1
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Osakabe A, Takizawa Y, Horikoshi N, Hatazawa S, Negishi L, Sato S, Berger F, Kakutani T, Kurumizaka H. Molecular and structural basis of the chromatin remodeling activity by Arabidopsis DDM1. Nat Commun 2024; 15:5187. [PMID: 38992002 PMCID: PMC11239853 DOI: 10.1038/s41467-024-49465-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 06/05/2024] [Indexed: 07/13/2024] Open
Abstract
The histone H2A variant H2A.W occupies transposons and thus prevents access to them in Arabidopsis thaliana. H2A.W is deposited by the chromatin remodeler DDM1, which also promotes the accessibility of chromatin writers to heterochromatin by an unknown mechanism. To shed light on this question, we solve the cryo-EM structures of nucleosomes containing H2A and H2A.W, and the DDM1-H2A.W nucleosome complex. These structures show that the DNA end flexibility of the H2A nucleosome is higher than that of the H2A.W nucleosome. In the DDM1-H2A.W nucleosome complex, DDM1 binds to the N-terminal tail of H4 and the nucleosomal DNA and increases the DNA end flexibility of H2A.W nucleosomes. Based on these biochemical and structural results, we propose that DDM1 counters the low accessibility caused by nucleosomes containing H2A.W to enable the maintenance of repressive epigenetic marks on transposons and prevent their activity.
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Affiliation(s)
- Akihisa Osakabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Naoki Horikoshi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Suguru Hatazawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Lumi Negishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Shoko Sato
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Tetsuji Kakutani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Hitoshi Kurumizaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.
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2
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Moran EA, Salas-Briceno K, Zhao W, Enya T, Aguilera AN, Acosta I, Alonzo F, Kiani D, Behnsen J, Alvarez C, Keane TM, Adams DJ, Lilue J, Ross SR. IFI207, a young and fast-evolving protein, controls retroviral replication via the STING pathway. mBio 2024:e0120924. [PMID: 38860764 DOI: 10.1128/mbio.01209-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 05/03/2024] [Indexed: 06/12/2024] Open
Abstract
Mammalian AIM-2-like receptor (ALR) proteins bind nucleic acids and initiate production of type I interferons or inflammasome assembly, thereby contributing to host innate immunity. In mice, the Alr locus is highly polymorphic at the sequence and copy number level, and we show here that it is one of the most dynamic regions of the genome. One rapidly evolving gene within this region, Ifi207, was introduced to the Mus genome by gene conversion or an unequal recombination event a few million years ago. Ifi207 has a large, distinctive repeat region that differs in sequence and length among Mus species and even closely related inbred Mus musculus strains. We show that IFI207 controls murine leukemia virus (MLV) infection in vivo and that it plays a role in the STING-mediated response to cGAMP, dsDNA, DMXXA, and MLV. IFI207 binds to STING, and inclusion of its repeat region appears to stabilize STING protein. The Alr locus and Ifi207 provide a clear example of the evolutionary innovation of gene function, possibly as a result of host-pathogen co-evolution.IMPORTANCEThe Red Queen hypothesis predicts that the arms race between pathogens and the host may accelerate evolution of both sides, and therefore causes higher diversity in virulence factors and immune-related proteins, respectively . The Alr gene family in mice has undergone rapid evolution in the last few million years and includes the creation of two novel members, MndaL and Ifi207. Ifi207, in particular, became highly divergent, with significant genetic changes between highly related inbred mice. IFI207 protein acts in the STING pathway and contributes to anti-retroviral resistance via a novel mechanism. The data show that under the pressure of host-pathogen coevolution in a dynamic locus, gene conversion and recombination between gene family members creates new genes with novel and essential functions that play diverse roles in biological processes.
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Affiliation(s)
- Eileen A Moran
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Karen Salas-Briceno
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Wenming Zhao
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Takuji Enya
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Alexya N Aguilera
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Ivan Acosta
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Francis Alonzo
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Dara Kiani
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
| | | | - Thomas M Keane
- EMBL-EBI, Wellcome Genome Campus, Cambridge, United Kingdom
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Jingtao Lilue
- Gulbenkian Institute of Science, Oeiras, Portugal
- Oujiang Laboratory, Wenzhou, Zhejiang, China
| | - Susan R Ross
- Department of Microbiology and Immunology, University of Illinois at Chicago College of Medicine, Chicago, Illinois, USA
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Münch L, Helmprobst F, Volff JN, Chalopin D, Schartl M, Kneitz S. Transposable Element Expression Profiles in Premalignant Pigment Cell Lesions and Melanoma of Xiphophorus. Genes (Basel) 2024; 15:620. [PMID: 38790249 PMCID: PMC11121471 DOI: 10.3390/genes15050620] [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: 03/28/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
Transposable elements (TEs) are characterized by their ability to change their genomic position. Through insertion or recombination leading to deletions and other chromosomal aberrations, they can cause genetic instability. The extent to which they thereby exert regulatory influence on cellular functions is unclear. To better characterize TEs in processes such as carcinogenesis, we used the well-established Xiphophorus melanoma model. By transcriptome sequencing, we show that an increasing total number in transposons correlates with progression of malignancy in melanoma samples from Xiphophorus interspecific hybrids. Further, by comparing the presence of TEs in the parental genomes of Xiphophorus maculatus and Xiphophorus hellerii, we could show that even in closely related species, genomic location and spectrum of TEs are considerably different.
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Affiliation(s)
- Luca Münch
- Neurology Asklepios Klinik Barmbek, Rübenkamp 220, 22307 Hamburg, Germany;
| | - Frederik Helmprobst
- Institute of Neuropathology, Philipps-University Marburg, 35037 Marburg, Germany;
| | | | | | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 786666, USA
- Developmental Biochemistry, University of Würzburg, 97974 Würzburg, Germany
| | - Susanne Kneitz
- Biochemistry and Cell Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany;
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4
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Boyboy BAG, Ichiyanagi K. Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse. Mob DNA 2024; 15:11. [PMID: 38730323 PMCID: PMC11084082 DOI: 10.1186/s13100-024-00321-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Gene expression divergence between populations and between individuals can emerge from genetic variations within the genes and/or in the cis regulatory elements. Since epigenetic modifications regulate gene expression, it is conceivable that epigenetic variations in cis regulatory elements can also be a source of gene expression divergence. RESULTS In this study, we compared histone acetylation (namely, H3K9ac) profiles in two mouse strains of different subspecies origin, C57BL/6 J (B6) and MSM/Ms (MSM), as well as their F1 hybrids. This identified 319 regions of strain-specific acetylation, about half of which were observed between the alleles of F1 hybrids. While the allele-specific presence of the interferon regulatory factor 3 (IRF3) binding sequence was associated with allele-specific histone acetylation, we also revealed that B6-specific insertions of a short 3' fragment of LINE-1 (L1) retrotransposon occur within or proximal to MSM-specific acetylated regions. Furthermore, even in hyperacetylated domains, flanking regions of non-polymorphic 3' L1 fragments were hypoacetylated, suggesting a general activity of the 3' L1 fragment to induce hypoacetylation. Indeed, we confirmed the binding of the 3' region of L1 by three Krüppel-associated box domain-containing zinc finger proteins (KZFPs), which interact with histone deacetylases. These results suggest that even a short insertion of L1 would be excluded from gene- and acetylation-rich regions by natural selection. Finally, mRNA-seq analysis for F1 hybrids was carried out, which disclosed a link between allele-specific promoter/enhancer acetylation and gene expression. CONCLUSIONS This study disclosed a number of genetic changes that have changed the histone acetylation levels during the evolution of mouse subspecies, a part of which is associated with gene expression changes. Insertions of even a very short L1 fragment can decrease the acetylation level in their neighboring regions and thereby have been counter-selected in gene-rich regions, which may explain a long-standing mystery of discrete genomic distribution of LINEs and SINEs.
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Affiliation(s)
- Beverly Ann G Boyboy
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.
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5
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Huang Y, Lee YCG. Blessing or curse: how the epigenetic resolution of host-transposable element conflicts shapes their evolutionary dynamics. Proc Biol Sci 2024; 291:20232775. [PMID: 38593848 PMCID: PMC11003778 DOI: 10.1098/rspb.2023.2775] [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: 12/08/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024] Open
Abstract
Transposable elements (TEs) are selfish genetic elements whose antagonistic interactions with hosts represent a common genetic conflict in eukaryotes. To resolve this conflict, hosts have widely adopted epigenetic silencing that deposits repressive marks at TEs. However, this mechanism is imperfect and fails to fully halt TE replication. Furthermore, TE epigenetic silencing can inadvertently spread repressive marks to adjacent functional sequences, a phenomenon considered a 'curse' of this conflict resolution. Here, we used forward simulations to explore how TE epigenetic silencing and its harmful side effects shape the evolutionary dynamics of TEs and their hosts. Our findings reveal that epigenetic silencing allows TEs and their hosts to stably coexist under a wide range of conditions, because the underlying molecular mechanisms give rise to copy-number dependency of the strength of TE silencing. Interestingly, contrary to intuitive expectations that TE epigenetic silencing should evolve to be as strong as possible, we found a selective benefit for modifier alleles that weaken TE silencing under biologically feasible conditions. These results reveal that the dual nature of TE epigenetic silencing, with both positive and negative effects, complicates its evolutionary trajectory and makes it challenging to determine whether TE epigenetic silencing is a 'blessing' or a 'curse'.
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Affiliation(s)
- Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
| | - Yuh Chwen G. Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
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6
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Le Breton A, Bettencourt MP, Gendrel AV. Navigating the brain and aging: exploring the impact of transposable elements from health to disease. Front Cell Dev Biol 2024; 12:1357576. [PMID: 38476259 PMCID: PMC10927736 DOI: 10.3389/fcell.2024.1357576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that constitute on average 45% of mammalian genomes. Their presence and activity in genomes represent a major source of genetic variability. While this is an important driver of genome evolution, TEs can also have deleterious effects on their hosts. A growing number of studies have focused on the role of TEs in the brain, both in physiological and pathological contexts. In the brain, their activity is believed to be important for neuronal plasticity. In neurological and age-related disorders, aberrant activity of TEs may contribute to disease etiology, although this remains unclear. After providing a comprehensive overview of transposable elements and their interactions with the host, this review summarizes the current understanding of TE activity within the brain, during the aging process, and in the context of neurological and age-related conditions.
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Affiliation(s)
| | | | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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7
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Guo Y, Li TD, Modzelewski AJ, Siomi H. Retrotransposon renaissance in early embryos. Trends Genet 2024; 40:39-51. [PMID: 37949723 DOI: 10.1016/j.tig.2023.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Despite being the predominant genetic elements in mammalian genomes, retrotransposons were often dismissed as genomic parasites with ambiguous biological significance. However, recent studies reveal their functional involvement in early embryogenesis, encompassing crucial processes such as zygotic genome activation (ZGA) and cell fate decision. This review underscores the paradigm shift in our understanding of retrotransposon roles during early preimplantation development, as well as their rich functional reservoir that is exploited by the host to provide cis-regulatory elements, noncoding RNAs, and functional proteins. The rapid advancement in long-read sequencing, low input multiomics profiling, advanced in vitro systems, and precise gene editing techniques encourages further dissection of retrotransposon functions that were once obscured by the intricacies of their genomic footprints.
