151
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Pfaff AL, Singleton LM, Kõks S. Mechanisms of disease-associated SINE-VNTR-Alus. Exp Biol Med (Maywood) 2022; 247:756-764. [PMID: 35387528 DOI: 10.1177/15353702221082612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
SINE-VNTR-Alus (SVAs) are the youngest retrotransposon family in the human genome. Their ongoing mobilization has generated genetic variation within the human population. At least 24 insertions to date, detailed in this review, have been associated with disease. The predominant mechanisms through which this occurs are alterations to normal splicing patterns, exonic insertions causing loss-of-function mutations, and large genomic deletions. Dissecting the functional impact of these SVAs and the mechanism through which they cause disease provides insight into the consequences of their presence in the genome and how these elements could influence phenotypes. Many of these disease-associated SVAs have been difficult to characterize and would not have been identified through routine analyses. However, the number identified has increased in recent years as DNA and RNA sequencing data became more widely available. Therefore, as the search for complex structural variation in disease continues, it is likely to yield further disease-causing SVA insertions.
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Affiliation(s)
- Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Lewis M Singleton
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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152
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A hypothesis: Retrotransposons as a relay of epigenetic marks in intergenerational epigenetic inheritance. Gene 2022; 817:146229. [PMID: 35063571 DOI: 10.1016/j.gene.2022.146229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/13/2021] [Accepted: 01/13/2022] [Indexed: 12/19/2022]
Abstract
Epigenetic marks in gametes, which both respond to the parental environmental factors and shape offspring phenotypes, are usually positioned to mediate intergenerational or transgenerational epigenetic inheritance. Nonetheless, the mechanisms through which gametic epigenetic signatures encode parental acquired phenotypes, and further initiate a cascade of molecular events to affect offspring phenotypes during early embryonic development, remain unclear. Retrotransposons are mobile DNA elements that could resist to genomic epigenetic reprogramming at specific loci and rewire the core regulatory networks of embryogenesis. Increasing evidences show that retrotransposons in the embryonic genome could interact with gametic epigenetic marks, which provides a tentative possibility that retrotransposons may serve as a relay of gametic epigenetic marks to transmit parental acquired traits. Here, we summarize the recent progress in exploring the crosstalk between gametic epigenetic marks and retrotransposons, and the regulation of gene expression and early embryonic development by retrotransposons. Accordingly, deciphering the mystery of interactions between gametic epigenetic marks and retrotransposons during early embryonic development will provide valuable insights into the intergenerational or transgenerational transmission of acquired traits.
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153
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Westerdahl H, Mellinger S, Sigeman H, Kutschera VE, Proux-Wéra E, Lundberg M, Weissensteiner M, Churcher A, Bunikis I, Hansson B, Wolf JBW, Strandh M. The genomic architecture of the passerine MHC region: high repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes. Mol Ecol Resour 2022; 22:2379-2395. [PMID: 35348299 DOI: 10.1111/1755-0998.13614] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 12/01/2022]
Abstract
The Major Histocompatibility Complex (MHC) is of central importance to the immune system, and an optimal MHC diversity is believed to maximize pathogen elimination. Birds show substantial variation in MHC diversity, ranging from few genes in most bird orders to very many genes in passerines. Our understanding of the evolutionary trajectories of the MHC in passerines is hampered by lack of data on genomic organization. Therefore, we assemble and annotate the MHC genomic region of the great reed warbler (Acrocephalus arundinaceus), using long-read sequencing and optical mapping. The MHC region is large (>5.5Mb), characterized by structural changes compared to hitherto investigated bird orders and shows higher repeat content than the genome average. These features were supported by analyses in three additional passerines. MHC genes in passerines are found in two different chromosomal arrangements, either as single copy MHC genes located among non-MHC genes, or as tandemly duplicated tightly linked MHC genes. Some single copy MHC genes are old and putative orthologs among species. In contrast tandemly duplicated MHC genes are monophyletic within species and have evolved by simultaneous gene duplication of several MHC genes. Structural differences in the MHC genomic region among bird orders seem substantial compared to mammals and have possibly been fuelled by clade-specific immune system adaptations. Our study provides methodological guidance in characterizing complex genomic regions, constitutes a resource for MHC research in birds, and calls for a revision of the general belief that avian MHC has a conserved gene order and small size compared to mammals.
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Affiliation(s)
- Helena Westerdahl
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Samantha Mellinger
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Hanna Sigeman
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121, Solna, Sweden
| | - Estelle Proux-Wéra
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121, Solna, Sweden
| | - Max Lundberg
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Matthias Weissensteiner
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Allison Churcher
- National Bioinformatics Infrastructure Sweden, Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden
| | - Ignas Bunikis
- Uppsala Genome Center, Science for Life Laboratory, Dept. of Immunology, Genetics and Pathology, Uppsala University, BMC, Box 815, SE-752 37, Uppsala, Sweden
| | - Bengt Hansson
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
| | - Jochen B W Wolf
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Grosshaderner Str. 2, 82152, Planegg-Martinsried, Germany
| | - Maria Strandh
- Molecular Ecology and Evolution Lab, Department of Biology, Lund University, Sölvegatan 37, SE-223 62, Lund, Sweden
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154
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Pinter TB, Ervin CS, Deb A, Penner-Hahn JE, Pecoraro VL. Cu(I) Binding to Designed Proteins Reveals a Putative Copper Binding Site of the Human Line1 Retrotransposon Protein ORF1p. Inorg Chem 2022; 61:5084-5091. [PMID: 35286080 PMCID: PMC10754372 DOI: 10.1021/acs.inorgchem.2c00057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long interspersed nuclear elements-1 (L1) are autonomous retrotransposons that encode two proteins in different open reading frames (ORF1 and ORF2). The ORF1p, which may be an RNA binding and chaperone protein, contains a three-stranded coiled coil (3SCC) domain that facilitates the formation of the biologically active homotrimer. This 3SCC domain is composed of seven amino acid (heptad) repeats as found in native and designed peptides and a stammer that modifies the helical structure. Cysteine residues occur at three hydrophobic positions (2 a and 1 d sites) within this domain. We recently showed that the cysteine layers in ORF1p and model de novo designed peptides bind the toxic metalloid lead(II) with high affinities, a feature that had not been previously recognized. However, there is little understanding of how essential metal ions might interact with this metal binding domain. We have, therefore, investigated the copper(I) binding properties of analogous de novo designed 3SCCs that contain cysteine layers within the hydrophobic core. The results from UV-visible and X-ray absorption spectroscopy show that these designed peptides bind Cu(I) with high affinity in a pH-dependent manner. At pH 9, monomeric trigonal planar Cu(I)S3 centers are formed with 1 equiv of metal, while dinuclear centers form with a second equivalent of metal. At physiologic pH conditions, the dinuclear center forms cooperatively. These data suggest that ORF1p is capable of binding two copper ions to its tris(cysteine) layers. This has major implications for ORF1p coiled coil domain stability and dynamics, ultimately potentially impacting the resulting biological activity.
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Affiliation(s)
- Tyler B.J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- These authors contributed equally to this work
| | - Catherine S. Ervin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- These authors contributed equally to this work
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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155
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van Bree EJ, Guimarães RLFP, Lundberg M, Blujdea ER, Rosenkrantz JL, White FTG, Poppinga J, Ferrer-Raventós P, Schneider AFE, Clayton I, Haussler D, Reinders MJT, Holstege H, Ewing AD, Moses C, Jacobs FMJ. A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci. Genome Res 2022; 32:656-670. [PMID: 35332097 PMCID: PMC8997352 DOI: 10.1101/gr.275515.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
Abstract
Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SINE-VNTR-Alu (SVA) elements, a class of great ape-specific transposable elements with gene-regulatory roles, which represents a major source of structural variability in the human population. We highlight the presence of structurally variable SVAs (SV-SVAs) in neurological disease-associated loci, and we further associate SV-SVAs to disease-associated SNPs and differential gene expression using luciferase assays and expression quantitative trait loci data. Finally, we genetically deleted SV-SVAs in the BIN1 and CD2AP Alzheimer's disease-associated risk loci and in the BCKDK Parkinson's disease-associated risk locus and assessed multiple aspects of their gene-regulatory influence in a human neuronal context. Together, this study reveals a novel layer of genetic variation in transposable elements that may contribute to identification of the structural variants that are the actual drivers of disease associations of GWAS loci.
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Affiliation(s)
- Elisabeth J van Bree
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Rita L F P Guimarães
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.,Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - Mischa Lundberg
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Elena R Blujdea
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Jimi L Rosenkrantz
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Fred T G White
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Josse Poppinga
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Paula Ferrer-Raventós
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Anne-Fleur E Schneider
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Isabella Clayton
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - David Haussler
- UC Santa Cruz Genomics Institute, and Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, California 95064, USA
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands
| | - Henne Holstege
- Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands.,Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam, The Netherlands
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Colette Moses
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Frank M J Jacobs
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.,Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam, The Netherlands
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156
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Garland W, Müller I, Wu M, Schmid M, Imamura K, Rib L, Sandelin A, Helin K, Jensen TH. Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression. Mol Cell 2022; 82:1691-1707.e8. [PMID: 35349793 PMCID: PMC9433625 DOI: 10.1016/j.molcel.2022.03.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) are widespread genetic parasites known to be kept under tight transcriptional control. Here, we describe a functional connection between the mouse-orthologous “nuclear exosome targeting” (NEXT) and “human silencing hub” (HUSH) complexes, involved in nuclear RNA decay and the epigenetic silencing of TEs, respectively. Knocking out the NEXT component ZCCHC8 in embryonic stem cells results in elevated TE RNA levels. We identify a physical interaction between ZCCHC8 and the MPP8 protein of HUSH and establish that HUSH recruits NEXT to chromatin at MPP8-bound TE loci. However, while NEXT and HUSH both dampen TE RNA expression, their activities predominantly affect shorter non-polyadenylated and full-length polyadenylated transcripts, respectively. Indeed, our data suggest that the repressive action of HUSH promotes a condition favoring NEXT RNA decay activity. In this way, transcriptional and post-transcriptional machineries synergize to suppress the genotoxic potential of TE RNAs. Garland et al. report a physical and functional connection between the NEXT complex, involved in RNA decay, and the HUSH complex, involved in chromatin regulation. Together, NEXT and HUSH cooperate to control transposable element (TE) RNA expression in embryonic stem cells, suppressing pA− and pA+ transcripts, respectively.
