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Masson E, Maestri S, Bordeau V, Cooper DN, Férec C, Chen JM. Alu insertion-mediated dsRNA structure formation with pre-existing Alu elements as a disease-causing mechanism. Am J Hum Genet 2024; 111:2176-2189. [PMID: 39265574 DOI: 10.1016/j.ajhg.2024.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/14/2024] Open
Abstract
We previously identified a homozygous Alu insertion variant (Alu_Ins) in the 3'-untranslated region (3'-UTR) of SPINK1 as the cause of severe infantile isolated exocrine pancreatic insufficiency. Although we established that Alu_Ins leads to the complete loss of SPINK1 mRNA expression, the precise mechanisms remained elusive. Here, we aimed to elucidate these mechanisms through a hypothesis-driven approach. Initially, we speculated that, owing to its particular location, Alu_Ins could independently disrupt mRNA 3' end formation and/or affect other post-transcriptional processes such as nuclear export and translation. However, employing a 3'-UTR luciferase reporter assay, Alu_Ins was found to result in only an ∼50% reduction in luciferase activity compared to wild type, which is insufficient to account for the severe pancreatic deficiency in the Alu_Ins homozygote. We then postulated that double-stranded RNA (dsRNA) structures formed between Alu elements, an upstream mechanism regulating gene expression, might be responsible. Using RepeatMasker, we identified two Alu elements within SPINK1's third intron, both oriented oppositely to Alu_Ins. Through RNAfold predictions and full-length gene expression assays, we investigated orientation-dependent interactions between these Alu repeats. We provide compelling evidence to link the detrimental effect of Alu_Ins to extensive dsRNA structures formed between Alu_Ins and pre-existing intronic Alu sequences, including the restoration of SPINK1 mRNA expression by aligning all three Alu elements in the same orientation. Given the widespread presence of Alu elements in the human genome and the potential for new Alu insertions at almost any locus, our findings have important implications for detecting and interpreting Alu insertions in disease genes.
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Affiliation(s)
- Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France; CHRU Brest, 29200 Brest, France
| | - Sandrine Maestri
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France; CHRU Brest, 29200 Brest, France
| | - Valérie Bordeau
- Inserm U1230 BRM (Bacterial RNAs and Medicine), Université de Rennes, 35043 Rennes, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France.
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2
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Yano N, Chong PF, Kojima KK, Miyoshi T, Luqmen-Fatah A, Kimura Y, Kora K, Kayaki T, Maizuru K, Hayashi T, Yokoyama A, Ajiro M, Hagiwara M, Kondo T, Kira R, Takita J, Yoshida T. Long-read sequencing identifies an SVA_D retrotransposon insertion deep within the intron of ATP7A as a novel cause of occipital horn syndrome. J Med Genet 2024; 61:950-958. [PMID: 38960580 DOI: 10.1136/jmg-2024-110056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/25/2024] [Indexed: 07/05/2024]
Abstract
BACKGROUND SINE-VNTR-Alu (SVA) retrotransposons move from one genomic location to another in a 'copy-and-paste' manner. They continue to move actively and cause monogenic diseases through various mechanisms. Currently, disease-causing SVA retrotransposons are classified into human-specific young SVA_E or SVA_F subfamilies. In this study, we identified an evolutionarily old SVA_D retrotransposon as a novel cause of occipital horn syndrome (OHS). OHS is an X-linked, copper metabolism disorder caused by dysfunction of the copper transporter, ATP7A. METHODS We investigated a 16-year-old boy with OHS whose pathogenic variant could not be detected via routine molecular genetic analyses. RESULTS A 2.8 kb insertion was detected deep within the intron of the patient's ATP7A gene. This insertion caused aberrant mRNA splicing activated by a new donor splice site located within it. Long-read circular consensus sequencing enabled us to accurately read the entire insertion sequence, which contained highly repetitive and GC-rich segments. Consequently, the insertion was identified as an SVA_D retrotransposon. Antisense oligonucleotides (AOs) targeting the new splice site restored the expression of normal transcripts and functional ATP7A proteins. AO treatment alleviated excessive accumulation of copper in patient fibroblasts in a dose-dependent manner. Pedigree analysis revealed that the retrotransposon had moved into the OHS-causing position two generations ago. CONCLUSION This is the first report of a human monogenic disease caused by the SVA_D retrotransposon. The fact that the evolutionarily old SVA_D is still actively transposed, leading to increased copy numbers may make a notable impact on rare genetic disease research.
