn α-spectrin variant with increased susceptibility to tryptic digestion, αII/47, was previously observed in a child with severe, recessively inherited, poikilocytic anemia. The molecular basis of this variant, spectrin St Claude, has now been identified as a splicing mutation of the α-spectrin gene due to a T → G mutation in the 3′ acceptor splice site of exon 20. This polypyrimidine tract mutation creates a new acceptor splice site, AT → AG, and leads to the production of two novel mRNAs. One mRNA contains a 12 intronic nucleotide insertion upstream of exon 20. This insertion introduces a termination codon into the reading frame and is predicted to encode a truncated protein (108 kD) that lacks the nucleation site and thus cannot be assembled in the membrane. In the other mRNA, there is in-frame skipping of exon 20, predicting a truncated (277 kD) α-spectrin chain. The homozygous propositus has only truncated 277 kD α-spectrin chains in his erythrocyte membranes. His heterozygous parents are clinically and biochemically normal. This allele was identified in 3% of asymptomatic individuals from Benin, Africa.
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Gallagher PG, Forget BG. Hematologically important mutations: spectrin variants in hereditary elliptocytosis and hereditary pyropoikilocytosis. Blood Cells Mol Dis 1996; 22:254-8. [PMID: 9075575 DOI: 10.1006/bcmd.1996.0105] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- P G Gallagher
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520-8064, USA.
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Abstract
Hereditary elliptocytosis (HE), its aggravated form hereditary pyropoikilocytosis (HPP), and hereditary spherocytosis (HS) designate a set of congenital hemolytic syndromes. The responsible mutations lie in several genes encoding proteins of the red cell membrane. In particular, they involve the SPTA1 and SPTB genes that encode erythroid spectrin alpha- and beta-chains, respectively. In situ, spectrin is a alpha 2 beta 2 fibrillar tetramer resulting from the head-to-head self-association of two alpha beta dimers. In HE, the 24 known alpha-chain mutations lie in the self-association site or its vicinity, whereas the 17 beta-chain mutations occur in the self-association site itself (record of November 30, 1995). Allele alpha LELY (LELY: Low Expression LYon) is found in ethnic groups remote from one another with a uniform frequency (20-30% of all alpha-alleles). It allows an expanded expression of any HE alpha-allele located in trans and results in severe HE or in HPP. In HS, a number of spectrin mutations have been recorded recently. Allele alpha LEPRA (LEPRA: Low Expression PRAgue) would occur in a recurrent fashion.
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Affiliation(s)
- P Maillet
- Laboratoire de Génétique Moléculaire Humaine CNRS URA 1171, Institut Pasteur de Lyon, France
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MESH Headings
- Adaptation, Physiological
- Amino Acid Sequence
- Anemia, Dyserythropoietic, Congenital/genetics
- Anemia, Hemolytic, Congenital/blood
- Anemia, Hemolytic, Congenital/classification
- Anemia, Hemolytic, Congenital/genetics
- Animals
- Base Sequence
- Blood Group Antigens/genetics
- Blood Proteins/chemistry
- Blood Proteins/genetics
- Blood Proteins/metabolism
- Disease Models, Animal
- Elliptocytosis, Hereditary/genetics
- Erythrocyte Membrane/metabolism
- Erythrocyte Membrane/ultrastructure
- Erythrocytes, Abnormal/metabolism
- Hemoglobinuria, Paroxysmal/genetics
- Humans
- Immunity, Innate
- Malaria
- Membrane Lipids/blood
- Membrane Proteins/blood
- Membrane Proteins/chemistry
- Membrane Proteins/genetics
- Molecular Sequence Data
- Spherocytosis, Hereditary/genetics
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Affiliation(s)
- J Delaunay
- CNRS URA 1171, Institut Pasteur de Lyon, France
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Xu W, Kozak CA, Desnick RJ. Uroporphyrinogen-III synthase: molecular cloning, nucleotide sequence, expression of a mouse full-length cDNA, and its localization on mouse chromosome 7. Genomics 1995; 26:556-62. [PMID: 7607680 DOI: 10.1016/0888-7543(95)80175-l] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Uroporphyrinogen-III synthase (URO-S; EC 4.2.1.75), the fourth enzyme in the heme biosynthetic pathway, is responsible for the conversion of hydroxymethylbilane to the cyclic tetrapyrrole, uroporphyrinogen III. The deficient activity of URO-S is the enzymatic defect in congenital erythropoietic porphyria (CEP), an autosomal recessive disorder. For the generation of a mouse model of CEP, the human URO-S cDNA was used to screen 2 x 10(6) recombinants from a mouse adult liver cDNA library. Ten positive clones were isolated, and dideoxy sequencing of the entire 1.6-kb insert of clone pmUROS-1 revealed 5' and 3' untranslated sequences of 144 and 623 bp, respectively, and an open reading frame of 798 bp encoding a 265-amino-acid polypeptide with a predicted molecular mass of 28,501 Da. The mouse and human coding sequences had 80.5 and 77.8% nucleotide and amino acid identity, respectively. The authenticity of the mouse cDNA was established by expression of the active monomeric enzyme in Escherichia coli. In addition, the analysis of two multilocus genetic crosses localized the mouse gene on chromosome 7, consistent with the mapping of the human gene to a position of conserved synteny on chromosome 10. The isolation, expression, and chromosomal mapping of this full-length cDNA should facilitate studies of the structure and organization of the mouse genomic sequence and the development of a mouse model of CEP for characterization of the disease pathogenesis and evaluation of gene therapy.
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Affiliation(s)
- W Xu
- Department of Human Genetics, Mount Sinai School of Medicine, New York, New York 10029-6574, USA
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