1
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Hong Y, Bie L, Zhang T, Yan X, Jin G, Chen Z, Wang Y, Li X, Pei G, Zhang Y, Hong Y, Gong L, Li P, Xie W, Zhu Y, Shen X, Liu N. SAFB restricts contact domain boundaries associated with L1 chimeric transcription. Mol Cell 2024; 84:1637-1650.e10. [PMID: 38604171 DOI: 10.1016/j.molcel.2024.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/05/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024]
Abstract
Long interspersed element-1 (LINE-1 or L1) comprises 17% of the human genome, continuously generates genetic variations, and causes disease in certain cases. However, the regulation and function of L1 remain poorly understood. Here, we uncover that L1 can enrich RNA polymerase IIs (RNA Pol IIs), express L1 chimeric transcripts, and create contact domain boundaries in human cells. This impact of L1 is restricted by a nuclear matrix protein scaffold attachment factor B (SAFB) that recognizes transcriptionally active L1s by binding L1 transcripts to inhibit RNA Pol II enrichment. Acute inhibition of RNA Pol II transcription abolishes the domain boundaries associated with L1 chimeric transcripts, indicating a transcription-dependent mechanism. Deleting L1 impairs domain boundary formation, and L1 insertions during evolution have introduced species-specific domain boundaries. Our data show that L1 can create RNA Pol II-enriched regions that alter genome organization and that SAFB regulates L1 and RNA Pol II activity to preserve gene regulation.
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Affiliation(s)
- Yaqiang Hong
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Luyao Bie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Tao Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohan Yan
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangpu Jin
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhuo Chen
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yang Wang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiufeng Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Gaofeng Pei
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yongyan Zhang
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yantao Hong
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Liang Gong
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Pilong Li
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yanfen Zhu
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu 322000, China
| | - Xiaohua Shen
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Nian Liu
- Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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2
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Zehrbach NM, Oh N, Ishak CA. Insights into LINE-1 reverse transcription guide therapy development. Trends Cancer 2024; 10:286-288. [PMID: 38499453 DOI: 10.1016/j.trecan.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024]
Abstract
Subsets of long interspersed nuclear element 1 (LINE-1) retrotransposons can 'retrotranspose' throughout the human genome at a cost to host cell fitness, as observed in some cancers. Pharmacological inhibition of LINE-1 retrotransposition requires a comprehensive understanding of the LINE-1 ORF2p reverse transcriptase. Two recent publications, by Thawani et al. and Baldwin et al., report structures of LINE-1 ORF2p and address long-standing mechanistic gaps regarding LINE-1 retrotransposition. Both studies will be critical to design new specific inhibitors of the LINE-1 ORF2p reverse transcriptase.
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Affiliation(s)
- Nicholas M Zehrbach
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nakyung Oh
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles A Ishak
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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3
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Li Y, Shen S, Guo H, Li H, Zhang L, Zhang B, Yu XF, Wei W. Pharmacological inhibition of neddylation impairs long interspersed element 1 retrotransposition. Cell Rep 2024; 43:113749. [PMID: 38329876 DOI: 10.1016/j.celrep.2024.113749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/25/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
Aberrant long interspersed element 1 (LINE-1 or L1) activity can cause insertional mutagenesis and chromosomal rearrangements and has been detected in several types of cancers. Here, we show that neddylation, a post-translational modification process, is essential for L1 transposition. The antineoplastic drug MLN4924 is an L1 inhibitor that suppresses NEDD8-activating enzyme activity. Neddylation inhibition by MLN4924 selectively impairs ORF2p-mediated L1 reverse transcription and blocks the generation of L1 cDNA. Consistent with these results, MLN4924 treatment suppresses the retrotransposition activity of the non-autonomous retrotransposons short interspersed nuclear element R/variable number of tandem repeat/Alu and Alu, which rely on the reverse transcription activity of L1 ORF2p. The E2 enzyme UBE2M in the neddylation pathway, rather than UBE2F, is required for L1 ORF2p and retrotransposition. Interference with the functions of certain neddylation-dependent Cullin-really interesting new gene E3 ligases disrupts L1 reverse transcription and transposition activity. Our findings provide insights into the regulation of L1 retrotransposition and the identification of therapeutic targets for L1 dysfunctions.
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Affiliation(s)
- Yan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin 130021, China; Department of Pathology, The First Bethune Hospital of Jilin University, Changchun, China
| | - Siyu Shen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin 130021, China
| | - Haoran Guo
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin 130021, China
| | - Huili Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin 130021, China
| | - Lili Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin 130021, China
| | - Boyin Zhang
- Department of Orthopedics Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Xiao-Fang Yu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - Wei Wei
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Institute of Translational Medicine, First Hospital, Jilin University, Changchun, Jilin 130021, China; Institute of Virology and AIDS Research, First Hospital, Jilin University, Changchun, Jilin 130021, China.
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4
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Perkiö A, Pradhan B, Genc F, Pirttikoski A, Pikkusaari S, Erkan EP, Falco MM, Huhtinen K, Narva S, Hynninen J, Kauppi L, Vähärautio A. Locus-specific LINE-1 expression in clinical ovarian cancer specimens at the single-cell level. Sci Rep 2024; 14:4322. [PMID: 38383551 PMCID: PMC10881972 DOI: 10.1038/s41598-024-54113-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 02/08/2024] [Indexed: 02/23/2024] Open
Abstract
Long interspersed nuclear elements (LINE-1s/L1s) are a group of retrotransposons that can copy themselves within a genome. In humans, it is the most successful transposon in nucleotide content. L1 expression is generally mild in normal human tissues, but the activity has been shown to increase significantly in many cancers. Few studies have examined L1 expression at single-cell resolution, thus it is undetermined whether L1 reactivation occurs solely in malignant cells within tumors. One of the cancer types with frequent L1 activity is high-grade serous ovarian carcinoma (HGSOC). Here, we identified locus-specific L1 expression with 3' single-cell RNA sequencing in pre- and post-chemotherapy HGSOC sample pairs from 11 patients, and in fallopian tube samples from five healthy women. Although L1 expression quantification with the chosen technique was challenging due to the repetitive nature of the element, we found evidence of L1 expression primarily in cancer cells, but also in other cell types, e.g. cancer-associated fibroblasts. The expression levels were similar in samples taken before and after neoadjuvant chemotherapy, indicating that L1 transcriptional activity was unaffected by clinical platinum-taxane treatment. Furthermore, L1 activity was negatively associated with the expression of MYC target genes, a finding that supports earlier literature of MYC being an L1 suppressor.
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Affiliation(s)
- Anna Perkiö
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Barun Pradhan
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Fatih Genc
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Anna Pirttikoski
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Sanna Pikkusaari
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Erdogan Pekcan Erkan
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Matias Marin Falco
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
| | - Kaisa Huhtinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku and Turku University Hospital, 20521, Turku, Finland
| | - Sara Narva
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, 20521, Turku, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, 20521, Turku, Finland
| | - Liisa Kauppi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
| | - Anna Vähärautio
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, 00290, Helsinki, Finland.
- Foundation for the Finnish Cancer Institute (FCI), Helsinki, Finland.
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5
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Workman S, Richardson SR. Every repeat is unique: Exploring the genomic impact of human L1 retrotransposons at locus-specific resolution. Cell Genom 2024; 4:100504. [PMID: 38359785 PMCID: PMC10879126 DOI: 10.1016/j.xgen.2024.100504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/17/2024]
Abstract
Fully understanding the impact of the human retrotransposon L1 requires that each of ∼500,000 L1 copies be evaluated as a potentially unique genomic entity. In this issue of Cell Genomics, Lanciano et al.1 strive toward this goal, illuminating the reciprocal regulatory influence between individual L1s and their genomic integration sites.
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Affiliation(s)
- Stephanie Workman
- Mater Research Institute-University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Sandra R Richardson
- Mater Research Institute-University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia.
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6
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Lanciano S, Philippe C, Sarkar A, Pratella D, Domrane C, Doucet AJ, van Essen D, Saccani S, Ferry L, Defossez PA, Cristofari G. Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites. Cell Genom 2024; 4:100498. [PMID: 38309261 PMCID: PMC10879037 DOI: 10.1016/j.xgen.2024.100498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
Long interspersed element 1 (L1) retrotransposons are implicated in human disease and evolution. Their global activity is repressed by DNA methylation, but deciphering the regulation of individual copies has been challenging. Here, we combine short- and long-read sequencing to unveil L1 methylation heterogeneity across cell types, families, and individual loci and elucidate key principles involved. We find that the youngest primate L1 families are specifically hypomethylated in pluripotent stem cells and the placenta but not in most tumors. Locally, intronic L1 methylation is intimately associated with gene transcription. Conversely, the L1 methylation state can propagate to the proximal region up to 300 bp. This phenomenon is accompanied by the binding of specific transcription factors, which drive the expression of L1 and chimeric transcripts. Finally, L1 hypomethylation alone is typically insufficient to trigger L1 expression due to redundant silencing pathways. Our results illuminate the epigenetic and transcriptional interplay between retrotransposons and their host genome.
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Affiliation(s)
- Sophie Lanciano
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Claude Philippe
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Arpita Sarkar
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - David Pratella
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Cécilia Domrane
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Aurélien J Doucet
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Dominic van Essen
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Simona Saccani
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Laure Ferry
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | | | - Gael Cristofari
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France.
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7
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Thawani A, Ariza AJF, Nogales E, Collins K. Template and target-site recognition by human LINE-1 in retrotransposition. Nature 2024; 626:186-193. [PMID: 38096901 PMCID: PMC10830416 DOI: 10.1038/s41586-023-06933-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
The long interspersed element-1 (LINE-1, hereafter L1) retrotransposon has generated nearly one-third of the human genome and serves as an active source of genetic diversity and human disease1. L1 spreads through a mechanism termed target-primed reverse transcription, in which the encoded enzyme (ORF2p) nicks the target DNA to prime reverse transcription of its own or non-self RNAs2. Here we purified full-length L1 ORF2p and biochemically reconstituted robust target-primed reverse transcription with template RNA and target-site DNA. We report cryo-electron microscopy structures of the complete human L1 ORF2p bound to structured template RNAs and initiating cDNA synthesis. The template polyadenosine tract is recognized in a sequence-specific manner by five distinct domains. Among them, an RNA-binding domain bends the template backbone to allow engagement of an RNA hairpin stem with the L1 ORF2p C-terminal segment. Moreover, structure and biochemical reconstitutions demonstrate an unexpected target-site requirement: L1 ORF2p relies on upstream single-stranded DNA to position the adjacent duplex in the endonuclease active site for nicking of the longer DNA strand, with a single nick generating a staggered DNA break. Our research provides insights into the mechanism of ongoing transposition in the human genome and informs the engineering of retrotransposon proteins for gene therapy.
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Affiliation(s)
- Akanksha Thawani
- California Institute for Quantitative Biosciences (QB3), Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
| | - Alfredo Jose Florez Ariza
- California Institute for Quantitative Biosciences (QB3), Berkeley, CA, USA
- Biophysics Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Kathleen Collins
- California Institute for Quantitative Biosciences (QB3), Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
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8
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Baldwin ET, van Eeuwen T, Hoyos D, Zalevsky A, Tchesnokov EP, Sánchez R, Miller BD, Di Stefano LH, Ruiz FX, Hancock M, Işik E, Mendez-Dorantes C, Walpole T, Nichols C, Wan P, Riento K, Halls-Kass R, Augustin M, Lammens A, Jestel A, Upla P, Xibinaku K, Congreve S, Hennink M, Rogala KB, Schneider AM, Fairman JE, Christensen SM, Desrosiers B, Bisacchi GS, Saunders OL, Hafeez N, Miao W, Kapeller R, Zaller DM, Sali A, Weichenrieder O, Burns KH, Götte M, Rout MP, Arnold E, Greenbaum BD, Romero DL, LaCava J, Taylor MS. Structures, functions and adaptations of the human LINE-1 ORF2 protein. Nature 2024; 626:194-206. [PMID: 38096902 PMCID: PMC10830420 DOI: 10.1038/s41586-023-06947-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The LINE-1 (L1) retrotransposon is an ancient genetic parasite that has written around one-third of the human genome through a 'copy and paste' mechanism catalysed by its multifunctional enzyme, open reading frame 2 protein (ORF2p)1. ORF2p reverse transcriptase (RT) and endonuclease activities have been implicated in the pathophysiology of cancer2,3, autoimmunity4,5 and ageing6,7, making ORF2p a potential therapeutic target. However, a lack of structural and mechanistic knowledge has hampered efforts to rationally exploit it. We report structures of the human ORF2p 'core' (residues 238-1061, including the RT domain) by X-ray crystallography and cryo-electron microscopy in several conformational states. Our analyses identified two previously undescribed folded domains, extensive contacts to RNA templates and associated adaptations that contribute to unique aspects of the L1 replication cycle. Computed integrative structural models of full-length ORF2p show a dynamic closed-ring conformation that appears to open during retrotransposition. We characterize ORF2p RT inhibition and reveal its underlying structural basis. Imaging and biochemistry show that non-canonical cytosolic ORF2p RT activity can produce RNA:DNA hybrids, activating innate immune signalling through cGAS/STING and resulting in interferon production6-8. In contrast to retroviral RTs, L1 RT is efficiently primed by short RNAs and hairpins, which probably explains cytosolic priming. Other biochemical activities including processivity, DNA-directed polymerization, non-templated base addition and template switching together allow us to propose a revised L1 insertion model. Finally, our evolutionary analysis demonstrates structural conservation between ORF2p and other RNA- and DNA-dependent polymerases. We therefore provide key mechanistic insights into L1 polymerization and insertion, shed light on the evolutionary history of L1 and enable rational drug development targeting L1.
