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Kohlrausch FB, Wang F, McKerrow W, Grivainis M, Fenyo D, Keefe DL. Mapping of long interspersed element-1 (L1) insertions by TIPseq provides information about sub chromosomal genetic variation in human embryos. J Assist Reprod Genet 2024; 41:2257-2269. [PMID: 38951360 DOI: 10.1007/s10815-024-03176-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
PURPOSE Retrotransposons play important roles during early development when they are transiently de-repressed during epigenetic reprogramming. Long interspersed element-1 (L1), the only autonomous retrotransposon in humans, comprises 17% of the human genome. We applied the Single Cell Transposon Insertion Profiling by Sequencing (scTIPseq) to characterize and map L1 insertions in human embryos. METHODS Sixteen cryopreserved, genetically tested, human blastocysts, were accessed from consenting couples undergoing IVF at NYU Langone Fertility Center. Additionally, four trios (father, mother, and embryos) were also evaluated. scTIPseq was applied to map L1 insertions in all samples, using L1 locations reported in the 1000 Genomes as controls. RESULTS Twenty-nine unknown and unique insertions were observed in the sixteen embryos. Most were intergenic; no insertions were located in exons or immediately upstream of genes. The location or number of unknown insertions did not differ between euploid and aneuploid embryos, suggesting they are not merely markers of aneuploidy. Rather, scTIPseq provides novel information about sub-chromosomal structural variation in human embryos. Trio analyses showed a parental origin of all L1 insertions in embryos. CONCLUSION Several studies have measured L1 expression at different stages of development in mice, but this study for the first time reports unknown insertions in human embryos that were inherited from one parent, confirming no de novo L1 insertions occurred in parental germline or during embryogenesis. Since one-third of euploid embryo transfers fail, future studies would be useful for understanding whether these sub-chromosomal genetic variants or de novo L1 insertions affect embryo developmental potential.
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Affiliation(s)
- Fabiana B Kohlrausch
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, 24210-201, Brazil.
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA.
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - Mark Grivainis
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - David Fenyo
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA
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2
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Betancourt AJ, Wei KHC, Huang Y, Lee YCG. Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective. Annu Rev Genomics Hum Genet 2024; 25:1-25. [PMID: 38603565 DOI: 10.1146/annurev-genom-120822-105708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Transposable elements (TEs) are genomic parasites found in nearly all eukaryotes, including humans. This evolutionary success of TEs is due to their replicative activity, involving insertion into new genomic locations. TE activity varies at multiple levels, from between taxa to within individuals. The rapidly accumulating evidence of the influence of TE activity on human health, as well as the rapid growth of new tools to study it, motivated an evaluation of what we know about TE activity thus far. Here, we discuss why TE activity varies, and the consequences of this variation, from an evolutionary perspective. By studying TE activity in nonhuman organisms in the context of evolutionary theories, we can shed light on the factors that affect TE activity. While the consequences of TE activity are usually deleterious, some have lasting evolutionary impacts by conferring benefits on the host or affecting other evolutionary processes.
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Affiliation(s)
- Andrea J Betancourt
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Kevin H-C Wei
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Yuh Chwen G Lee
- Center for Complex Biological Systems, University of California, Irvine, California, USA;
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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3
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Karkas R, Abdullah KSA, Kaizer L, Ürmös Á, Raya M, Tiszlavicz L, Pankotai T, Nagy I, Mátés L, Sükösd F. LINE-1 ORF1p is a Promising Biomarker in Cervical Intraepithelial Neoplasia Degree Assessment. Int J Gynecol Pathol 2024:00004347-990000000-00166. [PMID: 38920137 DOI: 10.1097/pgp.0000000000001035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Cervical intraepithelial neoplasia (CIN) represents a spectrum of preinvasive squamous lesions within the cervical epithelium, whose identification is a diagnostic challenge due to subtle histomorphological differences among its categories. This study explores ORF1p, a nucleic acid-binding protein derived from long interspersed nuclear element-1 (LINE-1), as a potential biomarker for enhancing CIN diagnosis. A comprehensive analysis of 143 cervical specimens, encompassing CIN I (n=20), CIN II (n=46), CIN III (n=14), invasive cancer (n=32), and nondysplastic cases (normal cervical epithelia (n=24) and atrophy (n=7) were conducted. ORF1p, Ki67, and p16 expressions were evaluated using immunohistochemistry. ORF1p immunopositivity was detected in the vast majority [110/112 (98.2%)] of dysplastic and neoplastic (CIN and invasive cancer) specimens, whereas 19/24 (79.2%) of normal cervical specimens lacked ORF1p expression. The observed pattern of ORF1p expression showed a progressively increasing extent and intensity with advancing CIN grades. CIN I exhibited mild ORF1p expression in the lower one or two-thirds of the cervical epithelium [14/16 (87.5%)], whereas CIN II demonstrated moderate to strong ORF1p expression spanning the lower two-thirds [29/46 (63.0%)]. Pronounced transepithelial ORF1p immunopositivity characterized CIN III cases [13/14 (92.8%)] and cervical cancer [30/32 (93.8%)]. These findings propose ORF1p as a valuable indicator even for detecting CIN I, effectively discerning them from normal cervical tissue (p < 0.0001). Our findings underscore the potential of ORF1p as an early diagnostic marker for cervical neoplasia.
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Affiliation(s)
- Réka Karkas
- Laboratory of Cancer Genome Research, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Albert Szent-Györgyi Medical School, Szeged, Hungary
| | - Khaldoon Sadiq Ahmed Abdullah
- Laboratory of Cancer Genome Research, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Albert Szent-Györgyi Medical School, Szeged, Hungary
| | - László Kaizer
- Department of Pathology, Albert Szent-Györgyi Health Centre, University of Szeged, Szeged, Hungary
| | - Ádám Ürmös
- Genome Integrity and DNA Repair Core Group, Hungarian Centre of Excellence for Molecular Medicine, Szeged, Hungary
| | - May Raya
- Laboratory of Cancer Genome Research, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Albert Szent-Györgyi Medical School, Szeged, Hungary
| | - Lilla Tiszlavicz
- Department of Pediatrics and Pediatric Health Centre, Albert Szent-Györgyi Health Centre, University of Szeged, Szeged, Hungary
| | - Tibor Pankotai
- Department of Pathology, Albert Szent-Györgyi Health Centre, University of Szeged, Szeged, Hungary
- Genome Integrity and DNA Repair Core Group, Hungarian Centre of Excellence for Molecular Medicine, Szeged, Hungary
- Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation, University of Szeged, Hungary
| | - István Nagy
- Seqomics Biotechnology Ltd, Mórahalom, Hungary
- Sequencing Platform, Institute of Biochemistry, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Lajos Mátés
- Laboratory of Cancer Genome Research, Institute of Genetics, HUN-REN Biological Research Centre, Szeged, Hungary
| | - Farkas Sükösd
- Department of Pathology, Albert Szent-Györgyi Health Centre, University of Szeged, Szeged, Hungary
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4
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Talley MJ, Longworth MS. Retrotransposons in embryogenesis and neurodevelopment. Biochem Soc Trans 2024; 52:1159-1171. [PMID: 38716891 PMCID: PMC11346457 DOI: 10.1042/bst20230757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/27/2024]
Abstract
Retrotransposable elements (RTEs) are genetic elements that can replicate and insert new copies into different genomic locations. RTEs have long been identified as 'parasitic genes', as their mobilization can cause mutations, DNA damage, and inflammation. Interestingly, high levels of retrotransposon activation are observed in early embryogenesis and neurodevelopment, suggesting that RTEs may possess functional roles during these stages of development. Recent studies demonstrate that RTEs can function as transcriptional regulatory elements through mechanisms such as chromatin organization and noncoding RNAs. It is clear, however, that RTE expression and activity must be restrained at some level during development, since overactivation of RTEs during neurodevelopment is associated with several developmental disorders. Further investigation is needed to understand the importance of RTE expression and activity during neurodevelopment and the balance between RTE-regulated development and RTE-mediated pathogenesis.
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Affiliation(s)
- Mary Jo Talley
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, U.S.A
| | - Michelle S. Longworth
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, U.S.A
- Cleveland Clinic Lerner College of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44195, U.S.A
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5
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Deng X, Liang S, Tang Y, Li Y, Xu R, Luo L, Wang Q, Zhang X, Liu Y. Adverse effects of bisphenol A and its analogues on male fertility: An epigenetic perspective. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123393. [PMID: 38266695 DOI: 10.1016/j.envpol.2024.123393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/11/2023] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
In recent years, there has been growing concern about the adverse effects of endocrine disrupting chemicals (EDCs) on male fertility. Epigenetic modification is critical for male germline development, and has been suggested as a potential mechanism for impaired fertility induced by EDCs. Bisphenol A (BPA) has been recognized as a typical EDC. BPA and its analogues, which are still widely used in various consumer products, have garnered increasing attention due to their reproductive toxicity and the potential to induce epigenetic alteration. This literature review provides an overview of studies investigating the adverse effects of bisphenol exposures on epigenetic modifications and male fertility. Existing studies provide evidence that exposure to bisphenols can lead to adverse effects on male fertility, including declined semen quality, altered reproductive hormone levels, and adverse reproductive outcomes. Epigenetic patterns, including DNA methylation, histone modification, and non-coding RNA expression, can be altered by bisphenol exposures. Transgenerational effects, which influence the fertility and epigenetic patterns of unexposed generations, have also been identified. However, the magnitude and direction of certain outcomes varied across different studies. Investigations into the dynamics of histopathological and epigenetic alterations associated with bisphenol exposures during developmental stages can enhance the understanding of the epigenetic effects of bisphenols, the implication of epigenetic alteration on male fertility, and the health of successive generation.
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Affiliation(s)
- Xinyi Deng
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Sihan Liang
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yuqian Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute, Guangdong Provincial Fertility Hospital, Guangzhou, China
| | - Yingxin Li
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ruijun Xu
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Lu Luo
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qiling Wang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute, Guangdong Provincial Fertility Hospital, Guangzhou, China
| | - Xinzong Zhang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute, Guangdong Provincial Fertility Hospital, Guangzhou, China
| | - Yuewei Liu
- Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China.
