1
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Blumenstiel JP. From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements. Semin Cell Dev Biol 2025; 164:1-12. [PMID: 38823219 DOI: 10.1016/j.semcdb.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/28/2024] [Accepted: 05/06/2024] [Indexed: 06/03/2024]
Abstract
Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.
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Affiliation(s)
- Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045, United States.
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2
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Wu K, Qin D, Qian Y, Liu H. A new era of mutation rate analyses: Concepts and methods. Zool Res 2024; 45:767-780. [PMID: 38894520 PMCID: PMC11298668 DOI: 10.24272/j.issn.2095-8137.2024.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
The mutation rate is a pivotal biological characteristic, intricately governed by natural selection and historically garnering considerable attention. Recent advances in high-throughput sequencing and analytical methodologies have profoundly transformed our understanding in this domain, ushering in an unprecedented era of mutation rate research. This paper aims to provide a comprehensive overview of the key concepts and methodologies frequently employed in the study of mutation rates. It examines various types of mutations, explores the evolutionary dynamics and associated theories, and synthesizes both classical and contemporary hypotheses. Furthermore, this review comprehensively explores recent advances in understanding germline and somatic mutations in animals and offers an overview of experimental methodologies, mutational patterns, molecular mechanisms, and driving forces influencing variations in mutation rates across species and tissues. Finally, it proposes several potential research directions and pressing questions for future investigations.
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Affiliation(s)
- Kun Wu
- Center for Evolutionary & Organismal Biology and the Fourth Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Danqi Qin
- Center for Evolutionary & Organismal Biology and the Fourth Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yang Qian
- Center for Evolutionary & Organismal Biology and the Fourth Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Haoxuan Liu
- Center for Evolutionary & Organismal Biology and the Fourth Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China. E-mail:
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3
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Sasani TA, Quinlan AR, Harris K. Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice. eLife 2024; 12:RP89096. [PMID: 38381482 PMCID: PMC10942616 DOI: 10.7554/elife.89096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations - the frequencies of C>T, A>G, etc. - will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al., 2022, Ashbrook et al., 2021). In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh (David et al., 2007). Its effect depends on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci have greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.
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Affiliation(s)
- Thomas A Sasani
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
| | - Aaron R Quinlan
- Department of Human Genetics, University of UtahSalt Lake CityUnited States
- Department of Biomedical Informatics, University of UtahSalt Lake CityUnited States
| | - Kelley Harris
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Herbold Computational Biology Program, Fred Hutch Cancer CenterSeattleUnited States
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4
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Lum GR, Ha SM, Olson CA, Blencowe M, Paramo J, Reyes B, Matsumoto JH, Yang X, Hsiao EY. Ketogenic diet therapy for pediatric epilepsy is associated with alterations in the human gut microbiome that confer seizure resistance in mice. Cell Rep 2023; 42:113521. [PMID: 38070135 PMCID: PMC10769314 DOI: 10.1016/j.celrep.2023.113521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/13/2023] [Accepted: 11/14/2023] [Indexed: 12/30/2023] Open
Abstract
The gut microbiome modulates seizure susceptibility and the anti-seizure effects of the ketogenic diet (KD) in animal models, but whether these relationships translate to KD therapies for human epilepsy is unclear. We find that the clinical KD alters gut microbial function in children with refractory epilepsy. Colonizing mice with KD-associated microbes promotes seizure resistance relative to matched pre-treatment controls. Select metagenomic and metabolomic features, including those related to anaplerosis, fatty acid β-oxidation, and amino acid metabolism, are seen with human KD therapy and preserved upon microbiome transfer to mice. Mice colonized with KD-associated gut microbes exhibit altered hippocampal transcriptomes, including pathways related to ATP synthesis, glutathione metabolism, and oxidative phosphorylation, and are linked to susceptibility genes identified in human epilepsy. Our findings reveal key microbial functions that are altered by KD therapies for pediatric epilepsy and linked to microbiome-induced alterations in brain gene expression and seizure protection in mice.
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Affiliation(s)
- Gregory R Lum
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Sung Min Ha
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christine A Olson
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Montgomery Blencowe
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jorge Paramo
- UCLA Goodman-Luskin Microbiome Center, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Beck Reyes
- Department of Pediatrics, Division of Pediatric Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joyce H Matsumoto
- Department of Pediatrics, Division of Pediatric Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elaine Y Hsiao
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; UCLA Goodman-Luskin Microbiome Center, Vatche and Tamar Manoukian Division of Digestive Diseases, David Geffen School of Medicine, Los Angeles, CA 90095, USA.
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5
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Sasani TA, Quinlan AR, Harris K. Epistasis between mutator alleles contributes to germline mutation spectra variability in laboratory mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.537217. [PMID: 37162999 PMCID: PMC10168256 DOI: 10.1101/2023.04.25.537217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair [1], mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations - the frequencies of C>T, A>G, etc. - will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs [2,3]. In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh [4]. Its effect depended on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci had greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.
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Affiliation(s)
| | - Aaron R. Quinlan
- Department of Human Genetics, University of Utah; Department of Biomedical Informatics, University of Utah · Funded by NIH/NHGRI R01HG012252
| | - Kelley Harris
- Department of Genome Sciences, University of Washington · Funded by NIH/NIGMS R35GM133428; Burroughs Wellcome Career Award at the Scientific Interface; Searle Scholarship; Pew Scholarship; Sloan Fellowship; Allen Discovery Center for Cell Lineage Tracing
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6
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Oliveira DS, Fablet M, Larue A, Vallier A, Carareto CA, Rebollo R, Vieira C. ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements. Nucleic Acids Res 2023; 51:9764-9784. [PMID: 37615575 PMCID: PMC10570057 DOI: 10.1093/nar/gkad671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 07/25/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Transposable elements (TEs) produce structural variants and are considered an important source of genetic diversity. Notably, TE-gene fusion transcripts, i.e. chimeric transcripts, have been associated with adaptation in several species. However, the identification of these chimeras remains hindered due to the lack of detection tools at a transcriptome-wide scale, and to the reliance on a reference genome, even though different individuals/cells/strains have different TE insertions. Therefore, we developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts through two different modes. Mode 1 is the reference-guided approach that employs canonical genome alignment, and Mode 2 identifies chimeras derived from fixed or insertionally polymorphic TEs without any reference genome. We have validated both modes using RNA-seq data from four Drosophila melanogaster wild-type strains. We found ∼1.12% of all genes generating chimeric transcripts, most of them from TE-exonized sequences. Approximately ∼23% of all detected chimeras were absent from the reference genome, indicating that TEs belonging to chimeric transcripts may be recent, polymorphic insertions. ChimeraTE is the first pipeline able to automatically uncover chimeric transcripts without a reference genome, consisting of two running Modes that can be used as a tool to investigate the contribution of TEs to transcriptome plasticity.
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Affiliation(s)
- Daniel S Oliveira
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
- Institut Universitaire de France (IUF), Paris, Île-de-FranceF-75231, France
| | - Anaïs Larue
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Agnès Vallier
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Claudia M A Carareto
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
| | - Rita Rebollo
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
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7
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Coronado-Zamora M, González J. Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains. Genome Res 2023; 33:1541-1553. [PMID: 37793782 PMCID: PMC10620055 DOI: 10.1101/gr.277565.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 08/08/2023] [Indexed: 10/06/2023]
Abstract
Transcriptomes are dynamic, with cells, tissues, and body parts expressing particular sets of transcripts. Transposable elements (TEs) are a known source of transcriptome diversity; however, studies often focus on a particular type of chimeric transcript, analyze single body parts or cell types, or are based on incomplete TE annotations from a single reference genome. In this work, we have implemented a method based on de novo transcriptome assembly that minimizes the potential sources of errors while identifying a comprehensive set of gene-TE chimeras. We applied this method to the head, gut, and ovary dissected from five Drosophila melanogaster natural strains, with individual reference genomes available. We found that ∼19% of body part-specific transcripts are gene-TE chimeras. Overall, chimeric transcripts contribute a mean of 43% to the total gene expression, and they provide protein domains for DNA binding, catalytic activity, and DNA polymerase activity. Our comprehensive data set is a rich resource for follow-up analysis. Moreover, because TEs are present in virtually all species sequenced to date, their role in spatially restricted transcript expression is likely not exclusive to the species analyzed in this work.
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Affiliation(s)
| | - Josefa González
- Institute of Evolutionary Biology, CSIC, UPF, Barcelona 08003, Spain
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8
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Chakrabarty P, Sen R, Sengupta S. From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution. Funct Integr Genomics 2023; 23:278. [PMID: 37610667 DOI: 10.1007/s10142-023-01206-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Transposable elements, often referred to as "jumping genes," have long been recognized as genomic parasites due to their ability to integrate and disrupt normal gene function and induce extensive genomic alterations, thereby compromising the host's fitness. To counteract this, the host has evolved a plethora of mechanisms to suppress the activity of the transposons. Recent research has unveiled the host-transposon relationships to be nuanced and complex phenomena, resulting in the coevolution of both entities. Transposition increases the mutational rate in the host genome, often triggering physiological pathways such as immune and stress responses. Current gene transfer technologies utilizing transposable elements have potential drawbacks, including off-target integration, induction of mutations, and modifications of cellular machinery, which makes an in-depth understanding of the host-transposon relationship imperative. This review highlights the dynamic interplay between the host and transposable elements, encompassing various factors and components of the cellular machinery. We provide a comprehensive discussion of the strategies employed by transposable elements for their propagation, as well as the mechanisms utilized by the host to mitigate their parasitic effects. Additionally, we present an overview of recent research identifying host proteins that act as facilitators or inhibitors of transposition. We further discuss the evolutionary outcomes resulting from the genetic interactions between the host and the transposable elements. Finally, we pose open questions in this field and suggest potential avenues for future research.