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Affiliation(s)
| | - Trevor van Eeuwen
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arthur Zalevsky
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Egor P Tchesnokov
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | | | - Bryant D Miller
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Luciano H Di Stefano
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Matthew Hancock
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Esin Işik
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Carlos Mendez-Dorantes
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Thomas Walpole
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Charles Nichols
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Paul Wan
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Kirsi Riento
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | - Rowan Halls-Kass
- Charles River Laboratories, Chesterford Research Park, Saffron Walden, UK
| | | | - Alfred Lammens
- Proteros Biostructures GmbH, Martinsried, Planegg, Germany
| | - Anja Jestel
- Proteros Biostructures GmbH, Martinsried, Planegg, Germany
| | - Paula Upla
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Kera Xibinaku
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | | | | | - Kacper B Rogala
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Anna M Schneider
- Structural Biology of Selfish RNA, Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | | | | | | | | | | | | | | | | | | | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biology Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Oliver Weichenrieder
- Structural Biology of Selfish RNA, Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Kathleen H Burns
- Department of Pathology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
| | - Matthias Götte
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA.
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
| | | | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA.
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, The Netherlands.
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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9
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Kines KJ, Sokolowski M, DeFreece C, Shareef A, deHaro DL, Belancio VP. Large Deletions, Cleavage of the Telomeric Repeat Sequence, and Reverse Transcriptase-Mediated DNA Damage Response Associated with Long Interspersed Element-1 ORF2p Enzymatic Activities. Genes (Basel) 2024; 15:143. [PMID: 38397133 PMCID: PMC10887698 DOI: 10.3390/genes15020143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/25/2024] Open
Abstract
L1 elements can cause DNA damage and genomic variation via retrotransposition and the generation of endonuclease-dependent DNA breaks. These processes require L1 ORF2p protein that contains an endonuclease domain, which cuts genomic DNA, and a reverse transcriptase domain, which synthesizes cDNA. The complete impact of L1 enzymatic activities on genome stability and cellular function remains understudied, and the spectrum of L1-induced mutations, other than L1 insertions, is mostly unknown. Using an inducible system, we demonstrate that an ORF2p containing functional reverse transcriptase is sufficient to elicit DNA damage response even in the absence of the functional endonuclease. Using a TK/Neo reporter system that captures misrepaired DNA breaks, we demonstrate that L1 expression results in large genomic deletions that lack any signatures of L1 involvement. Using an in vitro cleavage assay, we demonstrate that L1 endonuclease efficiently cuts telomeric repeat sequences. These findings support that L1 could be an unrecognized source of disease-promoting genomic deletions, telomere dysfunction, and an underappreciated source of chronic RT-mediated DNA damage response in mammalian cells. Our findings expand the spectrum of biological processes that can be triggered by functional and nonfunctional L1s, which have impactful evolutionary- and health-relevant consequences.
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Affiliation(s)
- Kristine J. Kines
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Mark Sokolowski
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Cecily DeFreece
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Afzaal Shareef
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Dawn L. deHaro
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Victoria P. Belancio
- Department of Structural and Cellular Biology, Tulane School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
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10
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Yang L, Metzger GA, Padilla Del Valle R, Delgadillo Rubalcaba D, McLaughlin RN. Evolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome. EMBO J 2024; 43:112-131. [PMID: 38177314 PMCID: PMC10883270 DOI: 10.1038/s44318-023-00007-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/18/2023] [Accepted: 11/10/2023] [Indexed: 01/06/2024] Open
Abstract
Transposable elements have created the majority of the sequence in many genomes. In mammals, LINE-1 retrotransposons have been expanding for more than 100 million years as distinct, consecutive lineages; however, the drivers of this recurrent lineage emergence and disappearance are unknown. Most human genome assemblies provide a record of this ancient evolution, but fail to resolve ongoing LINE-1 retrotranspositions. Utilizing the human CHM1 long-read-based haploid assembly, we identified and cloned all full-length, intact LINE-1s, and found 29 LINE-1s with measurable in vitro retrotransposition activity. Among individuals, these LINE-1s varied in their presence, their allelic sequences, and their activity. We found that recently retrotransposed LINE-1s tend to be active in vitro and polymorphic in the population relative to more ancient LINE-1s. However, some rare allelic forms of old LINE-1s retain activity, suggesting older lineages can persist longer than expected. Finally, in LINE-1s with in vitro activity and in vivo fitness, we identified mutations that may have increased replication in ancient genomes and may prove promising candidates for mechanistic investigations of the drivers of LINE-1 evolution and which LINE-1 sequences contribute to human disease.
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Affiliation(s)
- Lei Yang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | - Ricky Padilla Del Valle
- Pacific Northwest Research Institute, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | | | - Richard N McLaughlin
- Pacific Northwest Research Institute, Seattle, WA, USA.
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA.
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11
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Baba Y, Yasuda N, Bundo M, Nakachi Y, Ueda J, Ishimoto T, Iwatsuki M, Miyamoto Y, Yoshida N, Oshiumi H, Iwamoto K, Baba H. LINE-1 hypomethylation, increased retrotransposition and tumor-specific insertion in upper gastrointestinal cancer. Cancer Sci 2024; 115:247-256. [PMID: 38013627 PMCID: PMC10823286 DOI: 10.1111/cas.16007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/29/2023] Open
Abstract
The long interspersed nuclear element-1 (LINE-1) retrotransposons are a major family of mobile genetic elements, comprising approximately 17% of the human genome. The methylation state of LINE-1 is often used as an indicator of global DNA methylation levels and it regulates the retrotransposition and somatic insertion of the genetic element. We have previously reported the significant relationship between LINE-1 hypomethylation and poor prognosis in upper gastrointestinal (GI) cancers. However, the causal relationships between LINE-1 hypomethylation, retrotransposition, and tumor-specific insertion in upper GI cancers remain unknown. We used bisulfite-pyrosequencing and quantitative real-time PCR to verify LINE-1 methylation and copy number in tissue samples of 101 patients with esophageal and 103 patients with gastric cancer. Furthermore, we analyzed the LINE-1 retrotransposition profile with an originally developed L1Hs-seq. In tumor samples, LINE-1 methylation levels were significantly lower than non-tumor controls, while LINE-1 copy numbers were markedly increased. As such, there was a significant inverse correlation between the LINE-1 methylation level and copy number in tumor tissues, with lower LINE-1 methylation levels corresponding to higher LINE-1 copy numbers. Of particular importance is that somatic LINE-1 insertions were more numerous in tumor than normal tissues. Furthermore, we observed that LINE-1 was inserted evenly across all chromosomes, and most often within genomic regions associated with tumor-suppressive genes. LINE-1 hypomethylation in upper GI cancers is related to increased LINE-1 retrotransposition and tumor-specific insertion events, which may collectively contribute to the acquisition of aggressive tumor features through the inactivation of tumor-suppressive genes.
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Affiliation(s)
- Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
- Department of Next‐Generation Surgical Therapy DevelopmentKumamoto University HospitalKumamotoJapan
| | - Noriko Yasuda
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Junko Ueda
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Takatsugu Ishimoto
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
| | - Masaaki Iwatsuki
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
| | - Yuji Miyamoto
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
| | - Hiroyuki Oshiumi
- Department of Immunology, Graduate School of Medical Sciences, Faculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
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12
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Tong B, Sun Y. Activation of Young LINE-1 Elements by CRISPRa. Int J Mol Sci 2023; 25:424. [PMID: 38203595 PMCID: PMC10778729 DOI: 10.3390/ijms25010424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Long interspersed element-1 (LINE-1; L1s) are mobile genetic elements that comprise nearly 20% of the human genome. L1s have been shown to have important functions in various biological processes, and their dysfunction is thought to be linked with diseases and cancers. However, the roles of the repetitive elements are largely not understood. While the CRISPR activation (CRISPRa) system based on catalytically deadCas9 (dCas9) is widely used for genome-wide interrogation of gene function and genetic interaction, few studies have been conducted on L1s. Here, we report using the CRISPRa method to efficiently activate L1s in human L02 cells, a derivative of the HeLa cancer cell line. After CRISPRa, the young L1 subfamilies such as L1HS/L1PA1 and L1PA2 are found to be expressed at higher levels than the older L1s. The L1s with high levels of transcription are closer to full-length and are more densely occupied by the YY1 transcription factor. The activated L1s can either be mis-spliced to form chimeric transcripts or act as alternative promoters or enhancers to facilitate the expression of neighboring genes. The method described here can be used for studying the functional roles of young L1s in cultured cells of interest.
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Affiliation(s)
- Bei Tong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yuhua Sun
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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13
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Mendez-Dorantes C, Burns KH. LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities. Genes Dev 2023; 37:948-967. [PMID: 38092519 PMCID: PMC10760644 DOI: 10.1101/gad.351051.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Long interspersed element 1 (LINE-1) is the only protein-coding transposon that is active in humans. LINE-1 propagates in the genome using RNA intermediates via retrotransposition. This activity has resulted in LINE-1 sequences occupying approximately one-fifth of our genome. Although most copies of LINE-1 are immobile, ∼100 copies are retrotransposition-competent. Retrotransposition is normally limited via epigenetic silencing, DNA repair, and other host defense mechanisms. In contrast, LINE-1 overexpression and retrotransposition are hallmarks of cancers. Here, we review mechanisms of LINE-1 regulation and how LINE-1 may promote genetic heterogeneity in tumors. Finally, we discuss therapeutic strategies to exploit LINE-1 biology in cancers.
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Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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14
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Vylegzhanina AV, Bespalov IA, Novototskaya-Vlasova KA, Hall BM, Gleiberman AS, Yu H, Leontieva OV, Leonova KI, Kurnasov OV, Osterman AL, Dy GK, Komissarov AA, Vasilieva E, Gehlhausen J, Iwasaki A, Ambrosone CB, Tsuji T, Matsuzaki J, Odunsi K, Andrianova EL, Gudkov AV. Cancer Relevance of Circulating Antibodies Against LINE-1 Antigens in Humans. Cancer Res Commun 2023; 3:2256-2267. [PMID: 37870410 PMCID: PMC10631453 DOI: 10.1158/2767-9764.crc-23-0289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/16/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023]
Abstract
Long interspersed nuclear element-1 (LINE-1 or L1), the most abundant family of autonomous retrotransposons occupying over 17% of human DNA, is epigenetically silenced in normal tissues by the mechanisms involving p53 but is frequently derepressed in cancer, suggesting that L1-encoded proteins may act as tumor-associated antigens recognized by the immune system. In this study, we established an immunoassay to detect circulating autoantibodies against L1 proteins in human blood. Using this assay in >2,800 individuals with or without cancer, we observed significantly higher IgG titers against L1-encoded ORF1p and ORF2p in patients with lung, pancreatic, ovarian, esophageal, and liver cancers than in healthy individuals. Remarkably, elevated levels of anti-ORF1p-reactive IgG were observed in patients with cancer with disease stages 1 and 2, indicating that the immune response to L1 antigens can occur in the early phases of carcinogenesis. We concluded that the antibody response against L1 antigens could contribute to the diagnosis and determination of immunoreactivity of tumors among cancer types that frequently escape early detection. SIGNIFICANCE The discovery of autoantibodies against antigens encoded by L1 retrotransposons in patients with five poorly curable cancer types has potential implications for the detection of an ongoing carcinogenic process and tumor immunoreactivity.