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6
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Saha K, Nielsen GI, Nandani R, Kong L, Ye P, An W. YY1 is a transcriptional activator of mouse LINE-1 Tf subfamily. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.03.573552. [PMID: 38260579 PMCID: PMC10802269 DOI: 10.1101/2024.01.03.573552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Long interspersed element type 1 (LINE-1, L1) is an active autonomous transposable element (TE) in the human genome. The first step of L1 replication is transcription, which is controlled by an internal RNA polymerase II promoter in the 5' untranslated region (UTR) of a full-length L1. It has been shown that transcription factor YY1 binds to a conserved sequence motif at the 5' end of the human L1 5'UTR and dictates where transcription initiates but not the level of transcription. Putative YY1-binding motifs have been predicted in the 5'UTRs of two distinct mouse L1 subfamilies, Tf and Gf. Using site-directed mutagenesis, in vitro binding, and gene knockdown assays, we experimentally tested the role of YY1 in mouse L1 transcription. Our results indicate that Tf, but not Gf subfamily, harbors functional YY1-binding sites in its 5'UTR monomers. In contrast to its role in human L1, YY1 functions as a transcriptional activator for the mouse Tf subfamily. Furthermore, YY1-binding motifs are solely responsible for the synergistic interaction between monomers, consistent with a model wherein distant monomers act as enhancers for mouse L1 transcription. The abundance of YY1-binding sites in Tf elements also raise important implications for gene regulation at the genomic level.
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Affiliation(s)
- Karabi Saha
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Grace I. Nielsen
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Raj Nandani
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Lingqi Kong
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Ping Ye
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD 57007, USA
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7
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Zolzaya S, Narumoto A, Katsuyama Y. Genomic variation in neurons. Dev Growth Differ 2024; 66:35-42. [PMID: 37855730 DOI: 10.1111/dgd.12898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/20/2023]
Abstract
Neurons born during the fetal period have extreme longevity and survive until the death of the individual because the human brain has highly limited tissue regeneration. The brain is comprised of an enormous variety of neurons each exhibiting different morphological and physiological characteristics and recent studies have further reported variations in their genome including chromosomal abnormalities, copy number variations, and single nucleotide mutations. During the early stages of brain development, the increasing number of neurons generated at high speeds has been proposed to lead to chromosomal instability. Additionally, mutations in the neuronal genome can occur in the mature brain. This observed genomic mosaicism in the brain can be produced by multiple endogenous and environmental factors and careful analyses of these observed variations in the neuronal genome remain central for our understanding of the genetic basis of neurological disorders.
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Affiliation(s)
- Sunjidmaa Zolzaya
- Division of Neuroanatomy, Department of Anatomy, Shiga University of Medical Science, Otsu, Japan
| | - Ayano Narumoto
- Division of Neuroanatomy, Department of Anatomy, Shiga University of Medical Science, Otsu, Japan
| | - Yu Katsuyama
- Division of Neuroanatomy, Department of Anatomy, Shiga University of Medical Science, Otsu, Japan
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8
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Zhang X, Celic I, Mitchell H, Stuckert S, Vedula L, Han JS. Comprehensive profiling of L1 retrotransposons in mouse. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566638. [PMID: 38014156 PMCID: PMC10680791 DOI: 10.1101/2023.11.13.566638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
L1 elements are retrotransposons currently active in mammals. Although L1s are typically silenced in most normal tissues, elevated L1 expression is associated with a variety of conditions, including cancer, aging, infertility, and neurological disease. These associations have raised interest in the mapping of human endogenous de novo L1 insertions, and a variety of methods have been developed for this purpose. Adapting these methods to mouse genomes would allow us to monitor endogenous in vivo L1 activity in controlled, experimental conditions using mouse disease models. Here we use a modified version of transposon insertion profiling, called nanoTIPseq, to selectively enrich young mouse L1s. By linking this amplification step with nanopore sequencing, we identified >95% annotated L1s from C57BL/6 genomic DNA using only 200,000 sequencing reads. In the process, we discovered 82 unannotated L1 insertions from a single C57BL/6 genome. Most of these unannotated L1s were near repetitive sequence and were not found with short-read TIPseq. We used nanoTIPseq on individual mouse breast cancer cells and were able to identify the annotated and unannotated L1s, as well as new insertions specific to individual cells, providing proof of principle for using nanoTIPseq to interrogate retrotransposition activity at the single cell level in vivo .
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Bona N, Crossan GP. Fanconi anemia DNA crosslink repair factors protect against LINE-1 retrotransposition during mouse development. Nat Struct Mol Biol 2023; 30:1434-1445. [PMID: 37580626 PMCID: PMC10584689 DOI: 10.1038/s41594-023-01067-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 07/13/2023] [Indexed: 08/16/2023]
Abstract
Long interspersed nuclear element 1 (LINE-1) is the only autonomous retrotransposon in humans and new integrations are a major source of genetic variation between individuals. These events can also lead to de novo germline mutations, giving rise to heritable genetic diseases. Recently, a role for DNA repair in regulating these events has been identified. Here we find that Fanconi anemia (FA) DNA crosslink repair factors act in a common pathway to prevent retrotransposition. We purify recombinant SLX4-XPF-ERCC1, the crosslink repair incision complex, and find that it cleaves putative nucleic acid intermediates of retrotransposition. Mice deficient in upstream crosslink repair signaling (FANCA), a downstream component (FANCD2) or the nuclease XPF-ERCC1 show increased LINE-1 retrotransposition in vivo. Organisms limit retrotransposition through transcriptional silencing but this protection is attenuated during early development leaving the zygote vulnerable. We find that during this window of vulnerability, DNA crosslink repair acts as a failsafe to prevent retrotransposition. Together, our results indicate that the FA DNA crosslink repair pathway acts together to protect against mutation by restricting LINE-1 retrotransposition.
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Luqman-Fatah A, Miyoshi T. Human LINE-1 retrotransposons: impacts on the genome and regulation by host factors. Genes Genet Syst 2023; 98:121-154. [PMID: 36436935 DOI: 10.1266/ggs.22-00038] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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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Berteli TS, Wang F, Navarro PA, Kohlrausch FB, Keefe DL. A pilot study of LINE-1 copy number and telomere length with aging in human sperm. J Assist Reprod Genet 2023; 40:1845-1854. [PMID: 37382785 PMCID: PMC10371944 DOI: 10.1007/s10815-023-02857-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/03/2023] [Indexed: 06/30/2023] Open
Abstract
PURPOSE Unlike other cells in the body, in sperm, telomere length (TL) increases with age. TL can regulate nearby genes, and the subtelomeric region is rich in retrotransposons. We hypothesized that age-related telomere lengthening in sperm might suppress Long Interspersed Element 1 (LINE-1/L1), the only competent retrotransposon in humans. METHODS We measured L1 copy number (L1-CN) and sperm telomere length (STL) from young and older men to evaluate the relationship between age, TL and L1-CN. We also evaluated L1-CN and TL in individual sperm to determine whether these variables influence sperm morphology. STL was assayed by Multiplex quantitative polymerase chain reaction method (mmqPCR) and L1-CN by Quantitative polymerase chain reaction (qPCR). RESULTS We found that STL increased, and L1-CN decreased significantly with paternal age. STL in normal single sperm was significantly higher than in abnormal sperm. L1-CN did not differ between normal and abnormal sperm. Furthermore, morphologically normal sperm have longer telomeres than abnormal sperm. CONCLUSIONS Elongation of telomeres in the male germline could repress retrotransposition, which tends to increase with cellular aging. More studies in larger cohorts across a wide age span are needed to confirm our conclusions and explore their biological and clinical significance.
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Affiliation(s)
- Thalita S Berteli
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA.
- Human Reproduction Division, Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil.
| | - Fang Wang
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA
| | - Paula A Navarro
- Human Reproduction Division, Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA
- Human Genetics Laboratory, Fluminense Federal University, Niteroi, RJ, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, Langone Medical Center, New York University, 462, 1st Avenue, New York, NY, 10016, USA
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12
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Berteli TS, Wang F, McKerrow W, Navarro PA, Fenyo D, Boeke JD, Kohlrausch FB, Keefe DL. Transposon insertion profiling by sequencing (TIPseq) identifies novel LINE-1 insertions in human sperm. J Assist Reprod Genet 2023; 40:1835-1843. [PMID: 37310664 PMCID: PMC10371950 DOI: 10.1007/s10815-023-02852-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/01/2023] [Indexed: 06/14/2023] Open
Abstract
PURPOSE Long interspersed nuclear element-1 (LINE-1 or L1) comprises 17% of the human genome. Retrotransposons may perturb gene integrity or alter gene expression by altering regulatory regions in the genome. The germline employs a number of mechanisms, including cytosine methylation, to repress retrotransposon transcription throughout most of life. Demethylation during germ cell and early embryo development de-represses retrotransposons. Intriguingly, de novo genetic variation appearing in sperm has been implicated in a number of disorders in offspring, including autism spectrum disorder, schizophrenia, and bipolar disorder. We hypothesize that human sperm exhibit de novo retrotransposition and employ a new sequencing method, single cell transposon insertion profiling by sequencing (scTIPseq) to map them in small amounts of human sperm. METHODS Cross-sectional case-control study of sperm samples (n=10 men; ages 32-55 years old) from consenting men undergoing IVF at NYU Langone Fertility Center. scTIPseq identified novel LINE-1 insertions in individual sperm and TIPseqHunter, a custom bioinformatics pipeline, compared the architecture of sperm LINE-1 to known LINE-1 insertions from the European database of Human specific LINE-1 (L1Hs) retrotransposon insertions (euL1db). RESULTS scTIPseq identified 17 novel insertions in sperm. New insertions were mainly intergenic or intronic. Only one sample did not exhibit new insertions. The location or number of novel insertions did not differ by paternal age. CONCLUSION This study for the first time reports novel LINE-1 insertions in human sperm, demonstrating the feasibility of scTIPseq, and identifies new contributors to genetic diversity in the human germ line.
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Affiliation(s)
- Thalita S Berteli
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA.