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Affiliation(s)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iris Müller
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mengjun Wu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Leonor Rib
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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157
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Colonna Romano N, Fanti L. Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns. Cells 2022; 11:cells11061048. [PMID: 35326499 PMCID: PMC8947103 DOI: 10.3390/cells11061048] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome to another, in all organisms. For this reason, on the one hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality in individuals. On the other hand, TEs can increase genetic variability, making populations better equipped to respond adaptively to environmental change. To counteract the deleterious effects of TEs, organisms have evolved strategies to avoid their activation. However, their mobilization does occur. Usually, TEs are maintained silent through several mechanisms, but they can be reactivated during certain developmental windows. Moreover, TEs can become de-repressed because of drastic changes in the external environment. Here, we describe the ‘double life’ of TEs, being both ‘parasites’ and ‘symbionts’ of the genome. We also argue that the transposition of TEs contributes to two important evolutionary processes: the temporal dynamic of evolution and the induction of genetic variability. Finally, we discuss how the interplay between two TE-dependent phenomena, insertional mutagenesis and epigenetic plasticity, plays a role in the process of evolution.
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158
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Rodems TS, Juang DS, Stahlfeld CN, Gilsdorf CS, Krueger TEG, Heninger E, Zhao SG, Sperger JM, Beebe DJ, Haffner MC, Lang JM. SEEMLIS: a flexible semi-automated method for enrichment of methylated DNA from low-input samples. Clin Epigenetics 2022; 14:37. [PMID: 35272673 PMCID: PMC8908705 DOI: 10.1186/s13148-022-01252-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/18/2022] [Indexed: 01/02/2023] Open
Abstract
Background DNA methylation alterations have emerged as hallmarks of cancer and have been proposed as screening, prognostic, and predictive biomarkers. Traditional approaches for methylation analysis have relied on bisulfite conversion of DNA, which can damage DNA and is not suitable for targeted gene analysis in low-input samples. Here, we have adapted methyl-CpG-binding domain protein 2 (MBD2)-based DNA enrichment for use on a semi-automated exclusion-based sample preparation (ESP) platform for robust and scalable enrichment of methylated DNA from low-input samples, called SEEMLIS. Results We show that combining methylation-sensitive enzyme digestion with ESP-based MBD2 enrichment allows for single gene analysis with high sensitivity for GSTP1 in highly impure, heterogenous samples. We also show that ESP-based MBD2 enrichment coupled with targeted pre-amplification allows for analysis of multiple genes with sensitivities approaching the single cell level in pure samples for GSTP1 and RASSF1 and sensitivity down to 14 cells for these genes in highly impure samples. Finally, we demonstrate the potential clinical utility of SEEMLIS by successful detection of methylated gene signatures in circulating tumor cells (CTCs) from patients with prostate cancer with varying CTC number and sample purity. Conclusions SEEMLIS is a robust assay for targeted DNA methylation analysis in low-input samples, with flexibility at multiple steps. We demonstrate the feasibility of this assay to analyze DNA methylation in prostate cancer cells using CTCs from patients with prostate cancer as a real-world example of a low-input analyte of clinical importance. In summary, this novel assay provides a platform for determining methylation signatures in rare cell populations with broad implications for research as well as clinical applications. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01252-4.
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Affiliation(s)
- Tamara S Rodems
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Duane S Juang
- Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA
| | - Charlotte N Stahlfeld
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Cole S Gilsdorf
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Tim E G Krueger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Erika Heninger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Jamie M Sperger
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - David J Beebe
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA.,Department of Pathology, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, N., Seattle, WA, 98109, USA.,Department of Pathology, University of Washington, 1959 NE Pacific St., Seattle, WA, 98195, USA.,Department of Pathology, Johns Hopkins School of Medicine, 600 N Wolfe St., Baltimore, MD, 21287, USA
| | - Joshua M Lang
- University of Wisconsin Carbone Cancer Center, Madison, 1111 Highland Ave., Madison, WI, 53705, USA. .,Department of Medicine, University of Wisconsin, Madison, 1111 Highland Ave., Madison, WI, 53705, USA. .,7151 WI Institutes for Medical Research, 1111 Highland Ave., Madison, WI, 53705, USA.
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159
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Yang D, Cho S, Cho SI, Kim M, Seong MW, Park SS. Genetic mutation spectrum of pantothenate kinase-associated neurodegeneration expanded by breakpoint sequencing in pantothenate kinase 2 gene. Orphanet J Rare Dis 2022; 17:111. [PMID: 35246191 PMCID: PMC8896100 DOI: 10.1186/s13023-022-02251-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neurodegeneration with brain iron accumulation describes a group of rare heterogeneous progressive neurodegenerative disorders characterized by excessive iron accumulation in the basal ganglia region. Pantothenate kinase-associated neurodegeneration (PKAN) is a major form of this disease. RESULTS A total of 7 unrelated patients were diagnosed with PKAN in a single tertiary center from August 2009 to February 2018. Ten variants in PANK2 including three novel sequence variants and one large exonic deletion were detected. Sequencing of the breakpoint was performed to predict the mechanism of large deletion and AluSx3 and AluSz6 were found with approximately 97.3% sequence homology. CONCLUSION The findings support the disease-causing role of PANK2 and indicate the possibility that exonic deletion of PANK2 found in PKAN is mediated through Alu-mediated homologous recombination.
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Affiliation(s)
- Dahae Yang
- Department of Laboratory Medicine, Kosin Gospel University Hospital, Busan, Korea
| | - Sanghyun Cho
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Manjin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Korea. .,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea.
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160
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Almeida MV, Vernaz G, Putman AL, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet 2022; 38:529-553. [DOI: 10.1016/j.tig.2022.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022]
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161
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Khor JM, Ettensohn CA. Architecture and evolution of the cis-regulatory system of the echinoderm kirrelL gene. eLife 2022; 11:72834. [PMID: 35212624 PMCID: PMC8903837 DOI: 10.7554/elife.72834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
The gene regulatory network (GRN) that underlies echinoderm skeletogenesis is a prominent model of GRN architecture and evolution. KirrelL is an essential downstream effector gene in this network and encodes an Ig-superfamily protein required for the fusion of skeletogenic cells and the formation of the skeleton. In this study, we dissected the transcriptional control region of the kirrelL gene of the purple sea urchin, Strongylocentrotus purpuratus. Using plasmid- and bacterial artificial chromosome-based transgenic reporter assays, we identified key cis-regulatory elements (CREs) and transcription factor inputs that regulate Sp-kirrelL, including direct, positive inputs from two key transcription factors in the skeletogenic GRN, Alx1 and Ets1. We next identified kirrelL cis-regulatory regions from seven other echinoderm species that together represent all classes within the phylum. By introducing these heterologous regulatory regions into developing sea urchin embryos we provide evidence of their remarkable conservation across ~500 million years of evolution. We dissected in detail the kirrelL regulatory region of the sea star, Patiria miniata, and demonstrated that it also receives direct inputs from Alx1 and Ets1. Our findings identify kirrelL as a component of the ancestral echinoderm skeletogenic GRN. They support the view that GRN subcircuits, including specific transcription factor–CRE interactions, can remain stable over vast periods of evolutionary history. Lastly, our analysis of kirrelL establishes direct linkages between a developmental GRN and an effector gene that controls a key morphogenetic cell behavior, cell–cell fusion, providing a paradigm for extending the explanatory power of GRNs.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States
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162
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Niu Y, Teng X, Zhou H, Shi Y, Li Y, Tang Y, Zhang P, Luo H, Kang Q, Xu T, He S. Characterizing mobile element insertions in 5675 genomes. Nucleic Acids Res 2022; 50:2493-2508. [PMID: 35212372 PMCID: PMC8934628 DOI: 10.1093/nar/gkac128] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/07/2022] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-scale genome sequencing are still lacking compared to those for SNPs and SVs. Here, we report a comprehensive map of 36 699 non-reference MEIs constructed from 5675 genomes, comprising 2998 Chinese samples (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 1KGP). We discovered that LINE-1 insertions were highly enriched in centromere regions, implying the role of chromosome context in retroelement insertion. After functional annotation, we estimated that MEIs are responsible for about 9.3% of all protein-truncating events per genome. Finally, we built a companion database named HMEID for public use. This resource represents the latest and largest genomewide study on MEIs and will have broad utility for exploration of human MEI findings.
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Affiliation(s)
- Yiwei Niu
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueyi Teng
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Honghong Zhou
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yirong Shi
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyan Li
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiheng Tang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Huaxia Luo
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Quan Kang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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163
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Prakrithi P, Singhal K, Sharma D, Jain A, Bhoyar RC, Imran M, Senthilvel V, Divakar MK, Mishra A, Scaria V, Sivasubbu S, Mukerji M. An Alu insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project. NAR Genom Bioinform 2022; 4:lqac009. [PMID: 35178516 PMCID: PMC8846365 DOI: 10.1093/nargab/lqac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Actively retrotransposing primate-specific Alu repeats display insertion-deletion (InDel) polymorphism through their insertion at new loci. In the global datasets, Indian populations remain under-represented and so do their Alu InDels. Here, we report the genomic landscape of Alu InDels from the recently released 1021 Indian Genomes (IndiGen) (available at https://clingen.igib.res.in/indigen). We identified 9239 polymorphic Alu insertions that include private (3831), rare (3974) and common (1434) insertions with an average of 770 insertions per individual. We achieved an 89% PCR validation of the predicted genotypes in 94 samples tested. About 60% of identified InDels are unique to IndiGen when compared to other global datasets; 23% of sites were shared with both SGDP and HGSVC; among these, 58% (1289 sites) were common polymorphisms in IndiGen. The insertions not only show a bias for genic regions, with a preference for introns but also for the associated genes showing enrichment for processes like cell morphogenesis and neurogenesis (P-value < 0.05). Approximately, 60% of InDels mapped to genes present in the OMIM database. Finally, we show that 558 InDels can serve as ancestry informative markers to segregate global populations. This study provides a valuable resource for baseline Alu InDels that would be useful in population genomics.
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Affiliation(s)
- P Prakrithi
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Khushboo Singhal
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Disha Sharma
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Abhinav Jain
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Mohamed Imran
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Vigneshwar Senthilvel
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Anushree Mishra
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Mitali Mukerji
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
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164
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Li Y, Jiang N, Sun Y. AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes. PLANT PHYSIOLOGY 2022; 188:955-970. [PMID: 34792587 PMCID: PMC8825457 DOI: 10.1093/plphys/kiab524] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Short interspersed nuclear elements (SINEs) are a widespread type of small transposable element (TE). With increasing evidence for their impact on gene function and genome evolution in plants, accurate genome-scale SINE annotation becomes a fundamental step for studying the regulatory roles of SINEs and their relationship with other components in the genomes. Despite the overall promising progress made in TE annotation, SINE annotation remains a major challenge. Unlike some other TEs, SINEs are short and heterogeneous, and they usually lack well-conserved sequence or structural features. Thus, current SINE annotation tools have either low sensitivity or high false discovery rates. Given the demand and challenges, we aimed to provide a more accurate and efficient SINE annotation tool for plant genomes. The pipeline starts with maximizing the pool of SINE candidates via profile hidden Markov model-based homology search and de novo SINE search using structural features. Then, it excludes the false positives by integrating all known features of SINEs and the features of other types of TEs that can often be misannotated as SINEs. As a result, the pipeline substantially improves the tradeoff between sensitivity and accuracy, with both values close to or over 90%. We tested our tool in Arabidopsis thaliana and rice (Oryza sativa), and the results show that our tool competes favorably against existing SINE annotation tools. The simplicity and effectiveness of this tool would potentially be useful for generating more accurate SINE annotations for other plant species. The pipeline is freely available at https://github.com/yangli557/AnnoSINE.