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Affiliation(s)
| | | | | | | | | | - Han Yu
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | | | - Oleg V Kurnasov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Grace K Dy
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Alexey A Komissarov
- I.V. Davydovsky Clinical City Hospital, Moscow, Russia
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
| | - Elena Vasilieva
- I.V. Davydovsky Clinical City Hospital, Moscow, Russia
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
| | | | - Akiko Iwasaki
- Yale University, New Haven, Connecticut
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | | | - Takemasa Tsuji
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, Illinois
| | - Junko Matsuzaki
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, Illinois
| | - Kunle Odunsi
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, Illinois
| | | | - Andrei V Gudkov
- Genome Protection, Inc., Buffalo, New York
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
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15
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Garza R, Atacho DA, Adami A, Gerdes P, Vinod M, Hsieh P, Karlsson O, Horvath V, Johansson PA, Pandiloski N, Matas-Fuentes J, Quaegebeur A, Kouli A, Sharma Y, Jönsson ME, Monni E, Englund E, Eichler EE, Gale Hammell M, Barker RA, Kokaia Z, Douse CH, Jakobsson J. LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification. Sci Adv 2023; 9:eadh9543. [PMID: 37910626 PMCID: PMC10619931 DOI: 10.1126/sciadv.adh9543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]
Abstract
The genetic mechanisms underlying the expansion in size and complexity of the human brain remain poorly understood. Long interspersed nuclear element-1 (L1) retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution are largely unknown. Using multiomics profiling, we here demonstrate that L1 promoters are dynamically active in the developing and the adult human brain. L1s generate hundreds of developmentally regulated and cell type-specific transcripts, many that are co-opted as chimeric transcripts or regulatory RNAs. One L1-derived long noncoding RNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. CRISPR interference silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain.
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Affiliation(s)
- Raquel Garza
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Diahann A. M. Atacho
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Anita Adami
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Patricia Gerdes
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Meghna Vinod
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Ofelia Karlsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Vivien Horvath
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Pia A. Johansson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Ninoslav Pandiloski
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
- Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC B11, Lund University, 221 84 Lund, Sweden
| | - Jon Matas-Fuentes
- Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC B11, Lund University, 221 84 Lund, Sweden
| | - Annelies Quaegebeur
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Clinical Neurosciences, University of Cambridge and Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Antonina Kouli
- Department of Clinical Neuroscience and Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, John van Geest Centre for Brain Repair, Cambridge CB2 0PY, UK
| | - Yogita Sharma
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Marie E. Jönsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
| | - Emanuela Monni
- Laboratory of Stem Cells and Restorative Neurology, Lund Stem Cell Center, Lund University, SE-22184 Lund, Sweden
| | - Elisabet Englund
- Department of Clinical Sciences Lund, Division of Pathology, Lund University, Lund, Sweden
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Molly Gale Hammell
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Institute for Systems Genetics, Department of Neuroscience and Physiology, NYU Langone Health, New York, NY 10016, USA
- Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Roger A. Barker
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Clinical Neuroscience and Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, John van Geest Centre for Brain Repair, Cambridge CB2 0PY, UK
| | - Zaal Kokaia
- Laboratory of Stem Cells and Restorative Neurology, Lund Stem Cell Center, Lund University, SE-22184 Lund, Sweden
| | - Christopher H. Douse
- Epigenetics and Chromatin Dynamics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC B11, Lund University, 221 84 Lund, Sweden
| | - Johan Jakobsson
- Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, Wallenberg Neuroscience Center and Lund Stem Cell Center, BMC A11, Lund University, 221 84 Lund, Sweden
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
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16
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Khan M, Shah S, Lv B, Lv Z, Ji N, Song Z, Wu P, Wang X, Mehmood A. Molecular Mechanisms of Alu and LINE-1 Interspersed Repetitive Sequences Reveal Diseases of Visual System Dysfunction. Ocul Immunol Inflamm 2023; 31:1848-1858. [PMID: 36040959 DOI: 10.1080/09273948.2022.2112238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/05/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Short interspersed nuclear elements (SINEs) and long interspersed nuclear elements (LINE-1s) are the abundant and well-characterized repetitive elements in the human genome. METHODS For this review, all relevant original research studies were assessed by searching electronic databases, including PubMed, Google Scholar, and Web of Science, by using relevant keywords. Accumulating evidence indicates that the disorder of gene expression regulated by these repetitive sequences is one of the causes of the diseases of visual system dysfunction, including retinal degenerations, glaucoma, retinitis punctata albescens, retinitis pigmentosa, geographic atrophy, and age-related macular degeneration, suggesting that SINEs and LINE-1s may have great potential implications in ophthalmology. RESULTS Alu elements belonging to the SINEs are present in more than one million copies, comprising 10% of the human genome. CONCLUSION This study offers recent advances in Alu and LINE-1 mechanisms in the development of eye diseases. The current study could advance our knowledge of the roles of SINEs and LINE-1s in the developing process of eye diseases, suggesting new diagnostic biomarkers, therapeutic strategies, and significant points for future studies.
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Affiliation(s)
- Murad Khan
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Suleman Shah
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Baixue Lv
- Department of Ultrasound, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, Hubei Province, China
| | - Zhanjun Lv
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Ning Ji
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Zhixue Song
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Peiyuan Wu
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Xiufang Wang
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei Province, China
| | - Arshad Mehmood
- Department of Neurology, the Second Hospital of Hebei Medical University, City Shijiazhuang, P.R. China
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17
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Li Z, Duan S, Hua X, Xu X, Li Y, Menolfi D, Zhou H, Lu C, Zha S, Goff SP, Zhang Z. Asymmetric distribution of parental H3K9me3 in S phase silences L1 elements. Nature 2023; 623:643-651. [PMID: 37938774 PMCID: PMC11034792 DOI: 10.1038/s41586-023-06711-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/04/2023] [Indexed: 11/08/2023]
Abstract
In eukaryotes, repetitive DNA sequences are transcriptionally silenced through histone H3 lysine 9 trimethylation (H3K9me3). Loss of silencing of the repeat elements leads to genome instability and human diseases, including cancer and ageing1-3. Although the role of H3K9me3 in the establishment and maintenance of heterochromatin silencing has been extensively studied4-6, the pattern and mechanism that underlie the partitioning of parental H3K9me3 at replicating DNA strands are unknown. Here we report that H3K9me3 is preferentially transferred onto the leading strands of replication forks, which occurs predominantly at long interspersed nuclear element (LINE) retrotransposons (also known as LINE-1s or L1s) that are theoretically transcribed in the head-on direction with replication fork movement. Mechanistically, the human silencing hub (HUSH) complex interacts with the leading-strand DNA polymerase Pol ε and contributes to the asymmetric segregation of H3K9me3. Cells deficient in Pol ε subunits (POLE3 and POLE4) or the HUSH complex (MPP8 and TASOR) show compromised H3K9me3 asymmetry and increased LINE expression. Similar results were obtained in cells expressing a MPP8 mutant defective in H3K9me3 binding and in TASOR mutants with reduced interactions with Pol ε. These results reveal an unexpected mechanism whereby the HUSH complex functions with Pol ε to promote asymmetric H3K9me3 distribution at head-on LINEs to suppress their expression in S phase.
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Affiliation(s)
- Zhiming Li
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Shoufu Duan
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Xiaowei Xu
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Yinglu Li
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Demis Menolfi
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Chao Lu
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Shan Zha
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Departments of Pathology and Cell Biology, Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Stephen P Goff
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Departments of Biochemistry and Molecular Biophysics, Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
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18
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Watanabe R, Nakachi Y, Matsubara H, Ueda J, Ishii T, Ukai W, Hashimoto E, Kasai K, Simizu S, Kato T, Bundo M, Iwamoto K. Identification of epigenetically active L1 promoters in the human brain and their relationship with psychiatric disorders. Neurosci Res 2023; 195:37-51. [PMID: 37141946 DOI: 10.1016/j.neures.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/09/2023] [Accepted: 05/01/2023] [Indexed: 05/06/2023]
Abstract
Long interspersed nuclear element-1 (LINE-1, L1) affects the transcriptome landscape in multiple ways. Promoter activity within its 5'UTR plays a critical role in regulating diverse L1 activities. However, the epigenetic status of L1 promoters in adult brain cells and their relationship with psychiatric disorders remain poorly understood. Here, we examined DNA methylation and hydroxymethylation of the full-length L1s in neurons and nonneurons and identified "epigenetically active" L1s. Notably, some of epigenetically active L1s were retrotransposition competent, which even had chimeric transcripts from the antisense promoters at their 5'UTRs. We also identified differentially methylated L1s in the prefrontal cortices of patients with psychiatric disorders. In nonneurons of bipolar disorder patients, one L1 was significantly hypomethylated and showed an inverse correlation with the expression level of the overlapping gene NREP. Finally, we observed that altered DNA methylation levels of L1 in patients with psychiatric disorders were not affected by the surrounding genomic regions but originated from the L1 sequences. These results suggested that altered epigenetic regulation of the L1 5'UTR in the brain was involved in the pathophysiology of psychiatric disorders.
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Affiliation(s)
- Risa Watanabe
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hikari Matsubara
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Junko Ueda
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takao Ishii
- Department of Occupational Therapy, Sapporo Medical University School of Health Sciences, Sapporo, Japan
| | - Wataru Ukai
- Department of Neuropsychiatry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Eri Hashimoto
- Department of Neuropsychiatry, Sapporo Medical University, School of Medicine, Sapporo, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; The International Research Center for Neurointelligence (WPI-IRCN), University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo, Japan; University of Tokyo Institute for Diversity and Adaptation of Human Mind (UTIDAHM), The University of Tokyo, Tokyo, Japan; UTokyo Center for Integrative Science of Human Behaviour (CiSHuB), The University of Tokyo, Tokyo, Japan
| | - Siro Simizu
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, Yokohama, Japan
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan.
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Saitama, Japan.
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19
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Abstract
Genome sequencing revealed that nearly half of the human genome is comprised of transposable elements. Although most of these elements have been rendered inactive due to mutations, full-length intact long interspersed element-1 (LINE-1 or L1) copies retain the ability to mobilize through RNA intermediates by a so-called "copy-and-paste" mechanism, termed retrotransposition. L1 is the only known autonomous mobile genetic element in the genome, and its retrotransposition contributes to inter- or intra-individual genetic variation within the human population. However, L1 retrotransposition also poses a threat to genome integrity due to gene disruption and chromosomal instability. Moreover, recent studies suggest that aberrant L1 expression can impact human health by causing diseases such as cancer and chronic inflammation that might lead to autoimmune disorders. To counteract these adverse effects, the host cells have evolved multiple layers of defense mechanisms at the epigenetic, RNA and protein levels. Intriguingly, several host factors have also been reported to facilitate L1 retrotransposition, suggesting that there is competition between negative and positive regulation of L1 by host factors. Here, we summarize the known host proteins that regulate L1 activity at different stages of the replication cycle and discuss how these factors modulate disease-associated phenotypes caused by L1.
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Affiliation(s)
- Ahmad Luqman-Fatah
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University
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20
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Rybacki K, Xia M, Ahsan MU, Xing J, Wang K. Assessing the Expression of Long INterspersed Elements (LINEs) via Long-Read Sequencing in Diverse Human Tissues and Cell Lines. Genes (Basel) 2023; 14:1893. [PMID: 37895242 PMCID: PMC10606529 DOI: 10.3390/genes14101893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Transposable elements, such as Long INterspersed Elements (LINEs), are DNA sequences that can replicate within genomes. LINEs replicate using an RNA intermediate followed by reverse transcription and are typically a few kilobases in length. LINE activity creates genomic structural variants in human populations and leads to somatic alterations in cancer genomes. Long-read RNA sequencing technologies, including Oxford Nanopore and PacBio, can directly sequence relatively long transcripts, thus providing the opportunity to examine full-length LINE transcripts. This study focuses on the development of a new bioinformatics pipeline for the identification and quantification of active, full-length LINE transcripts in diverse human tissues and cell lines. In our pipeline, we utilized RepeatMasker to identify LINE-1 (L1) transcripts from long-read transcriptome data and incorporated several criteria, such as transcript start position, divergence, and length, to remove likely false positives. Comparisons between cancerous and normal cell lines, as well as human tissue samples, revealed elevated expression levels of young LINEs in cancer, particularly at intact L1 loci. By employing bioinformatics methodologies on long-read transcriptome data, this study demonstrates the landscape of L1 expression in tissues and cell lines.
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Affiliation(s)
- Karleena Rybacki
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; (K.R.); (M.X.)
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Mingyi Xia
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; (K.R.); (M.X.)
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Mian Umair Ahsan
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kai Wang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; (K.R.); (M.X.)