- Human Reproduction Division, Department of Gynecology and Obstetrics, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP, Brazil.
| | - Fang Wang
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Paula A Navarro
- Human Reproduction Division, Department of Gynecology and Obstetrics, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - David Fenyo
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA
- Biology Institute, Department of General Biology, Fluminense Federal University (UFF), Niteroi, RJ, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA
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Singh M, Kondrashkina AM, Widmann TJ, Cortes JL, Bansal V, Wang J, Römer C, Garcia-Canadas M, Garcia-Perez JL, Hurst LD, Izsvák Z. A new human embryonic cell type associated with activity of young transposable elements allows definition of the inner cell mass. PLoS Biol 2023; 21:e3002162. [PMID: 37339119 DOI: 10.1371/journal.pbio.3002162] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 05/12/2023] [Indexed: 06/22/2023] Open
Abstract
There remains much that we do not understand about the earliest stages of human development. On a gross level, there is evidence for apoptosis, but the nature of the affected cell types is unknown. Perhaps most importantly, the inner cell mass (ICM), from which the foetus is derived and hence of interest in reproductive health and regenerative medicine, has proven hard to define. Here, we provide a multi-method analysis of the early human embryo to resolve these issues. Single-cell analysis (on multiple independent datasets), supported by embryo visualisation, uncovers a common previously uncharacterised class of cells lacking commitment markers that segregates after embryonic gene activation (EGA) and shortly after undergo apoptosis. The discovery of this cell type allows us to clearly define their viable ontogenetic sisters, these being the cells of the ICM. While ICM is characterised by the activity of an Old non-transposing endogenous retrovirus (HERVH) that acts to suppress Young transposable elements, the new cell type, by contrast, expresses transpositionally competent Young elements and DNA-damage response genes. As the Young elements are RetroElements and the cells are excluded from the developmental process, we dub these REject cells. With these and ICM being characterised by differential mobile element activities, the human embryo may be a "selection arena" in which one group of cells selectively die, while other less damaged cells persist.
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Affiliation(s)
- Manvendra Singh
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
- Max Planck Institute of Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | | | - Thomas J Widmann
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Jose L Cortes
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Vikas Bansal
- German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Jichang Wang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Christine Römer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Marta Garcia-Canadas
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Jose L Garcia-Perez
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
- Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
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14
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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] [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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15
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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: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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16
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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] [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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17
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De Novo Somatic Mosaicism of CYBB Caused by Intronic LINE-1 Element Insertion Resulting in Chronic Granulomatous Disease. J Clin Immunol 2023; 43:88-100. [PMID: 35997928 DOI: 10.1007/s10875-022-01347-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/10/2022] [Indexed: 01/21/2023]
Abstract
Chronic granulomatosis disease (CGD) is a rare inborn error of immunity, characterized by phagocytic respiratory outbreak dysfunction. Mutations causing CGD occur in CYBB on the X chromosome and in the autosomal genes CYBA, NCF1, NCF2, NCF4, RAC2, and CYBC1. Nevertheless, some patients are clinically diagnosed with CGD, due to abnormal respiratory outbursts, while the pathogenic gene mutation is unidentified. Here, we report a patient with CGD who first presented with Bacillus Calmette-Guérin disease and had recurrent pneumonia. He was diagnosed with CGD by nitro blue tetrazolium and respiratory burst tests. Detailed assessment of neutrophil activity revealed that patient neutrophils were almost entirely nonfunctional. Sanger sequencing detected a 6-kb insertion of a LINE-1 transposable element in the third intron of CYBB, leading to abnormal splicing and pseudoexon insertion, as well as introduction of a premature termination codon, resulting in predicted protein truncation. Clonal analysis demonstrated that the patient had somatic mosaicism, and the phagocytes were almost all variant CYBB, while the mosaicism rate of PBMC was about 65%. Finally, deep RNA sequencing and gp91phox expression analysis confirmed the pathogenicity of the mutation. In conclusion, we demonstrate that insertion of a LINE-1 transposon in a CYBB intron was responsible for CGD in our patient. Intron LINE-1 transposon element insertion should be examined in CGD patients without any known disease-causing gene mutation, in addition to identification of new genes.
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18
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Gerdes P, Lim SM, Ewing AD, Larcombe MR, Chan D, Sanchez-Luque FJ, Walker L, Carleton AL, James C, Knaupp AS, Carreira PE, Nefzger CM, Lister R, Richardson SR, Polo JM, Faulkner GJ. Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells. Nat Commun 2022; 13:7470. [PMID: 36463236 PMCID: PMC9719517 DOI: 10.1038/s41467-022-35180-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 11/22/2022] [Indexed: 12/04/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) can in principle differentiate into any cell of the body, and have revolutionized biomedical research and regenerative medicine. Unlike their human counterparts, mouse iPSCs (miPSCs) are reported to silence transposable elements and prevent transposable element-mediated mutagenesis. Here we apply short-read or Oxford Nanopore Technologies long-read genome sequencing to 38 bulk miPSC lines reprogrammed from 10 parental cell types, and 18 single-cell miPSC clones. While single nucleotide variants and structural variants restricted to miPSCs are rare, we find 83 de novo transposable element insertions, including examples intronic to Brca1 and Dmd. LINE-1 retrotransposons are profoundly hypomethylated in miPSCs, beyond other transposable elements and the genome overall, and harbor alternative protein-coding gene promoters. We show that treatment with the LINE-1 inhibitor lamivudine does not hinder reprogramming and efficiently blocks endogenous retrotransposition, as detected by long-read genome sequencing. These experiments reveal the complete spectrum and potential significance of mutations acquired by miPSCs.
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Affiliation(s)
- Patricia Gerdes
- grid.1003.20000 0000 9320 7537Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Sue Mei Lim
- grid.1002.30000 0004 1936 7857Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800 Australia
| | - Adam D. Ewing
- grid.1003.20000 0000 9320 7537Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Michael R. Larcombe
- grid.1002.30000 0004 1936 7857Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800 Australia
| | - Dorothy Chan
- grid.1003.20000 0000 9320 7537Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Francisco J. Sanchez-Luque
- grid.1003.20000 0000 9320 7537Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia ,grid.418805.00000 0004 0500 8423GENYO. Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS, Granada, 18016 Spain
| | - Lucinda Walker
- grid.1003.20000 0000 9320 7537Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Alexander L. Carleton
- grid.1003.20000 0000 9320 7537Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Cini James
- grid.1003.20000 0000 9320 7537Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Anja S. Knaupp
- grid.1002.30000 0004 1936 7857Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800 Australia
| | - Patricia E. Carreira
- grid.1003.20000 0000 9320 7537Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Christian M. Nefzger
- grid.1002.30000 0004 1936 7857Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800 Australia
| | - Ryan Lister
- grid.1012.20000 0004 1936 7910Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA 6009 Australia ,grid.431595.f0000 0004 0469 0045Harry Perkins Institute of Medical Research, Perth, WA 6009 Australia
| | - Sandra R. Richardson
- grid.1003.20000 0000 9320 7537Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Jose M. Polo
- grid.1002.30000 0004 1936 7857Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800 Australia ,grid.1002.30000 0004 1936 7857Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800 Australia ,grid.1010.00000 0004 1936 7304Adelaide Centre for Epigenetics and The South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5005 Australia
| | - Geoffrey J. Faulkner
- grid.1003.20000 0000 9320 7537Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia ,grid.1003.20000 0000 9320 7537Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
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19
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Li TD, Murano K, Kitano T, Guo Y, Negishi L, Siomi H. TDP-43 safeguards the embryo genome from L1 retrotransposition. SCIENCE ADVANCES 2022; 8:eabq3806. [PMID: 36417507 PMCID: PMC9683724 DOI: 10.1126/sciadv.abq3806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Transposable elements (TEs) are genomic parasites that propagate within the host genome and introduce mutations. Long interspersed nuclear element-1 (LINE-1 or L1) is the major TE class, which occupies nearly 20% of the mouse genome. L1 is highly active in mammalian preimplantation embryos, posing a major threat to genome integrity, but the mechanism of stage-specific protection against L1 retrotransposition is unknown. Here, we show that TAR DNA-binding protein 43 (TDP-43), mutations in which constitute a major risk factor for amyotrophic lateral sclerosis, inhibits L1 retrotransposition in mouse embryonic stem cells (mESCs) and preimplantation embryos. Knockdown of TDP-43 resulted in massive genomic L1 expansion and impaired cell growth in preimplantation embryos and ESCs. Functional analysis demonstrated that TDP-43 interacts with L1 open reading frame 1 protein (L1 ORF1p) to mediate genomic protection, and loss of this interaction led to derepression of L1 retrotransposition. Our results identify TDP-43 as a guardian of the embryonic genome.
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Affiliation(s)
- Ten D. Li
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kensaku Murano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomohiro Kitano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Youjia Guo
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Lumi Negishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
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20
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Mohiuddin M, Kooy RF, Pearson CE. De novo mutations, genetic mosaicism and human disease. Front Genet 2022; 13:983668. [PMID: 36226191 PMCID: PMC9550265 DOI: 10.3389/fgene.2022.983668] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/08/2022] [Indexed: 11/23/2022] Open
Abstract
Mosaicism—the existence of genetically distinct populations of cells in a particular organism—is an important cause of genetic disease. Mosaicism can appear as de novo DNA mutations, epigenetic alterations of DNA, and chromosomal abnormalities. Neurodevelopmental or neuropsychiatric diseases, including autism—often arise by de novo mutations that usually not present in either of the parents. De novo mutations might occur as early as in the parental germline, during embryonic, fetal development, and/or post-natally, through ageing and life. Mutation timing could lead to mutation burden of less than heterozygosity to approaching homozygosity. Developmental timing of somatic mutation attainment will affect the mutation load and distribution throughout the body. In this review, we discuss the timing of de novo mutations, spanning from mutations in the germ lineage (all ages), to post-zygotic, embryonic, fetal, and post-natal events, through aging to death. These factors can determine the tissue specific distribution and load of de novo mutations, which can affect disease. The disease threshold burden of somatic de novo mutations of a particular gene in any tissue will be important to define.