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Affiliation(s)
- Yang Li
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR, China
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165
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Jiang T, Zhang XO, Weng Z, Xue W. Deletion and replacement of long genomic sequences using prime editing. Nat Biotechnol 2022; 40:227-234. [PMID: 34650270 PMCID: PMC8847310 DOI: 10.1038/s41587-021-01026-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/19/2021] [Indexed: 12/21/2022]
Abstract
Genomic insertions, duplications and insertion/deletions (indels), which account for ~14% of human pathogenic mutations, cannot be accurately or efficiently corrected by current gene-editing methods, especially those that involve larger alterations (>100 base pairs (bp)). Here, we optimize prime editing (PE) tools for creating precise genomic deletions and direct the replacement of a genomic fragment ranging from ~1 kilobases (kb) to ~10 kb with a desired sequence (up to 60 bp) in the absence of an exogenous DNA template. By conjugating Cas9 nuclease to reverse transcriptase (PE-Cas9) and combining it with two PE guide RNAs (pegRNAs) targeting complementary DNA strands, we achieve precise and specific deletion and repair of target sequences via using this PE-Cas9-based deletion and repair (PEDAR) method. PEDAR outperformed other genome-editing methods in a reporter system and at endogenous loci, efficiently creating large and precise genomic alterations. In a mouse model of tyrosinemia, PEDAR removed a 1.38-kb pathogenic insertion within the Fah gene and precisely repaired the deletion junction to restore FAH expression in liver.
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Affiliation(s)
- Tingting Jiang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.
- Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA.
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166
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Huang Y, Xu F, Mei S, Liu X, Zhao F, Wei L, Fan Z, Hu Y, Wang L, Ai B, Cen S, Liang C, Guo F. MxB inhibits long interspersed element type 1 retrotransposition. PLoS Genet 2022; 18:e1010034. [PMID: 35171907 PMCID: PMC8849481 DOI: 10.1371/journal.pgen.1010034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/12/2022] [Indexed: 12/13/2022] Open
Abstract
Long interspersed element type 1 (LINE-1, also L1 for short) is the only autonomously transposable element in the human genome. Its insertion into a new genomic site may disrupt the function of genes, potentially causing genetic diseases. Cells have thus evolved a battery of mechanisms to tightly control LINE-1 activity. Here, we report that a cellular antiviral protein, myxovirus resistance protein B (MxB), restricts the mobilization of LINE-1. This function of MxB requires the nuclear localization signal located at its N-terminus, its GTPase activity and its ability to form oligomers. We further found that MxB associates with LINE-1 protein ORF1p and promotes sequestration of ORF1p to G3BP1-containing cytoplasmic granules. Since knockdown of stress granule marker proteins G3BP1 or TIA1 abolishes MxB inhibition of LINE-1, we conclude that MxB engages stress granule components to effectively sequester LINE-1 proteins within the cytoplasmic granules, thus hindering LINE-1 from accessing the nucleus to complete retrotransposition. Thus, MxB protein provides one mechanism for cells to control the mobility of retroelements. Retrotransposons occupy more than 40% of human genome, and have co-evolved with humans for millions of years. Long interspersed element type 1 (LINE-1, or L1) is the only retrotransposon that is able to jump to a new locus. LINE-1 retrotransposition causes genome instability, and is associated with genetic diseases including autoimmune diseases and cancer. To suppress this genome toxicity caused by LINE-1, humans have developed multi-layered mechanisms to control LINE-1 activity. MxB has been previously shown to inhibit LINE-1 mobility, thus contributing to host restriction of LINE-1. Here, we further demonstrate that MxB effectively restricts LINE-1 retrotransposition by sequestering LINE-1 ribonucleoprotein (RNP) within the cytoplasmic stress granules, thus guards genome stability. Hence our data attribute the restriction function of MxB to sequestering LINE-1 RNP to stress granules.
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Affiliation(s)
- Yu Huang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Fengwen Xu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Shan Mei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Xiaoman Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Fei Zhao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liang Wei
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Zhangling Fan
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Yamei Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Liming Wang
- Department of Medical Oncology, Beijing Hospital, Beijing, P. R. China
| | - Bin Ai
- Department of Medical Oncology, Beijing Hospital, Beijing, P. R. China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
| | - Chen Liang
- McGill Centre for Viral Diseases, Lady Davis Institute, Jewish General Hospital, Montreal, Canada
- * E-mail: (CL); (FG)
| | - Fei Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China
- * E-mail: (CL); (FG)
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167
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Freeman B, White T, Kaul T, Stow EC, Baddoo M, Ungerleider N, Morales M, Yang H, Deharo D, Deininger P, Belancio V. Analysis of epigenetic features characteristic of L1 loci expressed in human cells. Nucleic Acids Res 2022; 50:1888-1907. [PMID: 35100410 PMCID: PMC8887483 DOI: 10.1093/nar/gkac013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 12/27/2021] [Accepted: 01/24/2022] [Indexed: 12/26/2022] Open
Abstract
Only a select few L1 loci in the human genome are expressed in any given cell line or organ, likely to minimize damage done to the genome. The epigenetic features and requirements of expressed L1 loci are currently unknown. Using human cells and comprehensive epigenetic analysis of individual expressed and unexpressed L1 loci, we determined that endogenous L1 transcription depends on a combination of epigenetic factors, including open chromatin, activating histone modifications, and hypomethylation at the L1 promoter. We demonstrate that the L1 promoter seems to require interaction with enhancer elements for optimal function. We utilize epigenetic context to predict the expression status of L1Hs loci that are poorly mappable with RNA-Seq. Our analysis identified a population of ‘transitional’ L1 loci that likely have greater potential to be activated during the epigenetic dysregulation seen in tumors and during aging because they are the most responsive to targeted CRISPR-mediated delivery of trans-activating domains. We demonstrate that an engineered increase in endogenous L1 mRNA expression increases Alu mobilization. Overall, our findings present the first global and comprehensive analysis of epigenetic status of individual L1 loci based on their expression status and demonstrate the importance of epigenetic context for L1 expression heterogeneity.
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Affiliation(s)
- Benjamin Freeman
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Travis White
- Sloan Kettering Institute for Cancer Research, NY, NY 10065, USA
| | - Tiffany Kaul
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Emily C Stow
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Melody Baddoo
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA 70112, USA
| | - Maria Morales
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Hanlin Yang
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Dawn Deharo
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Prescott Deininger
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- To whom correspondence should be addressed. Tel: +1 504 988 4506; Fax: +1 504 988 1687;
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168
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Bonnet A, Lesage P. [Restriction of transposable elements and genome evolution: A fine balance to set up]. Med Sci (Paris) 2022; 38:18-20. [PMID: 35060878 DOI: 10.1051/medsci/2021231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Amandine Bonnet
- Université de Paris, Institut de recherche Saint-Louis, Inserm U944, CNRS UMR 7212, 75010 Paris, France
| | - Pascale Lesage
- Université de Paris, Institut de recherche Saint-Louis, Inserm U944, CNRS UMR 7212, 75010 Paris, France
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169
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Pradhan RK, Ramakrishna W. Transposons: Unexpected players in cancer. Gene 2022; 808:145975. [PMID: 34592349 DOI: 10.1016/j.gene.2021.145975] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 12/21/2022]
Abstract
Transposons are repetitive DNA sequences encompassing about half of the human genome. They play a vital role in genome stability maintenance and contribute to genomic diversity and evolution. Their activity is regulated by various mechanisms considering the deleterious effects of these mobile elements. Various genetic risk factors and environmental stress conditions affect the regulatory pathways causing alteration of transposon expression. Our knowledge of the biological role of transposons is limited especially in various types of cancers. Retrotransposons of different types (LTR-retrotransposons, LINEs and SINEs) regulate a plethora of genes that have a role in cell reprogramming, tumor suppression, cell cycle, apoptosis, cell adhesion and migration, and DNA repair. The regulatory mechanisms of transposons, their deregulation and different mechanisms underlying transposon-mediated carcinogenesis in humans focusing on the three most prevalent types, lung, breast and colorectal cancers, were reviewed. The modes of regulation employed include alternative splicing, deletion, insertion, duplication in genes and promoters resulting in upregulation, downregulation or silencing of genes.
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170
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Abstract
Modern genome-scale methods that identify new genes, such as proteogenomics and ribosome profiling, have revealed, to the surprise of many, that overlap in genes, open reading frames and even coding sequences is widespread and functionally integrated into prokaryotic, eukaryotic and viral genomes. In parallel, the constraints that overlapping regions place on genome sequences and their evolution can be harnessed in bioengineering to build more robust synthetic strains and constructs. With a focus on overlapping protein-coding and RNA-coding genes, this Review examines their discovery, topology and biogenesis in the context of their genome biology. We highlight exciting new uses for sequence overlap to control translation, compress synthetic genetic constructs, and protect against mutation.
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171
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Amweg A, Tusup M, Cheng P, Picardi E, Dummer R, Levesque MP, French LE, Guenova E, Läuchli S, Kundig T, Mellett M, Pascolo S. The A to I editing landscape in melanoma and its relation to clinical outcome. RNA Biol 2022; 19:996-1006. [PMID: 35993275 PMCID: PMC9415457 DOI: 10.1080/15476286.2022.2110390] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
RNA editing refers to non-transient RNA modifications that occur after transcription and prior to translation by the ribosomes. RNA editing is more widespread in cancer cells than in non-transformed cells and is associated with tumorigenesis of various cancer tissues. However, RNA editing can also generate neo-antigens that expose tumour cells to host immunosurveillance. Global RNA editing in melanoma and its relevance to clinical outcome currently remain poorly characterized. The present study compared RNA editing as well as gene expression in tumour cell lines from melanoma patients of short or long metastasis-free survival, patients relapsing or not after immuno- and targeted therapy and tumours harbouring BRAF or NRAS mutations. Overall, our results showed that NTRK gene expression can be a marker of resistance to BRAF and MEK inhibition and gives some insights of candidate genes as potential biomarkers. In addition, this study revealed an increase in Adenosine-to-Inosine editing in Alu regions and in non-repetitive regions, including the hyperediting of the MOK and DZIP3 genes in relapsed tumour samples during targeted therapy and of the ZBTB11 gene in NRAS mutated melanoma cells. Therefore, RNA editing could be a promising tool for identifying predictive markers, tumour neoantigens and targetable pathways that could help in preventing relapses during immuno- or targeted therapies.