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
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21
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Fröhlich A, Pfaff AL, Bubb VJ, Quinn JP, Koks S. Reference LINE-1 insertion polymorphisms correlate with Parkinson's disease progression and differential transcript expression in the PPMI cohort. Sci Rep 2023; 13:13857. [PMID: 37620405 PMCID: PMC10449770 DOI: 10.1038/s41598-023-41052-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023] Open
Abstract
Long interspersed nuclear element-1 (LINE-1/L1) retrotransposons make up 17% of the human genome. They represent one class of transposable elements with the capacity to both mobilize autonomously and in trans via the mobilization of other elements, primarily Alu and SVA elements. Reference LINE-1 elements are, by definition, found in the reference genome, however, due to the polymorphic nature of these elements, variation for presence or absence is present within the population. We used a combination of clinical and transcriptomic data from the Parkinson's Progression Markers Initiative (PPMI) and applied matrix expression quantitative trait loci analysis and linear mixed-effects models involving 114 clinical, biochemical and imaging data from the PPMI cohort to elucidate the role of reference LINE-1 insertion polymorphism on both gene expression genome-wide and progression of Parkinson's disease (PD). We demonstrate that most LINE-1 insertion polymorphisms are capable of regulating gene expression, preferentially in trans, including previously identified PD risk loci. In addition, we show that 70 LINE-1 elements were associated with longitudinal changes of at least one PD progression marker, including ipsilateral count density ratio and UPDRS scores which are indicators of degeneration and severity. In conclusion, this study highlights the effect of the polymorphic nature of LINE-1 retrotransposons on gene regulation and progression of PD which underlines the importance of analyzing transposable elements within complex 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
| | - 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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22
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Mangoni D, Simi A, Lau P, Armaos A, Ansaloni F, Codino A, Damiani D, Floreani L, Di Carlo V, Vozzi D, Persichetti F, Santoro C, Pandolfini L, Tartaglia GG, Sanges R, Gustincich S. LINE-1 regulates cortical development by acting as long non-coding RNAs. Nat Commun 2023; 14:4974. [PMID: 37591988 PMCID: PMC10435495 DOI: 10.1038/s41467-023-40743-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/07/2023] [Indexed: 08/19/2023] Open
Abstract
Long Interspersed Nuclear Elements-1s (L1s) are transposable elements that constitute most of the genome's transcriptional output yet have still largely unknown functions. Here we show that L1s are required for proper mouse brain corticogenesis operating as regulatory long non-coding RNAs. They contribute to the regulation of the balance between neuronal progenitors and differentiation, the migration of post-mitotic neurons and the proportions of different cell types. In cortical cultured neurons, L1 RNAs are mainly associated to chromatin and interact with the Polycomb Repressive Complex 2 (PRC2) protein subunits enhancer of Zeste homolog 2 (Ezh2) and suppressor of zeste 12 (Suz12). L1 RNA silencing influences PRC2's ability to bind a portion of its targets and the deposition of tri-methylated histone H3 (H3K27me3) marks. Our results position L1 RNAs as crucial signalling hubs for genome-wide chromatin remodelling, enabling the fine-tuning of gene expression during brain development and evolution.
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Affiliation(s)
- Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Alessandro Simi
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Pierre Lau
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Alexandros Armaos
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Federico Ansaloni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Azzurra Codino
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Devid Damiani
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Lavinia Floreani
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Valerio Di Carlo
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Diego Vozzi
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Francesca Persichetti
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Claudio Santoro
- Department of Health Sciences and Research Center on Autoimmune and Allergic Diseases (CAAD), University of Piemonte Orientale (UPO), Novara, Italy
| | - Luca Pandolfini
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | | | - Remo Sanges
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.
- Area of Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy.
| | - Stefano Gustincich
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), Genova, Italy.
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23
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Zürcher JF, Kleefeldt AA, Funke LFH, Birnbaum J, Fredens J, Grazioli S, Liu KC, Spinck M, Petris G, Murat P, Rehm FBH, Sale JE, Chin JW. Continuous synthesis of E. coli genome sections and Mb-scale human DNA assembly. Nature 2023; 619:555-562. [PMID: 37380776 PMCID: PMC7614783 DOI: 10.1038/s41586-023-06268-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 05/26/2023] [Indexed: 06/30/2023]
Abstract
Whole-genome synthesis provides a powerful approach for understanding and expanding organism function1-3. To build large genomes rapidly, scalably and in parallel, we need (1) methods for assembling megabases of DNA from shorter precursors and (2) strategies for rapidly and scalably replacing the genomic DNA of organisms with synthetic DNA. Here we develop bacterial artificial chromosome (BAC) stepwise insertion synthesis (BASIS)-a method for megabase-scale assembly of DNA in Escherichia coli episomes. We used BASIS to assemble 1.1 Mb of human DNA containing numerous exons, introns, repetitive sequences, G-quadruplexes, and long and short interspersed nuclear elements (LINEs and SINEs). BASIS provides a powerful platform for building synthetic genomes for diverse organisms. We also developed continuous genome synthesis (CGS)-a method for continuously replacing sequential 100 kb stretches of the E. coli genome with synthetic DNA; CGS minimizes crossovers1,4 between the synthetic DNA and the genome such that the output for each 100 kb replacement provides, without sequencing, the input for the next 100 kb replacement. Using CGS, we synthesized a 0.5 Mb section of the E. coli genome-a key intermediate in its total synthesis1-from five episomes in 10 days. By parallelizing CGS and combining it with rapid oligonucleotide synthesis and episome assembly5,6, along with rapid methods for compiling a single genome from strains bearing distinct synthetic genome sections1,7,8, we anticipate that it will be possible to synthesize entire E. coli genomes from functional designs in less than 2 months.
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Affiliation(s)
- Jérôme F Zürcher
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Askar A Kleefeldt
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Louise F H Funke
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Department of Biomedical Engineering, National University of Singapore, Singapore, Singapore
| | - Jakob Birnbaum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julius Fredens
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Synthetic Biology for Clinical and Technological Innovation, Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Simona Grazioli
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Martin Spinck
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Pierre Murat
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fabian B H Rehm
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Julian E Sale
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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24
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Du Q, Stow EC, LaCoste D, Freeman B, Baddoo M, Shareef A, Miller KM, Belancio VP. A novel role of TRIM28 B box domain in L1 retrotransposition and ORF2p-mediated cDNA synthesis. Nucleic Acids Res 2023; 51:4429-4450. [PMID: 37070200 PMCID: PMC10201437 DOI: 10.1093/nar/gkad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 04/19/2023] Open
Abstract
The long interspersed element 1 (LINE-1 or L1) integration is affected by many cellular factors through various mechanisms. Some of these factors are required for L1 amplification, while others either suppress or enhance specific steps during L1 propagation. Previously, TRIM28 has been identified to suppress transposable elements, including L1 expression via its canonical role in chromatin remodeling. Here, we report that TRIM28 through its B box domain increases L1 retrotransposition and facilitates shorter cDNA and L1 insert generation in cultured cells. Consistent with the latter, we observe that tumor specific L1 inserts are shorter in endometrial, ovarian, and prostate tumors with higher TRIM28 mRNA expression than in those with lower TRIM28 expression. We determine that three amino acids in the B box domain that are involved in TRIM28 multimerization are critical for its effect on both L1 retrotransposition and cDNA synthesis. We provide evidence that B boxes from the other two members in the Class VI TRIM proteins, TRIM24 and TRIM33, also increase L1 retrotransposition. Our findings could lead to a better understanding of the host/L1 evolutionary arms race in the germline and their interplay during tumorigenesis.
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Affiliation(s)
- Qianhui Du
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Emily C Stow
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Dawn LaCoste
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Benjamin Freeman
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Melody Baddoo
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Afzaal M Shareef
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 100 E 24th Street, Austin, TX 78712, USA
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
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25
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McKerrow W, Kagermazova L, Doudican N, Frazzette N, Kaparos E, Evans SA, Rocha A, Sedivy JM, Neretti N, Carucci J, Boeke J, Fenyö D. LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5' single-cell RNA-Seq. Nucleic Acids Res 2023; 51:2033-2045. [PMID: 36744437 PMCID: PMC10018344 DOI: 10.1093/nar/gkad049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 02/07/2023] Open
Abstract
LINE-1 retrotransposons are sequences capable of copying themselves to new genomic loci via an RNA intermediate. New studies implicate LINE-1 in a range of diseases, especially in the context of aging, but without an accurate understanding of where and when LINE-1 is expressed, a full accounting of its role in health and disease is not possible. We therefore developed a method-5' scL1seq-that makes use of a widely available library preparation method (10x Genomics 5' single cell RNA-seq) to measure LINE-1 expression in tens of thousands of single cells. We recapitulated the known pattern of LINE-1 expression in tumors-present in cancer cells, absent from immune cells-and identified hitherto undescribed LINE-1 expression in human epithelial cells and mouse hippocampal neurons. In both cases, we saw a modest increase with age, supporting recent research connecting LINE-1 to age related diseases.
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Affiliation(s)
- Wilson McKerrow
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Larisa Kagermazova
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Nicole Doudican
- Ronald O. Perelman Department of Dermatology, NYU Langone Health, New York, NY, USA
| | - Nicholas Frazzette
- Ronald O. Perelman Department of Dermatology, NYU Langone Health, New York, NY, USA
| | - Efiyenia Ismini Kaparos
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Shane A Evans
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Azucena Rocha
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
- Center on the Biology of Aging, Brown University, Providence, RI, USA
| | - Nicola Neretti
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - John Carucci
- Ronald O. Perelman Department of Dermatology, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn,NY11201, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
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26
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Zadran B, Sudhindar PD, Wainwright D, Bury Y, Luli S, Howarth R, McCain MV, Watson R, Huet H, Palinkas F, Berlinguer-Palmini R, Casement J, Mann DA, Oakley F, Lunec J, Reeves H, Faulkner GJ, Shukla R. Impact of retrotransposon protein L1 ORF1p expression on oncogenic pathways in hepatocellular carcinoma: the role of cytoplasmic PIN1 upregulation. Br J Cancer 2023; 128:1236-1248. [PMID: 36707636 PMCID: PMC10050422 DOI: 10.1038/s41416-023-02154-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Molecular characterisation of hepatocellular carcinoma (HCC) is central to the development of novel therapeutic strategies for the disease. We have previously demonstrated mutagenic consequences of Long-Interspersed Nuclear Element-1 (LINE1s/L1) retrotransposition. However, the role of L1 in HCC, besides somatic mutagenesis, is not well understood. METHODS We analysed L1 expression in the TCGA-HCC RNAseq dataset (n = 372) and explored potential relationships between L1 expression and clinical features. The findings were confirmed by immunohistochemical (IHC) analysis of an independent human HCC cohort (n = 48) and functional mechanisms explored using in vitro and in vivo model systems. RESULTS We observed positive associations between L1 and activated TGFβ-signalling, TP53 mutation, alpha-fetoprotein and tumour invasion. IHC confirmed a positive association between pSMAD3, a surrogate for TGFβ-signalling status, and L1 ORF1p (P < 0.0001, n = 32). Experimental modulation of L1 ORF1p levels revealed an influence of L1 ORF1p on key hepatocarcinogenesis-related pathways. Reduction in cell migration and invasive capacity was observed upon L1 ORF1 knockdown, both in vitro and in vivo. In particular, L1 ORF1p increased PIN1 cytoplasmic localisation. Blocking PIN1 activity abrogated L1 ORF1p-induced NF-κB-mediated inflammatory response genes while further activated TGFβ-signalling confirming differential alteration of PIN1 activity in cellular compartments by L1 ORF1p. DISCUSSION Our data demonstrate a causal link between L1 ORF1p and key oncogenic pathways mediated by PIN1, presenting a novel therapeutic avenue.
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Affiliation(s)
- Bassier Zadran
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Praveen Dhondurao Sudhindar
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Daniel Wainwright
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Yvonne Bury
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Saimir Luli
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Rachel Howarth
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Misti Vanette McCain
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Robyn Watson
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Hannah Huet
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Fanni Palinkas
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | | | - John Casement
- Bioinformatics Support Unit, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Derek A Mann
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
- Department of Gastroenterology and Hepatology, School of Medicine, Koç University, Istanbul, Turkey
| | - Fiona Oakley
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - John Lunec
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Helen Reeves
- Newcastle University Centre for Cancer, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
- Hepatopancreatobiliary Multidisciplinary Team, Freeman Hospital, Newcastle-upon-Tyne Hospitals NHS foundation, Newcastle-upon-Tyne, UK
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ruchi Shukla
- Newcastle University Centre for Cancer, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, NE1 8ST, UK.