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Affiliation(s)
- Mohiuddin Mohiuddin
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Edegem, Belgium
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- *Correspondence: Mohiuddin Mohiuddin, ; Christopher E. Pearson,
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21
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Billon V, Sanchez-Luque FJ, Rasmussen J, Bodea GO, Gerhardt DJ, Gerdes P, Cheetham SW, Schauer SN, Ajjikuttira P, Meyer TJ, Layman CE, Nevonen KA, Jansz N, Garcia-Perez JL, Richardson SR, Ewing AD, Carbone L, Faulkner GJ. Somatic retrotransposition in the developing rhesus macaque brain. Genome Res 2022; 32:1298-1314. [PMID: 35728967 PMCID: PMC9341517 DOI: 10.1101/gr.276451.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 12/03/2022]
Abstract
The retrotransposon LINE-1 (L1) is central to the recent evolutionary history of the human genome and continues to drive genetic diversity and germline pathogenesis. However, the spatiotemporal extent and biological significance of somatic L1 activity are poorly defined and are virtually unexplored in other primates. From a single L1 lineage active at the divergence of apes and Old World monkeys, successive L1 subfamilies have emerged in each descendant primate germline. As revealed by case studies, the presently active human L1 subfamily can also mobilize during embryonic and brain development in vivo. It is unknown whether nonhuman primate L1s can similarly generate somatic insertions in the brain. Here we applied approximately 40× single-cell whole-genome sequencing (scWGS), as well as retrotransposon capture sequencing (RC-seq), to 20 hippocampal neurons from two rhesus macaques (Macaca mulatta). In one animal, we detected and PCR-validated a somatic L1 insertion that generated target site duplications, carried a short 5' transduction, and was present in ∼7% of hippocampal neurons but absent from cerebellum and nonbrain tissues. The corresponding donor L1 allele was exceptionally mobile in vitro and was embedded in PRDM4, a gene expressed throughout development and in neural stem cells. Nanopore long-read methylome and RNA-seq transcriptome analyses indicated young retrotransposon subfamily activation in the early embryo, followed by repression in adult tissues. These data highlight endogenous macaque L1 retrotransposition potential, provide prototypical evidence of L1-mediated somatic mosaicism in a nonhuman primate, and allude to L1 mobility in the brain over the past 30 million years of human evolution.
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Affiliation(s)
- Victor Billon
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
- Biology Department, École Normale Supérieure Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Francisco J Sanchez-Luque
- GENYO. Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
- Institute of Parasitology and Biomedicine "Lopez-Neyra"-Spanish National Research Council, PTS Granada 18016, Spain
| | - Jay Rasmussen
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Gabriela O Bodea
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Daniel J Gerhardt
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Patricia Gerdes
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Seth W Cheetham
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Stephanie N Schauer
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Prabha Ajjikuttira
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
| | - Thomas J Meyer
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
| | - Cora E Layman
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Kimberly A Nevonen
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Natasha Jansz
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Jose L Garcia-Perez
- GENYO. Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Sandra R Richardson
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
| | - Lucia Carbone
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon 97006, USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, Oregon 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239, USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon 97239, USA
| | - Geoffrey J Faulkner
- Queensland Brain Institute, University of Queensland, St. Lucia, Queensland 4067, Australia
- Mater Research Institute-University of Queensland, Woolloongabba, Queensland 4102, Australia
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22
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Rajurkar M, Parikh AR, Solovyov A, You E, Kulkarni AS, Chu C, Xu KH, Jaicks C, Taylor MS, Wu C, Alexander KA, Good CR, Szabolcs A, Gerstberger S, Tran AV, Xu N, Ebright RY, Van Seventer EE, Vo KD, Tai EC, Lu C, Joseph-Chazan J, Raabe MJ, Nieman LT, Desai N, Arora KS, Ligorio M, Thapar V, Cohen L, Garden PM, Senussi Y, Zheng H, Allen JN, Blaszkowsky LS, Clark JW, Goyal L, Wo JY, Ryan DP, Corcoran RB, Deshpande V, Rivera MN, Aryee MJ, Hong TS, Berger SL, Walt DR, Burns KH, Park PJ, Greenbaum BD, Ting DT. Reverse Transcriptase Inhibition Disrupts Repeat Element Life Cycle in Colorectal Cancer. Cancer Discov 2022; 12:1462-1481. [PMID: 35320348 PMCID: PMC9167735 DOI: 10.1158/2159-8290.cd-21-1117] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/27/2022] [Accepted: 03/08/2022] [Indexed: 11/16/2022]
Abstract
Altered RNA expression of repetitive sequences and retrotransposition are frequently seen in colorectal cancer, implicating a functional importance of repeat activity in cancer progression. We show the nucleoside reverse transcriptase inhibitor 3TC targets activities of these repeat elements in colorectal cancer preclinical models with a preferential effect in p53-mutant cell lines linked with direct binding of p53 to repeat elements. We translate these findings to a human phase II trial of single-agent 3TC treatment in metastatic colorectal cancer with demonstration of clinical benefit in 9 of 32 patients. Analysis of 3TC effects on colorectal cancer tumorspheres demonstrates accumulation of immunogenic RNA:DNA hybrids linked with induction of interferon response genes and DNA damage response. Epigenetic and DNA-damaging agents induce repeat RNAs and have enhanced cytotoxicity with 3TC. These findings identify a vulnerability in colorectal cancer by targeting the viral mimicry of repeat elements. SIGNIFICANCE Colorectal cancers express abundant repeat elements that have a viral-like life cycle that can be therapeutically targeted with nucleoside reverse transcriptase inhibitors (NRTI) commonly used for viral diseases. NRTIs induce DNA damage and interferon response that provide a new anticancer therapeutic strategy. This article is highlighted in the In This Issue feature, p. 1397.
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Affiliation(s)
- Mihir Rajurkar
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Aparna R. Parikh
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Alexander Solovyov
- Computational Oncology, Department of Epidemiology and Biostatistics; Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eunae You
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | | | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
| | - Katherine H. Xu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Christopher Jaicks
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Martin S. Taylor
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Connie Wu
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School; Boston, MA, USA
| | - Katherine A. Alexander
- Epigenetics Institute, Departments of Cell and Developmental Biology, Genetics, and Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Charly R. Good
- Epigenetics Institute, Departments of Cell and Developmental Biology, Genetics, and Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - Annamaria Szabolcs
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Stefanie Gerstberger
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Antuan V. Tran
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
| | - Nova Xu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Richard Y. Ebright
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | | | - Kevin D. Vo
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Eric C. Tai
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Chenyue Lu
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | | | - Michael J. Raabe
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Linda T. Nieman
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Niyati Desai
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Kshitij S. Arora
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Matteo Ligorio
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Vishal Thapar
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
| | - Limor Cohen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School; Boston, MA, USA
| | - Padric M. Garden
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School; Boston, MA, USA
| | - Yasmeen Senussi
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School; Boston, MA, USA
| | - Hui Zheng
- Biostatistics Center, Massachusetts General Hospital, Boston, MA, USA
| | - Jill N. Allen
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Lawrence S. Blaszkowsky
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Jeffrey W. Clark
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Lipika Goyal
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Jennifer Y. Wo
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - David P. Ryan
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Ryan B. Corcoran
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Vikram Deshpande
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Miguel N. Rivera
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Martin J. Aryee
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Theodore S. Hong
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
| | - Shelley L. Berger
- Epigenetics Institute, Departments of Cell and Developmental Biology, Genetics, and Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, USA
| | - David R. Walt
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard Medical School; Boston, MA, USA
| | - Kathleen H. Burns
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School; Boston, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School; Boston, MA, USA
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
| | - Benjamin D. Greenbaum
- Computational Oncology, Department of Epidemiology and 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
| | - David T. Ting
- Mass General Cancer Center, Harvard Medical School; Charlestown, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School; Boston, MA, USA
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23
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Filipenko ML, Boyarskikh UA, Leskov LS, Subbotina KV, Khrapov EA, Sokolov AV, Stilidi IS, Kushlinskii NE. The Level of LINE-1 mRNA Is Increased in Extracellular Circulating Plasma RNA in Patients with Colorectal Cancer. Bull Exp Biol Med 2022; 173:261-264. [DOI: 10.1007/s10517-022-05530-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Indexed: 10/17/2022]
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24
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Okudaira N, Ishizaka Y, Tamamori-Adachi M. Resveratrol blocks retrotransposition of LINE-1 through PPAR α and sirtuin-6. Sci Rep 2022; 12:7772. [PMID: 35546166 PMCID: PMC9095727 DOI: 10.1038/s41598-022-11761-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 04/26/2022] [Indexed: 11/09/2022] Open
Abstract
The retroelement long interspersed element-1 (LINE-1 or L1) comprises about 17% of the human genome. L1 retrotransposition is known to cause genomic instability and related disorders, and resveratrol suppresses this retrotransposition; however, the underlying mechanism is still not elucidated. Recent observations showed that low-molecular-weight compounds might induce L1 retrotransposition through unknown mechanisms. This study aimed to determine polyphenol resveratrol (RV)'s effect on L1-RTP (retrotransposition) in somatic cells. Surprisingly, RV completely blocked L1-RTP. Experiments using the PPARα inhibitor GW6471 or siRNA-mediated PPARα depletion showed that RV-mediated L1-RTP's inhibition depended on peroxisome proliferator-activated receptor α (PPARα). We demonstrated that RV inhibits p38 and cAMP response element binding protein phosphorylation, which are involved in MAPK signaling, and the L1-ORF1 protein's chromatin recruitment. Furthermore, RV increased the expression of sirtuin-6 (SIRT6), which inhibited the activation of L1. The sirtuins family, SIRT1, SIRT6, and SIRT7, but not SIRT3, are involved in RV-mediated inhibition of L1-RTP. Overall, our findings suggest that RV directly modulates PPARα-mediated L1-RTP in somatic cells and that MAPK signaling interacts with SIRT6 closely and may play a role in preventing human diseases such as cancer.
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Affiliation(s)
- Noriyuki Okudaira
- Department of Biochemistry, Teikyo University School of Medicine, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan.
| | - Yukihito Ishizaka
- Department of Intractable Diseases, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Mimi Tamamori-Adachi
- Department of Biochemistry, Teikyo University School of Medicine, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
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25
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Cai J, Chen H, Xie S, Hu Z, Bai Y. Research Progress of Totipotent Stem Cells. Stem Cells Dev 2022; 31:335-345. [PMID: 35502477 DOI: 10.1089/scd.2022.0061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Totipotent stem cells (TSCs), can develop into complete organisms, used in biological fields such as regenerative medicine, mammalian breeding, and conservation. However, cells from early-stage embryos cultured are hard to self-renew and maintain developmental totipotency, which becomes a key factor limiting the research of TSCs. Fortunately, a break-through in the study of induced pluripotent stem cells returning to their totipotent state has been made, resulting in the establishment of multiple TSCs and igniting a new wave of stem cell research. Furthermore, the blastocyst-like structures can be generated by the established TSCs, which lays a foundation for synthetic embryos in vitro. In this review, we summarize the totipotent stage of the early embryos, the establishment and cultivation of TSCs, and the developmental ability exploration of TSCs to promote further research of TSCs.