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Affiliation(s)
- Youjia Guo
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Ten D Li
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA
| | - Andrew J Modzelewski
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA.
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo 160-8582, Japan.
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8
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Alkailani MI, Gibbings D. The Regulation and Immune Signature of Retrotransposons in Cancer. Cancers (Basel) 2023; 15:4340. [PMID: 37686616 PMCID: PMC10486412 DOI: 10.3390/cancers15174340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Advances in sequencing technologies and the bioinformatic analysis of big data facilitate the study of jumping genes' activity in the human genome in cancer from a broad perspective. Retrotransposons, which move from one genomic site to another by a copy-and-paste mechanism, are regulated by various molecular pathways that may be disrupted during tumorigenesis. Active retrotransposons can stimulate type I IFN responses. Although accumulated evidence suggests that retrotransposons can induce inflammation, the research investigating the exact mechanism of triggering these responses is ongoing. Understanding these mechanisms could improve the therapeutic management of cancer through the use of retrotransposon-induced inflammation as a tool to instigate immune responses to tumors.
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Affiliation(s)
- Maisa I. Alkailani
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Derrick Gibbings
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada;
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9
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Crane-Smith Z, De Castro SCP, Nikolopoulou E, Wolujewicz P, Smedley D, Lei Y, Mather E, Santos C, Hopkinson M, Pitsillides AA, Finnell RH, Ross ME, Copp AJ, Greene NDE. A non-coding insertional mutation of Grhl2 causes gene over-expression and multiple structural anomalies including cleft palate, spina bifida and encephalocele. Hum Mol Genet 2023; 32:2681-2692. [PMID: 37364051 PMCID: PMC10460492 DOI: 10.1093/hmg/ddad094] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/19/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Orofacial clefts, including cleft lip and palate (CL/P) and neural tube defects (NTDs) are among the most common congenital anomalies, but knowledge of the genetic basis of these conditions remains incomplete. The extent to which genetic risk factors are shared between CL/P, NTDs and related anomalies is also unclear. While identification of causative genes has largely focused on coding and loss of function mutations, it is hypothesized that regulatory mutations account for a portion of the unidentified heritability. We found that excess expression of Grainyhead-like 2 (Grhl2) causes not only spinal NTDs in Axial defects (Axd) mice but also multiple additional defects affecting the cranial region. These include orofacial clefts comprising midline cleft lip and palate and abnormalities of the craniofacial bones and frontal and/or basal encephalocele, in which brain tissue herniates through the cranium or into the nasal cavity. To investigate the causative mutation in the Grhl2Axd strain, whole genome sequencing identified an approximately 4 kb LTR retrotransposon insertion that disrupts the non-coding regulatory region, lying approximately 300 base pairs upstream of the 5' UTR. This insertion also lies within a predicted long non-coding RNA, oriented on the reverse strand, which like Grhl2 is over-expressed in Axd (Grhl2Axd) homozygous mutant embryos. Initial analysis of the GRHL2 upstream region in individuals with NTDs or cleft palate revealed rare or novel variants in a small number of cases. We hypothesize that mutations affecting the regulation of GRHL2 may contribute to craniofacial anomalies and NTDs in humans.
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Affiliation(s)
- Zoe Crane-Smith
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Sandra C P De Castro
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Evanthia Nikolopoulou
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Paul Wolujewicz
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Damian Smedley
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Emma Mather
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Chloe Santos
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Mark Hopkinson
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London NW1 0TU, UK
| | - Andrew A Pitsillides
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London NW1 0TU, UK
| | | | - Richard H Finnell
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - M Elisabeth Ross
- Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10065, USA
| | - Andrew J Copp
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Nicholas D E Greene
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
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10
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Kobayashi M, Kanbe F, Ishii R, Tsubouchi H, Hirai K, Miyasaka Y, Ohno T, Oda H, Ikeda S, Katoh H, Ichiyanagi K, Ishikawa A, Murai A, Horio F. C3H/HeNSlc mouse with low phospholipid transfer protein expression showed dyslipidemia. Sci Rep 2023; 13:13813. [PMID: 37620514 PMCID: PMC10449841 DOI: 10.1038/s41598-023-40917-9] [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: 03/28/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
High serum levels of triglycerides (TG) and low levels of high-density lipoprotein cholesterol (HDL-C) increase the risk of coronary heart disease in humans. Herein, we first reported that the C3H/HeNSlc (C3H-S) mouse, a C3H/HeN-derived substrain, is a novel model for dyslipidemia. C3H-S showed hypertriglyceridemia and low total cholesterol (TC), HDL-C, and phospholipid (PL) concentrations. To identify the gene locus causing dyslipidemia in C3H-S, we performed genetic analysis. In F2 intercrosses between C3H-S mice and strains with normal serum lipids, the locus associated with serum lipids was identified as 163-168 Mb on chromosome 2. The phospholipid transfer protein (Pltp) gene was a candidate gene within this locus. Pltp expression and serum PLTP activity were markedly lower in C3H-S mice. Pltp expression was negatively correlated with serum TG and positively correlated with serum TC and HDL-C in F2 mice. Genome sequencing analysis revealed that an endogenous retrovirus (ERV) sequence called intracisternal A particle was inserted into intron 12 of Pltp in C3H-S. These results suggest that ERV insertion within Pltp causes aberrant splicing, leading to reduced Pltp expression in C3H-S. This study demonstrated the contribution of C3H-S to our understanding of the relationship between TG, TC, and PL metabolism via PLTP.
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Affiliation(s)
- Misato Kobayashi
- Department of Nutritional Sciences, Nagoya University of Arts and Sciences, 57 Takenoyama, Iwasaki-Cho, Nisshin, Aichi, 470-0196, Japan.
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan.
| | - Fumi Kanbe
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Reika Ishii
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Hiroki Tsubouchi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Kana Hirai
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Yuki Miyasaka
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, Aichi, Japan
| | - Tamio Ohno
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, Aichi, Japan
| | - Hiroaki Oda
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Saiko Ikeda
- Department of Nutritional Sciences, Nagoya University of Arts and Sciences, 57 Takenoyama, Iwasaki-Cho, Nisshin, Aichi, 470-0196, Japan
| | - Hirokazu Katoh
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Kenji Ichiyanagi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Akira Ishikawa
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Atsushi Murai
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
| | - Fumihiko Horio
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi, Japan
- Department of Life Studies and Environmental Science, Nagoya Women's University, Aichi, Japan
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11
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Liu S, Heumüller SE, Hossinger A, Müller SA, Buravlova O, Lichtenthaler SF, Denner P, Vorberg IM. Reactivated endogenous retroviruses promote protein aggregate spreading. Nat Commun 2023; 14:5034. [PMID: 37596282 PMCID: PMC10439213 DOI: 10.1038/s41467-023-40632-z] [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: 06/21/2022] [Accepted: 08/02/2023] [Indexed: 08/20/2023] Open
Abstract
Prion-like spreading of protein misfolding is a characteristic of neurodegenerative diseases, but the exact mechanisms of intercellular protein aggregate dissemination remain unresolved. Evidence accumulates that endogenous retroviruses, remnants of viral germline infections that are normally epigenetically silenced, become upregulated in neurodegenerative diseases such as amyotrophic lateral sclerosis and tauopathies. Here we uncover that activation of endogenous retroviruses affects prion-like spreading of proteopathic seeds. We show that upregulation of endogenous retroviruses drastically increases the dissemination of protein aggregates between cells in culture, a process that can be inhibited by targeting the viral envelope protein or viral protein processing. Human endogenous retrovirus envelopes of four different clades also elevate intercellular spreading of proteopathic seeds, including pathological Tau. Our data support a role of endogenous retroviruses in protein misfolding diseases and suggest that antiviral drugs could represent promising candidates for inhibiting protein aggregate spreading.
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Affiliation(s)
- Shu Liu
- German Center for Neurodegenerative Diseases Bonn (DZNE), Venusberg Campus 1/ 99, 53127, Bonn, Germany
- German Federal Institute for Risk Assessment (BfR), German Centre for the Protection of Laboratory Animals (Bf3R), Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | | | - André Hossinger
- German Center for Neurodegenerative Diseases Bonn (DZNE), Venusberg Campus 1/ 99, 53127, Bonn, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Oleksandra Buravlova
- German Center for Neurodegenerative Diseases Bonn (DZNE), Venusberg Campus 1/ 99, 53127, Bonn, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, 81675, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Philip Denner
- German Center for Neurodegenerative Diseases Bonn (DZNE), Venusberg Campus 1/ 99, 53127, Bonn, Germany
| | - Ina M Vorberg
- German Center for Neurodegenerative Diseases Bonn (DZNE), Venusberg Campus 1/ 99, 53127, Bonn, Germany.
- Department of Neurology, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany, Venusberg-Campus 1, 53127, Bonn, Germany.
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12
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Senner CE, Dong Z, Prater M, Branco MR, Watson ED. One-carbon metabolism is required for epigenetic stability in the mouse placenta. Front Cell Dev Biol 2023; 11:1209928. [PMID: 37440923 PMCID: PMC10333575 DOI: 10.3389/fcell.2023.1209928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/02/2023] [Indexed: 07/15/2023] Open
Abstract
One-carbon metabolism, including the folate cycle, has a crucial role in fetal development though its molecular function is complex and unclear. The hypomorphic Mtrr gt allele is known to disrupt one-carbon metabolism, and thus methyl group availability, leading to several developmental phenotypes (e.g., neural tube closure defects, fetal growth anomalies). Remarkably, previous studies showed that some of the phenotypes were transgenerationally inherited. Here, we explored the genome-wide epigenetic impact of one-carbon metabolism in placentas associated with fetal growth phenotypes and determined whether specific DNA methylation changes were inherited. Firstly, methylome analysis of Mtrr gt/gt homozygous placentas revealed genome-wide epigenetic instability. Several differentially methylated regions (DMRs) were identified including at the Cxcl1 gene promoter and at the En2 gene locus, which may have phenotypic implications. Importantly, we discovered hypomethylation and ectopic expression of a subset of ERV elements throughout the genome of Mtrr gt/gt placentas with broad implications for genomic stability. Next, we determined that known spermatozoan DMRs in Mtrr gt/gt males were reprogrammed in the placenta with little evidence of direct or transgenerational germline DMR inheritance. However, some spermatozoan DMRs were associated with placental gene misexpression despite normalisation of DNA methylation, suggesting the inheritance of an alternative epigenetic mechanism. Integration of published wildtype histone ChIP-seq datasets with Mtrr gt/gt spermatozoan methylome and placental transcriptome datasets point towards H3K4me3 deposition at key loci. These data suggest that histone modifications might play a role in epigenetic inheritance in this context. Overall, this study sheds light on the mechanistic complexities of one-carbon metabolism in development and epigenetic inheritance.