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Luqman-Fatah A, Watanabe Y, Uno K, Ishikawa F, Moran JV, Miyoshi T. The interferon stimulated gene-encoded protein HELZ2 inhibits human LINE-1 retrotransposition and LINE-1 RNA-mediated type I interferon induction. Nat Commun 2023; 14:203. [PMID: 36639706 PMCID: PMC9839780 DOI: 10.1038/s41467-022-35757-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
Some interferon stimulated genes (ISGs) encode proteins that inhibit LINE-1 (L1) retrotransposition. Here, we use immunoprecipitation followed by liquid chromatography-tandem mass spectrometry to identify proteins that associate with the L1 ORF1-encoded protein (ORF1p) in ribonucleoprotein particles. Three ISG proteins that interact with ORF1p inhibit retrotransposition: HECT and RLD domain containing E3 ubiquitin-protein ligase 5 (HERC5); 2'-5'-oligoadenylate synthetase-like (OASL); and helicase with zinc finger 2 (HELZ2). HERC5 destabilizes ORF1p, but does not affect its cellular localization. OASL impairs ORF1p cytoplasmic foci formation. HELZ2 recognizes sequences and/or structures within the L1 5'UTR to reduce L1 RNA, ORF1p, and ORF1p cytoplasmic foci levels. Overexpression of WT or reverse transcriptase-deficient L1s lead to a modest induction of IFN-α expression, which is abrogated upon HELZ2 overexpression. Notably, IFN-α expression is enhanced upon overexpression of an ORF1p RNA binding mutant, suggesting ORF1p binding might protect L1 RNA from "triggering" IFN-α induction. Thus, ISG proteins can inhibit retrotransposition by different mechanisms.
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Affiliation(s)
- Ahmad Luqman-Fatah
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuzo Watanabe
- Proteomics Facility, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazuko Uno
- Division of Basic Research, Louis Pasteur Center for Medical Research, Kyoto, 606-8225, Japan
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
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Abstract
By silencing L1 retrotransposons, DNA methylation protects mammalian genomes from potent endogenous mutagens. However, some loci can escape this repressive mechanism and become active, particularly in carcinomas. Alterations of L1 DNA methylation can also locally influence gene expression. Comprehensive measurement of L1 DNA methylation at the locus level remains challenging. Here, we present bs-ATLAS-seq, a genome-wide approach to locate full-length L1 elements in the human genome, and assess their methylation levels at single-base and single-locus resolutions. This strategy targets the youngest, and only retrotransposition-competent family, L1HS, but also detects a significant fraction of older elements (L1PA2 to L1PA8). Bs-ATLAS-seq evaluates methylation at the first 15 CpGs of L1 5' UTR, which corresponds to the first half of the sense promoter. It relies on random fragmentation of the genomic DNA, adapter ligation, bisulfite treatment and suppression PCR, and ends by asymmetrical paired-end sequencing. A dedicated pipeline provides the location of L1 elements and their methylation status, including for non-reference loci, as well as their single-molecule DNA profiles.
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29
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Garcia-Cañadas M, Sanchez-Luque FJ, Sanchez L, Rojas J, Garcia Perez JL. LINE-1 Retrotransposition Assays in Embryonic Stem Cells. Methods Mol Biol 2023; 2607:257-309. [PMID: 36449167 DOI: 10.1007/978-1-0716-2883-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The ongoing mobilization of active non-long terminal repeat (LTR) retrotransposons continues to impact the genomes of most mammals, including humans and rodents. Non-LTR retrotransposons mobilize using an intermediary RNA and a copy-and-paste mechanism termed retrotransposition. Non-LTR retrotransposons are subdivided into long and short interspersed elements (LINEs and SINEs, respectively), depending on their size and autonomy; while active class 1 LINEs (LINE-1s or L1s) encode the enzymatic machinery required to mobilize in cis, active SINEs use the enzymatic machinery of active LINE-1s to mobilize in trans. The mobilization mechanism used by LINE-1s/SINEs was exploited to develop ingenious plasmid-based retrotransposition assays in cultured cells, which typically exploit a reporter gene that can only be activated after a round of retrotransposition. Retrotransposition assays, in cis or in trans, are instrumental tools to study the biology of mammalian LINE-1s and SINEs. In fact, these and other biochemical/genetic assays were used to uncover that endogenous mammalian LINE-1s/SINEs naturally retrotranspose during early embryonic development. However, embryonic stem cells (ESCs) are typically used as a cellular model in these and other studies interrogating LINE-1/SINE expression/regulation during early embryogenesis. Thus, human and mouse ESCs represent an excellent model to understand how active retrotransposons are regulated and how their activity impacts the germline. Here, we describe robust and quantitative protocols to study human/mouse LINE-1 (in cis) and SINE (in trans) retrotransposition using (human and mice) ESCs. These protocols are designed to study the mobilization of active non-LTR retrotransposons in a cellular physiologically relevant context.
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Affiliation(s)
- Marta Garcia-Cañadas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain.
| | - Francisco J Sanchez-Luque
- Institute of Parasitology and Biomedicine "Lopez-Neyra" (IPBLN), Spanish National Research Council (CSIC), PTS Granada, Granada, Spain
| | - Laura Sanchez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Johana Rojas
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain
| | - Jose L Garcia Perez
- Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research (GENYO), PTS Granada, Granada, Spain.
- MRC Human Genetics Unit, Institute of Genetics and Cancer (IGC)/University of Edinburgh, Western General Hospital Campus, Edinburgh, UK.
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Abstract
Over the past 20 years, high-throughput genomic assays have fundamentally changed how transposable elements (TEs) are studied. While short-read DNA sequencing has been at the heart of these efforts, novel technologies that generate longer reads are driving a shift in the field. Long-read sequencing now permits locus-specific approaches to locate individual TE insertions and understand their epigenetic and transcriptional regulation, while still profiling TE activity genome-wide. Here we provide detailed guidelines to implement Oxford Nanopore Technologies (ONT) sequencing to identify polymorphic TE insertions and profile TE epigenetic landscapes. Using human long interspersed element-1 (LINE-1, L1) as an example, we explain the procedures involved, including final visualization, and potential bottlenecks and pitfalls. ONT sequencing will be, in our view, a workhorse technology for the foreseeable future in the TE field.
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Affiliation(s)
- Nathan Smits
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia.
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, Australia.
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31
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Ramini D, Latini S, Giuliani A, Matacchione G, Sabbatinelli J, Mensà E, Bacalini MG, Garagnani P, Rippo MR, Bronte G, Bonafè M, Cardelli M, Olivieri F. Replicative Senescence-Associated LINE1 Methylation and LINE1-Alu Expression Levels in Human Endothelial Cells. Cells 2022; 11:cells11233799. [PMID: 36497059 PMCID: PMC9739197 DOI: 10.3390/cells11233799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
One of the main challenges of current research on aging is to identify the complex epigenetic mechanisms involved in the acquisition of the cellular senescent phenotype. Despite some evidence suggested that epigenetic changes of DNA repetitive elements, including transposable elements (TE) sequences, are associated with replicative senescence of fibroblasts, data on different types of cells are scarce. We previously analysed genome-wide DNA methylation of young and replicative senescent human endothelial cells (HUVECs), highlighting increased levels of demethylated sequences in senescent cells. Here, we aligned the most significantly demethylated single CpG sites to the reference genome and annotated their localization inside TE sequences and found a significant hypomethylation of sequences belonging to the Long-Interspersed Element-1 (LINE-1 or L1) subfamilies L1M, L1P, and L1HS. To verify the hypothesis that L1 demethylation could be associated with increased transcription/activation of L1s and/or Alu elements (non-autonomous retroelements that usually depend on L1 sequences for reverse transcription and retrotransposition), we quantified the RNA expression levels of both L1 (generic L1 elements or site-specific L1PA2 on chromosome 14) and Alu elements in young and senescent HUVECs and human dermal fibroblasts (NHDFs). The RNA expression of Alu and L1 sequences was significantly increased in both senescent HUVECs and NHDFs, whereas the RNA transcript of L1PA2 on chromosome 14 was not significantly modulated in senescent cells. Moreover, we found an increased amount of TE DNA copies in the cytoplasm of senescent HUVECs and NHDFs. Our results support the hypothesis that TE, which are significantly increased in senescent cells, could be retrotranscribed to DNA sequences.
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Affiliation(s)
- Deborah Ramini
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
| | - Silvia Latini
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Angelica Giuliani
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
- Correspondence: ; Tel.: +39-071-220-6243
| | - Giulia Matacchione
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Jacopo Sabbatinelli
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
- Laboratory Medicine Unit, Azienda Ospedaliero Universitaria delle Marche, 60126 Ancona, Italy
| | - Emanuela Mensà
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, 40126 Bologna, Italy
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”-Unit of Bologna, 40126 Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, 141 86 Huddinge, Sweden
| | - Maria Rita Rippo
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Giuseppe Bronte
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
| | - Massimiliano Bonafè
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| | - Maurizio Cardelli
- Advanced Technology Center for Aging Research, IRCCS INRCA, 60121 Ancona, Italy
| | - Fabiola Olivieri
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, 60121 Ancona, Italy
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, 60126 Ancona, Italy
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32
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Lavia P, Sciamanna I, Spadafora C. An Epigenetic LINE-1-Based Mechanism in Cancer. Int J Mol Sci 2022; 23:ijms232314610. [PMID: 36498938 PMCID: PMC9738484 DOI: 10.3390/ijms232314610] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
In the last fifty years, large efforts have been deployed in basic research, clinical oncology, and clinical trials, yielding an enormous amount of information regarding the molecular mechanisms of cancer and the design of effective therapies. The knowledge that has accumulated underpins the complexity, multifactoriality, and heterogeneity of cancer, disclosing novel landscapes in cancer biology with a key role of genome plasticity. Here, we propose that cancer onset and progression are determined by a stress-responsive epigenetic mechanism, resulting from the convergence of upregulation of LINE-1 (long interspersed nuclear element 1), the largest family of human retrotransposons, genome damage, nuclear lamina fragmentation, chromatin remodeling, genome reprogramming, and autophagy activation. The upregulated expression of LINE-1 retrotransposons and their protein products plays a key role in these processes, yielding an increased plasticity of the nuclear architecture with the ensuing reprogramming of global gene expression, including the reactivation of embryonic transcription profiles. Cancer phenotypes would thus emerge as a consequence of the unscheduled reactivation of embryonic gene expression patterns in an inappropriate context, triggering de-differentiation and aberrant proliferation in differentiated cells. Depending on the intensity of the stressing stimuli and the level of LINE-1 response, diverse degrees of malignity would be generated.
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Affiliation(s)
- Patrizia Lavia
- Institute of Molecular Biology and Pathology (IBPM), CNR Consiglio Nazionale delle Ricerche, c/o Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
- Correspondence: or
| | - Ilaria Sciamanna
- Center for Animal Research and Welfare (BENA), ISS Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Corrado Spadafora
- Institute of Translational Pharmacology (IFT), CNR Consiglio Nazionale delle Ricerche, 00133 Rome, Italy
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Savage AL, Iacoangeli A, Schumann GG, Rubio-Roldan A, Garcia-Perez JL, Al Khleifat A, Koks S, Bubb VJ, Al-Chalabi A, Quinn JP. Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis. Gene 2022; 843:146799. [PMID: 35963498 DOI: 10.1016/j.gene.2022.146799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/15/2022] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The genetics of an individual is a crucial factor in understanding the risk of developing the neurodegenerative disease amyotrophic lateral sclerosis (ALS). There is still a large proportion of the heritability of ALS, particularly in sporadic cases, to be understood. Among others, active transposable elements drive inter-individual variability, and in humans long interspersed element 1 (LINE1, L1), Alu and SINE-VNTR-Alu (SVA) retrotransposons are a source of polymorphic insertions in the population. We undertook a pilot study to characterise the landscape of non-reference retrotransposon insertion polymorphisms (non-ref RIPs) in 15 control and 15 ALS individuals' whole genomes from Project MinE, an international project to identify potential genetic causes of ALS. The combination of two bioinformatics tools (mobile element locator tool (MELT) and TEBreak) identified on average 1250 Alu, 232 L1 and 77 SVA non-ref RIPs per genome across the 30 analysed. Further PCR validation of individual polymorphic retrotransposon insertions showed a similar level of accuracy for MELT and TEBreak. Our preliminary study did not identify a specific RIP or a significant difference in the total number of non-ref RIPs in ALS compared to control genomes. The use of multiple bioinformatic tools improved the accuracy of non-ref RIP detection and our study highlights the potential importance of studying these elements further in ALS.
