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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: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [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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2
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Lou C, Goodier JL, Qiang R. A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage. Reprod Biol Endocrinol 2020; 18:6. [PMID: 31964400 PMCID: PMC6971995 DOI: 10.1186/s12958-020-0564-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022] Open
Abstract
LINE1 retrotransposons are mobile DNA elements that copy and paste themselves into new sites in the genome. To ensure their evolutionary success, heritable new LINE-1 insertions accumulate in cells that can transmit genetic information to the next generation (i.e., germ cells and embryonic stem cells). It is our hypothesis that LINE1 retrotransposons, insertional mutagens that affect expression of genes, may be causal agents of early miscarriage in humans. The cell has evolved various defenses restricting retrotransposition-caused mutation, but these are occasionally relaxed in certain somatic cell types, including those of the early embryo. We predict that reduced suppression of L1s in germ cells or early-stage embryos may lead to excessive genome mutation by retrotransposon insertion, or to the induction of an inflammatory response or apoptosis due to increased expression of L1-derived nucleic acids and proteins, and so disrupt gene function important for embryogenesis. If correct, a novel threat to normal human development is revealed, and reverse transcriptase therapy could be one future strategy for controlling this cause of embryonic damage in patients with recurrent miscarriages.
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Affiliation(s)
- Chao Lou
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
| | - John L. Goodier
- 0000 0001 2171 9311grid.21107.35McKusick-Nathans Deartment of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Rong Qiang
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
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Kawano K, Doucet AJ, Ueno M, Kariya R, An W, Marzetta F, Kuroki M, Turelli P, Sukegawa S, Okada S, Strebel K, Trono D, Ariumi Y. HIV-1 Vpr and p21 restrict LINE-1 mobility. Nucleic Acids Res 2019; 46:8454-8470. [PMID: 30085096 PMCID: PMC6144823 DOI: 10.1093/nar/gky688] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/18/2018] [Indexed: 01/12/2023] Open
Abstract
Long interspersed element-1 (LINE-1, L1) composes ∼17% of the human genome. However, genetic interactions between L1 and human immunodeficiency virus type 1 (HIV-1) remain poorly understood. In this study, we found that HIV-1 suppresses L1 retrotransposition. Notably, HIV-1 Vpr strongly inhibited retrotransposition without inhibiting L1 promoter activity. Since Vpr is known to regulate host cell cycle, we examined the possibility whether Vpr suppresses L1 retrotransposition in a cell cycle dependent manner. We showed that the inhibitory effect of a mutant Vpr (H71R), which is unable to arrest the cell cycle, was significantly relieved compared with that of wild-type Vpr, suggesting that Vpr suppresses L1 mobility in a cell cycle dependent manner. Furthermore, a host cell cycle regulator p21Waf1 strongly suppressed L1 retrotransposition. The N-terminal kinase inhibitory domain (KID) of p21 was required for this inhibitory effect. Another KID-containing host cell cycle regulator p27Kip1 also strongly suppressed L1 retrotransposition. We showed that Vpr and p21 coimmunoprecipitated with L1 ORF2p and they suppressed the L1 reverse transcriptase activity in LEAP assay, suggesting that Vpr and p21 inhibit ORF2p-mediated reverse transcription. Altogether, our results suggest that viral and host cell cycle regulatory machinery limit L1 mobility in cultured cells.
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Affiliation(s)
- Koudai Kawano
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Aurélien J Doucet
- Institute for Research on Cancer and Aging, Nice (IRCAN), INSERM U1081, CNRS UMR 7284, Université de Nice-Sophia-Antipolis, Faculté de Médecine, 06107 Nice Cedex 2, France
| | - Mikinori Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Ryusho Kariya
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Flavia Marzetta
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Misao Kuroki
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Sayaka Sukegawa
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0460, USA.,Clinical Research Center, Nagoya Medical Center, Nagoya 460-0001, Japan
| | - Seiji Okada
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
| | - Klaus Strebel
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-0460, USA
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Yasuo Ariumi
- Center for AIDS Research, Kumamoto University, Kumamoto 860-0811, Japan
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4
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Philippe C, Vargas-Landin DB, Doucet AJ, van Essen D, Vera-Otarola J, Kuciak M, Corbin A, Nigumann P, Cristofari G. Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. eLife 2016; 5. [PMID: 27016617 PMCID: PMC4866827 DOI: 10.7554/elife.13926] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/25/2016] [Indexed: 12/26/2022] Open
Abstract
LINE-1 (L1) retrotransposons represent approximately one sixth of the human genome, but only the human-specific L1HS-Ta subfamily acts as an endogenous mutagen in modern humans, reshaping both somatic and germline genomes. Due to their high levels of sequence identity and the existence of many polymorphic insertions absent from the reference genome, the transcriptional activation of individual genomic L1HS-Ta copies remains poorly understood. Here we comprehensively mapped fixed and polymorphic L1HS-Ta copies in 12 commonly-used somatic cell lines, and identified transcriptional and epigenetic signatures allowing the unambiguous identification of active L1HS-Ta copies in their genomic context. Strikingly, only a very restricted subset of L1HS-Ta loci - some being polymorphic among individuals - significantly contributes to the bulk of L1 expression, and these loci are differentially regulated among distinct cell lines. Thus, our data support a local model of L1 transcriptional activation in somatic cells, governed by individual-, locus-, and cell-type-specific determinants. DOI:http://dx.doi.org/10.7554/eLife.13926.001 Retrotransposons, also known as jumping genes, have invaded the genomes of most living organisms. These fragments of DNA have the ability to move or copy themselves from one location of a chromosome to another. Depending on where they insert themselves, retrotransposons can modify the sequence of nearby genes, which can alter or even abolish their activity. Although these genetic modifications have contributed significantly to the evolution of different species, retrotransposons can also have detrimental effects; for example, by causing new cases of genetic diseases. Adult human cells have a number of mechanisms that work to keep the activity of retrotransposons at a very low level. However, in many types of cancers retrotransposons escape these defense mechanisms and ‘jump’ actively. This is thought to contribute to the development and spread of cancerous tumors. To understand how jumping genes are mobilized, a fundamental question must be answered: is the high jumping gene activity observed in some cell types a result of activating many copies of the retrotransposons, or only a few of them? This question has been difficult to address because there are more than one hundred copies of retrotransposons that could potentially move in humans, many of which have not even been referenced in the human genome map. Furthermore, each copy is almost identical to another one, making it difficult to discriminate between them. Philippe et al. have now developed an approach that can map where individual retrotransposons are located in the genome of normal and cancerous cells and measure how active these jumping genes are. This revealed that only a very restricted number of them are active in any given cell type. Moreover, different subsets of jumping genes are active in different cell types, and their locations in the genome often do not overlap. Thus, whether jumping genes are activated depends on the cell type and their position in the genome. These results are in contrast to the prevalent view that retrotransposons are activated in a more widespread manner across the genome, at least in cancerous cells. Overall, Philippe et al.’s findings pave the way towards characterizing the chromosome regions in which retrotransposons are frequently activated and understanding how they contribute to cancer and other diseases. DOI:http://dx.doi.org/10.7554/eLife.13926.002
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Affiliation(s)
- Claude Philippe
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
| | - Dulce B Vargas-Landin
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,Ecole Normale Supérieure, Paris, France
| | - Aurélien J Doucet
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
| | - Dominic van Essen
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Jorge Vera-Otarola
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Monika Kuciak
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,Ecole Normale Supérieure de Lyon, Lyon, France
| | | | - Pilvi Nigumann
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Gaël Cristofari
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
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