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Affiliation(s)
- Naoko Yano
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Pin Fee Chong
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Kenji K Kojima
- Genetic Information Research Institute, Cupertino, CA, USA
| | - Tomoichiro Miyoshi
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Gene Mechanisms, Kyoto University Graduate School of Biostudies, Kyoto, Japan
| | - Ahmad Luqmen-Fatah
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yu Kimura
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Kengo Kora
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Taisei Kayaki
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kanako Maizuru
- Department of Pediatrics, Tenri Yorozu Hospital, Tenri, Japan
| | - Takahiro Hayashi
- Department of Pediatrics, Kurashiki Central Hospital, Kurashiki, Japan
| | - Atsushi Yokoyama
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiko Ajiro
- Division of Cancer RNA Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Masatoshi Hagiwara
- Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Anatomy and Developmental Biology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Teruyuki Kondo
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ryutaro Kira
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Junko Takita
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takeshi Yoshida
- Department of Pediatrics, Kyoto University Graduate School of Medicine, Kyoto, Japan
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3
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Wang ZY, Ge LP, Ouyang Y, Jin X, Jiang YZ. Targeting transposable elements in cancer: developments and opportunities. Biochim Biophys Acta Rev Cancer 2024; 1879:189143. [PMID: 38936517 DOI: 10.1016/j.bbcan.2024.189143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Transposable elements (TEs), comprising nearly 50% of the human genome, have transitioned from being perceived as "genomic junk" to key players in cancer progression. Contemporary research links TE regulatory disruptions with cancer development, underscoring their therapeutic potential. Advances in long-read sequencing, computational analytics, single-cell sequencing, proteomics, and CRISPR-Cas9 technologies have enriched our understanding of TEs' clinical implications, notably their impact on genome architecture, gene regulation, and evolutionary processes. In cancer, TEs, including long interspersed element-1 (LINE-1), Alus, and long terminal repeat (LTR) elements, demonstrate altered patterns, influencing both tumorigenic and tumor-suppressive mechanisms. TE-derived nucleic acids and tumor antigens play critical roles in tumor immunity, bridging innate and adaptive responses. Given their central role in oncology, TE-targeted therapies, particularly through reverse transcriptase inhibitors and epigenetic modulators, represent a novel avenue in cancer treatment. Combining these TE-focused strategies with existing chemotherapy or immunotherapy regimens could enhance efficacy and offer a new dimension in cancer treatment. This review delves into recent TE detection advancements, explores their multifaceted roles in tumorigenesis and immune regulation, discusses emerging diagnostic and therapeutic approaches centered on TEs, and anticipates future directions in cancer research.
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Affiliation(s)
- Zi-Yu Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li-Ping Ge
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Ouyang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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Betancourt AJ, Wei KHC, Huang Y, Lee YCG. Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective. Annu Rev Genomics Hum Genet 2024; 25:1-25. [PMID: 38603565 DOI: 10.1146/annurev-genom-120822-105708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Transposable elements (TEs) are genomic parasites found in nearly all eukaryotes, including humans. This evolutionary success of TEs is due to their replicative activity, involving insertion into new genomic locations. TE activity varies at multiple levels, from between taxa to within individuals. The rapidly accumulating evidence of the influence of TE activity on human health, as well as the rapid growth of new tools to study it, motivated an evaluation of what we know about TE activity thus far. Here, we discuss why TE activity varies, and the consequences of this variation, from an evolutionary perspective. By studying TE activity in nonhuman organisms in the context of evolutionary theories, we can shed light on the factors that affect TE activity. While the consequences of TE activity are usually deleterious, some have lasting evolutionary impacts by conferring benefits on the host or affecting other evolutionary processes.
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Affiliation(s)
- Andrea J Betancourt
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Kevin H-C Wei
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Yuh Chwen G Lee
- Center for Complex Biological Systems, University of California, Irvine, California, USA;
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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5
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Fröhlich A, Pfaff AL, Middlehurst B, Hughes LS, Bubb VJ, Quinn JP, Koks S. Deciphering the role of a SINE-VNTR-Alu retrotransposon polymorphism as a biomarker of Parkinson's disease progression. Sci Rep 2024; 14:10932. [PMID: 38740892 DOI: 10.1038/s41598-024-61753-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are transposable elements which represent a source of genetic variation. We previously demonstrated that the presence/absence of a human-specific SVA, termed SVA_67, correlated with the progression of Parkinson's disease (PD). In the present study, we demonstrate that SVA_67 acts as expression quantitative trait loci, thereby exhibiting a strong regulatory effect across the genome using whole genome and transcriptomic data from the Parkinson's progression markers initiative cohort. We further show that SVA_67 is polymorphic for its variable number tandem repeat domain which correlates with both regulatory properties in a luciferase reporter gene assay in vitro and differential expression of multiple genes in vivo. Additionally, this variation's utility as a biomarker is reflected in a correlation with a number of PD progression markers. These experiments highlight the plethora of transcriptomic and phenotypic changes associated with SVA_67 polymorphism which should be considered when investigating the missing heritability of neurodegenerative diseases.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lauren S Hughes
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia.
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.
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6
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Gathings A, Zaman V, Banik NL, Haque A. Insights into Calpain Activation and Rho-ROCK Signaling in Parkinson's Disease and Aging. Biomedicines 2024; 12:1074. [PMID: 38791036 PMCID: PMC11117523 DOI: 10.3390/biomedicines12051074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Parkinson's disease (PD), a progressive neurodegenerative disease, has no cure, and current therapies are not effective at halting disease progression. The disease affects mid-brain dopaminergic neurons and, subsequently, the spinal cord, contributing to many debilitating symptoms associated with PD. The GTP-binding protein, Rho, plays a significant role in the cellular pathology of PD. The downstream effector of Rho, Rho-associated kinase (ROCK), plays multiple functions, including microglial activation and induction of inflammatory responses. Activated microglia have been implicated in the pathology of many neurodegenerative diseases, including PD, that initiate inflammatory responses, leading to neuron death. Calpain expression and activity is increased following glial activation, which triggers the Rho-ROCK pathway and induces inflammatory T cell activation and migration as well as mediates toxic α-synuclein (α-syn) aggregation and neuron death, indicating a pivotal role for calpain in the inflammatory and degenerative processes in PD. Increased calpain activity and Rho-ROCK activation may represent a new mechanism for increased oxidative damage in aging. This review will summarize calpain activation and the role of the Rho-ROCK pathway in oxidative stress and α-syn aggregation, their influence on the neurodegenerative process in PD and aging, and possible strategies and research directions for therapeutic intervention.