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Affiliation(s)
- Claire E. Senner
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Ziqi Dong
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Malwina Prater
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Miguel R. Branco
- Centre for Genomics and Child Health, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Erica D. Watson
- Centre for Trophoblast Research, University of Cambridge, Cambridge, United Kingdom
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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13
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De Luca C, Gupta A, Bortvin A. Retrotransposon LINE-1 bodies in the cytoplasm of piRNA-deficient mouse spermatocytes: Ribonucleoproteins overcoming the integrated stress response. PLoS Genet 2023; 19:e1010797. [PMID: 37307272 DOI: 10.1371/journal.pgen.1010797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 05/23/2023] [Indexed: 06/14/2023] Open
Abstract
Transposable elements (TE) are mobile DNA sequences whose excessive proliferation endangers the host. Although animals have evolved robust TE-targeting defenses, including Piwi-interacting (pi)RNAs, retrotransposon LINE-1 (L1) still thrives in humans and mice. To gain insights into L1 endurance, we characterized L1 Bodies (LBs) and ORF1p complexes in germ cells of piRNA-deficient Maelstrom null mice. We report that ORF1p interacts with TE RNAs, genic mRNAs, and stress granule proteins, consistent with earlier studies. We also show that ORF1p associates with the CCR4-NOT deadenylation complex and PRKRA, a Protein Kinase R factor. Despite ORF1p interactions with these negative regulators of RNA expression, the stability and translation of LB-localized mRNAs remain unchanged. To scrutinize these findings, we studied the effects of PRKRA on L1 in cultured cells and showed that it elevates ORF1p levels and L1 retrotransposition. These results suggest that ORF1p-driven condensates promote L1 propagation, without affecting the metabolism of endogenous RNAs.
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Affiliation(s)
- Chiara De Luca
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, United States of Americ
| | - Anuj Gupta
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland, United States of Americ
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14
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Cao J, Yu T, Xu B, Hu Z, Zhang XO, Theurkauf W, Weng Z. Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster. Nucleic Acids Res 2023; 51:2066-2086. [PMID: 36762470 PMCID: PMC10018349 DOI: 10.1093/nar/gkad054] [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: 11/02/2022] [Revised: 01/12/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Transposons are mobile genetic elements prevalent in the genomes of most species. The distribution of transposons within a genome reflects the actions of two opposing processes: initial insertion site selection, and selective pressure from the host. By analyzing whole-genome sequencing data from transposon-activated Drosophila melanogaster, we identified 43 316 de novo and 237 germline insertions from four long-terminal-repeat (LTR) transposons, one LINE transposon (I-element), and one DNA transposon (P-element). We found that all transposon types favored insertion into promoters de novo, but otherwise displayed distinct insertion patterns. De novo and germline P-element insertions preferred replication origins, often landing in a narrow region around transcription start sites and in regions of high chromatin accessibility. De novo LTR transposon insertions preferred regions with high H3K36me3, promoters and exons of active genes; within genes, LTR insertion frequency correlated with gene expression. De novo I-element insertion density increased with distance from the centromere. Germline I-element and LTR transposon insertions were depleted in promoters and exons, suggesting strong selective pressure to remove transposons from functional elements. Transposon movement is associated with genome evolution and disease; therefore, our results can improve our understanding of genome and disease biology.
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Affiliation(s)
| | - Tianxiong Yu
- Correspondence may also be addressed to Tianxiong Yu. Tel: +1 774 641 0409; Fax: +1 508 856 0017;
| | - Bo Xu
- The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhongren Hu
- The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiao-ou Zhang
- The School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zhiping Weng
- To whom correspondence should be addressed. Tel: +1 508 856 8866; Fax: +1 508 856 0017;
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15
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Liu M, Jia L, Guo X, Zhai X, Li H, Liu Y, Han J, Zhang B, Wang X, Li T, Wang Y, Li J, Yu C, Li L. Identification and Characterization of the HERV-K (HML-8) Group of Human Endogenous Retroviruses in the Genome. AIDS Res Hum Retroviruses 2023; 39:176-194. [PMID: 36656667 DOI: 10.1089/aid.2022.0084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Human endogenous retroviruses (HERVs) can be vertically transmitted in a Mendelian fashion, are stably maintained in the human genome, and are estimated to constitute ∼8% of the genome. HERVs affect human physiology and pathology through their provirus-encoded protein or long terminal repeat (LTR) element effect. Characterization of the genomic distribution is an essential step to understanding the relationships between endogenous retrovirus expression and diseases. However, the poor characterization of human MMTV-like (HML)-8 prevents a detailed understanding of the regulation of the expression of this family in humans and its impact on the host genome. In light of this, the definition of an accurate and updated HERV-K HML-8 genomic map is urgently needed. In this study, we report the results of a comprehensive analysis of HERV-K HML-8 sequence presence and distribution within the human genome and hominoids, with a detailed description of the different structural and phylogenetic aspects characterizing the group. A total of 40 proviruses and 5 solo LTR elements for human were characterized, which included a detailed description of provirus structure, integration time, potentially regulated genes, transcription factor-binding sites, and primer-binding site features. Besides, 9 chimpanzee sequences, 8 gorilla sequences, and 10 orangutan sequences belonging to the HML-8 subgroup were identified. The integration time results showed that the HML-8 elements were integrated into the primate lineage around 35 and 42 million years ago (mya), during primates evolutionary speciation. Overall, the results clarified the composition of the HML-8 groups, providing an exhaustive background for subsequent functional studies.
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Affiliation(s)
- Mengying Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xing Guo
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China.,Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Xiuli Zhai
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China.,Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Tianyi Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yanglan Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lin Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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16
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Miyasaka Y, Kobayashi T, Gotoh N, Kuga M, Kobayashi M, Horio F, Hashimoto K, Kawabe T, Ohno T. Neonatal lethality of mouse A/J-7 SM consomic strain is caused by an insertion mutation in the Dchs1 gene. Mamm Genome 2023; 34:32-43. [PMID: 36434174 DOI: 10.1007/s00335-022-09966-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/19/2022] [Indexed: 11/27/2022]
Abstract
Homosomic mice of the A/J-7SM consomic mouse strain that introduced the entire chromosome 7 (Chr 7) of SM/J into the A/J strain exhibited neonatal lethality. We tentatively maintained segregating inbred strains (A/J-7ASM and A/J-7DSM) in which the central portion of Chr 7 was heterozygous for the A/J and SM/J strains, and the centromeric and telomeric sides of Chr 7 were homozygous for the SM/J strain, instead of the A/J-7SM strain. Based on the chromosomal constitution of Chr 7 in A/J-7ASM and A/J-7DSM mice, the causative gene for neonatal lethality in homosomic mice was suggested to be located within an approximately 1.620 Mb region between D7Mit125 (104.879 Mb) and D7Mit355 (106.499 Mb) on Chr 7. RT-PCR analysis revealed that homosomic mice lacked dachsous cadherin-related 1 (Dchs1), which is located within the D7Mit125 to D7Mit355 region and functions in the regulation of planar cell polarity. Screening for mutations in Dchs1 indicated that homosomic mice possessed an early transposable (ETn)-like sequence in intron 1 of Dchs1. Moreover, an allelism test between Dchs1 ETn-like-insertion alleles detected in homosomic mice and CRISPR/Cas9-induced Dchs1 deletion alleles revealed that Dchs1 is a causative gene for neonatal lethality in homosomic mice. Based on these results, we concluded that in the A/J-7SM strain, ETn-like elements were inserted into intron 1 of SM/J-derived Dchs1 during strain development, which dramatically reduced Dchs1 expression, thus resulting in neonatal lethality in homosomic mice. Additionally, it was suggested that the timing of lethality in Dchs1 mutant mice is influenced by the genetic background.
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Affiliation(s)
- Yuki Miyasaka
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan.
| | - Takeshi Kobayashi
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan
| | - Naoya Gotoh
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan
| | - Masako Kuga
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan
| | - Misato Kobayashi
- Department of Nutritional Sciences, Nagoya University of Arts and Sciences, 57 Takenoyama, Iwasaki-Cho, Nisshin, Aichi, 470-0196, Japan
| | - Fumihiko Horio
- Department of Life Studies and Environmental Science, Nagoya Women's University, 3-40 Shioji-Cho, Mizuho-Ku, Nagoya, Aichi, 467-8610, Japan
| | - Katsunori Hashimoto
- Faculty of Medical Sciences, Shubun University, 6 Nikko-Cho, Ichinomiya, Aichi, 491-0938, Japan
| | - Tsutomu Kawabe
- Department of Pathophysiological Laboratory Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Dikou-Minami, Higashi-Ku, Nagoya, Aichi, 461-8673, Japan
| | - Tamio Ohno
- Division of Experimental Animals, Graduate School of Medicine, Nagoya University, 65 Tsurumai-Cho, Showa-Ku, Nagoya, Aichi, 466-8550, Japan.
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17
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Stamidis N, Żylicz JJ. RNA-mediated heterochromatin formation at repetitive elements in mammals. EMBO J 2023; 42:e111717. [PMID: 36847618 PMCID: PMC10106986 DOI: 10.15252/embj.2022111717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 12/12/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023] Open
Abstract
The failure to repress transcription of repetitive genomic elements can lead to catastrophic genome instability and is associated with various human diseases. As such, multiple parallel mechanisms cooperate to ensure repression and heterochromatinization of these elements, especially during germline development and early embryogenesis. A vital question in the field is how specificity in establishing heterochromatin at repetitive elements is achieved. Apart from trans-acting protein factors, recent evidence points to a role of different RNA species in targeting repressive histone marks and DNA methylation to these sites in mammals. Here, we review recent discoveries on this topic and predominantly focus on the role of RNA methylation, piRNAs, and other localized satellite RNAs.
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Affiliation(s)
- Nikolaos Stamidis
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
| | - Jan Jakub Żylicz
- Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW, University of Copenhagen, Copenhagen, Denmark
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18
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Berger F, Muegge K, Richards EJ. Seminars in cell and development biology on histone variants remodelers of H2A variants associated with heterochromatin. Semin Cell Dev Biol 2023; 135:93-101. [PMID: 35249811 PMCID: PMC9440159 DOI: 10.1016/j.semcdb.2022.02.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/04/2023]
Abstract
Variants of the histone H2A occupy distinct locations in the genome. There is relatively little known about the mechanisms responsible for deposition of specific H2A variants. Notable exceptions are chromatin remodelers that control the dynamics of H2A.Z at promoters. Here we review the steps that identified the role of a specific class of chromatin remodelers, including LSH and DDM1 that deposit the variants macroH2A in mammals and H2A.W in plants, respectively. The function of these remodelers in heterochromatin is discussed together with their multiple roles in genome stability.