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Affiliation(s)
- Jianfeng Cai
- Foshan University School of Life Science and Engineering, 118208, Foshan, China, 528000;
| | - Huifang Chen
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
| | - Shiting Xie
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
| | - Zhichao Hu
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
| | - Yinshan Bai
- Foshan University School of Life Science and Engineering, 118208, Foshan, China;
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26
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Domazet-Lošo T. mRNA Vaccines: Why Is the Biology of Retroposition Ignored? Genes (Basel) 2022; 13:719. [PMID: 35627104 PMCID: PMC9141755 DOI: 10.3390/genes13050719] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 02/07/2023] Open
Abstract
The major advantage of mRNA vaccines over more conventional approaches is their potential for rapid development and large-scale deployment in pandemic situations. In the current COVID-19 crisis, two mRNA COVID-19 vaccines have been conditionally approved and broadly applied, while others are still in clinical trials. However, there is no previous experience with the use of mRNA vaccines on a large scale in the general population. This warrants a careful evaluation of mRNA vaccine safety properties by considering all available knowledge about mRNA molecular biology and evolution. Here, I discuss the pervasive claim that mRNA-based vaccines cannot alter genomes. Surprisingly, this notion is widely stated in the mRNA vaccine literature but never supported by referencing any primary scientific papers that would specifically address this question. This discrepancy becomes even more puzzling if one considers previous work on the molecular and evolutionary aspects of retroposition in murine and human populations that clearly documents the frequent integration of mRNA molecules into genomes, including clinical contexts. By performing basic comparisons, I show that the sequence features of mRNA vaccines meet all known requirements for retroposition using L1 elements-the most abundant autonomously active retrotransposons in the human genome. In fact, many factors associated with mRNA vaccines increase the possibility of their L1-mediated retroposition. I conclude that is unfounded to a priori assume that mRNA-based therapeutics do not impact genomes and that the route to genome integration of vaccine mRNAs via endogenous L1 retroelements is easily conceivable. This implies that we urgently need experimental studies that would rigorously test for the potential retroposition of vaccine mRNAs. At present, the insertional mutagenesis safety of mRNA-based vaccines should be considered unresolved.
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Affiliation(s)
- Tomislav Domazet-Lošo
- Laboratory of Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, HR-10000 Zagreb, Croatia;
- School of Medicine, Catholic University of Croatia, Ilica 242, HR-10000 Zagreb, Croatia
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27
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Zhou S, Sakashita A, Yuan S, Namekawa SH. Retrotransposons in the Mammalian Male Germline. Sex Dev 2022:1-19. [PMID: 35231923 DOI: 10.1159/000520683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/25/2021] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons are a subset of DNA sequences that constitute a large part of the mammalian genome. They can translocate autonomously or non-autonomously, potentially jeopardizing the heritable germline genome. Retrotransposons coevolved with the host genome, and the germline is the prominent battlefield between retrotransposons and the host genome to maximize their mutual fitness. Host genomes have developed various mechanisms to suppress and control retrotransposons, including DNA methylation, histone modifications, and Piwi-interacting RNA (piRNA), for their own benefit. Thus, rapidly evolved retrotransposons often acquire positive functions, including gene regulation within the germline, conferring reproductive fitness in a species over the course of evolution. The male germline serves as an ideal model to examine the regulation and evolution of retrotransposons, resulting in genomic co-evolution with the host genome. In this review, we summarize and discuss the regulatory mechanisms of retrotransposons, stage-by-stage, during male germ cell development, with a particular focus on mice as an extensively studied mammalian model, highlighting suppression mechanisms and emerging functions of retrotransposons in the male germline.
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Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
| | - Satoshi H Namekawa
- Department of Microbiology and Molecular Genetics, University of California, Davis, California, USA
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28
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McKerrow W, Wang X, Mendez-Dorantes C, Mita P, Cao S, Grivainis M, Ding L, LaCava J, Burns KH, Boeke JD, Fenyö D. LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint. Proc Natl Acad Sci U S A 2022; 119:e2115999119. [PMID: 35169076 PMCID: PMC8872788 DOI: 10.1073/pnas.2115999119] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
Retrotransposons are genomic DNA sequences that copy themselves to new genomic locations via RNA intermediates; LINE-1 is the only active and autonomous retrotransposon in the human genome. The mobility of LINE-1 is largely repressed in somatic tissues but is derepressed in many cancers, where LINE-1 retrotransposition is correlated with p53 mutation and copy number alteration (CNA). In cell lines, inducing LINE-1 expression can cause double-strand breaks (DSBs) and replication stress. Reanalyzing multiomic data from breast, ovarian, endometrial, and colon cancers, we confirmed correlations between LINE-1 expression, p53 mutation status, and CNA. We observed a consistent correlation between LINE-1 expression and the abundance of DNA replication complex components, indicating that LINE-1 may also induce replication stress in human tumors. In endometrial cancer, high-quality phosphoproteomic data allowed us to identify the DSB-induced ATM-MRN-SMC S phase checkpoint pathway as the primary DNA damage response (DDR) pathway associated with LINE-1 expression. Induction of LINE-1 expression in an in vitro model led to increased phosphorylation of MRN complex member RAD50, suggesting that LINE-1 directly activates this pathway.
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Affiliation(s)
- Wilson McKerrow
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Xuya Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Carlos Mendez-Dorantes
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Pathology, Harvard Medical School, Boston, MA 02115
| | - Paolo Mita
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Song Cao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108
| | - Mark Grivainis
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
| | - Kathleen H Burns
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Pathology, Harvard Medical School, Boston, MA 02115
| | - Jef D Boeke
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016;
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
- Department of Biomedical Engineering, Tandon School of Engineering, Brooklyn, NY11201
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016;
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016
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29
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Transposable Element Dynamics and Regulation during Zygotic Genome Activation in Mammalian Embryos and Embryonic Stem Cell Model Systems. Stem Cells Int 2021; 2021:1624669. [PMID: 34691189 PMCID: PMC8536462 DOI: 10.1155/2021/1624669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic sequences capable of duplicating and reintegrating at new regions within the genome. A growing body of evidence has demonstrated that these elements play important roles in host genome evolution, despite being traditionally viewed as parasitic elements. To prevent ectopic activation of TE transposition and transcription, they are epigenetically silenced in most somatic tissues. Intriguingly, a specific class of TEs-retrotransposons-is transiently expressed at discrete phases during mammalian development and has been linked to the establishment of totipotency during zygotic genome activation (ZGA). While mechanisms controlling TE regulation in somatic tissues have been extensively studied, the significance underlying the unique transcriptional reactivation of retrotransposons during ZGA is only beginning to be uncovered. In this review, we summarize the expression dynamics of key retrotransposons during ZGA, focusing on findings from in vivo totipotent embryos and in vitro totipotent-like embryonic stem cells (ESCs). We then dissect the functions of retrotransposons and discuss how their transcriptional activities are finetuned during early stages of mammalian development.
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30
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Wang F, Chamani IJ, Luo D, Chan K, Navarro PA, Keefe DL. Inhibition of LINE-1 retrotransposition represses telomere reprogramming during mouse 2-cell embryo development. J Assist Reprod Genet 2021; 38:3145-3153. [PMID: 34618297 DOI: 10.1007/s10815-021-02331-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/23/2021] [Indexed: 12/22/2022] Open
Abstract
PURPOSE To investigate whether inhibition of LINE-1 affects telomere reprogramming during 2-cell embryo development. METHODS Mouse zygotes were cultured with or without 1 µM azidothymidine (AZT) for up to 15 h (early 2-cell, G1/S) or 24 h (late 2-cell, S/G2). Gene expression and DNA copy number were determined by RT-qPCR and qPCR respectively. Immunostaining and telomeric PNA-FISH were performed for co-localization between telomeres and ZSCAN4 or LINE-1-Orf1p. RESULTS LINE-1 copy number was remarkably reduced in later 2-cell embryos by exposure to 1 µM AZT, and telomere lengths in late 2-cell embryos with AZT were significantly shorter compared to control embryos (P = 0.0002). Additionally, in the absence of LINE-1 inhibition, Dux, Zscan4, and LINE-1 were highly transcribed in early 2-cell embryos, as compared to late 2-cell embryos (P < 0.0001), suggesting that these 2-cell genes are activated at the early 2-cell stage. However, in early 2-cell embryos with AZT treatment, mRNA levels of Dux, Zscan4, and LINE-1 were significantly decreased. Furthermore, both Zscan4 and LINE-1 encoded proteins localized to telomere regions in 2-cell embryos, but this co-localization was dramatically reduced after AZT treatment (P < 0.001). CONCLUSIONS Upon inhibition of LINE-1 retrotransposition in mouse 2-cell embryos, Dux, Zscan4, and LINE-1 were significantly downregulated, and telomere elongation was blocked. ZSCAN4 foci and their co-localization with telomeres were also significantly decreased, indicating that ZSCAN4 is an essential component of the telomere reprogramming that occurs in mice at the 2-cell stage. Our findings also suggest that LINE-1 may directly contribute to telomere reprogramming in addition to regulating gene expression.
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Affiliation(s)
- Fang Wang
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY, 10016, USA.
| | - Isaac J Chamani
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Danxia Luo
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Kasey Chan
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY, 10016, USA
| | - Paula Andrea Navarro
- Human Reproduction Division, Department of Gynecology and Obstetrics, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirão Preto, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University Grossman School of Medicine, New York, NY, 10016, USA
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31
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Factors Regulating the Activity of LINE1 Retrotransposons. Genes (Basel) 2021; 12:genes12101562. [PMID: 34680956 PMCID: PMC8535693 DOI: 10.3390/genes12101562] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/15/2022] Open
Abstract
LINE-1 (L1) is a class of autonomous mobile genetic elements that form somatic mosaicisms in various tissues of the organism. The activity of L1 retrotransposons is strictly controlled by many factors in somatic and germ cells at all stages of ontogenesis. Alteration of L1 activity was noted in a number of diseases: in neuropsychiatric and autoimmune diseases, as well as in various forms of cancer. Altered activity of L1 retrotransposons for some pathologies is associated with epigenetic changes and defects in the genes involved in their repression. This review discusses the molecular genetic mechanisms of the retrotransposition and regulation of the activity of L1 elements. The contribution of various factors controlling the expression and distribution of L1 elements in the genome occurs at all stages of the retrotransposition. The regulation of L1 elements at the transcriptional, post-transcriptional and integration into the genome stages is described in detail. Finally, this review also focuses on the evolutionary aspects of L1 accumulation and their interplay with the host regulation system.