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Affiliation(s)
- Austeja Amweg
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Marina Tusup
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Phil Cheng
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Bari, Italy
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Lars E French
- Department of Dermatology and Allergy, University Hospital, LMU Munich, Munich, Germany.,Dr. Philip Frost, Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Emmanuella Guenova
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland.,Department of Dermatology, Lausanne University Hospital (CHUV) and University of Lausanne, Lausanne, Switzerland
| | - Severin Läuchli
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Thomas Kundig
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Mark Mellett
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
| | - Steve Pascolo
- Department of Dermatology, University Hospital Zürich (USZ), Zürich, Switzerland.,Faculty of Medicine, University of Zürich (UZH), Zürich, Switzerland
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172
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Zhang J, Zhang W, Liu Y, Pi M, Jiang Y, Ainiwaer A, Mao S, Chen H, Ran Y, Sun S, Li W, Yao X, Chang Z, Yan Y. Emerging roles and potential application of PIWI-interacting RNA in urological tumors. Front Endocrinol (Lausanne) 2022; 13:1054216. [PMID: 36733811 PMCID: PMC9887041 DOI: 10.3389/fendo.2022.1054216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
The piRNA (PIWI-interacting RNA) is P-Element induced wimpy testis (PIWI)-interacting RNA which is a small molecule, non-coding RNA with a length of 24-32nt. It was originally found in germ cells and is considered a regulator of germ cell function. It can interact with PIWI protein, a member of the Argonaute family, and play a role in the regulation of gene transcription and epigenetic silencing of transposable factors in the nucleus. More and more studies have shown that piRNAs are abnormally expressed in a variety of cancer tissues and patient fluids, and may become diagnostic tools, therapeutic targets, staging markers, and prognostic evaluation tools for cancer. This article reviews the recent research on piRNA and summarizes the structural characteristics, production mechanism, applications, and its role in urological tumors, to provide a reference value for piRNA to regulate urological tumors.
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Affiliation(s)
- Jingcheng Zhang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Wentao Zhang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Yuchao Liu
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Man Pi
- Department of Pathology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yufeng Jiang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Ailiyaer Ainiwaer
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Shiyu Mao
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Haotian Chen
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Yuefei Ran
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Shuwen Sun
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
- Center of Clinical Oncology, the Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wei Li
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Yang Yan, ; Zhengyan Chang, ; Xudong Yao,
| | - Zhengyan Chang
- Department of Pathology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Yang Yan, ; Zhengyan Chang, ; Xudong Yao,
| | - Yang Yan
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Yang Yan, ; Zhengyan Chang, ; Xudong Yao,
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173
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Riquelme I, Pérez-Moreno P, Letelier P, Brebi P, Roa JC. The Emerging Role of PIWI-Interacting RNAs (piRNAs) in Gastrointestinal Cancers: An Updated Perspective. Cancers (Basel) 2021; 14:202. [PMID: 35008366 PMCID: PMC8750603 DOI: 10.3390/cancers14010202] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 02/07/2023] Open
Abstract
Gastrointestinal (GI) cancers produce ~3.4 million related deaths worldwide, comprising 35% of all cancer-related deaths. The high mortality among GI cancers is due to late diagnosis, the presence of metastasis and drug resistance development. Additionally, current clinical markers do not adequately guide patient management, thereby new and more reliable biomarkers and therapeutic targets are still needed for these diseases. RNA-seq technology has allowed the discovery of new types of RNA transcripts including PIWI-interacting RNAs (piRNAs), which have particular characteristics that enable these molecules to act via diverse molecular mechanisms for regulating gene expression. Cumulative evidence has described the potential role of piRNAs in the development of several tumor types as a likely explanation for certain genomic abnormalities and signaling pathways' deregulations observed in cancer. In addition, these piRNAs might be also proposed as promising diagnostic or prognostic biomarkers or as potential therapeutic targets in malignancies. This review describes important topics about piRNAs including their molecular characteristics, biosynthesis processes, gene expression silencing mechanisms, and the manner in which these transcripts have been studied in samples and cell lines of GI cancers to elucidate their implications in these diseases. Moreover, this article discusses the potential clinical usefulness of piRNAs as biomarkers and therapeutic targets in GI cancers.
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Affiliation(s)
- Ismael Riquelme
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Temuco 4810101, Chile;
| | - Pablo Pérez-Moreno
- Millennium Institute on Immunology and Immunotherapy, Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8380000, Chile;
| | - Pablo Letelier
- Precision Health Research Laboratory, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Manuel Montt 56, Temuco 4813302, Chile;
| | - Priscilla Brebi
- Millennium Institute on Immunology and Immunotherapy, Laboratory of Integrative Biology (LIBi), Center for Excellence in Translational Medicine—Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile;
| | - Juan Carlos Roa
- Millennium Institute on Immunology and Immunotherapy, Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8380000, Chile;
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174
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PRDM9-directed recombination hotspots depleted near meiotically transcribed genes. Gene 2021; 813:146123. [PMID: 34952174 DOI: 10.1016/j.gene.2021.146123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/22/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022]
Abstract
PRDM9 drives recombination hotspots in some mammals, including mice and apes. Non-functional orthologs of PRDM9 are present in a wide variety of vertebrates, but why it is functionally maintained in some lineages is not clear. One possible explanation is that PRDM9 plays a role in ensuring that meiosis is successful. During meiosis, available DNA may be a limiting resource given the tight packaging of chromosomes and could lead to competition between two key processes: meiotic transcription and recombination. Here we explore this potential competition and the role that PRDM9 might play in their interaction. Leveraging existing mouse genomic data, we use resampling schemes that simulate shuffled features along the genome and models that account for the rarity of features in the genome, to test if PRDM9 influences interactions between recombination hotspots and meiotic transcription in a whole genome framework. We also explored possible DNA sequence motifs associated to clusters of hotspots not tied to transcription or PRDM9. We find evidence of competition between meiotic transcription and recombination, with PRDM9 appearing to relocate recombination to avoid said conflict. We also find that retrotransposons may be playing a role in directing hotspots in the absence of other factors.
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175
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Complex Genetic Interactions between Piwi and HP1a in the Repression of Transposable Elements and Tissue-Specific Genes in the Ovarian Germline. Int J Mol Sci 2021; 22:ijms222413430. [PMID: 34948223 PMCID: PMC8707237 DOI: 10.3390/ijms222413430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/03/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Insertions of transposable elements (TEs) in eukaryotic genomes are usually associated with repressive chromatin, which spreads to neighbouring genomic sequences. In ovaries of Drosophila melanogaster, the Piwi-piRNA pathway plays a key role in the transcriptional silencing of TEs considered to be exerted mostly through the establishment of H3K9me3 histone marks recruiting Heterochromatin Protein 1a (HP1a). Here, using RNA-seq, we investigated the expression of TEs and the adjacent genomic regions upon Piwi and HP1a germline knockdowns sharing a similar genetic background. We found that the depletion of Piwi and HP1a led to the derepression of only partially overlapping TE sets. Several TEs were silenced predominantly by HP1a, whereas the upregulation of some other TEs was more pronounced upon Piwi knockdown and, surprisingly, was diminished upon a Piwi/HP1a double-knockdown. We revealed that HP1a loss influenced the expression of thousands of protein-coding genes mostly not adjacent to TE insertions and, in particular, downregulated a putative transcriptional factor required for TE activation. Nevertheless, our results indicate that Piwi and HP1a cooperatively exert repressive effects on the transcription of euchromatic loci flanking the insertions of some Piwi-regulated TEs. We suggest that this mechanism controls the silencing of a small set of TE-adjacent tissue-specific genes, preventing their inappropriate expression in ovaries.
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176
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Cayir A. RNA modifications as emerging therapeutic targets. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 13:e1702. [PMID: 34816607 DOI: 10.1002/wrna.1702] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022]
Abstract
The field of epitranscriptome, posttranscriptional modifications to RNAs, is still growing up and has presented substantial evidences for the role of RNA modifications in diseases. In terms of new drug development, RNA modifications have a great promise for therapy. For example, more than 170 type of modifications exist in various types of RNAs. Regulatory genes and their roles in critical biological process have been identified and they are associated with several diseases. Current data, for example, identification of inhibitors targeting RNA modifications regulatory genes, strongly support the idea that RNA modifications have potential as emerging therapeutic targets. Therefore, in this review, RNA modifications and regulatory genes were comprehensively documented in terms of drug development by summarizing the findings from previous studies. It was discussed how RNA modifications or regulatory genes can be targeted by altering molecular mechanisms. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > RNA Editing and Modification.
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Affiliation(s)
- Akin Cayir
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey.,Akershus Universitetssykehus, Medical Department, Lørenskog, Norway
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177
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A hypothetical model of trans-acting R-loops-mediated promoter-enhancer interactions by Alu elements. J Genet Genomics 2021; 48:1007-1019. [PMID: 34531149 DOI: 10.1016/j.jgg.2021.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/24/2021] [Accepted: 07/07/2021] [Indexed: 12/22/2022]
Abstract
Enhancers modulate gene expression by interacting with promoters. Models of enhancer-promoter interactions (EPIs) in the literature involve the activity of many components, including transcription factors and nucleic acid. However, the role that sequence similarity plays in EPIs remains largely unexplored. Herein, we report that Alu-derived sequences dominate sequence similarity between enhancers and promoters. After rejecting alternative DNA:DNA and DNA:RNA triplex models, we propose that enhancer-associated RNAs (eRNAs) may directly contact their targeted promoters by forming trans-acting R-loops at those Alu sequences. We show how the characteristic distribution of functional genomic data, such as RNA-DNA proximate ligation reads, binding of transcription factors, and RNA-binding proteins, all align with the Alu sequences of EPIs. We also show that these aligned Alu sequences may be subject to the constraint of coevolution, further implying the functional significance of these R-loop hybrids. Finally, our results imply that eRNA and Alu elements associate in a manner previously unrecognized in EPIs and the evolution of gene regulation networks in mammals.
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178
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Helmy M, Selvarajoo K. Systems Biology to Understand and Regulate Human Retroviral Proinflammatory Response. Front Immunol 2021; 12:736349. [PMID: 34867957 PMCID: PMC8635014 DOI: 10.3389/fimmu.2021.736349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/21/2021] [Indexed: 01/13/2023] Open
Abstract
The majority of human genome are non-coding genes. Recent research have revealed that about half of these genome sequences make up of transposable elements (TEs). A branch of these belong to the endogenous retroviruses (ERVs), which are germline viral infection that occurred over millions of years ago. They are generally harmless as evolutionary mutations have made them unable to produce viral agents and are mostly epigenetically silenced. Nevertheless, ERVs are able to express by still unknown mechanisms and recent evidences have shown links between ERVs and major proinflammatory diseases and cancers. The major challenge is to elucidate a detailed mechanistic understanding between them, so that novel therapeutic approaches can be explored. Here, we provide a brief overview of TEs, human ERVs and their links to microbiome, innate immune response, proinflammatory diseases and cancer. Finally, we recommend the employment of systems biology approaches for future HERV research.