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Affiliation(s)
- Amy Gathings
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (A.G.); (N.L.B.)
- Department of Neurosurgery, Medical University of South Carolina, 96 Jonathan Lucas Street, Charleston, SC 29425, USA;
| | - Vandana Zaman
- Department of Neurosurgery, Medical University of South Carolina, 96 Jonathan Lucas Street, Charleston, SC 29425, USA;
- Ralph H. Johnson Veterans Administration Medical Center, 109 Bee Street, Charleston, SC 29401, USA
| | - Narendra L. Banik
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (A.G.); (N.L.B.)
- Department of Neurosurgery, Medical University of South Carolina, 96 Jonathan Lucas Street, Charleston, SC 29425, USA;
- Ralph H. Johnson Veterans Administration Medical Center, 109 Bee Street, Charleston, SC 29401, USA
| | - Azizul Haque
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA; (A.G.); (N.L.B.)
- Department of Neurosurgery, Medical University of South Carolina, 96 Jonathan Lucas Street, Charleston, SC 29425, USA;
- Ralph H. Johnson Veterans Administration Medical Center, 109 Bee Street, Charleston, SC 29401, USA
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7
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Guo Y, Li TD, Modzelewski AJ, Siomi H. Retrotransposon renaissance in early embryos. Trends Genet 2024; 40:39-51. [PMID: 37949723 DOI: 10.1016/j.tig.2023.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Despite being the predominant genetic elements in mammalian genomes, retrotransposons were often dismissed as genomic parasites with ambiguous biological significance. However, recent studies reveal their functional involvement in early embryogenesis, encompassing crucial processes such as zygotic genome activation (ZGA) and cell fate decision. This review underscores the paradigm shift in our understanding of retrotransposon roles during early preimplantation development, as well as their rich functional reservoir that is exploited by the host to provide cis-regulatory elements, noncoding RNAs, and functional proteins. The rapid advancement in long-read sequencing, low input multiomics profiling, advanced in vitro systems, and precise gene editing techniques encourages further dissection of retrotransposon functions that were once obscured by the intricacies of their genomic footprints.
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Affiliation(s)
- Youjia Guo
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Ten D Li
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA
| | - Andrew J Modzelewski
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA.
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo 160-8582, Japan.
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Kulski JK, Pfaff AL, Marney LD, Fröhlich A, Bubb VJ, Quinn JP, Koks S. Regulation of expression quantitative trait loci by SVA retrotransposons within the major histocompatibility complex. Exp Biol Med (Maywood) 2023; 248:2304-2318. [PMID: 38031415 PMCID: PMC10903234 DOI: 10.1177/15353702231209411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
Genomic and transcriptomic studies of expression quantitative trait loci (eQTL) revealed that SINE-VNTR-Alu (SVA) retrotransposon insertion polymorphisms (RIPs) within human genomes markedly affect the co-expression of many coding and noncoding genes by coordinated regulatory processes. This study examined the polymorphic SVA modulation of gene co-expression within the major histocompatibility complex (MHC) genomic region where more than 160 coding genes are involved in innate and adaptive immunity. We characterized the modulation of SVA RIPs utilizing the genomic and transcriptomic sequencing data obtained from whole blood of 1266 individuals in the Parkinson's Progression Markers Initiative (PPMI) cohort that included an analysis of human leukocyte antigen (HLA)-A regulation in a subpopulation of the cohort. The regulatory properties of eight SVAs located within the class I and class II MHC regions were associated with differential co-expression of 71 different genes within and 75 genes outside the MHC region. Some of the same genes were affected by two or more different SVA. Five SVA are annotated in the human genomic reference sequence GRCh38.p14/hg38, whereas the other three were novel insertions within individuals. We also examined and found distinct structural effects (long and short variants and the CT internal variants) for one of the SVA (R_SVA_24) insertions on the differential expression of the HLA-A gene within a subpopulation (550 individuals) of the PPMI cohort. This is the first time that many HLA and non-HLA genes (multilocus expression units) and splicing mechanisms have been shown to be regulated by eight structurally polymorphic SVA within the MHC genomic region by applying precise statistical analysis of RNA data derived from the blood samples of a human cohort population. This study shows that SVA within the MHC region are important regulators or rheostats of gene co-expression that might have potential roles in diversity, health, and disease.