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Kitsou C, Lazaros L, Papoudou-Bai A, Sakaloglou P, Mastora E, Lykovardakis T, Giaka K, Vartholomatos G, Bouba I, Markoula S, Batistatou A, Georgiou I. Reverse Transcriptase Affects Gametogenesis and Preimplantation Development in Mouse. In Vivo 2021; 34:2269-2276. [PMID: 32871749 DOI: 10.21873/invivo.12037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM The expression of reverse transcriptase (RT) in ovaries, testes, gametes and embryos highlights its critical role in cell growth and differentiation. We sought to investigate the effects of the potent RT inhibitor lamivudine in gametogenesis and mouse embryo preimplantation development. MATERIALS AND METHODS Male and female FVB/N mice were treated with the reverse transcriptase inhibitor Lamivudine for seven consecutive weeks. Following treatment, mouse sperm parameters, testicular and ovarian morphology as well as post-IVF embryo development were evaluated. RESULTS Lamivudine impaired the sperm parameters and the testicular structure in male mice, the number of primordial germ cells and primary oocytes in ovaries of female mice, and the embryos' morphology and development up to the blastocyst stage during in vitro culture. CONCLUSION The administration of lamivudine affected the processes of spermatogenesis and oogenesis as well as the in vitro preimplantation development of mouse embryos.
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Affiliation(s)
- Chrysoula Kitsou
- Laboratory of Medical Genetics of Human Reproduction, Medical School, Ioannina University, Ioannina, Greece
| | - Leandros Lazaros
- Laboratory of Medical Genetics of Human Reproduction, Medical School, Ioannina University, Ioannina, Greece.,Genesis Genoma Lab, Genetic Diagnosis-Clinical Genetics-Research, Athens, Greece
| | | | - Prodromos Sakaloglou
- Laboratory of Medical Genetics of Human Reproduction, Medical School, Ioannina University, Ioannina, Greece
| | - Eirini Mastora
- Laboratory of Medical Genetics of Human Reproduction, Medical School, Ioannina University, Ioannina, Greece
| | - Theodoros Lykovardakis
- Laboratory of Medical Genetics of Human Reproduction, Medical School, Ioannina University, Ioannina, Greece
| | - Katerina Giaka
- Laboratory of Medical Genetics of Human Reproduction, Medical School, Ioannina University, Ioannina, Greece
| | - Georgios Vartholomatos
- Laboratory of Hematology, Molecular Biology Unit, Ioannina University Hospital, Ioannina, Greece
| | - Ioanna Bouba
- Laboratory of Medical Genetics of Human Reproduction, Medical School, Ioannina University, Ioannina, Greece
| | - Sofia Markoula
- Department of Neurology, Ioannina University Hospital, Ioannina, Greece
| | - Anna Batistatou
- Department of Pathology, Ioannina University Hospital, Ioannina, Greece
| | - Ioannis Georgiou
- Laboratory of Medical Genetics of Human Reproduction, Medical School, Ioannina University, Ioannina, Greece
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Abstract
Transposable elements (TEs) are mobile sequences that engender widespread mutations and thus are a major hazard that must be silenced. The most abundant active class of TEs in mammalian genomes is long interspersed element class 1 (LINE1). Here, we report that LINE1 transposition is suppressed in the male germline by transcription factors encoded by a rapidly evolving X-linked homeobox gene cluster. LINE1 transposition is repressed by many members of this RHOX transcription factor family, including those with different patterns of expression during spermatogenesis. One family member-RHOX10-suppresses LINE1 transposition during fetal development in vivo when the germline would otherwise be susceptible to LINE1 activation because of epigenetic reprogramming. We provide evidence that RHOX10 suppresses LINE transposition by inducing Piwil2, which encodes a key component in the Piwi-interacting RNA pathway that protects against TEs. The ability of RHOX transcription factors to suppress LINE1 is conserved in humans but is lost in RHOXF2 mutants from several infertile human patients, raising the possibility that loss of RHOXF2 causes human infertility by allowing uncontrolled LINE1 expression in the germline. Together, our results support a model in which the Rhox gene cluster is in an evolutionary arms race with TEs, resulting in expansion of the Rhox gene cluster to suppress TEs in different biological contexts.
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34
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Chen P, Kotov AA, Godneeva BK, Bazylev SS, Olenina LV, Aravin AA. piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline. Genes Dev 2021; 35:914-935. [PMID: 33985970 PMCID: PMC8168559 DOI: 10.1101/gad.345041.120] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 04/08/2021] [Indexed: 12/19/2022]
Abstract
Small noncoding piRNAs act as sequence-specific guides to repress complementary targets in Metazoa. Prior studies in Drosophila ovaries have demonstrated the function of the piRNA pathway in transposon silencing and therefore genome defense. However, the ability of the piRNA program to respond to different transposon landscapes and the role of piRNAs in regulating host gene expression remain poorly understood. Here, we comprehensively analyzed piRNA expression and defined the repertoire of their targets in Drosophila melanogaster testes. Comparison of piRNA programs between sexes revealed sexual dimorphism in piRNA programs that parallel sex-specific transposon expression. Using a novel bioinformatic pipeline, we identified new piRNA clusters and established complex satellites as dual-strand piRNA clusters. While sharing most piRNA clusters, the two sexes employ them differentially to combat the sex-specific transposon landscape. We found two piRNA clusters that produce piRNAs antisense to four host genes in testis, including CG12717/pirate, a SUMO protease gene. piRNAs encoded on the Y chromosome silence pirate, but not its paralog, to exert sex- and paralog-specific gene regulation. Interestingly, pirate is targeted by endogenous siRNAs in a sibling species, Drosophila mauritiana, suggesting distinct but related silencing strategies invented in recent evolution to regulate a conserved protein-coding gene.
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Affiliation(s)
- Peiwei Chen
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Alexei A Kotov
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow 123182, Russia
| | - Baira K Godneeva
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Sergei S Bazylev
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow 123182, Russia
| | - Ludmila V Olenina
- Institute of Molecular Genetics of National Research Center "Kurchatov Institute," Moscow 123182, Russia
| | - Alexei A Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
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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] [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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36
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Chen D, Cremona MA, Qi Z, Mitra RD, Chiaromonte F, Makova KD. Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. Mol Biol Evol 2021; 37:3576-3600. [PMID: 32722770 DOI: 10.1093/molbev/msaa194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. To fill this gap, we investigated three genome-wide data sets of L1s that integrated at different evolutionary times: 17,037 de novo L1s (from an L1 insertion cell-line experiment conducted in-house), and 1,212 polymorphic and 1,205 human-specific L1s (from public databases). We characterized 49 genomic features-proxying chromatin accessibility, transcriptional activity, replication, recombination, etc.-in the ±50 kb flanks of these elements. These features were contrasted between the three L1 data sets and L1-free regions using state-of-the-art Functional Data Analysis statistical methods, which treat high-resolution data as mathematical functions. Our results indicate that de novo, polymorphic, and human-specific L1s are surrounded by different genomic features acting at specific locations and scales. This led to an integrative model of L1 transposition, according to which L1s preferentially integrate into open-chromatin regions enriched in non-B DNA motifs, whereas they are fixed in regions largely free of purifying selection-depleted of genes and noncoding most conserved elements. Intriguingly, our results suggest that L1 insertions modify local genomic landscape by extending CpG methylation and increasing mononucleotide microsatellite density. Altogether, our findings substantially facilitate understanding of L1 integration and fixation preferences, pave the way for uncovering their role in aging and cancer, and inform their use as mutagenesis tools in genetic studies.
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Affiliation(s)
- Di Chen
- Intercollege Graduate Degree Program in Genetics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University, University Park, PA.,Department of Operations and Decision Systems, Université Laval, Québec, Canada
| | - Zongtai Qi
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Robi D Mitra
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, PA.,EMbeDS, Sant'Anna School of Advanced Studies, Pisa, Italy.,The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA
| | - Kateryna D Makova
- The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
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37
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Yin Y, Liu XZ, He X, Zhou LQ. Exogenous Coronavirus Interacts With Endogenous Retrotransposon in Human Cells. Front Cell Infect Microbiol 2021; 11:609160. [PMID: 33732659 PMCID: PMC7959850 DOI: 10.3389/fcimb.2021.609160] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/18/2021] [Indexed: 01/08/2023] Open
Abstract
There is an increased global outbreak of diseases caused by coronaviruses affecting respiratory tracts of birds and mammals. Recent dangerous coronaviruses are MERS-CoV, SARS-CoV, and SARS-CoV-2, causing respiratory illness and even failure of several organs. However, profound impact of coronavirus on host cells remains elusive. In this study, we analyzed transcriptome of MERS-CoV, SARS-CoV, and SARS-CoV-2 infected human lung-derived cells, and observed that infection of these coronaviruses all induced increase of retrotransposon expression with upregulation of TET genes. Upregulation of retrotransposon was also observed in SARS-CoV-2 infected human intestinal organoids. Retrotransposon upregulation may lead to increased genome instability and enhanced expression of genes with readthrough from retrotransposons. Therefore, people with higher basal level of retrotransposon such as cancer patients and aged people may have increased risk of symptomatic infection. Additionally, we show evidence supporting long-term epigenetic inheritance of retrotransposon upregulation. We also observed chimeric transcripts of retrotransposon and SARS-CoV-2 RNA for potential human genome invasion of viral fragments, with the front and the rear part of SARS-CoV-2 genome being easier to form chimeric RNA. Thus, we suggest that primers and probes for nucleic acid detection should be designed in the middle of virus genome to identify live virus with higher probability. In summary, we propose our hypothesis that coronavirus invades human cells and interacts with retrotransposon, eliciting more severe symptoms in patients with underlying diseases. In the treatment of patients with coronavirus infection, it may be necessary to pay more attention to the potential harm contributed by retrotransposon dysregulation.
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Affiliation(s)
- Ying Yin
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao-zhao Liu
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, China
| | - Li-quan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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38
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Ukadike KC, Mustelin T. Implications of Endogenous Retroelements in the Etiopathogenesis of Systemic Lupus Erythematosus. J Clin Med 2021; 10:856. [PMID: 33669709 PMCID: PMC7922054 DOI: 10.3390/jcm10040856] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. While its etiology remains elusive, current understanding suggests a multifactorial process with contributions by genetic, immunologic, hormonal, and environmental factors. A hypothesis that combines several of these factors proposes that genomic elements, the L1 retrotransposons, are instrumental in SLE pathogenesis. L1 retroelements are transcriptionally activated in SLE and produce two proteins, ORF1p and ORF2p, which are immunogenic and can drive type I interferon (IFN) production by producing DNA species that activate cytosolic DNA sensors. In addition, these two proteins reside in RNA-rich macromolecular assemblies that also contain well-known SLE autoantigens like Ro60. We surmise that cells expressing L1 will exhibit all the hallmarks of cells infected by a virus, resulting in a cellular and humoral immune response similar to those in chronic viral infections. However, unlike exogenous viruses, L1 retroelements cannot be eliminated from the host genome. Hence, dysregulated L1 will cause a chronic, but perhaps episodic, challenge for the immune system. The clinical and immunological features of SLE can be at least partly explained by this model. Here we review the support for, and the gaps in, this hypothesis of SLE and its potential for new diagnostic, prognostic, and therapeutic options in SLE.