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Affiliation(s)
- Abigail L Savage
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Alejandro Rubio-Roldan
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain
| | - Jose L Garcia-Perez
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain; MRC-HGU Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, Western Australia 6009, Australia; Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Western Australia 6150, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
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Szigeti KA, Barták BK, Nagy ZB, Zsigrai S, Papp M, Márkus E, Igaz P, Takács I, Molnár B, Kalmár A. Methodological and Biological Factors Influencing Global DNA Methylation Results Measured by LINE-1 Pyrosequencing Assay in Colorectal Tissue and Liquid Biopsy Samples. Int J Mol Sci 2022; 23:ijms231911608. [PMID: 36232908 PMCID: PMC9569782 DOI: 10.3390/ijms231911608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE-1) bisulfite pyrosequencing is a widely used technique for genome-wide methylation analyses. We aimed to investigate the effects of experimental and biological factors on its results to improve the comparability. LINE-1 bisulfite pyrosequencing was performed on colorectal tissue (n = 222), buffy coat (n = 39), and plasma samples (n = 9) of healthy individuals and patients with colorectal tumors. Significantly altered methylation was observed between investigated LINE-1 CpG positions of non-tumorous tissues (p ≤ 0.01). Formalin-fixed, paraffin-embedded biopsies (73.0 ± 5.3%) resulted in lower methylation than fresh frozen samples (76.1 ± 2.8%) (p ≤ 0.01). DNA specimens after long-term storage showed higher methylation levels (+3.2%, p ≤ 0.01). In blood collection tubes with preservatives, cfDNA and buffy coat methylation significantly changed compared to K3EDTA tubes (p ≤ 0.05). Lower methylation was detected in older (>40 years, 76.8 ± 1.7%) vs. younger (78.1 ± 1.0%) female patients (p ≤ 0.05), and also in adenomatous tissues with MTHFR 677CT, or 1298AC mutations vs. wild-type (p ≤ 0.05) comparisons. Based on our findings, it is highly recommended to consider the application of standard DNA samples in the case of a possible clinical screening approach, as well as in experimental research studies.
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Affiliation(s)
- Krisztina A Szigeti
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-459-1500
| | - Barbara K Barták
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Zsófia B Nagy
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Sára Zsigrai
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Márton Papp
- Centre for Bioinformatics, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary
| | - Eszter Márkus
- Department of Anaesthesia and Intensive Care, Pest County Flor Ferenc Hospital, 2143 Kistarcsa, Hungary
| | - Peter Igaz
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
- Department of Endocrinology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - István Takács
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
| | - Alexandra Kalmár
- Department of Internal Medicine and Oncology, Faculty of Medicine, Semmelweis University, 1083 Budapest, Hungary
- MTA-SE Molecular Medicine Research Group, Eötvös Loránd Research Network, 1083 Budapest, Hungary
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Wei J, Yu X, Yang L, Liu X, Gao B, Huang B, Dou X, Liu J, Zou Z, Cui XL, Zhang LS, Zhao X, Liu Q, He PC, Sepich-Poore C, Zhong N, Liu W, Li Y, Kou X, Zhao Y, Wu Y, Cheng X, Chen C, An Y, Dong X, Wang H, Shu Q, Hao Z, Duan T, He YY, Li X, Gao S, Gao Y, He C. FTO mediates LINE1 m 6A demethylation and chromatin regulation in mESCs and mouse development. Science 2022; 376:968-973. [PMID: 35511947 PMCID: PMC9746489 DOI: 10.1126/science.abe9582] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification on mammalian messenger RNA. It is installed by a writer complex and can be reversed by erasers such as the fat mass and obesity-associated protein FTO. Despite extensive research, the primary physiological substrates of FTO in mammalian tissues and development remain elusive. Here, we show that FTO mediates m6A demethylation of long-interspersed element-1 (LINE1) RNA in mouse embryonic stem cells (mESCs), regulating LINE1 RNA abundance and the local chromatin state, which in turn modulates the transcription of LINE1-containing genes. FTO-mediated LINE1 RNA m6A demethylation also plays regulatory roles in shaping chromatin state and gene expression during mouse oocyte and embryonic development. Our results suggest broad effects of LINE1 RNA m6A demethylation by FTO in mammals.
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Affiliation(s)
- Jiangbo Wei
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Xianbin Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Lei Yang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xuelian Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Boyang Gao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Boxian Huang
- State Key Laboratory of Reproductive Medicine, Suzhou Affiliated Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Xiaoyang Dou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Jun Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Zhongyu Zou
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Xiao-Long Cui
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Li-Sheng Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Xingsen Zhao
- The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou 310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Qinzhe Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - P. Cody He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Caraline Sepich-Poore
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Nicole Zhong
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Wenqiang Liu
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanhe Li
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yanhong Zhao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - You Wu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Xuejun Cheng
- The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou 310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Chuan Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yiming An
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Xueyang Dong
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Huanyu Wang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Qiang Shu
- The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Ziyang Hao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
| | - Tao Duan
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yu-Ying He
- Department of Medicine, Section of Dermatology, University of Chicago, Chicago, IL 60637, USA
| | - Xuekun Li
- The Children's Hospital, School of Medicine, Zhejiang University, National Clinical Research Center for Child Health, Hangzhou 310052, China
- The Institute of Translational Medicine, School of Medicine, Zhejiang University, Hangzhou 310029, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yawei Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, Chicago, IL 60637, USA
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Pfaff AL, Bubb VJ, Quinn JP, Koks S. Locus specific reduction of L1 expression in the cortices of individuals with amyotrophic lateral sclerosis. Mol Brain 2022; 15:25. [PMID: 35346298 PMCID: PMC8961898 DOI: 10.1186/s13041-022-00914-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
The activation and dysregulation of retrotransposons has been identified in the CNS of individuals with the fatal neurodegenerative disorder Amyotrophic lateral sclerosis (ALS). This includes elements from multiple different families and subfamilies of retrotransposons, however there is limited knowledge of the specific loci from which this expression occurs in ALS. The long interspersed element-1 (L1) is the only autonomous retrotransposon in the human genome and members of this family of elements maintain the ability to mobilise. Despite L1s contributing to 17% of the human genome only 80-100 L1s encode the required proteins for mobilisation and are retrotransposition competent. Identifying the specific loci from which L1 expression occurs will inform on the potential functional consequences of their expression, such as the potential for somatic retrotransposition or DNA damage caused by the endonuclease activity of the ORF2 protein of the L1. Here we characterised L1 loci expression using the L1EM tool ( https://github.com/FenyoLab/L1EM ) in RNA sequencing data from 518 samples across four tissues (motor cortex, frontal cortex, cerebellum and cervical spinal cord) in the Target ALS cohort obtained from the New York Genome Center. There was a significant reduction in total intact L1 expression (those that encode functional proteins) in two brain regions of individuals with ALS compared to controls and clustering of the ALS brain regions occurred based on their intact L1 expression profile. Although overall the levels of L1 expression were reduced in ALS/ALS with other neurological disorder (ND) there were individuals in which L1s were expressed at much higher levels than the rest of the ALS/ALSND cohort. Expressed L1 loci were more frequently located in introns compared to those not expressed and the level of L1 expression positively correlated with the expression of the gene in which it was located. Significant differences were observed in the expression profiles of L1s in ALS and specific features of these elements, such as location in the genome and whether or not they are intact, were significantly associated with those that were expressed in the cohort.
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Affiliation(s)
- Abigail L. Pfaff
- Perron Institute for Neurological and Translational Science, Perth, 8 Verdun Street, Nedlands, WA 6009 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, 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, 8 Verdun Street, Nedlands, WA 6009 Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA Australia
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Huang Y, Xu F, Mei S, Liu X, Zhao F, Wei L, Fan Z, Hu Y, Wang L, Ai B, Cen S, Liang C, Guo F. MxB inhibits long interspersed element type 1 retrotransposition. PLoS Genet 2022; 18:e1010034. [PMID: 35171907 PMCID: PMC8849481 DOI: 10.1371/journal.pgen.1010034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/12/2022] [Indexed: 12/13/2022] Open
Abstract
Long interspersed element type 1 (LINE-1, also L1 for short) is the only autonomously transposable element in the human genome. Its insertion into a new genomic site may disrupt the function of genes, potentially causing genetic diseases. Cells have thus evolved a battery of mechanisms to tightly control LINE-1 activity. Here, we report that a cellular antiviral protein, myxovirus resistance protein B (MxB), restricts the mobilization of LINE-1. This function of MxB requires the nuclear localization signal located at its N-terminus, its GTPase activity and its ability to form oligomers. We further found that MxB associates with LINE-1 protein ORF1p and promotes sequestration of ORF1p to G3BP1-containing cytoplasmic granules. Since knockdown of stress granule marker proteins G3BP1 or TIA1 abolishes MxB inhibition of LINE-1, we conclude that MxB engages stress granule components to effectively sequester LINE-1 proteins within the cytoplasmic granules, thus hindering LINE-1 from accessing the nucleus to complete retrotransposition. Thus, MxB protein provides one mechanism for cells to control the mobility of retroelements. Retrotransposons occupy more than 40% of human genome, and have co-evolved with humans for millions of years. Long interspersed element type 1 (LINE-1, or L1) is the only retrotransposon that is able to jump to a new locus. LINE-1 retrotransposition causes genome instability, and is associated with genetic diseases including autoimmune diseases and cancer. To suppress this genome toxicity caused by LINE-1, humans have developed multi-layered mechanisms to control LINE-1 activity. MxB has been previously shown to inhibit LINE-1 mobility, thus contributing to host restriction of LINE-1. Here, we further demonstrate that MxB effectively restricts LINE-1 retrotransposition by sequestering LINE-1 ribonucleoprotein (RNP) within the cytoplasmic stress granules, thus guards genome stability. Hence our data attribute the restriction function of MxB to sequestering LINE-1 RNP to stress granules.
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Affiliation(s)
- Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiaoman Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Zhangling Fan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yamei Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liming Wang
- Department of Medical Oncology, Beijing Hospital, Beijing, P. R. China
| | - Bin Ai
- Department of Medical Oncology, Beijing Hospital, Beijing, P. R. China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Chen Liang
- McGill Centre for Viral Diseases, Lady Davis Institute, Jewish General Hospital, Montreal, Canada
- * E-mail: (CL); (FG)
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- * E-mail: (CL); (FG)
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Abstract
All life forms defend their genome against DNA invasion. Eukaryotic cells recognize incoming DNA and limit its transcription through repressive chromatin modifications. The human silencing hub (HUSH) complex transcriptionally represses long interspersed element-1 retrotransposons (L1s) and retroviruses through histone H3 lysine 9 trimethylation (H3K9me3)1-3. How HUSH recognizes and initiates silencing of these invading genetic elements is unknown. Here we show that HUSH is able to recognize and transcriptionally repress a broad range of long, intronless transgenes. Intron insertion into HUSH-repressed transgenes counteracts repression, even in the absence of intron splicing. HUSH binds transcripts from the target locus, prior to and independent of H3K9me3 deposition, and target transcription is essential for both initiation and propagation of HUSH-mediated H3K9me3. Genomic data reveal how HUSH binds and represses a subset of endogenous intronless genes generated through retrotransposition of cellular mRNAs. Thus intronless cDNA-the hallmark of reverse transcription-provides a versatile way to distinguish invading retroelements from host genes and enables HUSH to protect the genome from 'non-self' DNA, despite there being no previous exposure to the invading element. Our findings reveal the existence of a transcription-dependent genome-surveillance system and explain how it provides immediate protection against newly acquired elements while avoiding inappropriate repression of host genes.
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Affiliation(s)
- Marta Seczynska
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Stuart Bloor
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Sergio Martinez Cuesta
- Data Sciences and Quantitative Biology, Discovery Sciences, AstraZeneca, Cambridge Biomedical Campus, Cambridge, UK
| | - Paul J Lehner
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
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Issah I, Arko-Mensah J, Rozek LS, Zarins KR, Agyekum TP, Dwomoh D, Basu N, Batterman S, Robins TG, Fobil JN. Global DNA (LINE-1) methylation is associated with lead exposure and certain job tasks performed by electronic waste workers. Int Arch Occup Environ Health 2021; 94:1931-1944. [PMID: 34148106 DOI: 10.1007/s00420-021-01733-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/28/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE This study assessed the associations between blood and urine levels of toxic metals; cadmium (Cd) and lead (Pb), and methylation levels of the LINE-1 gene among e-waste and control populations in Ghana. METHODS The study enrolled 100 male e-waste workers and 51 all-male non-e-waste workers or controls. The concentrations of Cd and Pb were measured in blood and urine using inductively coupled plasma mass spectrometry, while LINE1 methylation levels were assessed by pyrosequencing of bisulfite-converted DNA extracted from whole blood. Single and multiple metals linear regression models were used to determine the associations between metals and LINE1 DNA methylation. RESULTS Blood lead (BPb) and urine lead (UPb) showed higher median concentrations among the e-waste workers than the controls (76.82 µg/L vs 40.25 µg/L, p ≤ 0.001; and 6.89 µg/L vs 3.43 µg/L, p ≤ 0.001, respectively), whereas blood cadmium (BCd) concentration was lower in the e-waste workers compared to the controls (0.59 µg/L vs 0.81 µg/L, respectively, p = 0.003). There was no significant difference in LINE1 methylation between the e-waste and controls (85.16 ± 1.32% vs 85.17 ± 1.11%, p = 0.950). In our single metal linear regression models, BPb was significantly inversely associated with LINE1 methylation in the control group (βBPb = - 0.027, 95% CI - 0.045, - 0.010, p = 0.003). In addition, a weak association between BPb and LINE1 was observed in the multiple metals analysis in the e-waste worker group (βBPb = - 0.005, 95% CI - 0.011, 0.000, p = 0.058). CONCLUSION Continuous Pb exposure may interfere with LINE1 methylation, leading to epigenetic alterations, thus serving as an early epigenetic marker for future adverse health outcomes.