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Affiliation(s)
- Mohamed Helmy
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Department of Computer Science, Lakehead University, Thunder Bay, ON, Canada
| | - Kumar Selvarajoo
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
- Synthetic Biology Translational Research Program & SynCTI, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Kent Ridge, Singapore
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179
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Stochastic Effects in Retrotransposon Dynamics Revealed by Modeling under Competition for Cellular Resources. Life (Basel) 2021; 11:life11111209. [PMID: 34833085 PMCID: PMC8625273 DOI: 10.3390/life11111209] [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: 08/05/2021] [Revised: 10/30/2021] [Accepted: 11/06/2021] [Indexed: 11/17/2022] Open
Abstract
Transposons are genomic elements that can relocate within a host genome using a ‘cut’- or ‘copy-and-paste’ mechanism. They make up a significant part of many genomes, serve as a driving force for genome evolution, and are linked with Mendelian diseases and cancers. Interactions between two specific retrotransposon types, autonomous (e.g., LINE1/L1) and nonautonomous (e.g., Alu), may lead to fluctuations in the number of these transposons in the genome over multiple cell generations. We developed and examined a simple model of retrotransposon dynamics under conditions where transposon replication machinery competed for cellular resources: namely, free ribosomes and available energy (i.e., ATP molecules). Such competition is likely to occur in stress conditions that a malfunctioning cell may experience as a result of a malignant transformation. The modeling revealed that the number of actively replicating LINE1 and Alu elements in a cell decreases with the increasing competition for resources; however, stochastic effects interfere with this simple trend. We stochastically simulated the transposon dynamics in a cell population and showed that the population splits into pools with drastically different transposon behaviors. The early extinction of active Alu elements resulted in a larger number of LINE1 copies occurring in the first pool, as there was no competition between the two types of transposons in this pool. In the other pool, the competition process remained and the number of L1 copies was kept small. As the level of available resources reached a critical value, both types of dynamics demonstrated an increase in noise levels, and both the period and the amplitude of predator–prey oscillations rose in one of the cell pools. We hypothesized that the presented dynamical effects associated with the impact of the competition for cellular resources inflicted on the dynamics of retrotransposable elements could be used as a characteristic feature to assess a cell state, or to control the transposon activity.
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180
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Abante J, Kambhampati S, Feinberg AP, Goutsias J. Estimating DNA methylation potential energy landscapes from nanopore sequencing data. Sci Rep 2021; 11:21619. [PMID: 34732768 PMCID: PMC8566571 DOI: 10.1038/s41598-021-00781-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
High-throughput third-generation nanopore sequencing devices have enormous potential for simultaneously observing epigenetic modifications in human cells over large regions of the genome. However, signals generated by these devices are subject to considerable noise that can lead to unsatisfactory detection performance and hamper downstream analysis. Here we develop a statistical method, CpelNano, for the quantification and analysis of 5mC methylation landscapes using nanopore data. CpelNano takes into account nanopore noise by means of a hidden Markov model (HMM) in which the true but unknown (“hidden”) methylation state is modeled through an Ising probability distribution that is consistent with methylation means and pairwise correlations, whereas nanopore current signals constitute the observed state. It then estimates the associated methylation potential energy function by employing the expectation-maximization (EM) algorithm and performs differential methylation analysis via permutation-based hypothesis testing. Using simulations and analysis of published data obtained from three human cell lines (GM12878, MCF-10A, and MDA-MB-231), we show that CpelNano can faithfully estimate DNA methylation potential energy landscapes, substantially improving current methods and leading to a powerful tool for the modeling and analysis of epigenetic landscapes using nanopore sequencing data.
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Affiliation(s)
- Jordi Abante
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Sandeep Kambhampati
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew P Feinberg
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA.,Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - John Goutsias
- Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA. .,Department of Electrical & Computer Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
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181
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Górska A, Jabłońska E, Reszka E, Niedoszytko M, Lange M, Gruchała‐Niedoszytko M, Jarczak J, Strapagiel D, Górska‐Ponikowska M, Bastian P, Pelikant‐Małecka I, Kalinowski L, Nedoszytko B. DNA methylation profile in patients with indolent systemic mastocytosis. Clin Transl Allergy 2021; 11:e12074. [PMID: 34754417 PMCID: PMC8561632 DOI: 10.1002/clt2.12074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Mastocytosis is a clinically heterogeneous, usually acquired disease of the mast cells with a survival time that depends on the onset of the disease and ranges from skin-limited to systemic disease, including indolent and more aggressive variants. The crucial element in pathogenesis is the presence of oncogenic KIT somatic mutation D816V. Further epigenetic alterations are responsible for regulating the expression of genes. It is essential to identify indicators of disease progression, and the specific clinical picture to establish an appropriate therapeutic strategy. OBJECTIVE The aim of this study was to analyze the relation of mastocytosis symptoms and epigenetic changes, and to identify epigenetic predictors of the disease. METHODS Global DNA methylation profile analysis was performed in peripheral blood collected from 73 patients with indolent systemic mastocytosis (ISM) and 43 healthy adult volunteers. Levels of 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) were determined using an ELISA-based method, while the methylation of the Alu and LINE-1 repeats were assayed with the quantitative methylation-specific PCR technique. A questionnaire interview was conducted among the study participants to collect data on possible epigenetic modifiers. Additionally, the methylation profile was compared between three human mast cell lines: ROSA KIT D816V, ROSA KIT WT, and HMC-1.1 KIT V560G, in order to assess the association between KIT mutations and methylation profile. RESULTS A significantly lower level of DNA hydroxymethylation (5-hmC) in the blood was found in patients with ISM as compared to the controls (0.022% vs. 0.042%, p = 0.0001). Differences in the markers of global DNA methylation (5-mC, Alu, LINE-1) were not statistically significant, although they did indicate generally higher DNA methylation in patients with mastocytosis. The 5-hmC level was significantly associated with allergy (p = 0.011) in patients with ISM, showing a higher level of 5-hmC in patients with allergy as compared to patients without allergy. The in vitro study revealed significant differences between the studied cell lines at the level of 5-mC, Alu, and LINE-1. CONCLUSIONS This study confirms that epigenetic changes are involved in mastocytosis, and suggests that allergy may be an important epigenetic modifier of the disease. A possible association between KIT mutations and methylation status observed in human mast cell lines requires further investigation in human studies. CLINICAL IMPLICATIONS Epigenetic alterations are involved in mastocytosis pathology. The possible role of allergy as an important epigenetic modifier suggests the more impaired function of mast cells in ISM patients without allergy. CAPSULE SUMMARY Decreased DNA demethylation in the blood DNA of patients with ISM confirms that epigenetic alterations are involved in mastocytosis pathology. We observed a possible role of allergy as an important epigenetic modifier. There is a possible association between KIT mutations and the methylation status observed in human mast cell lines.
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Affiliation(s)
| | - Ewa Jabłońska
- Department of Translational ResearchNofer Institute of Occupational MedicineLodzPoland
| | - Edyta Reszka
- Department of Translational ResearchNofer Institute of Occupational MedicineLodzPoland
| | | | - Magdalena Lange
- Department of Dermatology, Venerology and AllergologyMedical University of GdanskGdanskPoland
| | | | - Justyna Jarczak
- Department of Molecular BiophysicsUniversity of LodzLodzPoland
| | | | | | - Paulina Bastian
- Department of Medical ChemistryMedical University of GdanskGdanskPoland
| | | | - Leszek Kalinowski
- Department of Clinical AnalyticsMedical University of GdanskGdanskPoland
| | - Bogusław Nedoszytko
- Department of Dermatology, Venerology and AllergologyMedical University of GdanskGdanskPoland
- Invicta Fertility and Reproductive CenterMolecular LaboratorySopotPoland
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182
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Programmed DNA elimination: silencing genes and repetitive sequences in somatic cells. Biochem Soc Trans 2021; 49:1891-1903. [PMID: 34665225 DOI: 10.1042/bst20190951] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/30/2022]
Abstract
In a multicellular organism, the genomes of all cells are in general the same. Programmed DNA elimination is a notable exception to this genome constancy rule. DNA elimination removes genes and repetitive elements in the germline genome to form a reduced somatic genome in various organisms. The process of DNA elimination within an organism is highly accurate and reproducible; it typically occurs during early embryogenesis, coincident with germline-soma differentiation. DNA elimination provides a mechanism to silence selected genes and repeats in somatic cells. Recent studies in nematodes suggest that DNA elimination removes all chromosome ends, resolves sex chromosome fusions, and may also promote the birth of novel genes. Programmed DNA elimination processes are diverse among species, suggesting DNA elimination likely has evolved multiple times in different taxa. The growing list of organisms that undergo DNA elimination indicates that DNA elimination may be more widespread than previously appreciated. These various organisms will serve as complementary and comparative models to study the function, mechanism, and evolution of programmed DNA elimination in metazoans.
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183
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Cui Y, Guo Y. The local integration preference of the Tf1 retrotransposon in Schizosaccharomyces pombe. Virology 2021; 565:52-57. [PMID: 34736160 DOI: 10.1016/j.virol.2021.10.008] [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: 05/12/2021] [Revised: 10/17/2021] [Accepted: 10/25/2021] [Indexed: 10/20/2022]
Abstract
Transposons are mobile DNAs that can move to different locations in host genomes. The integration site selection of transposons is critical for both themselves and host cells. Studies on the integration of retrotransposons and retroviruses have focused more on the global preference than on the local preference. The local preferences of retrotransposons are usually weak and of large diversity. Here, we analyzed hundreds of thousands of independent integration events of the Tf1 retrotransposon in Schizosaccharomyces pombe. The consensus sequence at the Tf1 integration sites shows a palindromic pattern, which can be divided into four sections, each of them contains one or more CGnTA units with a period of 10 base pairs, indicating interaction with subunits of the integrase oligomer in the pre-integration complex. Moreover, the analysis on the nucleosome occupancy flanking Tf1 target sites shows that Tf1 integration favors regions with one entire nucleosome depletion.