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Affiliation(s)
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington School of Medicine, 750 Republican Street, Seattle, WA 98109, USA;
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39
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Wu Y, Dong J, Feng S, Zhao Q, Duan P, Xiong M, Wen Y, Lv C, Wang X, Yuan S. Maternal UHRF1 Is Essential for Transcription Landscapes and Repression of Repetitive Elements During the Maternal-to-Zygotic Transition. Front Cell Dev Biol 2021; 8:610773. [PMID: 33634103 PMCID: PMC7902027 DOI: 10.3389/fcell.2020.610773] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/31/2020] [Indexed: 11/21/2022] Open
Abstract
Maternal factors that modulate maternal-to-zygotic transition (MZT) are essential for the growth from specialized oocytes to totipotent embryos. Despite several studies, the mechanisms regulating epigenetic reprogramming during MZT remain largely elusive. UHRF1 plays a role in maintaining GC methylation in oocytes and early embryos. However, little is known about its role in mouse MZT. Here, we explored the function of maternal UHRF1 in zygotic genome regulation during early embryonic development in mice. We showed that the conditional knockout (cKO) of UHRF1 in either primordial or growing oocytes causes infertility but differentially affects early embryonic development. UHRF1 deficiency in primordial oocytes led to early embryonic developmental arrest at the two-cell stage, accompanied by significant alterations in global DNA and H3K4me3 methylation patterns. In comparison, UHRF1 ablation in growing oocytes significantly reduced developmental competence from two-cell embryos to blastocysts. At the transcriptional level, the absence of maternal UHRF1 led to aberrant transcriptional regulation of the zygotic genome during MZT at the two-cell stage. Furthermore, we observed that retrotransposable elements in UHRF1-deficient oocytes and embryos were not silenced properly; in particular, the LINE-1 and long terminal repeat (LTR) subfamily were activated abnormally. Collectively, the findings of our study reveal that maternal UHRF1 plays a critical role in establishing the correct epigenetic chromatin reprogramming of early embryos, regulating essential genes during MZT, and preserving genome integrity that drives early embryonic development in mice.
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Affiliation(s)
- Yanqing Wu
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Juan Dong
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China.,Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shenglei Feng
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Qiang Zhao
- Central Laboratory, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China
| | - Peng Duan
- Laboratory of Gynecological Oncology and Reproductive Health, Department of Obstetrics and Gynaecology, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, China
| | - Mengneng Xiong
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Yujiao Wen
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Chunyu Lv
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoli Wang
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China
| | - Shuiqiao Yuan
- Tongji Medical College, Institute Reproductive Health, Huazhong University of Science and Technology, Wuhan, China.,Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, China
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40
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Kohlrausch FB, Berteli TS, Wang F, Navarro PA, Keefe DL. Control of LINE-1 Expression Maintains Genome Integrity in Germline and Early Embryo Development. Reprod Sci 2021; 29:328-340. [PMID: 33481218 DOI: 10.1007/s43032-021-00461-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/06/2021] [Indexed: 11/28/2022]
Abstract
Maintenance of genome integrity in the germline and in preimplantation embryos is crucial for mammalian development. Epigenetic remodeling during primordial germ cell (PGC) and preimplantation embryo development may contribute to genomic instability in these cells, since DNA methylation is an important mechanism to silence retrotransposons. Long interspersed elements 1 (LINE-1 or L1) are the most common autonomous retrotransposons in mammals, corresponding to approximately 17% of the human genome. Retrotransposition events are more frequent in germ cells and in early stages of embryo development compared with somatic cells. It has been shown that L1 activation and expression occurs in germline and is essential for preimplantation development. In this review, we focus on the role of L1 retrotransposon in mouse and human germline and early embryo development and discuss the possible relationship between L1 expression and genomic instability during these stages. Although several studies have addressed L1 expression at different stages of development, the developmental consequences of this expression remain poorly understood. Future research is still needed to highlight the relationship between L1 retrotransposition events and genomic instability during germline and early embryo development.
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Affiliation(s)
- Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Thalita S Berteli
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA
| | - Paula A Navarro
- Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.
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Shalini V, Bhaduri U, Ravikkumar AC, Rengarajan A, Satyanarayana RMR. Genome-wide occupancy reveals the localization of H1T2 (H1fnt) to repeat regions and a subset of transcriptionally active chromatin domains in rat spermatids. Epigenetics Chromatin 2021; 14:3. [PMID: 33407810 PMCID: PMC7788777 DOI: 10.1186/s13072-020-00376-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/23/2020] [Indexed: 11/10/2022] Open
Abstract
Background H1T2/H1FNT is a germ cell-specific linker histone variant expressed during spermiogenesis specifically in round and elongating spermatids. Infertile phenotype of homozygous H1T2 mutant male mice revealed the essential function of H1T2 for the DNA condensation and histone-to-protamine replacement in spermiogenesis. However, the mechanism by which H1T2 imparts the inherent polarity within spermatid nucleus including the additional protein partners and the genomic domains occupied by this linker histone are unknown. Results Sequence analysis revealed the presence of Walker motif, SR domains and putative coiled-coil domains in the C-terminal domain of rat H1T2 protein. Genome-wide occupancy analysis using highly specific antibody against the CTD of H1T2 demonstrated the binding of H1T2 to the LINE L1 repeat elements and to a significant percentage of the genic regions (promoter-TSS, exons and introns) of the rat spermatid genome. Immunoprecipitation followed by mass spectrometry analysis revealed the open chromatin architecture of H1T2 occupied chromatin encompassing the H4 acetylation and other histone PTMs characteristic of transcriptionally active chromatin. In addition, the present study has identified the interacting protein partners of H1T2-associated chromatin mainly as nucleo-skeleton components, RNA-binding proteins and chaperones. Conclusions Linker histone H1T2 possesses unique domain architecture which can account for the specific functions associated with chromatin remodeling events facilitating the initiation of histone to transition proteins/protamine transition in the polar apical spermatid genome. Our results directly establish the unique function of H1T2 in nuclear shaping associated with spermiogenesis by mediating the interaction between chromatin and nucleo-skeleton, positioning the epigenetically specialized chromatin domains involved in transcription coupled histone replacement initiation towards the apical pole of round/elongating spermatids.
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Affiliation(s)
- Vasantha Shalini
- From the Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India
| | - Utsa Bhaduri
- From the Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India.,Department of Life Sciences, University of Trieste, Trieste, Italy.,European Union's H2020 TRIM-NET ITN, Marie Sklodowska-Curie Actions (MSCA), Leiden, The Netherlands
| | - Anjhana C Ravikkumar
- From the Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India
| | - Anusha Rengarajan
- From the Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India
| | - Rao M R Satyanarayana
- From the Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore, 560064, India.
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42
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Profile of Haig H. Kazazian Jr. Proc Natl Acad Sci U S A 2020; 117:32185-32188. [DOI: 10.1073/pnas.2023398117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Komkov AY, Urazbakhtin SZ, Saliutina MV, Komech EA, Shelygin YA, Nugmanov GA, Shubin VP, Smirnova AO, Bobrov MY, Tsukanov AS, Snezhkina AV, Kudryavtseva AV, Lebedev YB, Mamedov IZ. SeqURE - a new copy-capture based method for sequencing of unknown Retroposition events. Mob DNA 2020; 11:33. [PMID: 33317630 PMCID: PMC7734759 DOI: 10.1186/s13100-020-00228-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/01/2020] [Indexed: 11/24/2022] Open
Abstract
Background Retroelements (REs) occupy a significant part of all eukaryotic genomes including humans. The majority of retroelements in the human genome are inactive and unable to retrotranspose. Dozens of active copies are repressed in most normal tissues by various cellular mechanisms. These copies can become active in normal germline and brain tissues or in cancer, leading to new retroposition events. The consequences of such events and their role in normal cell functioning and carcinogenesis are not yet fully understood. If new insertions occur in a small portion of cells they can be found only with the use of specific methods based on RE enrichment and high-throughput sequencing. The downside of the high sensitivity of such methods is the presence of various artifacts imitating real insertions, which in many cases cannot be validated due to lack of the initial template DNA. For this reason, adequate assessment of rare (< 1%) subclonal cancer specific RE insertions is complicated. Results Here we describe a new copy-capture technique which we implemented in a method called SeqURE for Sequencing Unknown of Retroposition Events that allows for efficient and reliable identification of new genomic RE insertions. The method is based on the capture of copies of target molecules (copy-capture), selective amplification and sequencing of genomic regions adjacent to active RE insertions from both sides. Importantly, the template genomic DNA remains intact and can be used for validation experiments. In addition, we applied a novel system for testing method sensitivity and precisely showed the ability of the developed method to reliably detect insertions present in 1 out of 100 cells and a substantial portion of insertions present in 1 out of 1000 cells. Using advantages of the method we showed the absence of somatic Alu insertions in colorectal cancer samples bearing tumor-specific L1HS insertions. Conclusions This study presents the first description and implementation of the copy-capture technique and provides the first methodological basis for the quantitative assessment of RE insertions present in a small portion of cells. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-020-00228-6.