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Affiliation(s)
- Prayas Chakrabarty
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
| | - Raneet Sen
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
- Institute of Bioorganic Chemistry, Department of RNA Metabolism, Polish Academy of Sciences, Poznan, Poland
| | - Sugopa Sengupta
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India.
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9
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Su C, Ding C, Zhao Y, He B, Nie R, Hao J. Diapause-Linked Gene Expression Pattern and Related Candidate Duplicated Genes of the Mountain Butterfly Parnassius glacialis (Lepidoptera: Papilionidae) Revealed by Comprehensive Transcriptome Profiling. Int J Mol Sci 2023; 24:5577. [PMID: 36982649 PMCID: PMC10058462 DOI: 10.3390/ijms24065577] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
The mountain butterfly Parnassius glacialis is a representative species of the genus Parnassius, which probably originated in the high-altitude Qinhai-Tibet Plateau in the Miocene and later dispersed eastward into relatively low-altitude regions of central to eastern China. However, little is known about the molecular mechanisms underlying the long-term evolutionary adaptation to heterogeneous environmental conditions of this butterfly species. In this study, we obtained the high-throughput RNA-Seq data from twenty-four adult individuals in eight localities, covering nearly all known distributional areas in China, and firstly identified the diapause-linked gene expression pattern that is likely to correlate with local adaptation in adult P. glacialis populations. Secondly, we found a series of pathways responsible for hormone biosynthesis, energy metabolism and immune defense that also exhibited unique enrichment patterns in each group that are probably related to habitat-specific adaptability. Furthermore, we also identified a suite of duplicated genes (including two transposable elements) that are mostly co-expressed to promote the plastic responses to different environmental conditions. Together, these findings can help us to better understand this species' successful colonization to distinct geographic areas from the western to eastern areas of China, and also provide us with some insights into the evolution of diapause in mountain Parnassius butterfly species.
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Affiliation(s)
| | | | | | | | | | - Jiasheng Hao
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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10
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Liu P, Cuerda-Gil D, Shahid S, Slotkin RK. The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond. Annu Rev Genet 2022; 56:63-87. [DOI: 10.1146/annurev-genet-072920-015534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Within the life cycle of a living organism, another life cycle exists for the selfish genome inhabitants, which are called transposable elements (TEs). These mobile sequences invade, duplicate, amplify, and diversify within a genome, increasing the genome's size and generating new mutations. Cells act to defend their genome, but rather than permanently destroying TEs, they use chromatin-level repression and epigenetic inheritance to silence TE activity. This level of silencing is ephemeral and reversible, leading to a dynamic equilibrium between TE suppression and reactivation within a host genome. The coexistence of the TE and host genome can also lead to the domestication of the TE to serve in host genome evolution and function. In this review, we describe the life cycle of a TE, with emphasis on how epigenetic regulation is harnessed to control TEs for host genome stability and innovation.
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Affiliation(s)
- Peng Liu
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Diego Cuerda-Gil
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
- Graduate Program in the Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Saima Shahid
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - R. Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
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11
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Nawae W, Sonthirod C, Yoocha T, Waiyamitra P, Soisook P, Tangphatsornruang S, Pootakham W. Genome assembly of the Pendlebury's roundleaf bat, Hipposideros pendleburyi, revealed the expansion of Tc1/Mariner DNA transposons in Rhinolophoidea. DNA Res 2022; 29:dsac026. [PMID: 36214371 PMCID: PMC9549598 DOI: 10.1093/dnares/dsac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Indexed: 11/16/2022] Open
Abstract
Bats (Chiroptera) constitute the second largest order of mammals and have several distinctive features, such as true self-powered flight and strong immunity. The Pendlebury's roundleaf bat, Hipposideros pendleburyi, is endemic to Thailand and listed as a vulnerable species. We employed the 10× Genomics linked-read technology to obtain a genome assembly of H. pendleburyi. The assembly size was 2.17 Gb with a scaffold N50 length of 15,398,518 bases. Our phylogenetic analysis placed H. pendleburyi within the rhinolophoid clade of the suborder Yinpterochiroptera. A synteny analysis showed that H. pendleburyi shared conserved chromosome segments (up to 105 Mb) with Rhinolophus ferrumequinum and Phyllostomus discolor albeit having different chromosome numbers and belonging different families. We found positive selection signals in genes involved in inflammation, spermatogenesis and Wnt signalling. The analyses of transposable elements suggested the contraction of short interspersed nuclear elements (SINEs) and the accumulation of young mariner DNA transposons in the analysed hipposiderids. Distinct mariners were likely horizontally transferred to hipposiderid genomes over the evolution of this family. The lineage-specific profiles of SINEs and mariners might involve in the evolution of hipposiderids and be associated with the phylogenetic separations of these bats from other bat families.
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Affiliation(s)
- Wanapinun Nawae
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Pitchaporn Waiyamitra
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Thailand
| | - Sithichoke Tangphatsornruang
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
| | - Wirulda Pootakham
- National Omics Center (NOC), National Science and Technology Development Agency, Thailand Science Park, Pathum Thani, Thailand
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12
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Kolacsek O, Wachtl G, Fóthi Á, Schamberger A, Sándor S, Pergel E, Varga N, Raskó T, Izsvák Z, Apáti Á, Orbán TI. Functional indications for transposase domestications - Characterization of the human piggyBac transposase derived (PGBD) activities. Gene 2022; 834:146609. [PMID: 35609796 DOI: 10.1016/j.gene.2022.146609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 12/13/2022]
Abstract
Transposable elements are widespread in all living organisms. In addition to self-reproduction, they are a major source of genetic variation that drives genome evolution but our knowledge of the functions of human genes derived from transposases is limited. There are examples of transposon-derived, domesticated human genes that lost (SETMAR) or retained (THAP9) their transposase activity, however, several remnants in the human genome have not been thoroughly investigated yet. These include the five human piggyBac-derived sequences (PGBD1-5) which share ancestry with the Trichoplusia ni originated piggyBac (PB) transposase. Since PB is widely used in gene delivery applications, the potential activities of endogenous PGBDs are important to address. However, previous data is controversial, especially with the claimed transposition activity of PGBD5, it awaits further investigations. Here, we aimed to systematically analyze all five human PGBD proteins from several aspects, including phylogenetic conservation, potential transposase activity, expression pattern and their regulation in different stress conditions. Among PGBDs, PGBD5 is under the highest purifying selection, and exhibits the most cell type specific expression pattern. In a two-component vector system, none of the human PGBDs could mobilize either the insect PB transposon or the endogenous human PB-like MER75 and MER85 elements with intact terminal sequences. When cells were exposed to various stress conditions, including hypoxia, oxidative or UV stress, the expression profiles of all PGBDs showed different, often cell type specific responses; however, the pattern of PGBD5 in most cases had the opposite tendency than that of the other piggyBac-derived elements. Taken together, our results indicate that human PGBD elements did not retain their mobilizing activity, but their cell type specific, and cellular stress related expression profiles point toward distinct domesticated functions that require further characterization.
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Affiliation(s)
- Orsolya Kolacsek
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gerda Wachtl
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary; Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ábel Fóthi
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Anita Schamberger
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Sára Sándor
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Enikő Pergel
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Nóra Varga
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás Raskó
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Zsuzsanna Izsvák
- Max Delbrück Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Ágota Apáti
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.
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13
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Brosh O, Fabian DK, Cogni R, Tolosana I, Day JP, Olivieri F, Merckx M, Akilli N, Szkuta P, Jiggins FM. A novel transposable element-mediated mechanism causes antiviral resistance in Drosophila through truncating the Veneno protein. Proc Natl Acad Sci U S A 2022; 119:e2122026119. [PMID: 35858337 PMCID: PMC9304006 DOI: 10.1073/pnas.2122026119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/18/2022] [Indexed: 01/13/2023] Open
Abstract
Hosts are continually selected to evolve new defenses against an ever-changing array of pathogens. To understand this process, we examined the genetic basis of resistance to the Drosophila A virus in Drosophila melanogaster. In a natural population, we identified a polymorphic transposable element (TE) insertion that was associated with an ∼19,000-fold reduction in viral titers, allowing flies to largely escape the harmful effects of infection by this virulent pathogen. The insertion occurs in the protein-coding sequence of the gene Veneno, which encodes a Tudor domain protein. By mutating Veneno with CRISPR-Cas9 in flies and expressing it in cultured cells, we show that the ancestral allele of the gene has no effect on viral replication. Instead, the TE insertion is a gain-of-function mutation that creates a gene encoding a novel resistance factor. Viral titers remained reduced when we deleted the TE sequence from the transcript, indicating that resistance results from the TE truncating the Veneno protein. This is a novel mechanism of virus resistance and a new way by which TEs can contribute to adaptation.