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Affiliation(s)
- Yujin Cui
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China; Guangzhou PharmaRays Technology Co., Ltd, Guangzhou, 510000, China
| | - Yabin Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
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184
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Bouras A, Leone M, Bonadona V, Lebrun M, Calender A, Boutry-Kryza N. Identification and Characterization of New Alu Element Insertion in the BRCA1 Exon 14 Associated with Hereditary Breast and Ovarian Cancer. Genes (Basel) 2021; 12:genes12111736. [PMID: 34828342 PMCID: PMC8623961 DOI: 10.3390/genes12111736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Abstract
Hereditary breast and ovarian cancer syndrome (HBOC) is an autosomal dominant cancer predisposition syndrome characterized by an increased risk of breast and ovarian cancers. Germline pathogenic variants in BRCA1 are found in about 7–10% of all familial breast cancers and 10% of ovarian cancers. Alu elements are the most abundant mobile DNA element in the human genome and are known to affect the human genome by different mechanisms leading to human disease. We report here the detection, by next-generation sequencing (NGS) analysis coupled with a suitable bioinformatics pipeline, of an AluYb8 element in exon 14 of the BRCA1 gene in a family with HBOC history first classified as BRCA-negative by Sanger sequencing and first NGS analysis. The c.4475_c.4476insAluYb8 mutation impacts splicing and induces the skipping of exon 14. As a result, the produced mRNA contains a premature stop, leading to the production of a short and likely non-functional protein (pAla1453Glyfs*10). Overall, our study allowed us to identify a novel pathogenic variant in BRCA1 and showed the importance of bioinformatics tool improvement and versioning.
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Affiliation(s)
- Ahmed Bouras
- Department of Molecular and Medical Genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France; (M.L.); (A.C.); (N.B.-K.)
- Correspondence:
| | - Melanie Leone
- Department of Molecular and Medical Genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France; (M.L.); (A.C.); (N.B.-K.)
| | - Valerie Bonadona
- Unit of Prevention and Genetic Epidemiology, UMR CNRS 5558, Centre Léon Bérard, 69008 Lyon, France;
| | - Marine Lebrun
- Department of Genetics, Saint Etienne University Hospital, 42270 Saint Priez en Jarez, France;
| | - Alain Calender
- Department of Molecular and Medical Genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France; (M.L.); (A.C.); (N.B.-K.)
| | - Nadia Boutry-Kryza
- Department of Molecular and Medical Genetics, Hospices Civils de Lyon, University Hospital, 69500 Bron, France; (M.L.); (A.C.); (N.B.-K.)
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185
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Nicolau M, Picault N, Moissiard G. The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation. Cells 2021; 10:cells10112952. [PMID: 34831175 PMCID: PMC8616336 DOI: 10.3390/cells10112952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.
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Affiliation(s)
- Melody Nicolau
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Nathalie Picault
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Guillaume Moissiard
- LGDP-UMR5096, CNRS, 66860 Perpignan, France; (M.N.); (N.P.)
- LGDP-UMR5096, Université de Perpignan Via Domitia, 66860 Perpignan, France
- Correspondence:
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186
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SINEUPs: a novel toolbox for RNA therapeutics. Essays Biochem 2021; 65:775-789. [PMID: 34623427 PMCID: PMC8564737 DOI: 10.1042/ebc20200114] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/22/2021] [Accepted: 08/23/2021] [Indexed: 12/17/2022]
Abstract
RNA molecules have emerged as a new class of promising therapeutics to expand the range of druggable targets in the genome. In addition to ‘canonical’ protein-coding mRNAs, the emerging richness of sense and antisense long non-coding RNAs (lncRNAs) provides a new reservoir of molecular tools for RNA-based drugs. LncRNAs are composed of modular structural domains with specific activities involving the recruitment of protein cofactors or directly interacting with nucleic acids. A single therapeutic RNA transcript can then be assembled combining domains with defined secondary structures and functions, and antisense sequences specific for the RNA/DNA target of interest. As the first representative molecules of this new pharmacology, we have identified SINEUPs, a new functional class of natural antisense lncRNAs that increase the translation of partially overlapping mRNAs. Their activity is based on the combination of two domains: an embedded mouse inverted SINEB2 element that enhances mRNA translation (effector domain) and an overlapping antisense region that provides specificity for the target sense transcript (binding domain). By genetic engineering, synthetic SINEUPs can potentially target any mRNA of interest increasing translation and therefore the endogenous level of the encoded protein. In this review, we describe the state-of-the-art knowledge of SINEUPs and discuss recent publications showing their potential application in diseases where a physiological increase of endogenous protein expression can be therapeutic.
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187
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Curty G, Iñiguez LP, Nixon DF, Soares MA, de Mulder Rougvie M. Hallmarks of Retroelement Expression in T-Cells Treated With HDAC Inhibitors. FRONTIERS IN VIROLOGY 2021. [DOI: 10.3389/fviro.2021.756635] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A wide spectrum of drugs have been assessed as latency reversal agents (LRA) to reactivate HIV-1 from cellular reservoirs and aid in viral eradication strategies. Histone deacetylase inhibitors (HDACi) have been studied in vitro and in vivo as potential candidates for HIV-1 latency reversion. Suberoylanilide hydroxamic acid (SAHA) and romidepsin (RMD) are two HDACi able to reverse HIV latency, however studies of potential off-target effects on retroelement expression have been limited. Retroelements constitute a large portion of the human genome, and some are considered “fossil viruses” as they constitute remnants of ancient exogenous retroviruses infections. Retroelements are reactivated during certain disease conditions like cancer or during HIV-1 infection. In this study, we analyzed differential expression of retroelements using publicly available RNA-seq datasets (GSE102187 and GSE114883) obtained from uninfected CD4+, and HIV-1 latently infected CD4+ T-cells treated with HDACi (SAHA and RMD). We found a total of 712 and 1,380 differentially expressed retroelements in HIV-1 latently infected cells following a 24-h SAHA and RMD treatment, respectively. Furthermore, we found that 531 retroelement sequences (HERVs and L1) were differentially expressed under both HDACi treatments, while 1,030 HERV/L1 were exclusively regulated by each drug. Despite differences in specific HERV loci expression, the overall pattern at the HERV family level was similar for both treatments. We detected differential expression of full-length HERV families including HERV-K, HERV-W and HERV-H. Furthermore, we analyzed the link between differentially expressed retroelements and nearby immune genes. TRAF2 (TNF receptor) and GBP5 (inflammasome activator) were upregulated in HDACi treated samples and their expression was correlated with nearby HERV (MERV101_9q34.3) and L1 (L1FLnI_1p22.2k, L1FLnI_1p22.2j, L1FLnI_1p22.2i). Our findings suggest that HDACi have an off-target effect on the expression of retroelements and on the expression of immune associated genes in treated CD4+ T-cells. Furthermore, our data highlights the importance of exploring the interaction between HIV-1 and retroelement expression in LRA treated samples to understand their role and impact on “shock and kill” strategies and their potential use as reservoir biomarkers.
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188
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Wang Y, Zhao B, Choi J, Lee EA. Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans. Mob DNA 2021; 12:22. [PMID: 34663455 PMCID: PMC8525043 DOI: 10.1186/s13100-021-00250-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/27/2021] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) significantly contribute to shaping the diversity of the human genome, and lines of evidence suggest TEs as one of driving forces of human brain evolution. Existing computational approaches, including cross-species comparative genomics and population genetic modeling, can be adapted for the study of the role of TEs in evolution. In particular, diverse ancient and archaic human genome sequences are increasingly available, allowing reconstruction of past human migration events and holding the promise of identifying and tracking TEs among other evolutionarily important genetic variants at an unprecedented spatiotemporal resolution. However, highly degraded short DNA templates and other unique challenges presented by ancient human DNA call for major changes in current experimental and computational procedures to enable the identification of evolutionarily important TEs. Ancient human genomes are valuable resources for investigating TEs in the evolutionary context, and efforts to explore ancient human genomes will potentially provide a novel perspective on the genetic mechanism of human brain evolution and inspire a variety of technological and methodological advances. In this review, we summarize computational and experimental approaches that can be adapted to identify and validate evolutionarily important TEs, especially for human brain evolution. We also highlight strategies that leverage ancient genomic data and discuss unique challenges in ancient transposon genomics.
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Affiliation(s)
- Yilan Wang
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Boxun Zhao
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Jaejoon Choi
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA.
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189
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Roquis D, Robertson M, Yu L, Thieme M, Julkowska M, Bucher E. Genomic impact of stress-induced transposable element mobility in Arabidopsis. Nucleic Acids Res 2021; 49:10431-10447. [PMID: 34551439 PMCID: PMC8501995 DOI: 10.1093/nar/gkab828] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impacts of stress induced TE mobilization in wild type Arabidopsis plants. We find that the heat-stress responsive ONSEN TE displays an insertion site preference that is associated with specific chromatin states, especially those rich in H2A.Z histone variant and H3K27me3 histone mark. In order to better understand how novel ONSEN insertions affect the plant's response to heat stress, we carried out an in-depth transcriptomic analysis. We find that in addition to simple gene knockouts, ONSEN can produce a plethora of gene expression changes such as: constitutive activation of gene expression, alternative splicing, acquisition of heat-responsiveness, exonisation and genesis of novel non-coding and antisense RNAs. This report shows how the mobilization of a single TE-family can lead to a rapid rise of its copy number increasing the host's genome size and contribute to a broad range of transcriptomic novelty on which natural selection can then act.
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Affiliation(s)
- David Roquis
- Plant Breeding and Genetic Resources, Agroscope, 1260 Nyon, Switzerland
| | - Marta Robertson
- Plant Breeding and Genetic Resources, Agroscope, 1260 Nyon, Switzerland
| | - Liang Yu
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA
| | - Michael Thieme
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | | | - Etienne Bucher
- Plant Breeding and Genetic Resources, Agroscope, 1260 Nyon, Switzerland
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190
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Meevassana J, Serirodom S, Prabsattru P, Boonsongserm P, Kamolratanakul S, Siritientong T, Mutirangura A, Angspatt A. Alu repetitive sequence CpG methylation changes in burn scars. Burns 2021; 48:1417-1424. [PMID: 34657766 DOI: 10.1016/j.burns.2021.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 11/25/2022]
Abstract
Alu elements are retrotransposons related to epigenetic modifications. To date, the role of epigenetics in hypertrophic scars from burn remains unknown. Here, our aim was to examine the pathophysiology of hypertrophic scars from an epigenetic perspective. For that, we performed a cross-sectional analytical study using tissue and blood samples from burned and healthy patients (n = 23 each) to detect Alu methylation levels and patterns. The results of the combined bisulfite restriction analysis technique were categorized into four groups based on the methylation status at the CpG dinucleotides from the 5' to the 3' ends of the Alu sequence: hypermethylated (mCmC), hypomethylated (uCuC), and partially methylated (uCmC and mCuC). Alu methylation levels were significantly lower in hypertrophic scar tissues than in normal skin (29.37 ± 2.49% vs. 35.56 ± 3.18%, p = 0.0002). In contrast, the levels were significantly higher in white blood cells from blood samples of burned patients than in those of control blood samples (26.92 ± 4.04% vs. 24.58 ± 3.34%, p = 0.0278). Alu total methylation (mC) and the uCmC pattern were significantly lower, whereas uCuC was significantly higher, in hypertrophic scar tissues than in normal skin (p < 0.0001). Receiver operating characteristic analysis indicated that the uCmC and uCuC patterns are useful as hypertrophic scar DNA methylation markers after burn, with 91.30% sensitivity and 96.23% specificity and 100% sensitivity and 94.23% specificity, respectively. Our findings suggest that epigenetic modifications play a major role in hypertrophic scar pathogenesis, and may be the starting point for developing a novel technique for burn scar treatment.