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Affiliation(s)
- Alexander Y Komkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia. .,Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.
| | | | - Maria V Saliutina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Yuri A Shelygin
- Ryzhikh National Medical Research Centre for Coloproctology of the Ministry of Health of Russia, Moscow, Russia
| | - Gaiaz A Nugmanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Vitaliy P Shubin
- Ryzhikh National Medical Research Centre for Coloproctology of the Ministry of Health of Russia, Moscow, Russia
| | | | - Mikhail Y Bobrov
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Alexey S Tsukanov
- Ryzhikh National Medical Research Centre for Coloproctology of the Ministry of Health of Russia, Moscow, Russia
| | - Anastasia V Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia. .,Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia. .,V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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Laureau R, Dyatel A, Dursuk G, Brown S, Adeoye H, Yue JX, De Chiara M, Harris A, Ünal E, Liti G, Adams IR, Berchowitz LE. Meiotic Cells Counteract Programmed Retrotransposon Activation via RNA-Binding Translational Repressor Assemblies. Dev Cell 2020; 56:22-35.e7. [PMID: 33278343 DOI: 10.1016/j.devcel.2020.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/25/2020] [Accepted: 11/06/2020] [Indexed: 12/14/2022]
Abstract
Retrotransposon proliferation poses a threat to germline integrity. While retrotransposons must be activated in developing germ cells in order to survive and propagate, how they are selectively activated in the context of meiosis is unclear. We demonstrate that the transcriptional activation of Ty3/Gypsy retrotransposons and host defense are controlled by master meiotic regulators. We show that budding yeast Ty3/Gypsy co-opts binding sites of the essential meiotic transcription factor Ndt80 upstream of the integration site, thereby tightly linking its transcriptional activation to meiotic progression. We also elucidate how yeast cells thwart Ty3/Gypsy proliferation by blocking translation of the retrotransposon mRNA using amyloid-like assemblies of the RNA-binding protein Rim4. In mammals, several inactive Ty3/Gypsy elements are undergoing domestication. We show that mammals utilize equivalent master meiotic regulators (Stra8, Mybl1, Dazl) to regulate Ty3/Gypsy-derived genes in developing gametes. Our findings inform how genes that are evolving from retrotransposons can build upon existing regulatory networks during domestication.
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Affiliation(s)
- Raphaelle Laureau
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Annie Dyatel
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gizem Dursuk
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samantha Brown
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hannah Adeoye
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jia-Xing Yue
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice 06107, France
| | | | - Anthony Harris
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Elçin Ünal
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Gianni Liti
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Nice 06107, France
| | - Ian R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Luke E Berchowitz
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Irving Medical Center, New York, NY 10032, USA.
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Ahmadi A, De Toma I, Vilor-Tejedor N, Eftekhariyan Ghamsari MR, Sadeghi I. Transposable elements in brain health and disease. Ageing Res Rev 2020; 64:101153. [PMID: 32977057 DOI: 10.1016/j.arr.2020.101153] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/22/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022]
Abstract
Transposable elements (TEs) occupy a large fraction of the human genome but only a small proportion of these elements are still active today. Recent works have suggested that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in behavior and cognition, and contribute to vulnerability to disease. As active TEs could induce genetic diversity and mutagenesis, their influences on human brain development and diseases are of great interest. In this review, we will focus on the active TEs in the human genome and discuss in detail their impacts on human brain development. Furthermore, the association between TEs and brain-related diseases is discussed.
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46
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Mustelin T, Ukadike KC. How Retroviruses and Retrotransposons in Our Genome May Contribute to Autoimmunity in Rheumatological Conditions. Front Immunol 2020; 11:593891. [PMID: 33281822 PMCID: PMC7691656 DOI: 10.3389/fimmu.2020.593891] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/19/2020] [Indexed: 12/14/2022] Open
Abstract
More than 200 human disorders include various manifestations of autoimmunity. The molecular events that lead to these diseases are still incompletely understood and their causes remain largely unknown. Numerous potential triggers of autoimmunity have been proposed over the years, but very few of them have been conclusively confirmed or firmly refuted. Viruses have topped the lists of suspects for decades, and it seems that many viruses, including those of the Herpesviridae family, indeed can influence disease initiation and/or promote exacerbations by a number of mechanisms that include prolonged anti-viral immunity, immune subverting factors, and mechanisms, and perhaps “molecular mimicry”. However, no specific virus has yet been established as being truly causative. Here, we discuss a different, but perhaps mechanistically related possibility, namely that retrotransposons or retroviruses that infected us in the past and left a lasting copy of themselves in our genome still can provoke an escalating immune response that leads to autoimmune disease. Many of these loci still encode for retroviral proteins that have retained some, or all, of their original functions. Importantly, these endogenous proviruses cannot be eliminated by the immune system the way it can eliminate exogenous viruses. Hence, if not properly controlled, they may drive a frustrated and escalating chronic, or episodic, immune response to the point of a frank autoimmune disorder. Here, we discuss the evidence and the proposed mechanisms, and assess the therapeutic options that emerge from the current understanding of this field.
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Affiliation(s)
- Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Kennedy C Ukadike
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
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Ewing AD, Smits N, Sanchez-Luque FJ, Faivre J, Brennan PM, Richardson SR, Cheetham SW, Faulkner GJ. Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling. Mol Cell 2020; 80:915-928.e5. [PMID: 33186547 DOI: 10.1016/j.molcel.2020.10.024] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape of mobile human TEs has to date proven largely inaccessible. Here, we apply new computational tools and long-read nanopore sequencing to directly infer CpG methylation of novel and extant TE insertions in hippocampus, heart, and liver, as well as paired tumor and non-tumor liver. As opposed to an indiscriminate stochastic process, we find pronounced demethylation of young long interspersed element 1 (LINE-1) retrotransposons in cancer, often distinct to the adjacent genome and other TEs. SINE-VNTR-Alu (SVA) retrotransposons, including their internal tandem repeat-associated CpG island, are near-universally methylated. We encounter allele-specific TE methylation and demethylation of aberrantly expressed young LINE-1s in normal tissues. Finally, we recover the complete sequences of tumor-specific LINE-1 insertions and their retrotransposition hallmarks, demonstrating how long-read sequencing can simultaneously survey the epigenome and detect somatic TE mobilization.
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Affiliation(s)
- Adam D Ewing
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Nathan Smits
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Francisco J Sanchez-Luque
- GENYO, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Jamila Faivre
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
| | - Paul M Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, Edinburgh EH16 4SB, UK
| | - Sandra R Richardson
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Seth W Cheetham
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, St. Lucia, QLD 4067, Australia.
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Potabattula R, Zacchini F, Ptak GE, Dittrich M, Müller T, El Hajj N, Hahn T, Drummer C, Behr R, Lucas‐Hahn A, Niemann H, Schorsch M, Haaf T. Increasing methylation of sperm rDNA and other repetitive elements in the aging male mammalian germline. Aging Cell 2020; 19:e13181. [PMID: 32608562 PMCID: PMC7431825 DOI: 10.1111/acel.13181] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/06/2020] [Accepted: 06/01/2020] [Indexed: 01/08/2023] Open
Abstract
In somatic cells/tissues, methylation of ribosomal DNA (rDNA) increases with age and age‐related pathologies, which has a direct impact on the regulation of nucleolar activity and cellular metabolism. Here, we used bisulfite pyrosequencing and show that methylation of the rDNA transcription unit including upstream control element (UCE), core promoter, 18S rDNA, and 28S rDNA in human sperm also significantly increases with donor's age. This positive correlation between sperm rDNA methylation and biological age is evolutionarily conserved among mammals with widely different life spans such as humans, marmoset, bovine, and mouse. Similar to the tandemly repeated rDNA, methylation of human α‐satellite and interspersed LINE1 repeats, marmoset α‐satellite, bovine alpha‐ and testis satellite I, mouse minor and major satellite, and LINE1‐T repeats increases in the aging male germline, probably related to their sperm histone packaging. Deep bisulfite sequencing of single rDNA molecules in human sperm revealed that methylation does not only depend on donor's age, but also depend on the region and sequence context (A vs. G alleles). Both average rDNA methylation of all analyzed DNA molecules and the number of fully (>50%) methylated alleles, which are thought to be epigenetically silenced, increase with donor's age. All analyzed CpGs in the sperm rDNA transcription unit show comparable age‐related methylation changes. Unlike other epigenetic aging markers, the rDNA clock appears to operate in similar ways in germline and soma in different mammalian species. We propose that sperm rDNA methylation, directly or indirectly, influences nucleolar formation and developmental potential in the early embryo.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Federica Zacchini
- Malopolska Centre of Biotechnology Jagiellonian University Krakow Poland
- Percuros B.V. Leiden The Netherlands
| | - Grazyna Ewa Ptak
- Malopolska Centre of Biotechnology Jagiellonian University Krakow Poland
| | - Marcus Dittrich
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
- Department of Bioinformatics Julius Maximilians University Würzburg Germany
| | - Tobias Müller
- Department of Bioinformatics Julius Maximilians University Würzburg Germany
| | - Nady El Hajj
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
- College of Health and Life Sciences Hamad Bin Khalifa University Doha Qatar
| | | | - Charis Drummer
- Platform Degenerative Diseases Leibniz Institute for Primate Research Göttingen Germany
- German Center for Cardiovascular Research, Partner Site Göttingen Göttingen Germany
| | - Rüdiger Behr
- Platform Degenerative Diseases Leibniz Institute for Primate Research Göttingen Germany
- German Center for Cardiovascular Research, Partner Site Göttingen Göttingen Germany
| | - Andrea Lucas‐Hahn
- Institute of Farm Animal Genetics Friedrich‐Loeffler‐Institute Mariensee/Neustadt Germany
| | - Heiner Niemann
- Clinic for Gastroenterology, Hepatology and Endocrinology Medical University Hannover Hannover Germany
| | | | - Thomas Haaf
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
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Abstract
Multicellular eukaryotic genomes show enormous differences in size. A substantial part of this variation is due to the presence of transposable elements (TEs). They contribute significantly to a cell's mass of DNA and have the potential to become involved in host gene control. We argue that the suppression of their activities by methylation of the C-phosphate-G (CpG) dinucleotide in DNA is essential for their long-term accommodation in the host genome and, therefore, to its expansion. An inevitable consequence of cytosine methylation is an increase in C-to-T transition mutations via deamination, which causes CpG loss. Cytosine deamination is often needed for TEs to take on regulatory functions in the host genome. Our study of the whole-genome sequences of 53 organisms showed a positive correlation between the size of a genome and the percentage of TEs it contains, as well as a negative correlation between size and the CpG observed/expected (O/E) ratio in both TEs and the host DNA. TEs are seldom found at promoters and transcription start sites, but they are found more at enhancers, particularly after they have accumulated C-to-T and other mutations. Therefore, the methylation of TE DNA allows for genome expansion and also leads to new opportunities for gene control by TE-based regulatory sites.
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50
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Dppa2 and Dppa4 counteract de novo methylation to establish a permissive epigenome for development. Nat Struct Mol Biol 2020; 27:706-716. [DOI: 10.1038/s41594-020-0445-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022]
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