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Affiliation(s)
- Osama Brosh
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Daniel K. Fabian
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Rodrigo Cogni
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
- Department of Ecology, University of São Paulo, 05508-220 São Paulo, Brazil
| | - Ignacio Tolosana
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Jonathan P. Day
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Francesca Olivieri
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Manon Merckx
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Nazli Akilli
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Piotr Szkuta
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
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14
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Fueyo R, Judd J, Feschotte C, Wysocka J. Roles of transposable elements in the regulation of mammalian transcription. Nat Rev Mol Cell Biol 2022; 23:481-497. [PMID: 35228718 PMCID: PMC10470143 DOI: 10.1038/s41580-022-00457-y] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 12/16/2022]
Abstract
Transposable elements (TEs) comprise about half of the mammalian genome. TEs often contain sequences capable of recruiting the host transcription machinery, which they use to express their own products and promote transposition. However, the regulatory sequences carried by TEs may affect host transcription long after the TEs have lost the ability to transpose. Recent advances in genome analysis and engineering have facilitated systematic interrogation of the regulatory activities of TEs. In this Review, we discuss diverse mechanisms by which TEs contribute to transcription regulation. Notably, TEs can donate enhancer and promoter sequences that influence the expression of host genes, modify 3D chromatin architecture and give rise to novel regulatory genes, including non-coding RNAs and transcription factors. We discuss how TEs spur regulatory evolution and facilitate the emergence of genetic novelties in mammalian physiology and development. By virtue of their repetitive and interspersed nature, TEs offer unique opportunities to dissect the effects of mutation and genomic context on the function and evolution of cis-regulatory elements. We argue that TE-centric studies hold the key to unlocking general principles of transcription regulation and evolution.
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Affiliation(s)
- Raquel Fueyo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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15
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Chang NC, Rovira Q, Wells J, Feschotte C, Vaquerizas JM. Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression. Genome Res 2022; 32:1408-1423. [PMID: 34987056 PMCID: PMC9341512 DOI: 10.1101/gr.275655.121] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 12/30/2021] [Indexed: 12/02/2022]
Abstract
There is considerable interest in understanding the effect of transposable elements (TEs) on embryonic development. Studies in humans and mice are limited by the difficulty of working with mammalian embryos and by the relative scarcity of active TEs in these organisms. The zebrafish is an outstanding model for the study of vertebrate development, and over half of its genome consists of diverse TEs. However, zebrafish TEs remain poorly characterized. Here we describe the demography and genomic distribution of zebrafish TEs and their expression throughout embryogenesis using bulk and single-cell RNA sequencing data. These results reveal a highly dynamic genomic ecosystem comprising nearly 2000 distinct TE families, which vary in copy number by four orders of magnitude and span a wide range of ages. Longer retroelements tend to be retained in intergenic regions, whereas short interspersed nuclear elements (SINEs) and DNA transposons are more frequently found nearby or within genes. Locus-specific mapping of TE expression reveals extensive TE transcription during development. Although two-thirds of TE transcripts are likely driven by nearby gene promoters, we still observe stage- and tissue-specific expression patterns in self-regulated TEs. Long terminal repeat (LTR) retroelements are most transcriptionally active immediately following zygotic genome activation, whereas DNA transposons are enriched among transcripts expressed in later stages of development. Single-cell analysis reveals several endogenous retroviruses expressed in specific somatic cell lineages. Overall, our study provides a valuable resource for using zebrafish as a model to study the impact of TEs on vertebrate development.
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Affiliation(s)
- Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Quirze Rovira
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
| | - Jonathan Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, 48149 Muenster, Germany
- MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom
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16
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Grau-Bové X, Navarrete C, Chiva C, Pribasnig T, Antó M, Torruella G, Galindo LJ, Lang BF, Moreira D, López-Garcia P, Ruiz-Trillo I, Schleper C, Sabidó E, Sebé-Pedrós A. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nat Ecol Evol 2022; 6:1007-1023. [PMID: 35680998 PMCID: PMC7613034 DOI: 10.1038/s41559-022-01771-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/21/2022] [Indexed: 02/06/2023]
Abstract
Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.
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Affiliation(s)
- Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Meritxell Antó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Bernd Franz Lang
- Robert Cedergren Centre in Bioinformatics and Genomics, Department of Biochemistry, Université de Montréal, Montréal, Quebec, Canada
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-Garcia
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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17
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Chesnokova E, Beletskiy A, Kolosov P. The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology. Int J Mol Sci 2022; 23:5847. [PMID: 35628657 PMCID: PMC9148063 DOI: 10.3390/ijms23105847] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) have been extensively studied for decades. In recent years, the introduction of whole-genome and whole-transcriptome approaches, as well as single-cell resolution techniques, provided a breakthrough that uncovered TE involvement in host gene expression regulation underlying multiple normal and pathological processes. Of particular interest is increased TE activity in neuronal tissue, and specifically in the hippocampus, that was repeatedly demonstrated in multiple experiments. On the other hand, numerous neuropathologies are associated with TE dysregulation. Here, we provide a comprehensive review of literature about the role of TEs in neurons published over the last three decades. The first chapter of the present review describes known mechanisms of TE interaction with host genomes in general, with the focus on mammalian and human TEs; the second chapter provides examples of TE exaptation in normal neuronal tissue, including TE involvement in neuronal differentiation and plasticity; and the last chapter lists TE-related neuropathologies. We sought to provide specific molecular mechanisms of TE involvement in neuron-specific processes whenever possible; however, in many cases, only phenomenological reports were available. This underscores the importance of further studies in this area.
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Affiliation(s)
- Ekaterina Chesnokova
- Laboratory of Cellular Neurobiology of Learning, Institute of Higher Nervous Activity and Neurophysiology of the Russian Academy of Sciences, 117485 Moscow, Russia; (A.B.); (P.K.)
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18
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Lié O, Renault S, Augé-Gouillou C. SETMAR, a case of primate co-opted genes: towards new perspectives. Mob DNA 2022; 13:9. [PMID: 35395947 PMCID: PMC8994322 DOI: 10.1186/s13100-022-00267-1] [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: 09/19/2021] [Accepted: 03/28/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We carry out a review of the history and biological activities of one domesticated gene in higher primates, SETMAR, by discussing current controversies. Our purpose is to open a new outlook that will serve as a framework for future work about SETMAR, possibly in the field of cognition development. MAIN BODY What is newly important about SETMAR can be summarized as follows: (1) the whole protein sequence is under strong purifying pressure; (2) its role is to strengthen existing biological functions rather than to provide new ones; (3) it displays a tissue-specific pattern of expression, at least for the alternative-splicing it undergoes. Studies reported here demonstrate that SETMAR protein(s) may be involved in essential networks regulating replication, transcription and translation. Moreover, during embryogenesis, SETMAR appears to contribute to brain development. SHORT CONCLUSION Our review underlines for the first time that SETMAR directly interacts with genes involved in brain functions related to vocalization and vocal learning. These findings pave the way for future works regarding SETMAR and the development of cognitive abilities in higher primates.
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Affiliation(s)
- Oriane Lié
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France.,iBrain, Team Neurogenomics and Neuronal physiopathology, Faculty of Medicine, 10 Bd Tonnellé, Cedex 1, 37032, Tours, France
| | - Sylvaine Renault
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France.,iBrain, Team Neurogenomics and Neuronal physiopathology, Faculty of Medicine, 10 Bd Tonnellé, Cedex 1, 37032, Tours, France
| | - Corinne Augé-Gouillou
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France. .,iBrain, Team Neurogenomics and Neuronal physiopathology, Faculty of Medicine, 10 Bd Tonnellé, Cedex 1, 37032, Tours, France.
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19
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Structural and genome-wide analyses suggest that transposon-derived protein SETMAR alters transcription and splicing. J Biol Chem 2022; 298:101894. [PMID: 35378129 PMCID: PMC9062482 DOI: 10.1016/j.jbc.2022.101894] [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: 12/18/2021] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 11/22/2022] Open
Abstract
Extensive portions of the human genome have unknown function, including those derived from transposable elements. One such element, the DNA transposon Hsmar1, entered the primate lineage approximately 50 million years ago leaving behind terminal inverted repeat (TIR) sequences and a single intact copy of the Hsmar1 transposase, which retains its ancestral TIR-DNA-binding activity, and is fused with a lysine methyltransferase SET domain to constitute the chimeric SETMAR gene. Here, we provide a structural basis for recognition of TIRs by SETMAR and investigate the function of SETMAR through genome-wide approaches. As elucidated in our 2.37 Å crystal structure, SETMAR forms a dimeric complex with each DNA-binding domain bound specifically to TIR-DNA through the formation of 32 hydrogen bonds. We found that SETMAR recognizes primarily TIR sequences (∼5000 sites) within the human genome as assessed by chromatin immunoprecipitation sequencing analysis. In two SETMAR KO cell lines, we identified 163 shared differentially expressed genes and 233 shared alternative splicing events. Among these genes are several pre–mRNA-splicing factors, transcription factors, and genes associated with neuronal function, and one alternatively spliced primate-specific gene, TMEM14B, which has been identified as a marker for neocortex expansion associated with brain evolution. Taken together, our results suggest a model in which SETMAR impacts differential expression and alternative splicing of genes associated with transcription and neuronal function, potentially through both its TIR-specific DNA-binding and lysine methyltransferase activities, consistent with a role for SETMAR in simian primate development.