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Affiliation(s)
- Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| | - Kathrin Muegge
- Epigenetics Section, Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA.
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19
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Sun YH, Cui H, Song C, Shen JT, Zhuo X, Wang RH, Yu X, Ndamba R, Mu Q, Gu H, Wang D, Murthy GG, Li P, Liang F, Liu L, Tao Q, Wang Y, Orlowski S, Xu Q, Zhou H, Jagne J, Gokcumen O, Anthony N, Zhao X, Li XZ. Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity. Nat Commun 2023; 14:812. [PMID: 36781861 PMCID: PMC9925758 DOI: 10.1038/s41467-023-36354-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023] Open
Abstract
Unlike PIWI-interacting RNA (piRNA) in other species that mostly target transposable elements (TEs), >80% of piRNAs in adult mammalian testes lack obvious targets. However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. Here, through comparative studies of chickens, ducks, mice, and humans, as well as long-read nanopore sequencing on diverse chicken breeds, we find that piRNA loci across amniotes experience: (1) a high local mutation rate of structural variations (SVs, mutations ≥ 50 bp in size); (2) positive selection to suppress young and actively mobilizing TEs commencing at the pachytene stage of meiosis during germ cell development; and (3) negative selection to purge deleterious SV hotspots. Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences.
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Affiliation(s)
- Yu H Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Hongxiao Cui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chi Song
- College of Public Health, Division of Biostatistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Jiafei Teng Shen
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, 322000, China
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ruoqiao Huiyi Wang
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaohui Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Rudo Ndamba
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Qian Mu
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Hanwen Gu
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Duolin Wang
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Gayathri Guru Murthy
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Pidong Li
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Fan Liang
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Lei Liu
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Qing Tao
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Sara Orlowski
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Qi Xu
- Department of Animal Science, McGill University, Quebec, H9X 3V9, Canada
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Jarra Jagne
- Animal Health Diagnostic Center, Cornell University College of Veterinary Medicine, Ithaca, NY, 14850, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Nick Anthony
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Xin Zhao
- Department of Animal Science, McGill University, Quebec, H9X 3V9, Canada.
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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20
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Luca CD, Gupta A, Bortvin A. Ribonucleoprotein condensation driven by retrotransposon LINE-1 sustains RNA integrity and translation in mouse spermatocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523313. [PMID: 36712121 PMCID: PMC9882024 DOI: 10.1101/2023.01.09.523313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Transposable elements (TE) are mobile DNA sequences whose excessive proliferation endangers the host. Although animals have evolved robust TE-targeting defenses, including Piwi-interacting (pi)RNAs, retrotransposon LINE-1 (L1) still thrives in humans and mice. To gain insights into L1 endurance, we characterized L1 Bodies (LBs) and ORF1p complexes in germ cells of piRNA-deficient Maelstrom null mice. We report that ORF1p interacts with TE RNAs, genic mRNAs, and stress granule proteins, consistent with earlier studies. We also show that ORF1p associates with the CCR4-NOT deadenylation complex and PRKRA, a Protein Kinase R factor. Despite ORF1p interactions with these negative regulators of RNA expression, the stability and translation of LB-localized mRNAs remain unchanged. To scrutinize these findings, we studied the effects of PRKRA on L1 in cultured cells and showed that it elevates ORF1p levels and L1 retrotransposition. These results suggest that ORF1p-driven condensates promote L1 propagation, without affecting the metabolism of endogenous RNAs.
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21
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Herrero F, Mueller FS, Gruchot J, Küry P, Weber-Stadlbauer U, Meyer U. Susceptibility and resilience to maternal immune activation are associated with differential expression of endogenous retroviral elements. Brain Behav Immun 2023; 107:201-214. [PMID: 36243285 DOI: 10.1016/j.bbi.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/26/2022] [Accepted: 10/09/2022] [Indexed: 12/05/2022] Open
Abstract
Endogenous retroviruses (ERVs) are ancestorial retroviral elements that were integrated into the mammalian genome through germline infections and insertions during evolution. While increased ERV expression has been repeatedly implicated in psychiatric and neurodevelopmental disorders, recent evidence suggests that aberrant endogenous retroviral activity may contribute to biologically defined subgroups of psychotic disorders with persisting immunological dysfunctions. Here, we explored whether ERV expression is altered in a mouse model of maternal immune activation (MIA), a transdiagnostic environmental risk factor of psychiatric and neurodevelopmental disorders. MIA was induced by maternal administration of poly(I:C) on gestation day 12 in C57BL/6N mice. Murine ERV transcripts were quantified in the placentae and fetal brains shortly after poly(I:C)-induced MIA, as well as in adult offspring that were stratified according to their behavioral profiles. We found that MIA increased and reduced levels of class II ERVs and syncytins, respectively, in placentae and fetal brain tissue. We also revealed abnormal ERV expression in MIA-exposed offspring depending on whether they displayed overt behavioral anomalies or not. Taken together, our findings provide a proof of concept that an inflammatory stimulus, even when initiated in prenatal life, has the potential of altering ERV expression across fetal to adult stages of development. Moreover, our data highlight that susceptibility and resilience to MIA are associated with differential ERV expression, suggesting that early-life exposure to inflammatory factors may play a role in determining disease susceptibility by inducing persistent alterations in the expression of endogenous retroviral elements.
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Affiliation(s)
- Felisa Herrero
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Flavia S Mueller
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Joel Gruchot
- Department of Neurology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Patrick Küry
- Department of Neurology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Ulrike Weber-Stadlbauer
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Urs Meyer
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.
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22
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Cipriani C, Tartaglione AM, Giudice M, D’Avorio E, Petrone V, Toschi N, Chiarotti F, Miele MT, Calamandrei G, Garaci E, Matteucci C, Sinibaldi-Vallebona P, Ricceri L, Balestrieri E. Differential Expression of Endogenous Retroviruses and Inflammatory Mediators in Female and Male Offspring in a Mouse Model of Maternal Immune Activation. Int J Mol Sci 2022; 23:ijms232213930. [PMID: 36430402 PMCID: PMC9695919 DOI: 10.3390/ijms232213930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
Maternal infections during pregnancy and the consequent maternal immune activation (MIA) are the major risk factors for autism spectrum disorder (ASD). Epidemiological evidence is corroborated by the preclinical models in which MIA leads to ASD-like behavioral abnormalities and altered neuroinflammatory profiles, with an increase in pro-inflammatory cytokines and microglial markers. In addition to neuroinflammatory response, an abnormal expression of endogenous retroviruses (ERVs) has been identified in neurodevelopmental disorders and have been found to correlate with disease severity. Our aim was to evaluate the transcriptional profile of several ERV families, ERV-related genes, and inflammatory mediators (by RT real-time PCR) in mouse offspring of both sexes, prenatally exposed to polyinosinic:polycytidylic acid (Poly I:C), a synthetic double-stranded RNA molecule targeting TLR-3 that mimics viral maternal infection during pregnancy. We found that prenatal exposure to Poly I:C deregulated the expression of some ERVs and ERV-related genes both in the prefrontal cortex (PFC) and hippocampus, while no changes were detected in the blood. Interestingly, sex-related differences in the expression levels of some ERVs, ERV-related genes, and inflammatory mediators that were higher in females than in males emerged only in PFC. Our findings support the tissue specificity of ERV and ERV-related transcriptional profiles in MIA mice.
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Affiliation(s)
- Chiara Cipriani
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Anna Maria Tartaglione
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità (ISS), 00161 Rome, Italy
| | - Martina Giudice
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Erica D’Avorio
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Vita Petrone
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Nicola Toschi
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy
- Martinos Center for Biomedical Imaging, Harvard Medical School, Boston, MA 02115, USA
| | - Flavia Chiarotti
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità (ISS), 00161 Rome, Italy
| | - Martino Tony Miele
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Gemma Calamandrei
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità (ISS), 00161 Rome, Italy
| | - Enrico Garaci
- University San Raffaele, 00166 Rome, Italy
- IRCCS San Raffaele Pisana, 00163 Rome, Italy
| | - Claudia Matteucci
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Paola Sinibaldi-Vallebona
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
| | - Laura Ricceri
- Center for Behavioral Sciences and Mental Health, Istituto Superiore di Sanità (ISS), 00161 Rome, Italy
| | - Emanuela Balestrieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- Correspondence:
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23
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Hijacking of transcriptional condensates by endogenous retroviruses. Nat Genet 2022; 54:1238-1247. [PMID: 35864192 PMCID: PMC9355880 DOI: 10.1038/s41588-022-01132-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 05/26/2022] [Indexed: 12/20/2022]
Abstract
Most endogenous retroviruses (ERVs) in mammals are incapable of retrotransposition; therefore, why ERV derepression is associated with lethality during early development has been a mystery. Here, we report that rapid and selective degradation of the heterochromatin adapter protein TRIM28 triggers dissociation of transcriptional condensates from loci encoding super-enhancer (SE)-driven pluripotency genes and their association with transcribed ERV loci in murine embryonic stem cells. Knockdown of ERV RNAs or forced expression of SE-enriched transcription factors rescued condensate localization at SEs in TRIM28-degraded cells. In a biochemical reconstitution system, ERV RNA facilitated partitioning of RNA polymerase II and the Mediator coactivator into phase-separated droplets. In TRIM28 knockout mouse embryos, single-cell RNA-seq analysis revealed specific depletion of pluripotent lineages. We propose that coding and noncoding nascent RNAs, including those produced by retrotransposons, may facilitate ‘hijacking’ of transcriptional condensates in various developmental and disease contexts. TRIM28 depletion in embryonic stem cells disconnects transcriptional condensates from super-enhancers, which is rescued by knockdown of endogenous retroviruses.
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24
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Jia L, Liu M, Yang C, Li H, Liu Y, Han J, Zhai X, Wang X, Li T, Li J, Zhang B, Yu C, Li L. Comprehensive identification and characterization of the HERV-K (HML-9) group in the human genome. Retrovirology 2022; 19:11. [PMID: 35676699 PMCID: PMC9178832 DOI: 10.1186/s12977-022-00596-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/09/2022] [Indexed: 12/14/2022] Open
Abstract
Background Human endogenous retroviruses (HERVs) result from ancestral infections caused by exogenous retroviruses that became incorporated into the germline DNA and evolutionarily fixed in the human genome. HERVs can be transmitted vertically in a Mendelian fashion and be stably maintained in the human genome, of which they are estimated to comprise approximately 8%. HERV-K (HML1-10) transcription has been confirmed to be associated with a variety of diseases, such as breast cancer, lung cancer, prostate cancer, melanoma, rheumatoid arthritis, and amyotrophic lateral sclerosis. However, the poor characterization of HML-9 prevents a detailed understanding of the regulation of the expression of this family in humans and its impact on the host genome. In light of this, a precise and updated HERV-K HML-9 genomic map is urgently needed to better evaluate the role of these elements in human health. Results We report a comprehensive analysis of the presence and distribution of HERV-K HML-9 elements within the human genome, with a detailed characterization of the structural and phylogenetic properties of the group. A total of 23 proviruses and 47 solo LTR elements were characterized, with a detailed description of the provirus structure, integration time, potential regulated genes, transcription factor binding sites (TFBS), and primer binding site (PBS) features. The integration time results showed that the HML-9 elements found in the human genome integrated into the primate lineage between 17.5 and 48.5 million years ago (mya). Conclusion The results provide a clear characterization of HML-9 and a comprehensive background for subsequent functional studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12977-022-00596-2.