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Affiliation(s)
- Ibrahim Issah
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana.
| | - John Arko-Mensah
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Katie R Zarins
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Thomas P Agyekum
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana
| | - Duah Dwomoh
- Department of Biostatistics, School of Public Health, University of Ghana, P.O. Box LG13, Accra, Ghana
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - Stuart Batterman
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Thomas G Robins
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Julius N Fobil
- Department of Biological, Environmental and Occupational Health Sciences, School of Public Health, University of Ghana, Legon, P.O. Box LG13, Accra, Ghana
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Abstract
LINE1 is the most active and abundant family of retrotransposons; it is implicated in a number of pathologies, as well as in early embryo development. We present a protocol to specifically knockdown LINE1 in mouse embryonic stem cells and embryos, including details for the nucleofection and zygote microinjection of LINE antisense oligos, followed by RNA FISH validation. This protocol can be used in development, as well as other cell types where LINE1 is believed to be expressed. For complete information on the use and execution of this protocol, please refer to Percharde et al. (2018).
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Affiliation(s)
- Michelle Percharde
- MRC London Institute of Medical Sciences (LMS), London W12 0NN, UK
- Institute of Clinical Sciences (ICS), Imperial College, London W12 0NN, UK
| | - Chih-Jen Lin
- The University of Edinburgh, MRC Centre for Reproductive Health, Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Miguel Ramalho-Santos
- Lunenfeld-Tanenbaum Research Institute and Department of Molecular Genetics, University of Toronto, Toronto M5T 3H7, Canada
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Mendes CC, Zampieri BL, Arantes LMRB, Melendez ME, Biselli JM, Carvalho AL, Eberlin MN, Riccio MF, Vannucchi H, Carvalho VM, Goloni-Bertollo EM, Pavarino ÉC. One-carbon metabolism and global DNA methylation in mothers of individuals with Down syndrome. Hum Cell 2021; 34:1671-1681. [PMID: 34410622 DOI: 10.1007/s13577-021-00586-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Down syndrome (DS) is the most common chromosomal disorder, resulting from the failure of normal chromosome 21 segregation. Studies have suggested that impairments within the one-carbon metabolic pathway can be of relevance for the global genome instability observed in mothers of individuals with DS. Based on the association between global DNA hypomethylation, genome instability, and impairments within the one-carbon metabolic pathway, the present study aimed to identify possible predictors, within the one-carbon metabolism, of global DNA methylation, measured by methylation patterns of LINE-1 and Alu repetitive sequences, in mothers of individuals with DS and mothers of individuals without the syndrome. In addition, we investigated one-carbon genetic polymorphisms and metabolites as maternal predisposing factors for the occurrence of trisomy 21 in children. Eighty-three samples of mothers of children with DS with karyotypically confirmed free trisomy 21 (case group) and 84 of mothers who had at least one child without DS or any other aneuploidy were included in the study. Pyrosequencing assays were performed to access global methylation. The results showed that group affiliation (case or control), betaine-homocysteine methyltransferase (BHMT) G742A and transcobalamin 2 (TCN2) C776G polymorphisms, and folate concentration were identified as predictors of global Alu DNA methylation values. In addition, thymidylate synthase (TYMS) 28-bp repeats 2R/3R or 3R/3R genotypes are independent maternal predisposing factors for having a child with DS. This study adds evidence that supports the association of impairments in the one-carbon metabolism, global DNA methylation, and the possibility of having a child with DS.
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Affiliation(s)
- Cristiani Cortez Mendes
- Unidade de Pesquisa em Genética e Biologia Molecular-UPGEM, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, Brazil
| | | | | | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Joice Matos Biselli
- Universidade Estadual Paulista Júlio de Mesquita Filho, Instituto de Biociências, Letras e Ciências Exatas de São José do Rio Preto, Departamento de Ciências Biológicas, São José do Rio Preto, São Paulo, Brazil
| | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Marcos Nogueira Eberlin
- Universidade Presbiteriana Mackenzie, Discovery-Mackenzie-Núcleo Mackenzie de Pesquisa, Núcleo Mackenzie de Pesquisas em Ciência, Fé e Sociedade, São Paulo, São Paulo, Brazil
| | | | - Hélio Vannucchi
- Laboratório de Nutrição, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto-USP, Ribeirão Preto, São Paulo, Brazil
| | | | - Eny Maria Goloni-Bertollo
- Unidade de Pesquisa em Genética e Biologia Molecular-UPGEM, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, Brazil
| | - Érika Cristina Pavarino
- Unidade de Pesquisa em Genética e Biologia Molecular-UPGEM, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, Brazil.
- , Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, São Paulo, 15090-000, Brazil.
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Mishra A, Zennami K, Velarde E, Thorek DLJ, Yegnasubramanian S, DeWeese TL, Lupold SE. Longitudinal measurement of subcutaneous and intratibial human prostate cancer xenograft growth and response to ionizing radiation by plasma Alu and LINE-1 ctDNA: A comparison to standard methods. Prostate 2021; 81:745-753. [PMID: 34032307 DOI: 10.1002/pros.24171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/28/2021] [Accepted: 05/07/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Current preclinical models of metastatic prostate cancer (PCa) require sophisticated technologies and/or genetically engineered cells for the noninvasive monitoring of tumors in remote sites, such as bone. Recent developments in circulating tumor DNA (ctDNA) analysis provide an alternative method for noninvasive tumor monitoring at a low cost. Here, we sought to evaluate human Alu and LINE-1 ctDNA for the longitudinal measurement of subcutaneous and intratibial human PCa xenograft growth and response to ionizing radiation (IR) through comparison with standard slide caliper and bioluminescence measurements. MATERIAL AND METHODS Intratibial and subcutaneous xenografts were established in male athymic nude mice using LNCaP cells that stably express firefly luciferase. A subset of tumors was treated with a single dose of IR (CT-guided focal IR, 6 Gy). Tumor measurements were simultaneously taken by slide caliper (subcutaneous only), in vivo bioluminescence imaging, and quantitative real-time PCR (qPCR) of human-specific Alu and LINE-1 ctDNA for several weeks. RESULTS Levels of ctDNA and bioluminescence increased concordantly with subcutaneous and intratibial tumor growth. A statistically significant correlation (Spearman) was observed between ctDNA and subcutaneous tumor volume (LINE-1, r = .94 and Alu, r = .95, p < .0001), ctDNA and bioluminescence (LINE-1, r = .66 and Alu, r = .60, p < .002), and bioluminescence and tumor volume (r = .66, p = .0003). Bioluminescence and ctDNA were also significantly correlated in intratibial tumors (LINE-1, r = .82 and Alu, r = .81, p < .0001). Following external beam IR, the tumor responses varied briefly by method of measurement, but followed a similar trend. Statistically significant correlations were maintained between ctDNA and slide caliper measurement in irradiated subcutaneous tumors (LINE-1, r = .64 and Alu, r = .44, p < .02), and ctDNA and bioluminescence in intratibial tumors (LINE-1, r = .55, p = .018). CONCLUSIONS Real-time qPCR of circulating human Alu and LINE-1 DNA provides an accurate measurement of subcutaneous and intratibial xenograft burden that is comparable with conventional bioluminescence imaging and slide caliper measurement. Transient differences in measurements were observed following tumor-targeted IR, but overall all measurements mirrored tumor growth and response.
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Affiliation(s)
- Alok Mishra
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kenji Zennami
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Esteban Velarde
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel L J Thorek
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Radiology and Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Srinivasan Yegnasubramanian
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Theodore L DeWeese
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Shawn E Lupold
- Department of Urology, The James Buchanan Brady Urologic Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Awada Z, Bouaoun L, Nasr R, Tfayli A, Cuenin C, Akika R, Boustany RM, Makoukji J, Tamim H, Zgheib NK, Ghantous A. LINE-1 methylation mediates the inverse association between body mass index and breast cancer risk: A pilot study in the Lebanese population. Environ Res 2021; 197:111094. [PMID: 33839117 DOI: 10.1016/j.envres.2021.111094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/28/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Lebanon is among the top countries worldwide in combined incidence and mortality of breast cancer, which raises concern about risk factors peculiar to this country. The underlying molecular mechanisms of breast cancer require elucidation, particularly epigenetics, which is recognized as a molecular sensor to environmental exposures. PURPOSE We aim to explore whether DNA methylation levels of AHRR (marker of cigarette smoking), SLC1A5 and TXLNA (markers of alcohol consumption), and LINE-1 (a genome-wide repetitive retrotransposon) can act as molecular mediators underlying putative associations between breast cancer risk and pertinent extrinsic (tobacco smoking and alcohol consumption) and intrinsic factors [age and body mass index (BMI)]. METHODS This is a cross-sectional pilot study which includes breast cancer cases (N = 65) and controls (N = 54). DNA methylation levels were measured using bisulfite pyrosequencing on available peripheral blood samples (N = 119), and Multivariate Imputation by Chained Equations (MICE) was used to impute missing DNA methylation values in remaining samples. Multiple mediation analysis was performed to assess direct and indirect (via DNA methylation) effects of intrinsic and extrinsic factors on breast cancer risk. RESULTS In relation to exposure, AHRR hypo-methylation was associated with cigarette but not waterpipe smoking, suggesting potentially different biomarkers of these two forms of tobacco use; SLC1A5 and TXLNA methylation were not associated with alcohol consumption; LINE-1 methylation was inversely associated with BMI (β-value [95% confidence interval (CI)] = -0.04 [-0.07, -0.02]), which remained significant after adjustment for age, smoking and alcohol consumption. In relation to breast cancer, there was no detectable association between AHRR, SLC1A5 or TXLNA methylation and cancer risk, but LINE-1 methylation was significantly higher in breast cancer cases when compared to controls (mean ± SD: 72.00 ± 0.66 versus 70.89 ± 0.73, P = 4.67 × 10-14). This difference remained significant after adjustment for confounders (odds ratio (OR) [95% CI] = 9.75[3.74, 25.39]). Moreover, LINE-1 hypo-methylation mediated 83% of the inverse effect of BMI on breast cancer risk. CONCLUSION This pilot study demonstrates that alterations in blood LINE-1 methylation mediate the inverse effect of BMI on breast cancer risk. This warrants large scale studies and stratification based on clinic-pathological types of breast cancer.
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Affiliation(s)
- Zainab Awada
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon; International Agency for Research on Cancer, Lyon, France
| | | | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Arafat Tfayli
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Cyrille Cuenin
- International Agency for Research on Cancer, Lyon, France
| | - Reem Akika
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Rose-Mary Boustany
- Department of Biochemistry and Molecular Genetics, American University of Beirut Faculty of Medicine, Beirut, Lebanon; Department of Neurology, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Joelle Makoukji
- Department of Biochemistry and Molecular Genetics, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Hani Tamim
- Department of Internal Medicine and Clinical Research Institute, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Nathalie K Zgheib
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon.
| | - Akram Ghantous
- International Agency for Research on Cancer, Lyon, France.
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Mukherjee K, Sur D, Singh A, Rai S, Das N, Sekar R, Narindi S, Dhingra VK, Jat B, Balraam KVV, Agarwal SP, Mandal PK. Robust expression of LINE-1 retrotransposon encoded proteins in oral squamous cell carcinoma. BMC Cancer 2021; 21:628. [PMID: 34044801 PMCID: PMC8161598 DOI: 10.1186/s12885-021-08174-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 04/07/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Oral Squamous Cell Carcinoma (OSCC) results from a series of genetic alteration in squamous cells. This particular type of cancer considers one of the most aggressive malignancies to control because of its frequent local invasions to the regional lymph node. Although several biomarkers have been reported, the key marker used to predict the behavior of the disease is largely unknown. Here we report Long INterpersed Element-1 (LINE1 or L1) retrotransposon activity in post-operative oral cancer samples. L1 is the only active retrotransposon occupying around 17% of the human genome with an estimated 500,000 copies. An active L1 encodes two proteins (L1ORF1p and L1ORF2p); both of which are critical in the process of retrotransposition. Several studies report that the L1 retrotransposon is highly active in many cancers. L1 activity is generally determined by assaying L1ORF1p because of its high expression and availability of the antibody. However, due to its lower expression and unavailability of a robust antibody, detection of L1ORF2p has been limited. L1ORF2p is the crucial protein in the process of retrotransposition as it provides endonuclease and reverse transcriptase (RT) activity. METHODS Immunohistochemistry and Western blotting were performed on the post-operative oral cancer samples and murine tissues. RESULTS Using in house novel antibodies against both the L1 proteins (L1ORF1p and L1ORF2p), we found L1 retrotransposon is extremely active in post-operative oral cancer tissues. Here, we report a novel human L1ORF2p antibody generated using an 80-amino-acid stretch from the RT domain, which is highly conserved among different species. The antibody detects significant L1ORF2p expression in human oral squamous cell carcinoma (OSCC) samples and murine germ tissues. CONCLUSIONS We report exceptionally high L1ORF1p and L1ORF2p expression in post-operative oral cancer samples. The novel L1ORF2p antibody reported in this study will serve as a useful tool to understand why L1 activity is deregulated in OSCC and how it contributes to the progression of this particular cancer. Cross-species reactivity of L1ORF2p antibody due to the conserved epitope will be useful to study the retrotransposon biology in mice and rat germ tissues.