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Affiliation(s)
- Jerzy K Kulski
- Department of Molecular Life Sciences, School of Medicine, Tokai University, Isehara, Kanagawa 259–1193, Japan
- Health and Medical Science. Division of Immunology and Microbiology, School of Biomedical Sciences, The University of Western Australia, Nedlands, WA 6009, Australia
| | - 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
| | - Luke D Marney
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Sulev Koks
- 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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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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10
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Fröhlich A, Hughes LS, Middlehurst B, Pfaff AL, Bubb VJ, Koks S, Quinn JP. CRISPR deletion of a SINE-VNTR- Alu (SVA_67) retrotransposon demonstrates its ability to differentially modulate gene expression at the MAPT locus. Front Neurol 2023; 14:1273036. [PMID: 37840928 PMCID: PMC10570551 DOI: 10.3389/fneur.2023.1273036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Background SINE-VNTR-Alu (SVA) retrotransposons are hominid-specific elements which have been shown to play important roles in processes such as chromatin structure remodelling and regulation of gene expression demonstrating that these repetitive elements exert regulatory functions. We have previously shown that the presence or absence of a specific SVA element, termed SVA_67, was associated with differential expression of several genes at the MAPT locus, a locus associated with Parkinson's Disease (PD) and frontotemporal dementia. However, we were not able to demonstrate that causation of differential gene expression was directed by the SVA due to lack of functional validation. Methods We performed CRISPR to delete SVA_67 in the HEK293 cell line. Quantification of target gene expression was performed using qPCR to assess the effects on expression in response to the deletion of SVA_67. Differences between CRISPR edit and control cell lines were analysed using two-tailed t-test with a minimum 95% confidence interval to determine statistical significance. Results In this study, we provide data highlighting the SVA-specific effect on differential gene expression. We demonstrate that the hemizygous deletion of the endogenous SVA_67 in CRISPR edited cell lines was associated with differential expression of several genes at the MAPT locus associated with neurodegenerative diseases including KANSL1, MAPT and LRRC37A. Discussion This data is consistent with our previous bioinformatic work of differential gene expression analysis using transcriptomic data from the Parkinson's Progression Markers Initiative (PPMI) cohort. As SVAs have regulatory influences on gene expression, and insertion polymorphisms contribute to interpersonal differences in expression patterns, these results highlight the potential contribution of these elements to complex diseases with potentially many genetic components, such as PD.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Lauren S. Hughes
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Abigail L. Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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de Tribolet-Hardy J, Thorball CW, Forey R, Planet E, Duc J, Coudray A, Khubieh B, Offner S, Pulver C, Fellay J, Imbeault M, Turelli P, Trono D. Genetic features and genomic targets of human KRAB-zinc finger proteins. Genome Res 2023; 33:1409-1423. [PMID: 37730438 PMCID: PMC10547255 DOI: 10.1101/gr.277722.123] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/18/2023] [Indexed: 09/22/2023]
Abstract
Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by gene and segment duplication since the gene family first emerged more than 400 million years ago. Previous work has revealed that many KZFPs recognize transposable element (TE)-embedded sequences as genomic targets, and that KZFPs facilitate the co-option of the regulatory potential of TEs for the benefit of the host. Here, we present a comprehensive survey of the genetic features and genomic targets of human KZFPs, notably completing past analyses by adding data on close to a hundred family members. General principles emerge from our study of the TE-KZFP regulatory system, which point to multipronged evolutionary mechanisms underlaid by highly complex and combinatorial modes of action with strong influences on human speciation.
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Affiliation(s)
- Jonas de Tribolet-Hardy
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Christian W Thorball
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Romain Forey
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Evarist Planet
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Julien Duc
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Alexandre Coudray
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Bara Khubieh
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Sandra Offner
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Cyril Pulver
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital (CHUV) and University of Lausanne, 1010 Lausanne, Switzerland
| | - Michael Imbeault
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland;
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12
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He J, Yu M, Chi C, Du Z, Zheng Y, Chen C, Moawad AS, Song C, Wang X. Insertion of 643bp Retrotransposon Upstream of PPARγ CDS Is Associated with Backfat of Large White Pigs. Animals (Basel) 2023; 13:2355. [PMID: 37508132 PMCID: PMC10376311 DOI: 10.3390/ani13142355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
PPARs are essential regulators of mammalian fatty acid and lipid metabolism. Although the effects of genetic variations, including single nucleotide polymorphisms (SNPs) in PPARs genes on the phenotype of domestic animals have been investigated, there is limited information on the impact of retrotransposon insertion polymorphisms (RIPs). In this study, a combined comparative genome and polymerase chain reaction (PCR) was used to excavate the RIPs in porcine PPARs. We also investigated the potential effects of retrotransposon insertion on phenotype and expression patterns. This study identified the two RIPs in PPARs genes, namely an ERV in intron 1 of PPARα and a combined retrotransposon in intron 2 of PPARγ, designated as PPARα-ERV-RIP and PPARγ-COM-RIP, respectively. These RIPs exhibited different distribution patterns among Chinese indigenous breeds and Western commercial breeds. Individuals with the PPARα-ERV-RIP+/+ genotype (+/+ indicated homozygous with insertion) among Large White pigs had significantly higher (p < 0.05) corrected backfat thickness compared to those with the other two genotypes. Similarly, those with the PPARγ-COM-RIP-/- genotype had significantly higher (p < 0.05) corrected backfat thickness than those with the other two genotypes in Large White pigs. Moreover, in 30-day-old Sujiang piglets, the PPARγ gene expression in the backfat of those with the PPARγ-COM-RIP-/- genotype (-/- indicated homozygous without insertion) was significantly greater (p < 0.01) than those with other genotypes. The dual luciferase reporter gene assay demonstrated that the combined retrotransposon insertion significantly reduced the activity of the MYC promoter in both C2C12 and 3T3-L1 cells (p < 0.01). Therefore, the combined retrotransposon insertion could function as a repressor to decrease the expression of PPARγ, making PPARγ-COM-RIP a valuable molecular marker for assisted selection of backfat thickness in pig breeding.