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20
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Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, Olson D, Rosen J, Smit AFA, Straight AF, Vollger MR, Wheeler TJ, Schatz MC, Eichler EE, Phillippy AM, Timp W, Miga KH, O’Neill RJ. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science 2022; 376:eabk3112. [PMID: 35357925 PMCID: PMC9301658 DOI: 10.1126/science.abk3112] [Citation(s) in RCA: 121] [Impact Index Per Article: 60.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.
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Affiliation(s)
- Savannah J. Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | | | - Gabrielle A. Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Patrick G. S. Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Charles Limouse
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Reza Halabian
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Luke Wojenski
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Matias Rodriguez
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leighton J. Core
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | | | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Daniel Olson
- Department of Computer Science, University of Montana, Missoula, MT, USA
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Travis J. Wheeler
- Department of Computer Science, University of Montana, Missoula, MT, USA
| | - Michael C. Schatz
- Department of Computer Science and Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Rachel J. O’Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
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21
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Nickoloff JA, Sharma N, Taylor L, Allen SJ, Hromas R. Nucleases and Co-Factors in DNA Replication Stress Responses. DNA 2022; 2:68-85. [PMID: 36203968 PMCID: PMC9534323 DOI: 10.3390/dna2010006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA replication stress is a constant threat that cells must manage to proliferate and maintain genome integrity. DNA replication stress responses, a subset of the broader DNA damage response (DDR), operate when the DNA replication machinery (replisome) is blocked or replication forks collapse during S phase. There are many sources of replication stress, such as DNA lesions caused by endogenous and exogenous agents including commonly used cancer therapeutics, and difficult-to-replicate DNA sequences comprising fragile sites, G-quadraplex DNA, hairpins at trinucleotide repeats, and telomeres. Replication stress is also a consequence of conflicts between opposing transcription and replication, and oncogenic stress which dysregulates replication origin firing and fork progression. Cells initially respond to replication stress by protecting blocked replisomes, but if the offending problem (e.g., DNA damage) is not bypassed or resolved in a timely manner, forks may be cleaved by nucleases, inducing a DNA double-strand break (DSB) and providing a means to accurately restart stalled forks via homologous recombination. However, DSBs pose their own risks to genome stability if left unrepaired or misrepaired. Here we focus on replication stress response systems, comprising DDR signaling, fork protection, and fork processing by nucleases that promote fork repair and restart. Replication stress nucleases include MUS81, EEPD1, Metnase, CtIP, MRE11, EXO1, DNA2-BLM, SLX1-SLX4, XPF-ERCC1-SLX4, Artemis, XPG, and FEN1. Replication stress factors are important in cancer etiology as suppressors of genome instability associated with oncogenic mutations, and as potential cancer therapy targets to enhance the efficacy of chemo- and radiotherapeutics.
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Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Lynn Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Sage J. Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO 80523, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
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22
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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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23
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Nickoloff JA, Sharma N, Taylor L, Allen SJ, Lee SH, Hromas R. Metnase and EEPD1: DNA Repair Functions and Potential Targets in Cancer Therapy. Front Oncol 2022; 12:808757. [PMID: 35155245 PMCID: PMC8831698 DOI: 10.3389/fonc.2022.808757] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/12/2022] [Indexed: 12/30/2022] Open
Abstract
Cells respond to DNA damage by activating signaling and DNA repair systems, described as the DNA damage response (DDR). Clarifying DDR pathways and their dysregulation in cancer are important for understanding cancer etiology, how cancer cells exploit the DDR to survive endogenous and treatment-related stress, and to identify DDR targets as therapeutic targets. Cancer is often treated with genotoxic chemicals and/or ionizing radiation. These agents are cytotoxic because they induce DNA double-strand breaks (DSBs) directly, or indirectly by inducing replication stress which causes replication fork collapse to DSBs. EEPD1 and Metnase are structure-specific nucleases, and Metnase is also a protein methyl transferase that methylates histone H3 and itself. EEPD1 and Metnase promote repair of frank, two-ended DSBs, and both promote the timely and accurate restart of replication forks that have collapsed to single-ended DSBs. In addition to its roles in HR, Metnase also promotes DSB repair by classical non-homologous recombination, and chromosome decatenation mediated by TopoIIα. Although mutations in Metnase and EEPD1 are not common in cancer, both proteins are frequently overexpressed, which may help tumor cells manage oncogenic stress or confer resistance to therapeutics. Here we focus on Metnase and EEPD1 DNA repair pathways, and discuss opportunities for targeting these pathways to enhance cancer therapy.
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Affiliation(s)
- Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Lynn Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Sage J Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States
| | - Suk-Hee Lee
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, United States
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24
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Tellier M. Structure, Activity, and Function of SETMAR Protein Lysine Methyltransferase. Life (Basel) 2021; 11:life11121342. [PMID: 34947873 PMCID: PMC8704517 DOI: 10.3390/life11121342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 12/21/2022] Open
Abstract
SETMAR is a protein lysine methyltransferase that is involved in several DNA processes, including DNA repair via the non-homologous end joining (NHEJ) pathway, regulation of gene expression, illegitimate DNA integration, and DNA decatenation. However, SETMAR is an atypical protein lysine methyltransferase since in anthropoid primates, the SET domain is fused to an inactive DNA transposase. The presence of the DNA transposase domain confers to SETMAR a DNA binding activity towards the remnants of its transposable element, which has resulted in the emergence of a gene regulatory function. Both the SET and the DNA transposase domains are involved in the different cellular roles of SETMAR, indicating the presence of novel and specific functions in anthropoid primates. In addition, SETMAR is dysregulated in different types of cancer, indicating a potential pathological role. While some light has been shed on SETMAR functions, more research and new tools are needed to better understand the cellular activities of SETMAR and to investigate the therapeutic potential of SETMAR.
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Affiliation(s)
- Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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25
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Watson AK, Lopez P, Bapteste E. Hundreds of out-of-frame remodelled gene families in the E. coli pangenome. Mol Biol Evol 2021; 39:6430988. [PMID: 34792602 PMCID: PMC8788219 DOI: 10.1093/molbev/msab329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesized to have formed de novo, from noncoding sequences, and recent work has begun to elucidate the processes by which de novo gene formation can occur. A special case of de novo gene formation, overprinting, describes the origin of new genes from noncoding alternative reading frames of existing open reading frames (ORFs). We argue that additionally, out-of-frame gene fission/fusion events of alternative reading frames of ORFs and out-of-frame lateral gene transfers could contribute to the origin of new gene families. To demonstrate this, we developed an original pattern-search in sequence similarity networks, enhancing the use of these graphs, commonly used to detect in-frame remodeled genes. We applied this approach to gene families in 524 complete genomes of Escherichia coli. We identified 767 gene families whose evolutionary history likely included at least one out-of-frame remodeling event. These genes with out-of-frame components represent ∼2.5% of all genes in the E. coli pangenome, suggesting that alternative reading frames of existing ORFs can contribute to a significant proportion of de novo genes in bacteria.
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Affiliation(s)
- Andrew K Watson
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, 7, quai Saint Bernard, Paris, 75005, France
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26
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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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Nickoloff JA, Sharma N, Taylor L, Allen SJ, Hromas R. The Safe Path at the Fork: Ensuring Replication-Associated DNA Double-Strand Breaks are Repaired by Homologous Recombination. Front Genet 2021; 12:748033. [PMID: 34646312 PMCID: PMC8502867 DOI: 10.3389/fgene.2021.748033] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/14/2021] [Indexed: 01/15/2023] Open
Abstract
Cells must replicate and segregate their DNA to daughter cells accurately to maintain genome stability and prevent cancer. DNA replication is usually fast and accurate, with intrinsic (proofreading) and extrinsic (mismatch repair) error-correction systems. However, replication forks slow or stop when they encounter DNA lesions, natural pause sites, and difficult-to-replicate sequences, or when cells are treated with DNA polymerase inhibitors or hydroxyurea, which depletes nucleotide pools. These challenges are termed replication stress, to which cells respond by activating DNA damage response signaling pathways that delay cell cycle progression, stimulate repair and replication fork restart, or induce apoptosis. Stressed forks are managed by rescue from adjacent forks, repriming, translesion synthesis, template switching, and fork reversal which produces a single-ended double-strand break (seDSB). Stressed forks also collapse to seDSBs when they encounter single-strand nicks or are cleaved by structure-specific nucleases. Reversed and cleaved forks can be restarted by homologous recombination (HR), but seDSBs pose risks of mis-rejoining by non-homologous end-joining (NHEJ) to other DSBs, causing genome rearrangements. HR requires resection of broken ends to create 3' single-stranded DNA for RAD51 recombinase loading, and resected ends are refractory to repair by NHEJ. This Mini Review highlights mechanisms that help maintain genome stability by promoting resection of seDSBs and accurate fork restart by HR.