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Affiliation(s)
- Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China
| | - Mengying Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Caiqin Yang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China
| | - Xiuli Zhai
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China
| | - Tianyi Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Lin Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China. .,State Key Laboratory of Pathogen and Biosecurity, Beijing, 100071, China.
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25
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Inadvertent Transfer of Murine VL30 Retrotransposons to CAR-T Cells. ADVANCES IN CELL AND GENE THERAPY 2022; 2022. [PMID: 36081760 PMCID: PMC9450689 DOI: 10.1155/2022/6435077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
For more than a decade, genetically engineered autologous T-cells have been successfully employed as immunotherapy drugs for patients with incurable blood cancers. The active components in some of these game-changing medicines are autologous T-cells that express viral vector-delivered chimeric antigen receptors (CARs), which specifically target proteins that are preferentially expressed on cancer cells. Some of these therapeutic CAR expressing T-cells (CAR-Ts) are engineered via transduction with
-retroviral vectors (
-RVVs) produced in a stable producer cell line that was derived from murine PG13 packaging cells (ATCC CRL-10686). Earlier studies reported on the copackaging of murine virus-like 30S RNA (VL30) genomes with
-retroviral vectors generated in murine stable packaging cells. In an earlier study, VL30 mRNA was found to enhance the metastatic potential of human melanoma cells. These findings raise biosafety concerns regarding the possibility that therapeutic CAR-Ts have been inadvertently contaminated with potentially oncogenic VL30 retrotransposons. In this study, we demonstrated the presence of infectious VL30 particles in PG13 cell-conditioned media and observed the ability of these particles to deliver transcriptionally active VL30 genomes to human cells. Notably, VL30 genomes packaged by HIV-1-based vector particles transduced naïve human cells in culture. Furthermore, we detected the transfer and expression of VL30 genomes in clinical-grade CAR-T cells generated by transduction with PG13 cell-derived
-retroviral vectors. Our findings raise biosafety concerns regarding the use of murine packaging cell lines in ongoing clinical applications.
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26
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Lewis MA, Ingham NJ, Chen J, Pearson S, Di Domenico F, Rekhi S, Allen R, Drake M, Willaert A, Rook V, Pass J, Keane T, Adams DJ, Tucker AS, White JK, Steel KP. Identification and characterisation of spontaneous mutations causing deafness from a targeted knockout programme. BMC Biol 2022; 20:67. [PMID: 35296311 PMCID: PMC8928630 DOI: 10.1186/s12915-022-01257-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background Mice carrying targeted mutations are important for investigating gene function and the role of genes in disease, but off-target mutagenic effects associated with the processes of generating targeted alleles, for instance using Crispr, and culturing embryonic stem cells, offer opportunities for spontaneous mutations to arise. Identifying spontaneous mutations relies on the detection of phenotypes segregating independently of targeted alleles, and having a broad estimate of the level of mutations generated by intensive breeding programmes is difficult given that many phenotypes are easy to miss if not specifically looked for. Here we present data from a large, targeted knockout programme in which mice were analysed through a phenotyping pipeline. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Results Twenty-five lines out of 1311 displayed different deafness phenotypes that did not segregate with the targeted allele. We observed a variety of phenotypes by Auditory Brainstem Response (ABR) and behavioural assessment and isolated eight lines showing early-onset severe progressive hearing loss, later-onset progressive hearing loss, low frequency hearing loss, or complete deafness, with vestibular dysfunction. The causative mutations identified include deletions, insertions, and point mutations, some of which involve new genes not previously associated with deafness while others are new alleles of genes known to underlie hearing loss. Two of the latter show a phenotype much reduced in severity compared to other mutant alleles of the same gene. We investigated the ES cells from which these lines were derived and determined that only one of the 8 mutations could have arisen in the ES cell, and in that case, only after targeting. Instead, most of the non-segregating mutations appear to have occurred during breeding of mutant mice. In one case, the mutation arose within the wildtype colony used for expanding mutant lines. Conclusions Our data show that spontaneous mutations with observable effects on phenotype are a common side effect of intensive breeding programmes, including those underlying targeted mutation programmes. Such spontaneous mutations segregating within mutant lines may confound phenotypic analyses, highlighting the importance of record-keeping and maintaining correct pedigrees. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01257-8.
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Affiliation(s)
- Morag A Lewis
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England. .,Wellcome Sanger Institute, Hinxton, CB10 1SA, England.
| | - Neil J Ingham
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Jing Chen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | | | - Francesca Di Domenico
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Sohinder Rekhi
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Rochelle Allen
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Matthew Drake
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Annelore Willaert
- Research Group of Experimental Oto-Rhino-Laryngology, Department of Neurosciences, KU Leuven - University of Leuven, Leuven, Belgium
| | - Victoria Rook
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England
| | - Johanna Pass
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Thomas Keane
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - David J Adams
- Wellcome Sanger Institute, Hinxton, CB10 1SA, England
| | - Abigail S Tucker
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, England
| | | | - Karen P Steel
- Wolfson Centre for Age-Related Diseases, King's College London, London, SE1 1UL, England.,Wellcome Sanger Institute, Hinxton, CB10 1SA, England
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27
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Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation. Nat Genet 2022; 54:1895-1906. [PMID: 36471082 PMCID: PMC9729108 DOI: 10.1038/s41588-022-01241-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 10/24/2022] [Indexed: 12/12/2022]
Abstract
Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes. To what extent this entails direct inhibition of transcription factor (TF) binding versus indirect inhibition via recruitment of methyl-CpG-binding domain (MBD) proteins is unclear. Here we show that combinatorial genetic deletions of all four proteins with functional MBDs in mouse embryonic stem cells, derived neurons or a human cell line do not reactivate genes or repeats with methylated promoters. These do, however, become activated by methylation-restricted TFs if DNA methylation is removed. We identify several causal TFs in neurons, including ONECUT1, which is methylation sensitive only at a motif variant. Rampantly upregulated retrotransposons in methylation-free neurons feature a CRE motif, which activates them in the absence of DNA methylation via methylation-sensitive binding of CREB1. Our study reveals methylation-sensitive TFs in vivo and argues that direct inhibition, rather than indirect repression by the tested MBD proteins, is the prevailing mechanism of methylation-mediated repression at regulatory regions and repeats.
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28
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Buttler CA, Chuong EB. Emerging roles for endogenous retroviruses in immune epigenetic regulation. Immunol Rev 2022; 305:165-178. [PMID: 34816452 PMCID: PMC8766910 DOI: 10.1111/imr.13042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/21/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023]
Abstract
In recent years, there has been significant progress toward understanding the transcriptional networks underlying mammalian immune responses, fueled by advances in regulatory genomic technologies. Epigenomic studies profiling immune cells have generated detailed genome-wide maps of regulatory elements that will be key to deciphering the regulatory networks underlying cellular immune responses and autoimmune disorders. Unbiased analyses of these genomic maps have uncovered endogenous retroviruses as an unexpected ally in the regulation of human immune systems. Despite their parasitic origins, studies are finding an increasing number of examples of retroviral sequences having been co-opted for beneficial immune function and regulation by the host cell. Here, we review how endogenous retroviruses have given rise to numerous regulatory elements that shape the epigenetic landscape of host immune responses. We will discuss the implications of these elements on the function, dysfunction, and evolution of innate immunity.
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29
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Lee YCG. Synergistic epistasis of the deleterious effects of transposable elements. Genetics 2021; 220:6458331. [PMID: 34888644 DOI: 10.1093/genetics/iyab211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 11/12/2022] Open
Abstract
The replicative nature and generally deleterious effects of transposable elements (TEs) raise an outstanding question about how TE copy number is stably contained in host populations. Classic theoretical analyses predict that, when the decline in fitness due to each additional TE insertion is greater than linear, or when there is synergistic epistasis, selection against TEs can result in a stable equilibrium of TE copy number. While several mechanisms are predicted to yield synergistic deleterious effects of TEs, we lack empirical investigations of the presence of such epistatic interactions. Purifying selection with synergistic epistasis generates repulsion linkage between deleterious alleles. We investigated this population genetic signal in the likely ancestral Drosophila melanogaster population and found evidence supporting the presence of synergistic epistasis among TE insertions, especially TEs expected to exert large fitness impacts. Even though synergistic epistasis of TEs has been predicted to arise through ectopic recombination and TE-mediated epigenetic silencing mechanisms, we only found mixed support for the associated predictions. We observed signals of synergistic epistasis for a large number of TE families, which is consistent with the expectation that such epistatic interaction mainly happens among copies of the same family. Curiously, significant repulsion linkage was also found among TE insertions from different families, suggesting the possibility that synergism of TEs' deleterious fitness effects could arise above the family level and through mechanisms similar to those of simple mutations. Our findings set the stage for investigating the prevalence and importance of epistatic interactions in the evolutionary dynamics of TEs.
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Affiliation(s)
- Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
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30
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Zhou X, Sam TW, Lee AY, Leung D. Mouse strain-specific polymorphic provirus functions as cis-regulatory element leading to epigenomic and transcriptomic variations. Nat Commun 2021; 12:6462. [PMID: 34753915 PMCID: PMC8578388 DOI: 10.1038/s41467-021-26630-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 10/14/2021] [Indexed: 12/27/2022] Open
Abstract
Polymorphic integrations of endogenous retroviruses (ERVs) have been previously detected in mouse and human genomes. While most are inert, a subset can influence the activity of the host genes. However, the molecular mechanism underlying how such elements affect the epigenome and transcriptome and their roles in driving intra-specific variation remain unclear. Here, by utilizing wildtype murine embryonic stem cells (mESCs) derived from distinct genetic backgrounds, we discover a polymorphic MMERGLN (GLN) element capable of regulating H3K27ac enrichment and transcription of neighboring loci. We demonstrate that this polymorphic element can enhance the neighboring Klhdc4 gene expression in cis, which alters the activity of downstream stress response genes. These results suggest that the polymorphic ERV-derived cis-regulatory element contributes to differential phenotypes from stimuli between mouse strains. Moreover, we identify thousands of potential polymorphic ERVs in mESCs, a subset of which show an association between proviral activity and nearby chromatin states and transcription. Overall, our findings elucidate the mechanism of how polymorphic ERVs can shape the epigenome and transcriptional networks that give rise to phenotypic divergence between individuals.