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Affiliation(s)
- Jia He
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Miao Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Chenglin Chi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhanyu Du
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Ali Shoaib Moawad
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- International Joint Research Laboratory in Universities of Jiangsu Province of China for Domestic Animal Germplasm Resources and Genetic Improvement, Yangzhou 225009, China
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13
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Möhner J, Scheuren M, Woronzow V, Schumann S, Zischler H. RDA coupled with deep sequencing detects somatic SVA-retrotranspositions and mosaicism in the human brain. Front Cell Dev Biol 2023; 11:1201258. [PMID: 37325565 PMCID: PMC10267396 DOI: 10.3389/fcell.2023.1201258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/19/2023] [Indexed: 06/17/2023] Open
Abstract
Cells of the developing human brain are affected by the progressive acquisition of genetic and epigenetic alterations that have been reported to contribute to somatic mosaicism in the adult brain and are increasingly considered a possible cause of neurogenetic disorders. A recent work uncovered that the copy-paste transposable element (TE) LINE-1 (L1) is mobilized during brain development, and thus mobile non-autonomous TEs like AluY and SINE-VNTR-Alu (SVA) families can use L1 activity in trans, leading to de novo insertions that may influence the variability of neural cells at genetic and epigenetic levels. In contrast to SNPs and when considering substitutional sequence evolution, the presence or absence of TEs at orthologous loci represents highly informative clade markers that provide insights into the lineage relationships between neural cells and how the nervous system evolves in health and disease. SVAs, as the 'youngest' class of hominoid-specific retrotransposons preferentially found in gene- and GC-rich regions, are thought to differentially co-regulate nearby genes and exhibit a high mobility in the human germline. Therefore, we determined whether this is reflected in the somatic brain and used a subtractive and kinetic enrichment technique called representational difference analysis (RDA) coupled with deep sequencing to compare different brain regions with respect to de novo SINE-VNTR-Alu insertion patterns. As a result, we detected somatic de novo SVA integrations in all human brain regions analyzed, and the majority of de novo insertions can be attributed to lineages of telencephalon and metencephalon, since most of the examined integrations are unique to different brain regions under scrutiny. The SVA positions were used as presence/absence markers, forming informative sites that allowed us to create a maximum parsimony phylogeny of brain regions. Our results largely recapitulated the generally accepted evo-devo patterns and revealed chromosome-wide rates of de novo SVA reintegration targets and preferences for specific genomic regions, e.g., GC- and TE-rich regions as well as close proximity to genes that tend to fall into neural-specific Gene Ontology pathways. We concluded that de novo SVA insertions occur in the germline and somatic brain cells at similar target regions, suggesting that similar retrotransposition modes are effective in the germline and soma.
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Affiliation(s)
- Jonas Möhner
- Division of Anthropology, Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maurice Scheuren
- Division of Anthropology, Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Valentina Woronzow
- Division of Anthropology, Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sven Schumann
- Institute of Anatomy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Hans Zischler
- Division of Anthropology, Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
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14
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Bowles H, Kabiljo R, Al Khleifat A, Jones A, Quinn JP, Dobson RJB, Swanson CM, Al-Chalabi A, Iacoangeli A. An assessment of bioinformatics tools for the detection of human endogenous retroviral insertions in short-read genome sequencing data. FRONTIERS IN BIOINFORMATICS 2023; 2:1062328. [PMID: 36845320 PMCID: PMC9945273 DOI: 10.3389/fbinf.2022.1062328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/12/2022] [Indexed: 02/10/2023] Open
Abstract
There is a growing interest in the study of human endogenous retroviruses (HERVs) given the substantial body of evidence that implicates them in many human diseases. Although their genomic characterization presents numerous technical challenges, next-generation sequencing (NGS) has shown potential to detect HERV insertions and their polymorphisms in humans. Currently, a number of computational tools to detect them in short-read NGS data exist. In order to design optimal analysis pipelines, an independent evaluation of the available tools is required. We evaluated the performance of a set of such tools using a variety of experimental designs and datasets. These included 50 human short-read whole-genome sequencing samples, matching long and short-read sequencing data, and simulated short-read NGS data. Our results highlight a great performance variability of the tools across the datasets and suggest that different tools might be suitable for different study designs. However, specialized tools designed to detect exclusively human endogenous retroviruses consistently outperformed generalist tools that detect a wider range of transposable elements. We suggest that, if sufficient computing resources are available, using multiple HERV detection tools to obtain a consensus set of insertion loci may be ideal. Furthermore, given that the false positive discovery rate of the tools varied between 8% and 55% across tools and datasets, we recommend the wet lab validation of predicted insertions if DNA samples are available.