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Affiliation(s)
- Koel Mukherjee
- Department of Biotechnology, IIT Roorkee, Roorkee, Uttarakhand India
| | - Debpali Sur
- Department of Biotechnology, IIT Roorkee, Roorkee, Uttarakhand India
| | - Abhijeet Singh
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
| | - Sandhya Rai
- Department of Biotechnology, IIT Roorkee, Roorkee, Uttarakhand India
| | | | - Rakshanya Sekar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu India
| | | | - Vandana Kumar Dhingra
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
| | - Bhinyaram Jat
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
| | | | - Satya Prakash Agarwal
- Department of Head-Neck Surgery and Oncology, AIIMS Rishikesh, Rishikesh, Uttarakhand India
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Gu Z, Liu Y, Zhang Y, Cao H, Lyu J, Wang X, Wylie A, Newkirk SJ, Jones AE, Lee M, Botten GA, Deng M, Dickerson KE, Zhang CC, An W, Abrams JM, Xu J. Silencing of LINE-1 retrotransposons is a selective dependency of myeloid leukemia. Nat Genet 2021; 53:672-682. [PMID: 33833453 PMCID: PMC8270111 DOI: 10.1038/s41588-021-00829-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 02/26/2021] [Indexed: 02/07/2023]
Abstract
Transposable elements or transposons are major players in genetic variability and genome evolution. Aberrant activation of long interspersed element-1 (LINE-1 or L1) retrotransposons is common in human cancers, yet their tumor-type-specific functions are poorly characterized. We identified MPHOSPH8/MPP8, a component of the human silencing hub (HUSH) complex, as an acute myeloid leukemia (AML)-selective dependency by epigenetic regulator-focused CRISPR screening. Although MPP8 is dispensable for steady-state hematopoiesis, MPP8 loss inhibits AML development by reactivating L1s to induce the DNA damage response and cell cycle exit. Activation of endogenous or ectopic L1s mimics the phenotype of MPP8 loss, whereas blocking retrotransposition abrogates MPP8-deficiency-induced phenotypes. Expression of AML oncogenic mutations promotes L1 suppression, and enhanced L1 silencing is associated with poor prognosis in human AML. Hence, while retrotransposons are commonly recognized for their cancer-promoting functions, we describe a tumor-suppressive role for L1 retrotransposons in myeloid leukemia.
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Affiliation(s)
- Zhimin Gu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuxuan Liu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yuannyu Zhang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hui Cao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Junhua Lyu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xun Wang
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Annika Wylie
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - Amanda E Jones
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Lee
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Giovanni A Botten
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mi Deng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kathryn E Dickerson
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cheng Cheng Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, USA
| | - John M Abrams
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jian Xu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Lee YR, Kim G, Lee HW, Tak WY, Park SY, Jang SY, Kweon YO, Park JG, Han YS, Chun JM, Han JR, Hur K. Long interspersed nuclear element-1 hypomethylation is associated with poor outcomes via the activation of ST18 in human hepatocellular carcinoma. Medicine (Baltimore) 2021; 100:e25552. [PMID: 33879706 PMCID: PMC8078304 DOI: 10.1097/md.0000000000025552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/25/2021] [Indexed: 01/04/2023] Open
Abstract
The level of long interspersed nuclear element-1 (LINE-1) methylation, representing the global deoxyribonucleic acid methylation level, could contribute to the prognosis of cancer via the activation of oncogenes. This study was performed to evaluate the prognostic implications of LINE-1 hypomethylation in patients with hepatocellular carcinoma (HCC) and the possible mechanisms related to oncogene activation.Seventy-seven HCC patients between October 2014 and September 2015 were enrolled in this prospective study. Quantitative pyrosequencing was performed to assess the LINE-1 methylation level of HCC and matched non-HCC tissue samples. The expression of suppression of tumorigenicity 18 was measured by immunohistochemistry and its correlation with LINE-1 methylation levels was examined.LINE-1 was significantly hypomethylated in the HCC tissue compared with the matched nontumor tissue (64.0 ± 11.6% vs 75.6 ± 4.0%, P < .001). LINE-1 hypomethylation was an independent risk factor for overall survival (hazard ratio = 27.291, P = .032) and disease progression (hazard ratio = 5.298, P = .005). The expression of suppression of tumorigenicity 18 was higher in the hypomethylated LINE-1 HCC tissue than the hypermethylated LINE-1 tumor tissue (P = .030).LINE-1 hypomethylation may serve as a potential prognostic marker for patients with HCC.
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Affiliation(s)
- Yu Rim Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital
| | - Gyeonghwa Kim
- Department of Biochemistry and Cell Biology, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University
| | - Hye Won Lee
- Department of Pathology, Keimyung University School of Medicine
| | - Won Young Tak
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital
| | - Soo Young Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital
| | - Se Young Jang
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital
| | - Young Oh Kweon
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital
| | - Jung Gil Park
- Department of Internal Medicine, College of Medicine, Yeungnam University
| | - Young Seok Han
- Department of Surgery, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Jae Min Chun
- Department of Surgery, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Ja Ryung Han
- Department of Surgery, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, South Korea
| | - Keun Hur
- Department of Biochemistry and Cell Biology, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University
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Szabo L, Molnar R, Tomesz A, Deutsch A, Darago R, Nowrasteh G, Varjas T, Nemeth B, Budan F, Kiss I. The effects of flavonoids, green tea polyphenols and coffee on DMBA induced LINE-1 DNA hypomethylation. PLoS One 2021; 16:e0250157. [PMID: 33878138 PMCID: PMC8057585 DOI: 10.1371/journal.pone.0250157] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
The intake of carcinogenic and chemopreventive compounds are important nutritional factors related to the development of malignant tumorous diseases. Repetitive long interspersed element-1 (LINE-1) DNA methylation pattern plays a key role in both carcinogenesis and chemoprevention. In our present in vivo animal model, we examined LINE-1 DNA methylation pattern as potential biomarker in the liver, spleen and kidney of mice consuming green tea (Camellia sinensis) extract (catechins 80%), a chinese bayberry (Morella rubra) extract (myricetin 80%), a flavonoid extract (with added resveratrol) and coffee (Coffee arabica) extract. In the organs examined, carcinogen 7,12-dimethylbenz(a)anthracene (DMBA)-induced hypomethylation was prevented by all test materials except chinese bayberry extract in the kidneys. Moreover, the flavonoid extract caused significant hypermethylation in the liver compared to untreated controls and to other test materials. The tested chemopreventive substances have antioxidant, anti-inflammatory properties and regulate molecular biological signaling pathways. They increase glutathione levels, induce antioxidant enzymes, which decrease free radical damage caused by DMBA, and ultimately, they are able to increase the activity of DNA methyltransferase enzymes. Furthermore, flavonoids in the liver may inhibit the procarcinogen to carcinogen activation of DMBA through the inhibition of CYP1A1 enzyme. At the same time, paradoxically, myricetin can act as a prooxidant as a result of free radical damage, which can explain that it did not prevent hypomethylation in the kidneys. Our results demonstrated that LINE-1 DNA methylation pattern is a useful potential biomarker for detecting and monitoring carcinogenic and chemopreventive effects of dietary compounds.
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Affiliation(s)
- Laszlo Szabo
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Richard Molnar
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Andras Tomesz
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Arpad Deutsch
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Richard Darago
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | | | - Timea Varjas
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Balazs Nemeth
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Ferenc Budan
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Institute of Environmental Engineering, Faculty of Engineering, University of Pannonia, Veszprém, Hungary
- Szentagothai Research Centre, University of Pécs, Pécs, Hungary
| | - Istvan Kiss
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
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Hanna R, Flamier A, Barabino A, Bernier G. G-quadruplexes originating from evolutionary conserved L1 elements interfere with neuronal gene expression in Alzheimer's disease. Nat Commun 2021; 12:1828. [PMID: 33758195 PMCID: PMC7987966 DOI: 10.1038/s41467-021-22129-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/03/2021] [Indexed: 02/06/2023] Open
Abstract
DNA sequences containing consecutive guanines organized in 4-interspaced tandem repeats can form stable single-stranded secondary structures, called G-quadruplexes (G4). Herein, we report that the Polycomb group protein BMI1 is enriched at heterochromatin regions containing putative G4 DNA sequences, and that G4 structures accumulate in cells with reduced BMI1 expression and/or relaxed chromatin, including sporadic Alzheimer's disease (AD) neurons. In AD neurons, G4 structures preferentially accumulate in lamina-associated domains, and this is rescued by re-establishing chromatin compaction. ChIP-seq analyses reveal that G4 peaks correspond to evolutionary conserved Long Interspersed Element-1 (L1) sequences predicted to be transcriptionally active. Hence, G4 structures co-localize with RNAPII, and inhibition of transcription can reverse the G4 phenotype without affecting chromatin's state, thus uncoupling both components. Intragenic G4 structures affecting splicing events are furthermore associated with reduced neuronal gene expression in AD. Active L1 sequences are thus at the origin of most G4 structures observed in human neurons.
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Affiliation(s)
- Roy Hanna
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Anthony Flamier
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
- Whitehead Institute of Biomedical Research, Cambridge, MA, USA
| | - Andrea Barabino
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Gilbert Bernier
- Stem Cell and Developmental Biology Laboratory, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada.
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada.
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Meyer A, Schloissnig S, Franchini P, Du K, Woltering JM, Irisarri I, Wong WY, Nowoshilow S, Kneitz S, Kawaguchi A, Fabrizius A, Xiong P, Dechaud C, Spaink HP, Volff JN, Simakov O, Burmester T, Tanaka EM, Schartl M. Giant lungfish genome elucidates the conquest of land by vertebrates. Nature 2021; 590:284-289. [PMID: 33461212 PMCID: PMC7875771 DOI: 10.1038/s41586-021-03198-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/06/2021] [Indexed: 01/29/2023]
Abstract
Lungfishes belong to lobe-fined fish (Sarcopterygii) that, in the Devonian period, 'conquered' the land and ultimately gave rise to all land vertebrates, including humans1-3. Here we determine the chromosome-quality genome of the Australian lungfish (Neoceratodus forsteri), which is known to have the largest genome of any animal. The vast size of this genome, which is about 14× larger than that of humans, is attributable mostly to huge intergenic regions and introns with high repeat content (around 90%), the components of which resemble those of tetrapods (comprising mainly long interspersed nuclear elements) more than they do those of ray-finned fish. The lungfish genome continues to expand independently (its transposable elements are still active), through mechanisms different to those of the enormous genomes of salamanders. The 17 fully assembled lungfish macrochromosomes maintain synteny to other vertebrate chromosomes, and all microchromosomes maintain conserved ancient homology with the ancestral vertebrate karyotype. Our phylogenomic analyses confirm previous reports that lungfish occupy a key evolutionary position as the closest living relatives to tetrapods4,5, underscoring the importance of lungfish for understanding innovations associated with terrestrialization. Lungfish preadaptations to living on land include the gain of limb-like expression in developmental genes such as hoxc13 and sall1 in their lobed fins. Increased rates of evolution and the duplication of genes associated with obligate air-breathing, such as lung surfactants and the expansion of odorant receptor gene families (which encode proteins involved in detecting airborne odours), contribute to the tetrapod-like biology of lungfishes. These findings advance our understanding of this major transition during vertebrate evolution.
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Affiliation(s)
- Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | | | - Paolo Franchini
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kang Du
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | | | - Iker Irisarri
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
| | - Wai Yee Wong
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | | | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Akane Kawaguchi
- Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | | | - Peiwen Xiong
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Corentin Dechaud
- Institut de Génomique Fonctionnelle, École Normale Superieure, Université Claude Bernard, Lyon, France
| | - Herman P Spaink
- Faculty of Science, Universiteit Leiden, Leiden, The Netherlands
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle, École Normale Superieure, Université Claude Bernard, Lyon, France
| | - Oleg Simakov
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria.
| | | | - Elly M Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna, Austria.
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Germany.
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
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