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Affiliation(s)
- Xuemeng Zhou
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
| | - Tsz Wing Sam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
| | - Ah Young Lee
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China
| | - Danny Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China. .,Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, SAR, China.
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31
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High Prevalence of Recombinant Porcine Endogenous Retroviruses (PERV-A/Cs) in Minipigs: A Review on Origin and Presence. Viruses 2021; 13:v13091869. [PMID: 34578447 PMCID: PMC8473008 DOI: 10.3390/v13091869] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/17/2022] Open
Abstract
Minipigs play an important role in biomedical research and they have also been used as donor animals for preclinical xenotransplantations. Since zoonotic microorganisms including viruses can be transmitted when pig cells, tissues or organs are transplanted, virus safety is an important feature in xenotransplantation. Whereas most porcine viruses can be eliminated from pig herds by different strategies, this is not possible for porcine endogenous retroviruses (PERVs). PERVs are integrated in the genome of pigs and some of them release infectious particles able to infect human cells. Whereas PERV-A and PERV-B are present in all pigs and can infect cells from humans and other species, PERV-C is present in most, but not all pigs and infects only pig cells. Recombinant viruses between PERV-A and PERV-C have been found in some pigs; these recombinants infect human cells and are characterized by high replication rates. PERV-A/C recombinants have been found mainly in minipigs of different origin. The possible reasons of this high prevalence of PERV-A/C in minipigs, including inbreeding and higher numbers and expression of replication-competent PERV-C in these animals, are discussed in this review. Based on these data, it is highly recommended to use only pig donors in clinical xenotransplantation that are negative for PERV-C.
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32
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Yang L, Malhotra R, Chikhi R, Elleder D, Kaiser T, Rong J, Medvedev P, Poss M. Recombination marks the evolutionary dynamics of a recently endogenized retrovirus. Mol Biol Evol 2021; 38:5423-5436. [PMID: 34480565 PMCID: PMC8662619 DOI: 10.1093/molbev/msab252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
All vertebrate genomes have been colonized by retroviruses along their evolutionary trajectory. Although endogenous retroviruses (ERVs) can contribute important physiological functions to contemporary hosts, such benefits are attributed to long-term coevolution of ERV and host because germline infections are rare and expansion is slow, and because the host effectively silences them. The genomes of several outbred species including mule deer (Odocoileus hemionus) are currently being colonized by ERVs, which provides an opportunity to study ERV dynamics at a time when few are fixed. We previously established the locus-specific distribution of cervid ERV (CrERV) in populations of mule deer. In this study, we determine the molecular evolutionary processes acting on CrERV at each locus in the context of phylogenetic origin, genome location, and population prevalence. A mule deer genome was de novo assembled from short- and long-insert mate pair reads and CrERV sequence generated at each locus. We report that CrERV composition and diversity have recently measurably increased by horizontal acquisition of a new retrovirus lineage. This new lineage has further expanded CrERV burden and CrERV genomic diversity by activating and recombining with existing CrERV. Resulting interlineage recombinants then endogenize and subsequently expand. CrERV loci are significantly closer to genes than expected if integration were random and gene proximity might explain the recent expansion of one recombinant CrERV lineage. Thus, in mule deer, retroviral colonization is a dynamic period in the molecular evolution of CrERV that also provides a burst of genomic diversity to the host population.
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Affiliation(s)
- Lei Yang
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Raunaq Malhotra
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Rayan Chikhi
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Daniel Elleder
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, 1083, 14220, Czech Republic Vídeňská Prague
| | - Theodora Kaiser
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jesse Rong
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Paul Medvedev
- Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Computer Science and Engineering, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mary Poss
- Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, PA, 16802, USA
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33
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Markouli M, Strepkos D, Piperi C. Structure, Activity and Function of the SETDB1 Protein Methyltransferase. Life (Basel) 2021; 11:life11080817. [PMID: 34440561 PMCID: PMC8397983 DOI: 10.3390/life11080817] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
The SET Domain Bifurcated Histone Lysine Methyltransferase 1 (SETDB1) is a prominent member of the Suppressor of Variegation 3–9 (SUV39)-related protein lysine methyltransferases (PKMTs), comprising three isoforms that differ in length and domain composition. SETDB1 is widely expressed in human tissues, methylating Histone 3 lysine 9 (H3K9) residues, promoting chromatin compaction and exerting negative regulation on gene expression. SETDB1 has a central role in normal physiology and nervous system development, having been implicated in the regulation of cell cycle progression, inactivation of the X chromosome, immune cells function, expression of retroelements and formation of promyelocytic leukemia (PML) nuclear bodies (NB). SETDB1 has been frequently deregulated in carcinogenesis, being implicated in the pathogenesis of gliomas, melanomas, as well as in lung, breast, gastrointestinal and ovarian tumors, where it mainly exerts an oncogenic role. Aberrant activity of SETDB1 has also been implicated in several neuropsychiatric, cardiovascular and gastrointestinal diseases, including schizophrenia, Huntington’s disease, congenital heart defects and inflammatory bowel disease. Herein, we provide an update on the unique structural and biochemical features of SETDB1 that contribute to its regulation, as well as its molecular and cellular impact in normal physiology and disease with potential therapeutic options.
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Yuan L, Sun B, Xu L, Chen L, Ou W. The Updating of Biological Functions of Methyltransferase SETDB1 and Its Relevance in Lung Cancer and Mesothelioma. Int J Mol Sci 2021; 22:ijms22147416. [PMID: 34299035 PMCID: PMC8306223 DOI: 10.3390/ijms22147416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/11/2022] Open
Abstract
SET domain bifurcated 1 (SETDB1) is a histone H3 lysine 9 (H3K9) methyltransferase that exerts important effects on epigenetic gene regulation. SETDB1 complexes (SETDB1-KRAB-KAP1, SETDB1-DNMT3A, SETDB1-PML, SETDB1-ATF7IP-MBD1) play crucial roles in the processes of histone methylation, transcriptional suppression and chromatin remodelling. Therefore, aberrant trimethylation at H3K9 due to amplification, mutation or deletion of SETDB1 may lead to transcriptional repression of various tumour-suppressing genes and other related genes in cancer cells. Lung cancer is the most common type of cancer worldwide in which SETDB1 amplification and H3K9 hypermethylation have been indicated as potential tumourigenesis markers. In contrast, frequent inactivation mutations of SETDB1 have been revealed in mesothelioma, an asbestos-associated, locally aggressive, highly lethal, and notoriously chemotherapy-resistant cancer. Above all, the different statuses of SETDB1 indicate that it may have different biological functions and be a potential diagnostic biomarker and therapeutic target in lung cancer and mesothelioma.
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Affiliation(s)
| | | | | | | | - Wenbin Ou
- Correspondence: ; Tel./Fax: +86-571-86843303
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Activation of Endogenous Retrovirus, Brain Infections and Environmental Insults in Neurodegeneration and Alzheimer's Disease. Int J Mol Sci 2021; 22:ijms22147263. [PMID: 34298881 PMCID: PMC8303979 DOI: 10.3390/ijms22147263] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/29/2021] [Accepted: 07/03/2021] [Indexed: 12/18/2022] Open
Abstract
Chronic neurodegenerative diseases are complex, and their pathogenesis is uncertain. Alzheimer’s disease (AD) is a neurodegenerative brain alteration that is responsible for most dementia cases in the elderly. AD etiology is still uncertain; however, chronic neuroinflammation is a constant component of brain pathology. Infections have been associated with several neurological diseases and viruses of the Herpes family appear to be a probable cause of AD neurodegenerative alterations. Several different factors may contribute to the AD clinical progression. Exogeneous viruses or other microbes and environmental pollutants may directly induce neurodegeneration by activating brain inflammation. In this paper, we suggest that exogeneous brain insults may also activate retrotransposons and silent human endogenous retroviruses (HERVs). The initial inflammation of small brain areas induced by virus infections or other brain insults may activate HERV dis-regulation that contributes to neurodegenerative mechanisms. Chronic HERV activation in turn may cause progressive neurodegeneration that thereafter merges in cognitive impairment and dementia in genetically susceptible people. Specific treatment for exogenous end endogenous pathogens and decreasing pollutant exposure may show beneficial effect in early intervention protocol to prevent the progression of cognitive deterioration in the elderly.
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Bertozzi TM, Takahashi N, Hanin G, Kazachenka A, Ferguson-Smith AC. A spontaneous genetically induced epiallele at a retrotransposon shapes host genome function. eLife 2021; 10:e65233. [PMID: 33755012 PMCID: PMC8084528 DOI: 10.7554/elife.65233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
Intracisternal A-particles (IAPs) are endogenous retroviruses (ERVs) responsible for most insertional mutations in the mouse. Full-length IAPs harbour genes flanked by long terminal repeats (LTRs). Here, we identify a solo LTR IAP variant (Iap5-1solo) recently formed in the inbred C57BL/6J mouse strain. In contrast to the C57BL/6J full-length IAP at this locus (Iap5-1full), Iap5-1solo lacks DNA methylation and H3K9 trimethylation. The distinct DNA methylation levels between the two alleles are established during preimplantation development, likely due to loss of KRAB zinc finger protein binding at the Iap5-1solo variant. Iap5-1solo methylation increases and becomes more variable in a hybrid genetic background yet is unresponsive to maternal dietary methyl supplementation. Differential epigenetic modification of the two variants is associated with metabolic differences and tissue-specific changes in adjacent gene expression. Our characterisation of Iap5-1 as a genetically induced epiallele with functional consequences establishes a new model to study transposable element repression and host-element co-evolution.
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Affiliation(s)
- Tessa M Bertozzi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Nozomi Takahashi
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Geula Hanin
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
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Elmer JL, Hay AD, Kessler NJ, Bertozzi TM, Ainscough EAC, Ferguson-Smith AC. Genomic properties of variably methylated retrotransposons in mouse. Mob DNA 2021; 12:6. [PMID: 33612119 PMCID: PMC7898769 DOI: 10.1186/s13100-021-00235-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/02/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are enriched in cytosine methylation, preventing their mobility within the genome. We previously identified a genome-wide repertoire of candidate intracisternal A particle (IAP) TEs in mice that exhibit inter-individual variability in this methylation (VM-IAPs) with implications for genome function. RESULTS Here we validate these metastable epialleles and discover a novel class that exhibit tissue specificity (tsVM-IAPs) in addition to those with uniform methylation in all tissues (constitutive- or cVM-IAPs); both types have the potential to regulate genes in cis. Screening for variable methylation at other TEs shows that this phenomenon is largely limited to IAPs, which are amongst the youngest and most active endogenous retroviruses. We identify sequences enriched within cVM-IAPs, but determine that these are not sufficient to confer epigenetic variability. CTCF is enriched at VM-IAPs with binding inversely correlated with DNA methylation. We uncover dynamic physical interactions between cVM-IAPs with low methylation ranges and other genomic loci, suggesting that VM-IAPs have the potential for long-range regulation. CONCLUSION Our findings indicate that a recently evolved interplay between genetic sequence, CTCF binding, and DNA methylation at young TEs can result in inter-individual variability in transcriptional outcomes with implications for phenotypic variation.