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Affiliation(s)
- Harry Bowles
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Renata Kabiljo
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Ahmad Al Khleifat
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - Ashley Jones
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard J. B. Dobson
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
- Institute of Health Informatics, University College London, London, United Kingdom
- NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Chad M. Swanson
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Neurology, King’s College Hospital, London, United Kingdom
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King’s College London, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- Department of Biostatistics and Health Informatics, King’s College London, Institute of Psychiatry, Psychology and Neuroscience, London, United Kingdom
- NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King’s College London, London, United Kingdom
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15
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Scheuren M, Möhner J, Zischler H. R-loop landscape in mature human sperm: Regulatory and evolutionary implications. Front Genet 2023; 14:1069871. [PMID: 37139234 PMCID: PMC10149866 DOI: 10.3389/fgene.2023.1069871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
R-loops are three-stranded nucleic acid structures consisting of an RNA:DNA hybrid and a displaced DNA strand. While R-loops pose a potential threat to genome integrity, they constitute 5% of the human genome. The role of R-loops in transcriptional regulation, DNA replication, and chromatin signature is becoming increasingly clear. R-loops are associated with various histone modifications, suggesting that they may modulate chromatin accessibility. To potentially harness transcription-coupled repair mechanisms in the germline, nearly the entire genome is expressed during the early stages of male gametogenesis in mammals, providing ample opportunity for the formation of a transcriptome-dependent R-loop landscape in male germ cells. In this study, our data demonstrated the presence of R-loops in fully mature human and bonobo sperm heads and their partial correspondence to transcribed regions and chromatin structure, which is massively reorganized from mainly histone to mainly protamine-packed chromatin in mature sperm. The sperm R-loop landscape resembles characteristic patterns of somatic cells. Surprisingly, we detected R-loops in both residual histone and protamine-packed chromatin and localize them to still-active retroposons, ALUs and SINE-VNTR-ALUs (SVAs), the latter has recently arisen in hominoid primates. We detected both evolutionarily conserved and species-specific localizations. Comparing our DNA-RNA immunoprecipitation (DRIP) data with published DNA methylation and histone chromatin immunoprecipitation (ChIP) data, we hypothesize that R-loops epigenetically reduce methylation of SVAs. Strikingly, we observe a strong influence of R-loops on the transcriptomes of zygotes from early developmental stages before zygotic genome activation. Overall, these findings suggest that chromatin accessibility influenced by R-loops may represent a system of inherited gene regulation.
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16
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Pozojevic J, von Holt BH, Westenberger A. Factors influencing reduced penetrance and variable expressivity in X-linked dystonia-parkinsonism. MED GENET-BERLIN 2022; 34:97-102. [PMID: 38835911 PMCID: PMC11007627 DOI: 10.1515/medgen-2022-2135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
X-linked dystonia-parkinsonism (XDP) is a neurodegenerative movement disorder that primarily affects adult Filipino men. It is caused by a founder retrotransposon insertion in TAF1 that contains a hexanucleotide repeat, the number of which differs among the patients and correlates with the age at disease onset (AAO) and other clinical parameters. A recent work has identified additional genetic modifiers of age-associated penetrance in XDP, bringing to light the DNA mismatch repair genes MSH3 and PMS2. Despite X-linked recessive inheritance, a minor subset of patients are female, manifesting the disease via various mechanisms such as homozygosity, imbalanced X-chromosome inactivation, or aneuploidy. Here, we summarize and discuss clinical and genetic aspects of XDP, with a focus on variable disease expressivity as a consequence of subtle genetic differences within a seemingly homogenous population of patients.
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Affiliation(s)
- Jelena Pozojevic
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, BMF, Building 67; Ratzeburger Allee 160, 23538 Lübeck, Germany
- Institute of Human Genetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Björn-Hergen von Holt
- Institute of Medical Biometry and Statistics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, BMF, Building 67; Ratzeburger Allee 160, 23538 Lübeck, Germany
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17
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Vialle RA, de Paiva Lopes K, Bennett DA, Crary JF, Raj T. Integrating whole-genome sequencing with multi-omic data reveals the impact of structural variants on gene regulation in the human brain. Nat Neurosci 2022; 25:504-514. [PMID: 35288716 PMCID: PMC9245608 DOI: 10.1038/s41593-022-01031-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 02/07/2022] [Indexed: 11/09/2022]
Abstract
Structural variants (SVs), which are genomic rearrangements of more than 50 base pairs, are an important source of genetic diversity and have been linked to many diseases. However, it remains unclear how they modulate human brain function and disease risk. Here we report 170,996 SVs discovered using 1,760 short-read whole genomes from aged adults and individuals with Alzheimer's disease. By applying quantitative trait locus (SV-xQTL) analyses, we quantified the impact of cis-acting SVs on histone modifications, gene expression, splicing and protein abundance in postmortem brain tissues. More than 3,200 SVs were associated with at least one molecular phenotype. We found reproducibility of 65-99% SV-eQTLs across cohorts and brain regions. SV associations with mRNA and proteins shared the same direction of effect in more than 87% of SV-gene pairs. Mediation analysis showed ~8% of SV-eQTLs mediated by histone acetylation and ~11% by splicing. Additionally, associations of SVs with progressive supranuclear palsy identified previously known and novel SVs.
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Affiliation(s)
- Ricardo A Vialle
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - John F Crary
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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18
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van Bree EJ, Guimarães RLFP, Lundberg M, Blujdea ER, Rosenkrantz JL, White FTG, Poppinga J, Ferrer-Raventós P, Schneider AFE, Clayton I, Haussler D, Reinders MJT, Holstege H, Ewing AD, Moses C, Jacobs FMJ. A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci. Genome Res 2022; 32:656-670. [PMID: 35332097 PMCID: PMC8997352 DOI: 10.1101/gr.275515.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
Abstract
Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SINE-VNTR-Alu (SVA) elements, a class of great ape-specific transposable elements with gene-regulatory roles, which represents a major source of structural variability in the human population. We highlight the presence of structurally variable SVAs (SV-SVAs) in neurological disease-associated loci, and we further associate SV-SVAs to disease-associated SNPs and differential gene expression using luciferase assays and expression quantitative trait loci data. Finally, we genetically deleted SV-SVAs in the BIN1 and CD2AP Alzheimer's disease-associated risk loci and in the BCKDK Parkinson's disease-associated risk locus and assessed multiple aspects of their gene-regulatory influence in a human neuronal context. Together, this study reveals a novel layer of genetic variation in transposable elements that may contribute to identification of the structural variants that are the actual drivers of disease associations of GWAS loci.