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Affiliation(s)
- Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO, United States
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO, United States
| | - Lynn Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO, United States
| | - Sage J Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Ft. Collins, CO, United States
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, United States
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28
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Brzáčová Z, Peťková M, Veljačiková K, Zajičková T, Tomáška Ľ. Reconstruction of human genome evolution in yeast: an educational primer for use with "systematic humanization of the yeast cytoskeleton discerns functionally replaceable from divergent human genes". Genetics 2021; 219:6380399. [PMID: 34849890 DOI: 10.1093/genetics/iyab118] [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: 06/16/2021] [Accepted: 07/14/2021] [Indexed: 01/01/2023] Open
Abstract
The evolution of eukaryotic organisms starting with the last eukaryotic common ancestor was accompanied by lineage-specific expansion of gene families. A paper by Garge et al. provides an excellent opportunity to have students explore how expansion of gene families via gene duplication results in protein specialization, in this case in the context of eukaryotic cytoskeletal organization . The authors tested hypotheses about conserved protein function by systematic "humanization" of the yeast cytoskeletal components while employing a wide variety of methodological approaches. We outline several exercises to promote students' ability to explore the genomic databases, perform bioinformatic analyses, design experiments for functional analysis of human genes in yeast and critically interpret results to address both specific and general questions.
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Affiliation(s)
- Zuzana Brzáčová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava 842 15, Slovakia
| | - Mária Peťková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava 842 15, Slovakia
| | - Katarína Veljačiková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava 842 15, Slovakia
| | - Terézia Zajičková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava 842 15, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava 842 15, Slovakia
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29
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Wanner NM, Faulk C. Suggested Absence of Horizontal Transfer of Retrotransposons between Humans and Domestic Mammal Species. Genes (Basel) 2021; 12:1223. [PMID: 34440397 PMCID: PMC8391136 DOI: 10.3390/genes12081223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/02/2021] [Accepted: 08/05/2021] [Indexed: 02/01/2023] Open
Abstract
Transposable element sequences are usually vertically inherited but have also spread across taxa via horizontal transfer. Previous investigations of ancient horizontal transfer of transposons have compared consensus sequences, but this method resists detection of recent single or low copy number transfer events. The relationship between humans and domesticated animals represents an opportunity for potential horizontal transfer due to the consistent shared proximity and exposure to parasitic insects, which have been identified as plausible transfer vectors. The relatively short period of extended human-animal contact (tens of thousands of years or less) makes horizontal transfer of transposons between them unlikely. However, the availability of high-quality reference genomes allows individual element comparisons to detect low copy number events. Using pairwise all-versus-all megablast searches of the complete suite of retrotransposons of thirteen domestic animals against human, we searched a total of 27,949,823 individual TEs. Based on manual comparisons of stringently filtered BLAST search results for evidence of vertical inheritance, no plausible instances of HTT were identified. These results indicate that significant recent HTT between humans and domesticated animals has not occurred despite the close proximity, either due to the short timescale, inhospitable recipient genomes, a failure of vector activity, or other factors.
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Affiliation(s)
- Nicole M. Wanner
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, 301 Veterinary Science Building, 1971 Commonwealth Avenue, St. Paul, MN 55108, USA;
| | - Christopher Faulk
- Department of Animal Science, College of Food, Agriculture, and Natural Resource Sciences, University of Minnesota, 277 Coffey Hall, 1420 Eckles Avenue, St. Paul, MN 55108, USA
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30
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Nickoloff JA, Sharma N, Allen CP, Taylor L, Allen SJ, Jaiswal AS, Hromas R. Roles of homologous recombination in response to ionizing radiation-induced DNA damage. Int J Radiat Biol 2021; 99:903-914. [PMID: 34283012 PMCID: PMC9629169 DOI: 10.1080/09553002.2021.1956001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/04/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE Ionizing radiation induces a vast array of DNA lesions including base damage, and single- and double-strand breaks (SSB, DSB). DSBs are among the most cytotoxic lesions, and mis-repair causes small- and large-scale genome alterations that can contribute to carcinogenesis. Indeed, ionizing radiation is a 'complete' carcinogen. DSBs arise immediately after irradiation, termed 'frank DSBs,' as well as several hours later in a replication-dependent manner, termed 'secondary' or 'replication-dependent DSBs. DSBs resulting from replication fork collapse are single-ended and thus pose a distinct problem from two-ended, frank DSBs. DSBs are repaired by error-prone nonhomologous end-joining (NHEJ), or generally error-free homologous recombination (HR), each with sub-pathways. Clarifying how these pathways operate in normal and tumor cells is critical to increasing tumor control and minimizing side effects during radiotherapy. CONCLUSIONS The choice between NHEJ and HR is regulated during the cell cycle and by other factors. DSB repair pathways are major contributors to cell survival after ionizing radiation, including tumor-resistance to radiotherapy. Several nucleases are important for HR-mediated repair of replication-dependent DSBs and thus replication fork restart. These include three structure-specific nucleases, the 3' MUS81 nuclease, and two 5' nucleases, EEPD1 and Metnase, as well as three end-resection nucleases, MRE11, EXO1, and DNA2. The three structure-specific nucleases evolved at very different times, suggesting incremental acceleration of replication fork restart to limit toxic HR intermediates and genome instability as genomes increased in size during evolution, including the gain of large numbers of HR-prone repetitive elements. Ionizing radiation also induces delayed effects, observed days to weeks after exposure, including delayed cell death and delayed HR. In this review we highlight the roles of HR in cellular responses to ionizing radiation, and discuss the importance of HR as an exploitable target for cancer radiotherapy.
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Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Christopher P. Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Microbiology, Immunology and Pathology, Flow Cytometry and Cell Sorting Facility, Colorado State University, Fort Collins, CO, USA
| | - Lynn Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Sage J. Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Aruna S. Jaiswal
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
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31
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Miskei M, Horváth A, Viola L, Varga L, Nagy É, Feró O, Karányi Z, Roszik J, Miskey C, Ivics Z, Székvölgyi L. Genome-wide mapping of binding sites of the transposase-derived SETMAR protein in the human genome. Comput Struct Biotechnol J 2021; 19:4032-4041. [PMID: 34377368 PMCID: PMC8327481 DOI: 10.1016/j.csbj.2021.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 01/04/2023] Open
Abstract
Throughout evolution, DNA transposons provide a recurrent supply of genetic information to give rise to novel gene functions by fusion of their transposase domain to various domains of host-encoded proteins. One of these "domesticated", transposase-derived factors is SETMAR/Metnase which is a naturally occurring fusion protein that consists of a histone-lysine methyltransferase domain and an HsMar1 transposase. To elucidate the biological role of SETMAR, it is crucial to identify genomic targets to which SETMAR specifically binds and link these sites to the regulation of gene expression. Herein, we mapped the genomic landscape of SETMAR binding in a near-haploid human leukemia cell line (HAP1) in order to identify on-target and off-target binding sites at high resolution and to elucidate their role in terms of gene expression. Our analysis revealed a perfect correlation between SETMAR and inverted terminal repeats (ITRs) of HsMar1 transposon remnants, which are considered as natural target sites for SETMAR binding. However, we did not detect any untargeted events at non-ITR sequences, calling into question previously proposed off-target binding sites. We identified sequence fidelity of the ITR motif as a key factor for determining the binding affinity of SETMAR for chromosomes, as higher conservation of ITR sequences resulted in increased affinity for chromatin and stronger repression of SETMAR-bound gene loci. These associations highlight how SETMAR's chromatin binding fine-tune gene regulatory networks in human tumour cells.
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Affiliation(s)
- Márton Miskei
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Adrienn Horváth
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Lívia Viola
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Laura Varga
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Éva Nagy
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Orsolya Feró
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
| | - Zsolt Karányi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
- Department of Internal Medicine, Faculty of Medicine, University of Debrecen, Hungary
| | - Jason Roszik
- Department of Melanoma Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Centre, University of Texas, USA
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen D-63225, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen D-63225, Germany
| | - Lóránt Székvölgyi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary
- Faculty of Pharmacy, University of Debrecen, Hungary
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32
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Almojil D, Bourgeois Y, Falis M, Hariyani I, Wilcox J, Boissinot S. The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes. Genes (Basel) 2021; 12:genes12060918. [PMID: 34203645 PMCID: PMC8232201 DOI: 10.3390/genes12060918] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.
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Affiliation(s)
- Dareen Almojil
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Yann Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK;
| | - Marcin Falis
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Imtiyaz Hariyani
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
| | - Justin Wilcox
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates; (D.A.); (M.F.); (I.H.); (J.W.)
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Correspondence:
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Antoine-Lorquin A, Arensburger P, Arnaoty A, Asgari S, Batailler M, Beauclair L, Belleannée C, Buisine N, Coustham V, Guyetant S, Helou L, Lecomte T, Pitard B, Stévant I, Bigot Y. Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells. Genomics 2021; 113:1589-1604. [PMID: 33812898 DOI: 10.1016/j.ygeno.2021.03.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 11/15/2022]
Abstract
Setmar is a gene specific to simian genomes. The function(s) of its isoforms are poorly understood and their existence in healthy tissues remains to be validated. Here we profiled SETMAR expression and its genome-wide binding landscape in colon tissue. We found isoforms V3 and V6 in healthy and tumour colon tissues as well as incell lines. In two colorectal cell lines SETMAR binds to several thousand Hsmar1 and MADE1 terminal ends, transposons mostly located in non-genic regions of active chromatin including in enhancers. It also binds to a 12-bp motifs similar to an inner motif in Hsmar1 and MADE1 terminal ends. This motif is interspersed throughout the genome and is enriched in GC-rich regions as well as in CpG islands that contain constitutive replication origins. It is also found in enhancers other than those associated with Hsmar1 and MADE1. The role of SETMAR in the expression of genes, DNA replication and in DNA repair are discussed.