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Affiliation(s)
- Jessica L. Elmer
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Amir D. Hay
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Noah J. Kessler
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
| | - Tessa M. Bertozzi
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH UK
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38
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Hintze M, Griesing S, Michels M, Blanck B, Wischhof L, Hartmann D, Bano D, Franz T. Alopecia in Harlequin mutant mice is associated with reduced AIF protein levels and expression of retroviral elements. Mamm Genome 2021; 32:12-29. [PMID: 33367954 PMCID: PMC7878237 DOI: 10.1007/s00335-020-09854-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/23/2020] [Indexed: 11/25/2022]
Abstract
We investigated the contribution of apoptosis-inducing factor (AIF), a key regulator of mitochondrial biogenesis, in supporting hair growth. We report that pelage abnormalities developed during hair follicle (HF) morphogenesis in Harlequin (Hq) mutant mice. Fragility of the hair cortex was associated with decreased expression of genes encoding structural hair proteins, though key transcriptional regulators of HF development were expressed at normal levels. Notably, Aifm1 (R200 del) knockin males and Aifm1(R200 del)/Hq females showed minor hair defects, despite substantially reduced AIF levels. Furthermore, we cloned the integrated ecotropic provirus of the Aifm1Hq allele. We found that its overexpression in wild-type keratinocyte cell lines led to down-regulation of HF-specific Krt84 and Krtap3-3 genes without altering Aifm1 or epidermal Krt5 expression. Together, our findings imply that pelage paucity in Hq mutant mice is mechanistically linked to severe AIF deficiency and is associated with the expression of retroviral elements that might potentially influence the transcriptional regulation of structural hair proteins.
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Affiliation(s)
- Maik Hintze
- Institute of Anatomy, Neuroanatomy, Medical Faculty, UKB, University of Bonn, Bonn, Germany.
- Medical Department, MSH Medical School Hamburg, Hamburg, Germany.
| | - Sebastian Griesing
- Institute of Anatomy, Neuroanatomy, Medical Faculty, UKB, University of Bonn, Bonn, Germany
- Dept. of Oncology, National Taiwan University Hospital, Taipei City, 100, Taiwan, ROC
| | - Marion Michels
- Institute of Anatomy, Neuroanatomy, Medical Faculty, UKB, University of Bonn, Bonn, Germany
| | - Birgit Blanck
- Institute of Anatomy, Neuroanatomy, Medical Faculty, UKB, University of Bonn, Bonn, Germany
| | - Lena Wischhof
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Dieter Hartmann
- Institute of Anatomy, Neuroanatomy, Medical Faculty, UKB, University of Bonn, Bonn, Germany
| | - Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Thomas Franz
- Institute of Anatomy, Neuroanatomy, Medical Faculty, UKB, University of Bonn, Bonn, Germany
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39
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Norin U, Rintisch C, Meng L, Forster F, Ekman D, Tuncel J, Klocke K, Bäcklund J, Yang M, Bonner MY, Lahore GF, James J, Shchetynsky K, Bergquist M, Gjertsson I, Hubner N, Bäckdahl L, Holmdahl R. Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation. Nat Commun 2021; 12:610. [PMID: 33504785 PMCID: PMC7840939 DOI: 10.1038/s41467-020-20586-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 12/07/2020] [Indexed: 11/18/2022] Open
Abstract
The introduction of the CTLA-4 recombinant fusion protein has demonstrated therapeutic effects by selectively modulating T-cell activation in rheumatoid arthritis. Here we show, using a forward genetic approach, that a mutation in the SH3gl1 gene encoding the endocytic protein Endophilin A2 is associated with the development of arthritis in rodents. Defective expression of SH3gl1 affects T cell effector functions and alters the activation threshold of autoreactive T cells, thereby leading to complete protection from chronic autoimmune inflammatory disease in both mice and rats. We further show that SH3GL1 regulates human T cell signaling and T cell receptor internalization, and its expression is upregulated in rheumatoid arthritis patients. Collectively our data identify SH3GL1 as a key regulator of T cell activation, and as a potential target for treatment of autoimmune diseases. The autoimmune disorder, rheumatoid arthritis (RA), has been associated with multiple pathophysiological factors. Here the authors show that deficiency in endophilin A2 in rodents protects them from experimental arthritis by altering T cell activation threshold and effector functions, thereby hinting a potential target for RA therapy.
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Affiliation(s)
- Ulrika Norin
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
| | - Carola Rintisch
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.,Medical Inflammation Research, Lund University, Lund, Sweden.,Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Liesu Meng
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.,The Second affiliated hospital to Xi'an Jiaotong University and the Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 710061, Xi'an, Shaanxi, China
| | - Florian Forster
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Diana Ekman
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.,Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Jonatan Tuncel
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Katrin Klocke
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Johan Bäcklund
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Min Yang
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Michael Y Bonner
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Gonzalo Fernandez Lahore
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Jaime James
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Klementy Shchetynsky
- Rheumatology Unit, Department of Medicine, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Maria Bergquist
- Department of Rheumatology and Inflammation Research, Institute for Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Medical Sciences, Clinical Physiology, Uppsala University, Uppsala, Sweden
| | - Inger Gjertsson
- Department of Rheumatology and Inflammation Research, Institute for Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany.,Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Liselotte Bäckdahl
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Rikard Holmdahl
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden. .,The Second affiliated hospital to Xi'an Jiaotong University and the Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 710061, Xi'an, Shaanxi, China.
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40
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Markouli M, Strepkos D, Chlamydas S, Piperi C. Histone lysine methyltransferase SETDB1 as a novel target for central nervous system diseases. Prog Neurobiol 2020; 200:101968. [PMID: 33279625 DOI: 10.1016/j.pneurobio.2020.101968] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/31/2020] [Accepted: 11/29/2020] [Indexed: 12/14/2022]
Abstract
Epigenetic changes that regulate chromatin structure have a major impact in genome stabilization and maintenance of cellular homeostasis, been recently implicated in the pathophysiology of central nervous system (CNS). Aberrant expression and dysregulation of histone modification enzymes has been associated with the development of several CNS disorders, revealing these enzymes as putative targets for drug development and novel therapeutic approaches. SETDB1 is a histone lysine methyltransferase responsible for the di- and tri-methylation of histone 3 (H3) at lysine (K) 9 in euchromatic regions further promoting gene silencing through heterochromatin formation. By this way, SETDB1 has been shown to regulate gene expression and influence normal cellular homeostasis required for nervous system function while it is also implicated in the pathogenesis of CNS disorders. Among them, brain tumors, schizophrenia, Huntington's disease, autism spectrum disorders along with alcohol-induced fetal neurobehavioral deficits and Prader-Willi syndrome are representative examples, indicating the aberrant expression and function of SETDB1 as a common pathogenic factor. In this review, we focus on SETDB1-associated molecular mechanisms implicated in CNS physiology and disease while we further discuss current pharmacological approaches targeting SETDB1 enzymatic activity with beneficial effects.
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Affiliation(s)
- Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Strepkos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Sarantis Chlamydas
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece.
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41
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Rahnama M, Novikova O, Starnes JH, Zhang S, Chen L, Farman ML. Transposon-mediated telomere destabilization: a driver of genome evolution in the blast fungus. Nucleic Acids Res 2020; 48:7197-7217. [PMID: 32558886 PMCID: PMC7367193 DOI: 10.1093/nar/gkaa287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 04/03/2020] [Accepted: 04/14/2020] [Indexed: 01/01/2023] Open
Abstract
The fungus Magnaporthe oryzae causes devastating diseases of crops, including rice and wheat, and in various grasses. Strains from ryegrasses have highly unstable chromosome ends that undergo frequent rearrangements, and this has been associated with the presence of retrotransposons (Magnaporthe oryzae Telomeric Retrotransposons-MoTeRs) inserted in the telomeres. The objective of the present study was to determine the mechanisms by which MoTeRs promote telomere instability. Targeted cloning, mapping, and sequencing of parental and novel telomeric restriction fragments (TRFs), along with MinION sequencing of genomic DNA allowed us to document the precise molecular alterations underlying 109 newly-formed TRFs. These included truncations of subterminal rDNA sequences; acquisition of MoTeR insertions by 'plain' telomeres; insertion of the MAGGY retrotransposons into MoTeR arrays; MoTeR-independent expansion and contraction of subtelomeric tandem repeats; and a variety of rearrangements initiated through breaks in interstitial telomere tracts that are generated during MoTeR integration. Overall, we estimate that alterations occurred in approximately sixty percent of chromosomes (one in three telomeres) analyzed. Most importantly, we describe an entirely new mechanism by which transposons can promote genomic alterations at exceptionally high frequencies, and in a manner that can promote genome evolution while minimizing collateral damage to overall chromosome architecture and function.
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Affiliation(s)
- Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Olga Novikova
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - John H Starnes
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Shouan Zhang
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Li Chen
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Mark L Farman
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
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42
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Son W, Choi KW. The Classic Lobe Eye Phenotype of Drosophila Is Caused by Transposon Insertion-Induced Misexpression of a Zinc-Finger Transcription Factor. Genetics 2020; 216:117-134. [PMID: 32641295 PMCID: PMC7463288 DOI: 10.1534/genetics.120.303486] [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: 08/02/2019] [Accepted: 07/06/2020] [Indexed: 11/18/2022] Open
Abstract
Drosophila Lobe (L) alleles were first discovered ∼100 years ago as spontaneous dominant mutants with characteristic developmental eye defects. However, the molecular basis for L dominant eye phenotypes has not been clearly understood. A previous work reported identification of CG10109/PRAS40 as the L gene, but subsequent analyses suggested that PRAS40 may not be related to L Here, we revisited the L gene to clarify this discrepancy and understand the basis for the dominance of L mutations. Genetic analysis localized the L gene to Oaz, which encodes a homolog of the vertebrate zinc finger protein 423 (Zfp423) family transcriptional regulators. We demonstrate that RNAi knockdown of Oaz almost completely restores all L dominant alleles tested. Lrev6-3 , a revertant allele of the L2 dominant eye phenotype, has an inframe deletion in the Oaz coding sequence. Molecular analysis of L dominant mutants identified allele-specific insertions of natural transposons (roo[ ]L1 , hopper[ ]L5 , and roo[ ]Lr ) or alterations of a preexisting transposon (L2 -specific mutations in roo[ ]Mohr) in the Oaz region. In addition, we generated additional L2 -reversion alleles by CRISPR targeting at Oaz These new loss-of-function Oaz mutations suppress the dominant L eye phenotype. Oaz protein is not expressed in wild-type eye disc but is expressed ectopically in L2/+ mutant eye disc. We induced male recombination between Oaz-GAL4 insertions and the L2 mutation through homologous recombination. By using the L2 -recombined GAL4 reporters, we show that Oaz-GAL4 is expressed ectopically in L2 eye imaginal disc. Taken together, our data suggest that neomorphic L eye phenotypes are likely due to misregulation of Oaz by spontaneous transposon insertions.