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Affiliation(s)
- Elisabeth J van Bree
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Rita L F P Guimarães
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.,Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - Mischa Lundberg
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Elena R Blujdea
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Jimi L Rosenkrantz
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Fred T G White
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Josse Poppinga
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Paula Ferrer-Raventós
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Anne-Fleur E Schneider
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Isabella Clayton
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - David Haussler
- UC Santa Cruz Genomics Institute, and Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, California 95064, USA
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands
| | - Henne Holstege
- Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands.,Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam, The Netherlands
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Colette Moses
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Frank M J Jacobs
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.,Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam, The Netherlands
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19
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Fröhlich A, Pfaff AL, Bubb VJ, Koks S, Quinn JP. Characterisation of the Function of a SINE-VNTR-Alu Retrotransposon to Modulate Isoform Expression at the MAPT Locus. Front Mol Neurosci 2022; 15:815695. [PMID: 35370538 PMCID: PMC8965460 DOI: 10.3389/fnmol.2022.815695] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/10/2022] [Indexed: 11/30/2022] Open
Abstract
SINE-VNTR-Alu retrotransposons represent one class of transposable elements which contribute to the regulation and evolution of the primate genome and have the potential to be involved in genetic instability and disease progression. However, these polymorphic elements have not been extensively analysed when addressing the missing heritability of neurodegenerative diseases, including Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS). SVA_67, a retrotransposon insertion polymorphism, is located in a 1.8 Mb region of high linkage disequilibrium, called the MAPT locus, which is known to contribute to increased risk of developing PD, frontotemporal dementia and other tauopathies. To investigate the role of SVA_67 in directing differential gene expression at this locus, we characterised the impact of SVA_67 allele dosage on isoform expression of several genes in the MAPT locus using the datasets from both the Parkinson’s Progression Markers Initiative and New York Genome Center Consortium Target ALS cohort. The Parkinson’s data was from gene expression in the blood and the ALS data from a variety of CNS regions and allowed us to demonstrate that SVA_67 presence or absence correlated with both isoform- and tissue-specific expression of multiple genes at this locus. This study highlights the importance of addressing SVA polymorphism in disease genetics to gain insight into a better understanding of the role of these regulatory domains to a variety of neurodegenerative diseases.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: Alexander Fröhlich,
| | - Abigail L. Pfaff
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Expression Quantitative Trait Loci (eQTLs) Associated with Retrotransposons Demonstrate their Modulatory Effect on the Transcriptome. Int J Mol Sci 2021; 22:ijms22126319. [PMID: 34204806 PMCID: PMC8231655 DOI: 10.3390/ijms22126319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/10/2021] [Indexed: 12/26/2022] Open
Abstract
Transposable elements (TEs) are repetitive elements that belong to a variety of functional classes and have an important role in shaping genome evolution. Around 50% of the human genome contains TEs, and they have been termed the "dark matter" of the genome because relatively little is known about their function. While TEs have been shown to participate in aberrant gene regulation and the pathogenesis of diseases, only a few studies have explored the systemic effect of TEs on gene expression. In the present study, we analysed whole genome sequences and blood whole transcriptome data from 570 individuals within the Parkinson's Progressive Markers Initiative (PPMI) cohort to identify expression quantitative trait loci (eQTL) regulating genome-wide gene expression associated with TEs. We identified 2132 reference TEs that were polymorphic for their presence or absence in our study cohort. The presence or absence of the TE element could change the expression of the gene or gene clusters from zero to tens of thousands of copies of RNA. The main finding is that many TEs possess very strong regulatory effects, and they have the potential to modulate large genetic networks with hundreds of target genes over the genome. We illustrate the plethora of regulatory mechanisms using examples of their action at the HLA gene cluster and data showing different TEs' convergence to modulate WFS1 gene expression. In conclusion, the presence or absence of polymorphisms of TEs has an eminent genome-wide regulatory function with large effect size at the level of the whole transcriptome. The role of TEs in explaining, in part, the missing heritability for complex traits is convincing and should be considered.