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Affiliation(s)
| | - Peter Arensburger
- Biological Sciences Department, California State Polytechnic University, Pomona, CA 91768, - United States
| | - Ahmed Arnaoty
- EA GICC, 7501, CHRU de Tours, 37044 TOURS, Cedex 09, France
| | - Sassan Asgari
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Martine Batailler
- PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France
| | - Linda Beauclair
- PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France
| | | | - Nicolas Buisine
- UMR CNRS 7221, Muséum National d'Histoire Naturelle, 75005 Paris, France
| | | | - Serge Guyetant
- Tumorothèque du CHRU de Tours, 37044 Tours, Cedex, France
| | - Laura Helou
- PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France
| | | | - Bruno Pitard
- Université de Nantes, CNRS ERL6001, Inserm 1232, CRCINA, F-44000 Nantes, France
| | - Isabelle Stévant
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon, 1, 46 allée d'Italie, 69364 Lyon, France
| | - Yves Bigot
- PRC, UMR INRA 0085, CNRS 7247, Centre INRA Val de Loire, 37380 Nouzilly, France.
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34
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Cosby RL, Judd J, Zhang R, Zhong A, Garry N, Pritham EJ, Feschotte C. Recurrent evolution of vertebrate transcription factors by transposase capture. Science 2021; 371:eabc6405. [PMID: 33602827 PMCID: PMC8186458 DOI: 10.1126/science.abc6405] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 12/18/2020] [Indexed: 12/13/2022]
Abstract
Genes with novel cellular functions may evolve through exon shuffling, which can assemble novel protein architectures. Here, we show that DNA transposons provide a recurrent supply of materials to assemble protein-coding genes through exon shuffling. We find that transposase domains have been captured-primarily via alternative splicing-to form fusion proteins at least 94 times independently over the course of ~350 million years of tetrapod evolution. We find an excess of transposase DNA binding domains fused to host regulatory domains, especially the Krüppel-associated box (KRAB) domain, and identify four independently evolved KRAB-transposase fusion proteins repressing gene expression in a sequence-specific fashion. The bat-specific KRABINER fusion protein binds its cognate transposons genome-wide and controls a network of genes and cis-regulatory elements. These results illustrate how a transcription factor and its binding sites can emerge.
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Affiliation(s)
- Rachel L Cosby
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Julius Judd
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Ruiling Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Alan Zhong
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Nathaniel Garry
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850, USA.
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35
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Affiliation(s)
- Aaron Wacholder
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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36
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Dupeyron M, Baril T, Bass C, Hayward A. Phylogenetic analysis of the Tc1/mariner superfamily reveals the unexplored diversity of pogo-like elements. Mob DNA 2020; 11:21. [PMID: 32612713 PMCID: PMC7325037 DOI: 10.1186/s13100-020-00212-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/08/2020] [Indexed: 01/18/2023] Open
Abstract
Background Tc1/mariner transposons are widespread DNA transposable elements (TEs) that have made important contributions to the evolution of host genomic complexity in metazoans. However, the evolution and diversity of the Tc1/mariner superfamily remains poorly understood. Following recent developments in genome sequencing and the availability of a wealth of new genomes, Tc1/mariner TEs have been identified in many new taxa across the eukaryotic tree of life. To date, the majority of studies focussing on Tc1/mariner elements have considered only a single host lineage or just a small number of host lineages. Thus, much remains to be learnt about the evolution of Tc1/mariner TEs by performing analyses that consider elements that originate from across host diversity. Results We mined the non-redundant database of NCBI using BLASTp searches, with transposase sequences from a diverse set of reference Tc1/mariner elements as queries. A total of 5158 Tc1/mariner elements were retrieved and used to reconstruct evolutionary relationships within the superfamily. The resulting phylogeny is well resolved and includes several new groups of Tc1/mariner elements. In particular, we identify a new family of plant-genome restricted Tc1/mariner elements, which we call PlantMar. We also show that the pogo family is much larger and more diverse than previously appreciated, and we review evidence for a potential revision of its status to become a separate superfamily. Conclusions Our study provides an overview of Tc1-mariner phylogeny and summarises the impressive diversity of Tc1-mariner TEs among sequenced eukaryotes. Tc1/mariner TEs are successful in a wide range of eukaryotes, especially unikonts (the taxonomic supergroup containing Amoebozoa, Opisthokonta, Breviatea, and Apusomonadida). In particular, ecdysozoa, and especially arthropods, emerge as important hosts for Tc1/mariner elements (except the PlantMar family). Meanwhile, the pogo family, which is by far the largest Tc1/mariner family, also includes many elements from fungal and chordate genomes. Moreover, there is evidence of the repeated exaptation of pogo elements in vertebrates, including humans, in addition to the well-known example of CENP-B. Collectively, our findings provide a considerable advancement in understanding of Tc1/mariner elements, and more generally they suggest that much work remains to improve understanding of the diversity and evolution of DNA TEs.
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Affiliation(s)
- Mathilde Dupeyron
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE UK
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Sharma N, Speed MC, Allen CP, Maranon DG, Williamson E, Singh S, Hromas R, Nickoloff JA. Distinct roles of structure-specific endonucleases EEPD1 and Metnase in replication stress responses. NAR Cancer 2020; 2:zcaa008. [PMID: 32743552 PMCID: PMC7380491 DOI: 10.1093/narcan/zcaa008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/20/2020] [Accepted: 05/31/2020] [Indexed: 12/16/2022] Open
Abstract
Accurate DNA replication and segregation are critical for maintaining genome integrity and suppressing cancer. Metnase and EEPD1 are DNA damage response (DDR) proteins frequently dysregulated in cancer and implicated in cancer etiology and tumor response to genotoxic chemo- and radiotherapy. Here, we examine the DDR in human cell lines with CRISPR/Cas9 knockout of Metnase or EEPD1. The knockout cell lines exhibit slightly slower growth rates, significant hypersensitivity to replication stress, increased genome instability and distinct alterations in DDR signaling. Metnase and EEPD1 are structure-specific nucleases. EEPD1 is recruited to and cleaves stalled forks to initiate fork restart by homologous recombination. Here, we demonstrate that Metnase is also recruited to stalled forks where it appears to dimethylate histone H3 lysine 36 (H3K36me2), raising the possibility that H3K36me2 promotes DDR factor recruitment or limits nucleosome eviction to protect forks from nucleolytic attack. We show that stalled forks are cleaved normally in the absence of Metnase, an important and novel result because a prior study indicated that Metnase nuclease is important for timely fork restart. A double knockout was as sensitive to etoposide as either single knockout, suggesting a degree of epistasis between Metnase and EEPD1. We propose that EEPD1 initiates fork restart by cleaving stalled forks, and that Metnase may promote fork restart by processing homologous recombination intermediates and/or inducing H3K36me2 to recruit DDR factors. By accelerating fork restart, Metnase and EEPD1 reduce the chance that stalled replication forks will adopt toxic or genome-destabilizing structures, preventing genome instability and cancer. Metnase and EEPD1 are overexpressed in some cancers and thus may also promote resistance to genotoxic therapeutics.
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Affiliation(s)
- Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, 1618 Campus Delivery, Fort Collins, CO 80523-1618, USA
| | - Michael C Speed
- Department of Environmental and Radiological Health Sciences, Colorado State University, 1618 Campus Delivery, Fort Collins, CO 80523-1618, USA
| | - Christopher P Allen
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1601Campus Delivery, Fort Collins, CO 80523-1601, USA
| | - David G Maranon
- Department of Environmental and Radiological Health Sciences, Colorado State University, 1618 Campus Delivery, Fort Collins, CO 80523-1618, USA
| | - Elizabeth Williamson
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas HealthScience Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Sudha Singh
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas HealthScience Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine, University of Texas HealthScience Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, 1618 Campus Delivery, Fort Collins, CO 80523-1618, USA
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Tellier M, Chalmers R. Compensating for over-production inhibition of the Hsmar1 transposon in Escherichia coli using a series of constitutive promoters. Mob DNA 2020; 11:5. [PMID: 31938044 PMCID: PMC6954556 DOI: 10.1186/s13100-020-0200-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/01/2020] [Indexed: 01/03/2023] Open
Abstract
Background Transposable elements (TEs) are a diverse group of self-mobilizing DNA elements. Transposition has been exploited as a powerful tool for molecular biology and genomics. However, transposition is sometimes limited because of auto-regulatory mechanisms that presumably allow them to cohabit within their hosts without causing excessive genomic damage. The papillation assay provides a powerful visual screen for hyperactive transposases. Transposition is revealed by the activation of a promoter-less lacZ gene when the transposon integrates into a non-essential gene on the host chromosome. Transposition events are detected as small blue speckles, or papillae, on the white background of the main Escherichia coli colony. Results We analysed the parameters of the papillation assay including the strength of the transposase transcriptional and translational signals. To overcome certain limitations of inducible promoters, we constructed a set of vectors based on constitutive promoters of different strengths to widen the range of transposase expression. We characterized and validated our expression vectors with Hsmar1, a member of the mariner transposon family. The highest rate of transposition was observed with the weakest promoters. We then took advantage of our approach to investigate how the level of transposition responds to selected point mutations and the effect of joining the transposase monomers into a single-chain dimer. Conclusions We generated a set of vectors to provide a wide range of transposase expression which will be useful for screening libraries of transposase mutants. The use of weak promoters should allow screening for truly hyperactive transposases rather than those that are simply resistant to auto-regulatory mechanisms, such as overproduction inhibition (OPI). We also found that mutations in the Hsmar1 dimer interface provide resistance to OPI in bacteria, which could be valuable for improving bacterial transposon mutagenesis techniques.