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Affiliation(s)
- Jiraroch Meevassana
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Division of Plastic and Reconstructive Surgery, Department of Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok, Thailand.
| | - Siwat Serirodom
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Piyawan Prabsattru
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok, Thailand
| | - Papatson Boonsongserm
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok, Thailand
| | - Supitcha Kamolratanakul
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tippawan Siritientong
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok, Thailand; Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apichai Angspatt
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok, Thailand
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191
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Ravel-Godreuil C, Znaidi R, Bonnifet T, Joshi RL, Fuchs J. Transposable elements as new players in neurodegenerative diseases. FEBS Lett 2021; 595:2733-2755. [PMID: 34626428 DOI: 10.1002/1873-3468.14205] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/23/2021] [Accepted: 10/03/2021] [Indexed: 01/02/2023]
Abstract
Neurodegenerative diseases (NDs), including the most prevalent Alzheimer's disease and Parkinson disease, share common pathological features. Despite decades of gene-centric approaches, the molecular mechanisms underlying these diseases remain widely elusive. In recent years, transposable elements (TEs), long considered 'junk' DNA, have gained growing interest as pathogenic players in NDs. Age is the major risk factor for most NDs, and several repressive mechanisms of TEs, such as heterochromatinization, fail with age. Indeed, heterochromatin relaxation leading to TE derepression has been reported in various models of neurodegeneration and NDs. There is also evidence that certain pathogenic proteins involved in NDs (e.g., tau, TDP-43) may control the expression of TEs. The deleterious consequences of TE activation are not well known but they could include DNA damage and genomic instability, altered host gene expression, and/or neuroinflammation, which are common hallmarks of neurodegeneration and aging. TEs might thus represent an overlooked pathogenic culprit for both brain aging and neurodegeneration. Certain pathological effects of TEs might be prevented by inhibiting their activity, pointing to TEs as novel targets for neuroprotection.
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Affiliation(s)
- Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Rania Znaidi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Tom Bonnifet
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Rajiv L Joshi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
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192
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Duan K, Si CY, Zhao SM, Ai ZY, Niu BH, Yin Y, Xiang LF, Ding H, Zheng Y. The Long Terminal Repeats of ERV6 Are Activated in Pre-Implantation Embryos of Cynomolgus Monkey. Cells 2021; 10:cells10102710. [PMID: 34685690 PMCID: PMC8534818 DOI: 10.3390/cells10102710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
Precise gene regulation is critical during embryo development. Long terminal repeat elements (LTRs) of endogenous retroviruses (ERVs) are dynamically expressed in blastocysts of mammalian embryos. However, the expression pattern of LTRs in monkey blastocyst is still unknown. By single-cell RNA-sequencing (seq) data of cynomolgus monkeys, we found that LTRs of several ERV families, including MacERV6, MacERV3, MacERV2, MacERVK1, and MacERVK2, were highly expressed in pre-implantation embryo cells including epiblast (EPI), trophectoderm (TrB), and primitive endoderm (PrE), but were depleted in post-implantation. We knocked down MacERV6-LTR1a in cynomolgus monkeys with a short hairpin RNA (shRNA) strategy to examine the potential function of MacERV6-LTR1a in the early development of monkey embryos. The silence of MacERV6-LTR1a mainly postpones the differentiation of TrB, EPI, and PrE cells in embryos at day 7 compared to control. Moreover, we confirmed MacERV6-LTR1a could recruit Estrogen Related Receptor Beta (ESRRB), which plays an important role in the maintenance of self-renewal and pluripotency of embryonic and trophoblast stem cells through different signaling pathways including FGF and Wnt signaling pathways. In summary, these results suggest that MacERV6-LTR1a is involved in gene regulation of the pre-implantation embryo of the cynomolgus monkeys.
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Affiliation(s)
- Kui Duan
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Chen-Yang Si
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Shu-Mei Zhao
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Zong-Yong Ai
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Bao-Hua Niu
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Yu Yin
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Li-Feng Xiang
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Hao Ding
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
| | - Yun Zheng
- Faculty of Environmental Science and Engineering, Kunming University of Science and Technology, Kunming 650500, China; (K.D.); (C.-Y.S.); (S.-M.Z.); (Z.-Y.A.); (B.-H.N.); (Y.Y.); (L.-F.X.); (H.D.)
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- Yunnan Provincial Academy of Science and Technology, Kunming 650500, China
- Correspondence:
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193
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Factors Regulating the Activity of LINE1 Retrotransposons. Genes (Basel) 2021; 12:genes12101562. [PMID: 34680956 PMCID: PMC8535693 DOI: 10.3390/genes12101562] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 12/15/2022] Open
Abstract
LINE-1 (L1) is a class of autonomous mobile genetic elements that form somatic mosaicisms in various tissues of the organism. The activity of L1 retrotransposons is strictly controlled by many factors in somatic and germ cells at all stages of ontogenesis. Alteration of L1 activity was noted in a number of diseases: in neuropsychiatric and autoimmune diseases, as well as in various forms of cancer. Altered activity of L1 retrotransposons for some pathologies is associated with epigenetic changes and defects in the genes involved in their repression. This review discusses the molecular genetic mechanisms of the retrotransposition and regulation of the activity of L1 elements. The contribution of various factors controlling the expression and distribution of L1 elements in the genome occurs at all stages of the retrotransposition. The regulation of L1 elements at the transcriptional, post-transcriptional and integration into the genome stages is described in detail. Finally, this review also focuses on the evolutionary aspects of L1 accumulation and their interplay with the host regulation system.
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194
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Troskie RL, Faulkner GJ, Cheetham SW. Processed pseudogenes: A substrate for evolutionary innovation: Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome. Bioessays 2021; 43:e2100186. [PMID: 34569081 DOI: 10.1002/bies.202100186] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 11/08/2022]
Abstract
Processed pseudogenes may serve as a genetic reservoir for evolutionary innovation. Here, we argue that through the activity of long interspersed element-1 retrotransposons, processed pseudogenes disperse coding and noncoding sequences rich with regulatory potential throughout the human genome. While these sequences may appear to be non-functional, a lack of contemporary function does not prohibit future development of biological activity. Here, we discuss the dynamic evolution of certain processed pseudogenes into coding and noncoding genes and regulatory elements, and their implication in wide-ranging biological and pathological processes. Also see the video abstract here: https://youtu.be/iUY_mteVoPI.
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Affiliation(s)
- Robin-Lee Troskie
- Mater Research Institute, University of Queensland, Woolloongabba, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Woolloongabba, Australia.,Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Seth W Cheetham
- Mater Research Institute, University of Queensland, Woolloongabba, Australia
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195
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Mantziou S, Markopoulos G, Thrasyvoulou S, Noutsopoulos D, Gkartziou F, Vartholomatos G, Tzavaras T. Tinzaparin inhibits VL30 retrotransposition induced by oxidative stress and/or VEGF in HC11 mouse progenitor mammary cells: Association between inhibition of cancer stem cell proliferation and mammosphere disaggregation. Oncol Rep 2021; 46:241. [PMID: 34558648 PMCID: PMC8485018 DOI: 10.3892/or.2021.8192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023] Open
Abstract
Tinzaparin is an anticoagulant and antiangiogenic drug with inhibitory properties against tumor growth. VEGF stimulates angiogenesis, while an association between reactive oxygen species (ROS) and angiogenesis is involved in tumor progression. The present study aimed to investigate the effect of tinzaparin on VL30 retrotransposition-positive mouse HC11 mammary stem-like epithelial cells, previously reported to be associated with induced mammosphere/cancer stem cell (CSC) generation and tumorigenesis. Under 24 h serum starvation, 15.2% nominal retrotransposition frequency was increased to 29%. Additionally, while treatment with 3–12 ng/ml VEGF further induced retrotransposition frequency in a dose-dependent manner (up to 40.3%), pre-incubation with tinzaparin (2 IU/ml) for 0.5–4 h reduced this frequency to 18.3% in a time-dependent manner, confirmed by analogous results in NIH3T3 fibroblasts. Treatment with 10–40 pg/ml glucose oxidase (GO) for 24 h induced HC11 cell retrotransposition in a dose-dependent manner (up to 82.5%), while a 3 h pre-incubation with tinzaparin (1 or 2 IU/ml) elicited a 13.5 or 25.5% reduction in retrotransposition, respectively. Regarding tumorigenic VL30 retrotransposition-positive HC11 cells, treatment with 2 IU/ml tinzaparin for 5 days reduced proliferation rate in a time-dependent manner (up to ~55%), and after 3 weeks, disaggregated soft agar-formed foci, as well as low-adherent mammospheres, producing single mesenchymal-like cells with a ~50% reduced retrotransposition. With respect to the VL30 retrotransposition mechanism: While 12 ng/ml VEGF increased the level of VL30 and endogenous reverse transcriptase (enRT) transcripts ~1.41- and ~1.16-fold, respectively, subsequent tinzaparin treatment reduced both endogenous/ROS- and VEGF-induced levels 1.15- and 0.40-fold (VL30) and 0.60- and 0.52-fold (enRT), respectively. To the best of our knowledge, these data demonstrate for the first time, the novel inhibition activity of tinzaparin against ROS- and VEGF-induced VL30 retrotransposition, and the proliferation and/or aggregation of mouse HC11 mammosphere/tumor-initiating CSCs, thus contributing to the inhibition of VL30 retrotransposition-induced primary tumor growth.