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CRISPR Deletion of a SVA Retrotransposon Demonstrates Function as a cis-Regulatory Element at the TRPV1/TRPV3 Intergenic Region. Int J Mol Sci 2021; 22:ijms22041911. [PMID: 33671852 PMCID: PMC7917899 DOI: 10.3390/ijms22041911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are a subclass of transposable elements (TEs) that exist only in primate genomes. TE insertions can be co-opted as cis-regulatory elements (CREs); however, the regulatory potential of SVAs has predominantly been demonstrated using bioinformatic approaches and reporter gene assays. The objective of this study was to demonstrate SVA cis-regulatory activity by CRISPR (clustered regularly interspaced short palindromic repeats) deletion and subsequent measurement of direct effects on local gene expression. We identified a region on chromosome 17 that was enriched with human-specific SVAs. Comparative gene expression analysis at this region revealed co-expression of TRPV1 and TRPV3 in multiple human tissues, which was not observed in mouse, highlighting key regulatory differences between the two species. Furthermore, the intergenic region between TRPV1 and TRPV3 coding sequences contained a human specific SVA insertion located upstream of the TRPV3 promoter and downstream of the 3′ end of TRPV1, highlighting this SVA as a candidate to study its potential cis-regulatory activity on both genes. Firstly, we generated SVA reporter gene constructs and demonstrated their transcriptional regulatory activity in HEK293 cells. We then devised a dual-targeting CRISPR strategy to facilitate the deletion of this entire SVA sequence and generated edited HEK293 clonal cell lines containing homozygous and heterozygous SVA deletions. In edited homozygous ∆SVA clones, we observed a significant decrease in both TRPV1 and TRPV3 mRNA expression, compared to unedited HEK293. In addition, we also observed an increase in the variability of mRNA expression levels in heterozygous ∆SVA clones. Overall, in edited HEK293 with SVA deletions, we observed a disruption to the co-expression of TRPV1 and TRPV3. Here we provide an example of a human specific SVA with cis-regulatory activity in situ, supporting the role of SVA retrotransposons as contributors to species-specific gene expression.
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Petrozziello T, Dios AM, Mueller KA, Vaine CA, Hendriks WT, Glajch KE, Mills AN, Mangkalaphiban K, Penney EB, Ito N, Fernandez-Cerado C, Legarda GPA, Velasco-Andrada MS, Acuña PJ, Ang MA, Muñoz EL, Diesta CCE, Macalintal-Canlas R, Acuña G, Sharma N, Ozelius LJ, Bragg DC, Sadri-Vakili G. SVA insertion in X-linked Dystonia Parkinsonism alters histone H3 acetylation associated with TAF1 gene. PLoS One 2020; 15:e0243655. [PMID: 33315879 PMCID: PMC7735578 DOI: 10.1371/journal.pone.0243655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022] Open
Abstract
X-linked Dystonia-Parkinsonism (XDP) is a neurodegenerative disease linked to an insertion of a SINE-VNTR-Alu (SVA)-type retrotransposon within an intron of TAF1. This SVA insertion induces aberrant TAF1 splicing and partial intron retention, thereby decreasing levels of the full-length transcript. Here we sought to determine if these altered transcriptional dynamics caused by the SVA are also accompanied by local changes in histone acetylation, given that these modifications influence gene expression. Because TAF1 protein may itself exhibit histone acetyltransferase activity, we also examined whether decreased TAF1 expression in XDP cell lines and post-mortem brain affects global levels of acetylated histone H3 (AcH3). The results demonstrate that total AcH3 are not altered in XDP post-mortem prefrontal cortex or cell lines. We also did not detect local differences in AcH3 associated with TAF1 exons or intronic sites flanking the SVA insertion. There was, however, a decrease in AcH3 association with the exon immediately proximal to the intronic SVA, and this decrease was normalized by CRISPR/Cas-excision of the SVA. Collectively, these data suggest that the SVA insertion alters histone status in this region, which may contribute to the dysregulation of TAF1 expression.
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Affiliation(s)
- Tiziana Petrozziello
- NeuroEpigenetics Laboratory, Healey Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Amanda M. Dios
- NeuroEpigenetics Laboratory, Healey Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kaly A. Mueller
- NeuroEpigenetics Laboratory, Healey Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Christine A. Vaine
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - William T. Hendriks
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kelly E. Glajch
- NeuroEpigenetics Laboratory, Healey Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Alexandra N. Mills
- NeuroEpigenetics Laboratory, Healey Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kotchaphorn Mangkalaphiban
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Ellen B. Penney
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Naoto Ito
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | | | | | | | - Patrick J. Acuña
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mark A. Ang
- Department of Pathology, College of Medicine, University of the Philippines, Manila, Philippines
| | - Edwin L. Muñoz
- Department of Pathology, College of Medicine, University of the Philippines, Manila, Philippines
| | | | | | - Geraldine Acuña
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Nutan Sharma
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Laurie J. Ozelius
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - D. Cristopher Bragg
- The Collaborative Center for X-linked Dystonia-Parkinsonism, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Ghazaleh Sadri-Vakili
- NeuroEpigenetics Laboratory, Healey Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, United States of America
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Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly. Viruses 2020; 12:v12101089. [PMID: 32993145 PMCID: PMC7650545 DOI: 10.3390/v12101089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022] Open
Abstract
The human genome has been under selective pressure to evolve in response to emerging pathogens and other environmental challenges. Genome evolution includes the acquisition of new genes or new isoforms of genes and changes to gene expression patterns. One source of genome innovation is from transposable elements (TEs), which carry their own promoters, enhancers and open reading frames and can act as ‘controlling elements’ for our own genes. TEs include LINE-1 elements, which can retrotranspose intracellularly and endogenous retroviruses (ERVs) that represent remnants of past retroviral germline infections. Although once pathogens, ERVs also represent an enticing source of incoming genetic material that the host can then repurpose. ERVs and other TEs have coevolved with host genes for millions of years, which has allowed them to become embedded within essential gene expression programmes. Intriguingly, these host genes are often subject to the same epigenetic control mechanisms that evolved to combat the TEs that now regulate them. Here, we illustrate the breadth of host gene regulation through TEs by focusing on examples of young (The New), ancient (The Old), and disease-causing (The Ugly) TE integrants.
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