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Affiliation(s)
- Michael Tellier
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH UK.,2Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE UK
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH UK
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Tellier M, Chalmers R. Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome. Nucleic Acids Res 2019; 47:122-133. [PMID: 30329085 PMCID: PMC6326780 DOI: 10.1093/nar/gky937] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022] Open
Abstract
Transposons impart dynamism to the genomes they inhabit and their movements frequently rewire the control of nearby genes. Occasionally, their proteins are domesticated when they evolve a new function. SETMAR is a protein methylase with a sequence-specific DNA binding domain. It began to evolve about 50 million years ago when an Hsmar1 transposon integrated downstream of a SET-domain methylase gene. Here we show that the DNA-binding domain of the transposase targets the enzyme to transposon-end remnants and that this is capable of regulating gene expression, dependent on the methylase activity. When SETMAR was modestly overexpressed in human cells, almost 1500 genes changed expression by more than 2-fold (65% up- and 35% down-regulated). These genes were enriched for the KEGG Pathways in Cancer and include several transcription factors important for development and differentiation. Expression of a similar level of a methylase-deficient SETMAR changed the expression of many fewer genes, 77% of which were down-regulated with no significant enrichment of KEGG Pathways. Our data is consistent with a model in which SETMAR is part of an anthropoid primate-specific regulatory network centered on the subset of genes containing a transposon end.
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Affiliation(s)
- Michael Tellier
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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Tellier M, Chalmers R. The roles of the human SETMAR (Metnase) protein in illegitimate DNA recombination and non-homologous end joining repair. DNA Repair (Amst) 2019; 80:26-35. [PMID: 31238295 PMCID: PMC6715855 DOI: 10.1016/j.dnarep.2019.06.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/18/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023]
Abstract
Full length SETMAR expression has no effect on DNA repair and integration in vivo. SETMAR putative nuclease activity is not required in vivo. Separate expression of the SET and MAR domains affects DNA repair and integration. SETMAR isoform with a truncated SET-domain is specific to species containing the MAR domain.
SETMAR is a fusion between a SET-domain methyltransferase gene and a mariner-family transposase gene, which is specific to anthropoid primates. However, the ancestral SET gene is present in all other mammals and birds. SETMAR is reported to be involved in transcriptional regulation and a diverse set of reactions related to DNA repair. Since the transcriptional effects of SETMAR depend on site-specific DNA binding, and are perturbed by inactivating the methyltransferase, we wondered whether we could differentiate the effects of the SET and MAR domains in DNA repair assays. We therefore generated several stable U2OS cell lines expressing either wild type SETMAR or truncation or point mutant variants. We tested these cell lines with in vivo plasmid-based assays to determine the relevance of the different domains and activities of SETMAR in DNA repair. Contrary to previous reports, we found that wild type SETMAR had little to no effect on the rate of cell division, DNA integration into the genome or non-homologous end joining. Also contrary to previous reports, we failed to detect any effect of a strong active-site mutation that should have knocked out the putative nuclease activity of SETMAR.
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Affiliation(s)
- Michael Tellier
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
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Renault S, Genty M, Gabori A, Boisneau C, Esnault C, Dugé de Bernonville T, Augé-Gouillou C. The epigenetic regulation of HsMar1, a human DNA transposon. BMC Genet 2019; 20:17. [PMID: 30764754 PMCID: PMC6375154 DOI: 10.1186/s12863-019-0719-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/29/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Both classes of transposable elements (DNA and RNA) are tightly regulated at the transcriptional level leading to the inactivation of transposition via epigenetic mechanisms. Due to the high copies number of these elements, the hypothesis has emerged that their regulation can coordinate a regulatory network of genes. Herein, we investigated whether transposition regulation of HsMar1, a human DNA transposon, differs in presence or absence of endogenous HsMar1 copies. In the case where HsMar1 transposition is regulated, the number of repetitive DNA sequences issued by HsMar1 and distributed in the human genome makes HsMar1 a good candidate to regulate neighboring gene expression by epigenetic mechanisms. RESULTS A recombinant active HsMar1 copy was inserted in HeLa (human) and CHO (hamster) cells and its genomic excision monitored. We show that HsMar1 excision is blocked in HeLa cells, whereas CHO cells are competent to promote HsMar1 excision. We demonstrate that de novo HsMar1 insertions in HeLa cells (human) undergo rapid silencing by cytosine methylation and apposition of H3K9me3 marks, whereas de novo HsMar1 insertions in CHO cells (hamster) are not repressed and enriched in H3K4me3 modifications. The overall analysis of HsMar1 endogenous copies in HeLa cells indicates that neither full-length endogenous inactive copies nor their Inverted Terminal Repeats seem to be specifically silenced, and are, in contrast, devoid of epigenetic marks. Finally, the setmar gene, derived from HsMar1, presents H3K4me3 modifications as expected for a human housekeeping gene. CONCLUSIONS Our work highlights that de novo and old HsMar1 are not similarly regulated by epigenetic mechanisms. Old HsMar1 are generally detected as lacking epigenetic marks, irrespective their localisation relative to the genes. Considering the putative existence of a network associating HsMar1 old copies and SETMAR, two non-mutually exclusive hypotheses are proposed: active and inactive HsMar1 copies are not similarly regulated or/and regulations concern only few loci (and few genes) that cannot be detected at the whole genome level.
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Affiliation(s)
- Sylvaine Renault
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
- UMR 1253, iBrain, University of Tours, INSERM, Tours, France
| | - Murielle Genty
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
- UMR 1253, iBrain, University of Tours, INSERM, Tours, France
| | - Alison Gabori
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
| | - Catherine Boisneau
- UMR CITERES CNRS 7324, Université de Tours, 35 Allée Ferdinand de Lesseps, 37200 Tours, France
| | - Charles Esnault
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
| | | | - Corinne Augé-Gouillou
- EA 6306 Instabilité génétique et cancer, Université de Tours, UFR Sciences et Techniques, UFR Pharmacie, 31 Avenue Monge, 37200 Tours, France
- UMR 1253, iBrain, University of Tours, INSERM, Tours, France
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Tobar-Tosse F, Veléz PE, Ocampo-Toro E, Moreno PA. Structure, clustering and functional insights of repeats configurations in the upstream promoter region of the human coding genes. BMC Genomics 2018; 19:862. [PMID: 30537933 PMCID: PMC6288848 DOI: 10.1186/s12864-018-5196-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Repetitive DNA sequences (Repeats) are significant regions in the human genome that have a specific genomic distribution, structure, and several binding sites for genome architecture and function. In consequence, the possible configurations of Repeats in specific and dynamic regions like the gene promoters could define footprints for molecular mechanisms, pathways, and cell function beyond their density in the genome. Here we explored the distribution of Repeats in the upstream promoter region of the human coding genes with the aim to identify specific configurations, clusters and functional meaning of those elements. Our method includes structural descriptions, hierarchical clustering, pathway association, and functional enrichment analysis. Results We report here several configurations of Repeats in the upstream promoter region (UPR), which define 2729 patterns for the 80% of the human coding genes. There are 47 types of Repeats in these configurations, where the most frequent were Alu, Low_complexity, MIR, Simple_repeat, LINE/L2, LINE/L1, hAT-Charlie, and ERV1. The distribution, length, and the high frequency of Repeats in the UPR defines several patterns and clusters, where the minimum frequency of configuration among Repeats was higher than 0.7. We found those clusters associated with cellular pathways and ontologies; thus, it was plausible to determine groups of Repeats to specific functional insights, for example, pathways for Genetic Information Processing or Metabolism shows particular groups of Repeats with specific configurations. Conclusion Based on these findings, we propose that specific configurations of repetitive elements describe frequent patterns in the upstream promoter for sets of human coding genes, which those correlated to specific and essential cell pathways and functions. Electronic supplementary material The online version of this article (10.1186/s12864-018-5196-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabian Tobar-Tosse
- Departamento de Ciencias Básicas de la Salud, Pontificia Universidad Javeriana Cali, Cali, Colombia
| | - Patricia E Veléz
- Departamento de Biología, FACNED, Universidad del Cauca, Popayán, Colombia
| | - Eliana Ocampo-Toro
- Especialización en Hematología y Oncología Clínica, Universidad Libre Seccional Cali, Cali, Colombia
| | - Pedro A Moreno
- Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Cali, Colombia.