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Affiliation(s)
- Wonseok Son
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Kwang-Wook Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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43
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Geis FK, Goff SP. Silencing and Transcriptional Regulation of Endogenous Retroviruses: An Overview. Viruses 2020; 12:v12080884. [PMID: 32823517 PMCID: PMC7472088 DOI: 10.3390/v12080884] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
Almost half of the human genome is made up of transposable elements (TEs), and about 8% consists of endogenous retroviruses (ERVs). ERVs are remnants of ancient exogenous retrovirus infections of the germ line. Most TEs are inactive and not detrimental to the host. They are tightly regulated to ensure genomic stability of the host and avoid deregulation of nearby gene loci. Histone-based posttranslational modifications such as H3K9 trimethylation are one of the main silencing mechanisms. Trim28 is one of the identified master regulators of silencing, which recruits most prominently the H3K9 methyltransferase Setdb1, among other factors. Sumoylation and ATP-dependent chromatin remodeling factors seem to contribute to proper localization of Trim28 to ERV sequences and promote Trim28 interaction with Setdb1. Additionally, DNA methylation as well as RNA-mediated targeting of TEs such as piRNA-based silencing play important roles in ERV regulation. Despite the involvement of ERV overexpression in several cancer types, autoimmune diseases, and viral pathologies, ERVs are now also appreciated for their potential positive role in evolution. ERVs can provide new regulatory gene elements or novel binding sites for transcription factors, and ERV gene products can even be repurposed for the benefit of the host.
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Affiliation(s)
- Franziska K. Geis
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
| | - Stephen P. Goff
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY 10032, USA;
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA
- Correspondence: ; Tel.: +1-212-305-3794
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44
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Timpano S, Picketts DJ. Neurodevelopmental Disorders Caused by Defective Chromatin Remodeling: Phenotypic Complexity Is Highlighted by a Review of ATRX Function. Front Genet 2020; 11:885. [PMID: 32849845 PMCID: PMC7432156 DOI: 10.3389/fgene.2020.00885] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 07/20/2020] [Indexed: 12/15/2022] Open
Abstract
The ability to determine the genetic etiology of intellectual disability (ID) and neurodevelopmental disorders (NDD) has improved immensely over the last decade. One prevailing metric from these studies is the large percentage of genes encoding epigenetic regulators, including many members of the ATP-dependent chromatin remodeling enzyme family. Chromatin remodeling proteins can be subdivided into five classes that include SWI/SNF, ISWI, CHD, INO80, and ATRX. These proteins utilize the energy from ATP hydrolysis to alter nucleosome positioning and are implicated in many cellular processes. As such, defining their precise roles and contributions to brain development and disease pathogenesis has proven to be complex. In this review, we illustrate that complexity by reviewing the roles of ATRX on genome stability, replication, and transcriptional regulation and how these mechanisms provide key insight into the phenotype of ATR-X patients.
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Affiliation(s)
- Sara Timpano
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.,Department of Medicine, University of Ottawa, Ottawa, ON, Canada.,University of Ottawa Brain and Mind Research Institute, Ottawa, ON, Canada
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45
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Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans-Acting Modifiers. Viruses 2020; 12:v12080810. [PMID: 32727076 PMCID: PMC7472028 DOI: 10.3390/v12080810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation.
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Rebollo R, Galvão-Ferrarini M, Gagnier L, Zhang Y, Ferraj A, Beck CR, Lorincz MC, Mager DL. Inter-Strain Epigenomic Profiling Reveals a Candidate IAP Master Copy in C3H Mice. Viruses 2020; 12:v12070783. [PMID: 32708087 PMCID: PMC7411935 DOI: 10.3390/v12070783] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
Insertions of endogenous retroviruses cause a significant fraction of mutations in inbred mice but not all strains are equally susceptible. Notably, most new Intracisternal A particle (IAP) ERV mutagenic insertions have occurred in C3H mice. We show here that strain-specific insertional polymorphic IAPs accumulate faster in C3H/HeJ mice, relative to other sequenced strains, and that IAP transcript levels are higher in C3H/HeJ embryonic stem (ES) cells compared to other ES cells. To investigate the mechanism for high IAP activity in C3H mice, we identified 61 IAP copies in C3H/HeJ ES cells enriched with H3K4me3 (a mark of active promoters) and, among those tested, all are unmethylated in C3H/HeJ ES cells. Notably, 13 of the 61 are specific to C3H/HeJ and are members of the non-autonomous 1Δ1 IAP subfamily that is responsible for nearly all new insertions in C3H. One copy is full length with intact open reading frames and hence potentially capable of providing proteins in trans to other 1Δ1 elements. This potential “master copy” is present in other strains, including 129, but its 5’ long terminal repeat (LTR) is methylated in 129 ES cells. Thus, the unusual IAP activity in C3H may be due to reduced epigenetic repression coupled with the presence of a master copy.
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Affiliation(s)
- Rita Rebollo
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC V5Z1L3, Canada; (L.G.); (Y.Z.)
- University of Lyon, INSA-Lyon, INRA, BF2i, UMR0203, F-69621 Villeurbanne, France;
- Correspondence: (R.R.); (D.L.M.)
| | | | - Liane Gagnier
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC V5Z1L3, Canada; (L.G.); (Y.Z.)
| | - Ying Zhang
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC V5Z1L3, Canada; (L.G.); (Y.Z.)
| | - Ardian Ferraj
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA; (A.F.); (C.R.B.)
| | - Christine R. Beck
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA; (A.F.); (C.R.B.)
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Matthew C. Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T1Z3, Canada;
| | - Dixie L. Mager
- Terry Fox Laboratory, British Columbia Cancer, Vancouver, BC V5Z1L3, Canada; (L.G.); (Y.Z.)
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T1Z3, Canada;
- Correspondence: (R.R.); (D.L.M.)
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Espinosa E, Paly E, Barre FX. High-Resolution Whole-Genome Analysis of Sister-Chromatid Contacts. Mol Cell 2020; 79:857-869.e3. [PMID: 32681820 DOI: 10.1016/j.molcel.2020.06.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022]
Abstract
Sister-chromatid cohesion describes the orderly association of newly replicated DNA molecules behind replication forks. It plays an essential role in the maintenance and faithful transmission of genetic information. Cohesion is created by DNA topological links and proteinaceous bridges, whose formation and deposition could be potentially affected by many processes. Current knowledge on cohesion has been mainly gained by fluorescence microscopy observation. However, the resolution limit of microscopy and the restricted number of genomic positions that can be simultaneously visualized considerably hampered progress. Here, we present a high-throughput methodology to monitor sister-chromatid contacts (Hi-SC2). Using the multi-chromosomal Vibrio cholerae bacterium as a model, we show that Hi-SC2 permits to monitor local variations in sister-chromatid cohesion at a high resolution over a whole genome.
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Affiliation(s)
- Elena Espinosa
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Evelyne Paly
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - François-Xavier Barre
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Université Paris Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
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Choi JY, Lee YCG. Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements. PLoS Genet 2020; 16:e1008872. [PMID: 32673310 PMCID: PMC7365398 DOI: 10.1371/journal.pgen.1008872] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Transposable elements (TEs) are genomic parasites that selfishly replicate at the expense of host fitness. Fifty years of evolutionary studies of TEs have concentrated on the deleterious genetic effects of TEs, such as their effects on disrupting genes and regulatory sequences. However, a flurry of recent work suggests that there is another important source of TEs’ harmful effects—epigenetic silencing. Host genomes typically silence TEs by the deposition of repressive epigenetic marks. While this silencing reduces the selfish replication of TEs and should benefit hosts, a picture is emerging that the epigenetic silencing of TEs triggers inadvertent spreading of repressive marks to otherwise expressed neighboring genes, ultimately jeopardizing host fitness. In this Review, we provide a long-overdue overview of the recent genome-wide evidence for the presence and prevalence of TEs’ epigenetic effects, highlighting both the similarities and differences across mammals, insects, and plants. We lay out the current understanding of the functional and fitness consequences of TEs’ epigenetic effects, and propose possible influences of such effects on the evolution of both hosts and TEs themselves. These unique evolutionary consequences indicate that TEs’ epigenetic effect is not only a crucial component of TE biology but could also be a significant contributor to genome function and evolution.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York State, United States of America
| | - Yuh Chwen G. Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
- * E-mail:
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Lanciano S, Cristofari G. Measuring and interpreting transposable element expression. Nat Rev Genet 2020; 21:721-736. [PMID: 32576954 DOI: 10.1038/s41576-020-0251-y] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
Abstract
Transposable elements (TEs) are insertional mutagens that contribute greatly to the plasticity of eukaryotic genomes, influencing the evolution and adaptation of species as well as physiology or disease in individuals. Measuring TE expression helps to understand not only when and where TE mobilization can occur but also how this process alters gene expression, chromatin accessibility or cellular signalling pathways. Although genome-wide gene expression assays such as RNA sequencing include transposon-derived transcripts, most computational analytical tools discard or misinterpret TE-derived reads. Emerging approaches are improving the identification of expressed TE loci and helping to discriminate TE transcripts that permit TE mobilization from chimeric gene-TE transcripts or pervasive transcription. Here we review the main challenges associated with the detection of TE expression, including mappability, insertional and internal sequence polymorphisms, and the diversity of the TE transcriptional landscape, as well as the different experimental and computational strategies to solve them.
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DNA methylation dynamics at transposable elements in mammals. Essays Biochem 2020; 63:677-689. [PMID: 31654072 DOI: 10.1042/ebc20190039] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/29/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022]
Abstract
Transposable elements dominate the mammalian genome, but their contribution to genetic and epigenetic regulation has been largely overlooked. This was in part due to technical limitations, which made the study of repetitive sequences at single copy resolution difficult. The advancement of next-generation sequencing assays in the last decade has greatly enhanced our understanding of transposable element function. In some instances, specific transposable elements are thought to have been co-opted into regulatory roles during both mouse and human development, while in disease such regulatory potential can contribute to malignancy. DNA methylation is arguably the best characterised regulator of transposable element activity. DNA methylation is associated with transposable element repression, and acts to limit their genotoxic potential. In specific developmental contexts, erasure of DNA methylation is associated with a burst of transposable element expression. Developmental regulation of DNA methylation enables transposon activation, ensuring their survival and propagation throughout the host genome, and also allows the host access to regulatory sequences encoded within the elements. Here I discuss DNA methylation at transposable elements, describing its function and dynamic regulation throughout murine and human development.
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