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Affiliation(s)
- Stefania Mantziou
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Georgios Markopoulos
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Soteroula Thrasyvoulou
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Dimitrios Noutsopoulos
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Foteini Gkartziou
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Georgios Vartholomatos
- Molecular Biology Unit, Hematology Laboratory, University Hospital of Ioannina, 45110 Ioannina, Greece
| | - Theodore Tzavaras
- Laboratory of General Biology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
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196
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Li J, Chen H, Gou M, Tian C, Wang H, Song X, Keefe DL, Bai X, Liu L. Molecular Features of Polycystic Ovary Syndrome Revealed by Transcriptome Analysis of Oocytes and Cumulus Cells. Front Cell Dev Biol 2021; 9:735684. [PMID: 34552933 PMCID: PMC8450412 DOI: 10.3389/fcell.2021.735684] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/09/2021] [Indexed: 01/21/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is typically characterized by a polycystic ovarian morphology, hyperandrogenism, ovulatory dysfunction, and infertility. Furthermore, PCOS patients undergoing ovarian stimulation have more oocytes; however, the poor quality of oocytes leads to lower fertilization and implantation rates, decreased pregnancy rates, and increased miscarriage rates. The complex molecular mechanisms underlying PCOS and the poor quality of oocytes remain to be elucidated. We obtained matched oocytes and cumulus cells (CCs) from PCOS patients, compared them with age-matched controls, and performed RNA sequencing analysis to explore the transcriptional characteristics of their oocytes and CCs. Moreover, we validated our newly confirmed candidate genes for PCOS by immunofluorescence. Unsupervised clustering analysis showed that the overall global gene expression patterns and transposable element (TE) expression profiles of PCOS patients tightly clustered together, clearly distinct from those of controls. Abnormalities in functionally important pathways are found in PCOS oocytes. Notably, genes involved in microtubule processes, TUBB8 and TUBA1C, are overexpressed in PCOS oocytes. The metabolic and oxidative phosphorylation pathways are also dysregulated in both oocytes and CCs from PCOS patients. Moreover, in oocytes, differentially expressed TEs are not uniformly dispersed in human chromosomes. Endogenous retrovirus 1 (ERV1) elements located on chromosomes 2, 3, 4, and 5 are rather highly upregulated. Interestingly, these correlate with the most highly expressed protein-coding genes, including tubulin-associated genes TUBA1C, TUBB8P8, and TUBB8, linking the ERV1 elements to the occurrence of PCOS. Our comprehensive analysis of gene expression in oocytes and CCs, including TE expression, revealed the specific molecular features of PCOS. The aberrantly elevated expression of TUBB8 and TUBA1C and ERV1 provides additional markers for PCOS and may contribute to the compromised oocyte developmental competence in PCOS patients. Our findings may also have implications for treatment strategies to improve oocyte maturation and the pregnancy outcomes for women with PCOS.
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Affiliation(s)
- Jie Li
- The State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Haixia Chen
- The Center for Reproductive Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Mo Gou
- The State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Chenglei Tian
- The State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Huasong Wang
- The State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
| | - Xueru Song
- The Center for Reproductive Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - David L Keefe
- Department of Obstetrics and Gynecology, NYU Langone Medical Center, New York, NY, United States
| | - Xiaohong Bai
- The Center for Reproductive Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Lin Liu
- The State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin, China
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197
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Pinter TBJ, Ruckthong L, Stuckey JA, Deb A, Penner-Hahn JE, Pecoraro VL. Open Reading Frame 1 Protein of the Human Long Interspersed Nuclear Element 1 Retrotransposon Binds Multiple Equivalents of Lead. J Am Chem Soc 2021; 143:15271-15278. [PMID: 34494819 PMCID: PMC11069406 DOI: 10.1021/jacs.1c06461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The human long interspersed nuclear element 1 (LINE1) has been implicated in numerous diseases and has been suggested to play a significant role in genetic evolution. Open reading frame 1 protein (ORF1p) is one of the two proteins encoded in this self-replicating mobile genetic element, both of which are essential for retrotransposition. The structure of the three-stranded coiled-coil domain of ORF1p was recently solved and showed the presence of tris-cysteine layers in the interior of the coiled-coil that could function as metal binding sites. Here, we demonstrate that ORF1p binds Pb(II). We designed a model peptide, GRCSL16CL23C, to mimic two of the ORF1p Cys3 layers and crystallized the peptide both as the apo-form and in the presence of Pb(II). Structural comparison of the ORF1p with apo-(GRCSL16CL23C)3 shows very similar Cys3 layers, preorganized for Pb(II) binding. We propose that exposure to heavy metals, such as lead, could influence directly the structural parameters of ORF1p and thus impact the overall LINE1 retrotransposition frequency, directly relating heavy metal exposure to genetic modification.
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Affiliation(s)
- Tyler B. J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Leela Ruckthong
- Department of Chemistry, Faculty of Science, King Mongkut’s University of Technology Thonburi (KMUTT), Bang Mod, Thung Khru, Bangkok, 10140, Thailand
| | - Jeanne A. Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, 48109, United States
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
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198
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Riba A, Fumagalli MR, Caselle M, Osella M. A Model-Driven Quantitative Analysis of Retrotransposon Distributions in the Human Genome. Genome Biol Evol 2021; 12:2045-2059. [PMID: 32986810 PMCID: PMC7750997 DOI: 10.1093/gbe/evaa201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2020] [Indexed: 12/21/2022] Open
Abstract
Retrotransposons, DNA sequences capable of creating copies of themselves, compose about half of the human genome and played a central role in the evolution of mammals. Their current position in the host genome is the result of the retrotranscription process and of the following host genome evolution. We apply a model from statistical physics to show that the genomic distribution of the two most populated classes of retrotransposons in human deviates from random placement, and that this deviation increases with time. The time dependence suggests a major role of the host genome dynamics in shaping the current retrotransposon distributions. Focusing on a neutral scenario, we show that a simple model based on random placement followed by genome expansion and sequence duplications can reproduce the empirical retrotransposon distributions, even though more complex and possibly selective mechanisms can have contributed. Besides the inherent interest in understanding the origin of current retrotransposon distributions, this work sets a general analytical framework to analyze quantitatively the effects of genome evolutionary dynamics on the distribution of genomic elements.
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Affiliation(s)
| | - Maria Rita Fumagalli
- Institute of Biophysics - CNR, National Research Council, Genova, Italy.,Department of Environmental Science and Policy, Center for Complexity and Biosystems, University of Milan, Milano, Italy
| | - Michele Caselle
- Department of Physics and INFN, University of Torino, Torino, Italy
| | - Matteo Osella
- Department of Physics and INFN, University of Torino, Torino, Italy
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199
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Zhao P, Du H, Jiang L, Zheng X, Feng W, Diao C, Zhou L, Liu GE, Zhang H, Chamba Y, Zhang Q, Li B, Liu JF. PRE-1 Revealed Previous Unknown Introgression Events in Eurasian Boars during the Middle Pleistocene. Genome Biol Evol 2021; 12:1751-1764. [PMID: 33151306 PMCID: PMC7643367 DOI: 10.1093/gbe/evaa142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2020] [Indexed: 12/22/2022] Open
Abstract
Introgression events and population admixture occurred among Sus species across the Eurasian mainland in the Middle Pleistocene, which reflects the local adaption of different populations and contributes to evolutionary novelty. Previous findings on these population introgressions were largely based on extensive genome-wide single-nucleotide polymorphism information, ignoring structural variants (SVs) as an important alternative resource of genetic variations. Here, we profiled the genome-wide SVs and explored the formation of pattern-related SVs, indicating that PRE1-SS is a recently active subfamily that was strongly associated with introgression events in multiple Asian and European pig populations. As reflected by the three different combination haplotypes from two specific patterns and known phylogenetic relationships in Eurasian boars, we identified the Asian Northern wild pigs as having experienced introgression from European wild boars around 0.5–0.2 Ma and having received latitude-related selection. During further exploration of the influence of pattern-related SVs on gene functions, we found substantial sequence changes in 199 intron regions of 54 genes and 3 exon regions of 3 genes (HDX, TRO, and SMIM1), implying that the pattern-related SVs were highly related to positive selection and adaption of pigs. Our findings revealed novel introgression events in Eurasian wild boars, providing a timeline of population admixture and divergence across the Eurasian mainland in the Middle Pleistocene.
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Affiliation(s)
- Pengju Zhao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Heng Du
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lin Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xianrui Zheng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wen Feng
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chenguang Diao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lei Zhou
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Maryland
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yangzom Chamba
- College of Animal Science and Technology, Tibet Agriculture and Animal Husbandry College, Linzhi, Tibet, China
| | - Qin Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China.,College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, PR China
| | - Bugao Li
- Department of Animal Sciences and Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | - Jian-Feng Liu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, Beijing, China
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200
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Mendes CC, Zampieri BL, Arantes LMRB, Melendez ME, Biselli JM, Carvalho AL, Eberlin MN, Riccio MF, Vannucchi H, Carvalho VM, Goloni-Bertollo EM, Pavarino ÉC. One-carbon metabolism and global DNA methylation in mothers of individuals with Down syndrome. Hum Cell 2021; 34:1671-1681. [PMID: 34410622 DOI: 10.1007/s13577-021-00586-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/26/2021] [Indexed: 10/20/2022]
Abstract
Down syndrome (DS) is the most common chromosomal disorder, resulting from the failure of normal chromosome 21 segregation. Studies have suggested that impairments within the one-carbon metabolic pathway can be of relevance for the global genome instability observed in mothers of individuals with DS. Based on the association between global DNA hypomethylation, genome instability, and impairments within the one-carbon metabolic pathway, the present study aimed to identify possible predictors, within the one-carbon metabolism, of global DNA methylation, measured by methylation patterns of LINE-1 and Alu repetitive sequences, in mothers of individuals with DS and mothers of individuals without the syndrome. In addition, we investigated one-carbon genetic polymorphisms and metabolites as maternal predisposing factors for the occurrence of trisomy 21 in children. Eighty-three samples of mothers of children with DS with karyotypically confirmed free trisomy 21 (case group) and 84 of mothers who had at least one child without DS or any other aneuploidy were included in the study. Pyrosequencing assays were performed to access global methylation. The results showed that group affiliation (case or control), betaine-homocysteine methyltransferase (BHMT) G742A and transcobalamin 2 (TCN2) C776G polymorphisms, and folate concentration were identified as predictors of global Alu DNA methylation values. In addition, thymidylate synthase (TYMS) 28-bp repeats 2R/3R or 3R/3R genotypes are independent maternal predisposing factors for having a child with DS. This study adds evidence that supports the association of impairments in the one-carbon metabolism, global DNA methylation, and the possibility of having a child with DS.
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Affiliation(s)
- Cristiani Cortez Mendes
- Unidade de Pesquisa em Genética e Biologia Molecular-UPGEM, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, Brazil
| | | | | | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Joice Matos Biselli
- Universidade Estadual Paulista Júlio de Mesquita Filho, Instituto de Biociências, Letras e Ciências Exatas de São José do Rio Preto, Departamento de Ciências Biológicas, São José do Rio Preto, São Paulo, Brazil
| | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Marcos Nogueira Eberlin
- Universidade Presbiteriana Mackenzie, Discovery-Mackenzie-Núcleo Mackenzie de Pesquisa, Núcleo Mackenzie de Pesquisas em Ciência, Fé e Sociedade, São Paulo, São Paulo, Brazil
| | | | - Hélio Vannucchi
- Laboratório de Nutrição, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto-USP, Ribeirão Preto, São Paulo, Brazil
| | | | - Eny Maria Goloni-Bertollo
- Unidade de Pesquisa em Genética e Biologia Molecular-UPGEM, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, Brazil
| | - Érika Cristina Pavarino
- Unidade de Pesquisa em Genética e Biologia Molecular-UPGEM, Departamento de Biologia Molecular, Faculdade de Medicina de São José do Rio Preto-FAMERP, São José do Rio Preto, São Paulo, Brazil.
- , Av. Brigadeiro Faria Lima, 5416, Vila São Pedro, São José do Rio Preto, São Paulo, 15090-000, Brazil.
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