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Horizontal acquisition of transposable elements and viral sequences: patterns and consequences. Curr Opin Genet Dev 2018; 49:15-24. [PMID: 29505963 DOI: 10.1016/j.gde.2018.02.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 12/30/2022]
Abstract
It is becoming clear that most eukaryotic transposable elements (TEs) owe their evolutionary success in part to horizontal transfer events, which enable them to invade new species. Recent large-scale studies are beginning to unravel the mechanisms and ecological factors underlying this mode of transmission. Viruses are increasingly recognized as vectors in the process but also as a direct source of genetic material horizontally acquired by eukaryotic organisms. Because TEs and endogenous viruses are major catalysts of variation and innovation in genomes, we argue that horizontal inheritance has had a more profound impact in eukaryotic evolution than is commonly appreciated. To support this proposal, we compile a list of examples, including some previously unrecognized, whereby new host functions and phenotypes can be directly attributed to horizontally acquired TE or viral sequences. We predict that the number of examples will rapidly grow in the future as the prevalence of horizontal transfer in the life cycle of TEs becomes even more apparent, firmly establishing this form of non-Mendelian inheritance as a consequential facet of eukaryotic evolution.
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Ellis MJ, Carfrae LA, Macnair CR, Trussler RS, Brown ED, Haniford DB. Silent but deadly: IS200 promotes pathogenicity in Salmonella Typhimurium. RNA Biol 2017; 15:176-181. [PMID: 29120256 DOI: 10.1080/15476286.2017.1403001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Bacterial transposons were long thought of as selfish mobile genetic elements that propagate at the expense of 'host' bacterium fitness. However, limited transposition can benefit the host organism by promoting DNA rearrangements and facilitating horizontal gene transfer. Here we discuss and provide context for our recently published work which reported the surprising finding that an otherwise dormant transposon, IS200, encodes a regulatory RNA in Salmonella Typhimurium. This previous work identified a trans-acting sRNA that is encoded in the 5'UTR of IS200 transposase mRNA (tnpA). This sRNA represses expression of genes encoded within Salmonella Pathogenicity Island 1 (SPI-1), and accordingly limits invasion into non-phagocytic cells in vitro. We present new data here that shows IS200 elements are important for colonization of the mouse gastrointestinal tract. We discuss our previous and current findings in the context of transposon biology and suggest that otherwise 'silent' transposons may in fact play an important role in controlling host gene expression.
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Affiliation(s)
- Michael J Ellis
- a Department of Biochemistry , University of Western Ontario , London , ON Canada
| | - Lindsey A Carfrae
- b Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research , McMaster University , Hamilton , ON Canada
| | - Craig R Macnair
- b Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research , McMaster University , Hamilton , ON Canada
| | - Ryan S Trussler
- a Department of Biochemistry , University of Western Ontario , London , ON Canada
| | - Eric D Brown
- b Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research , McMaster University , Hamilton , ON Canada
| | - David B Haniford
- a Department of Biochemistry , University of Western Ontario , London , ON Canada
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Delihas N. Enterobacterial Small Mobile Sequences Carry Open Reading Frames and are Found Intragenically–-Evolutionary Implications for Formation of New Peptides. GENE REGULATION AND SYSTEMS BIOLOGY 2017. [DOI: 10.1177/117762500700100017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Intergenic repeat units of 127-bp (RU-1) and 168-bp (RU-2), as well as a newly-found class of 103-bp (RU-3), represent small mobile sequences in enterobacterial genomes present in multiple intergenic regions. These repeat sequences display similarities to eukaryotic miniature inverted-repeat transposable elements (MITE). The RU mobile elements have not been reported to encode amino acid sequences. An in silico approach was used to scan genomes for location of repeat units. RU sequences are found to have open reading frames, which are present in annotated gene loci whereby the RU amino acid sequence is maintained. Gene loci that display repeat units include those that encode large proteins which are part of super families that carry conserved domains and those that carry predicted motifs such as signal peptide sequences and transmembrane domains. A putative exported protein in Y. pestis and a phylogenetically conserved putative inner membrane protein in Salmonella species represent some of the more interesting constructs. We hypothesize that a major outcome of RU open reading frame fusions is the evolutionary emergence of new proteins.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, SUNY, Stony Brook, NY 11794-5222, U.S.A
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Savvateeva-Popova EV, Zhuravlev AV, Brázda V, Zakharov GA, Kaminskaya AN, Medvedeva AV, Nikitina EA, Tokmatcheva EV, Dolgaya JF, Kulikova DA, Zatsepina OG, Funikov SY, Ryazansky SS, Evgen‘ev MB. Drosophila Model for the Analysis of Genesis of LIM-kinase 1-Dependent Williams-Beuren Syndrome Cognitive Phenotypes: INDELs, Transposable Elements of the Tc1/ Mariner Superfamily and MicroRNAs. Front Genet 2017; 8:123. [PMID: 28979292 PMCID: PMC5611441 DOI: 10.3389/fgene.2017.00123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/04/2017] [Indexed: 12/18/2022] Open
Abstract
Genomic disorders, the syndromes with multiple manifestations, may occur sporadically due to unequal recombination in chromosomal regions with specific architecture. Therefore, each patient may carry an individual structural variant of DNA sequence (SV) with small insertions and deletions (INDELs) sometimes less than 10 bp. The transposable elements of the Tc1/mariner superfamily are often associated with hotspots for homologous recombination involved in human genetic disorders, such as Williams Beuren Syndromes (WBS) with LIM-kinase 1-dependent cognitive defects. The Drosophila melanogaster mutant agnts3 has unusual architecture of the agnostic locus harboring LIMK1: it is a hotspot of chromosome breaks, ectopic contacts, underreplication, and recombination. Here, we present the analysis of LIMK1-containing locus sequencing data in agnts3 and three D. melanogaster wild-type strains-Canton-S, Berlin, and Oregon-R. We found multiple strain-specific SVs, namely, single base changes and small INDEls. The specific feature of agnts3 is 28 bp A/T-rich insertion in intron 1 of LIMK1 and the insertion of mobile S-element from Tc1/mariner superfamily residing ~460 bp downstream LIMK1 3'UTR. Neither of SVs leads to amino acid substitutions in agnts3 LIMK1. However, they apparently affect the nucleosome distribution, non-canonical DNA structure formation and transcriptional factors binding. Interestingly, the overall expression of miRNAs including the biomarkers for human neurological diseases, is drastically reduced in agnts3 relative to the wild-type strains. Thus, LIMK1 DNA structure per se, as well as the pronounced changes in total miRNAs profile, probably lead to LIMK1 dysregulation and complex behavioral dysfunctions observed in agnts3 making this mutant a simple plausible Drosophila model for WBS.
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Affiliation(s)
- Elena V. Savvateeva-Popova
- Department of Neurogenetics, Pavlov Institute of Physiology, Russian Academy of SciencesSt. Petersburg, Russia
| | - Aleksandr V. Zhuravlev
- Department of Neurogenetics, Pavlov Institute of Physiology, Russian Academy of SciencesSt. Petersburg, Russia
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech RepublicBrno, Czechia
| | - Gennady A. Zakharov
- Department of Neurogenetics, Pavlov Institute of Physiology, Russian Academy of SciencesSt. Petersburg, Russia
| | - Alena N. Kaminskaya
- Department of Neurogenetics, Pavlov Institute of Physiology, Russian Academy of SciencesSt. Petersburg, Russia
| | - Anna V. Medvedeva
- Department of Neurogenetics, Pavlov Institute of Physiology, Russian Academy of SciencesSt. Petersburg, Russia
| | - Ekaterina A. Nikitina
- Department of Neurogenetics, Pavlov Institute of Physiology, Russian Academy of SciencesSt. Petersburg, Russia
- Department of Human and Animal Anatomy and Physiology, Herzen State Pedagogical UniversitySt. Petersburg, Russia
| | - Elena V. Tokmatcheva
- Department of Neurogenetics, Pavlov Institute of Physiology, Russian Academy of SciencesSt. Petersburg, Russia
| | - Julia F. Dolgaya
- Department of Neurogenetics, Pavlov Institute of Physiology, Russian Academy of SciencesSt. Petersburg, Russia
| | - Dina A. Kulikova
- Department of Molecular Mechanisms of Development, Koltzov Institute of Developmental Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga G. Zatsepina
- Department of Molecular Mechanisms of Biological Adaptation, Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Sergei Y. Funikov
- Department of Molecular Mechanisms of Biological Adaptation, Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Sergei S. Ryazansky
- Department of Biochemical Genetics of Animals, Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia
| | - Michail B. Evgen‘ev
- Department of Molecular Mechanisms of Biological Adaptation, Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
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Dussaussois-Montagne A, Jaillet J, Babin L, Verrelle P, Karayan-Tapon L, Renault S, Rousselot-Denis C, Zemmoura I, Augé-Gouillou C. SETMAR isoforms in glioblastoma: A matter of protein stability. Oncotarget 2017; 8:9835-9848. [PMID: 28038463 PMCID: PMC5354774 DOI: 10.18632/oncotarget.14218] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/05/2016] [Indexed: 01/10/2023] Open
Abstract
Glioblastomas (GBMs) are the most frequent and the most aggressive brain tumors, known for their chemo- and radio-resistance, making them often incurable. We also know that SETMAR is a protein involved in chromatin dynamics and genome plasticity, of which overexpression confers chemo- and radio-resistance to some tumors. The relationships between SETMAR and GBM have never been explored. To fill this gap, we define the SETMAR status of 44 resected tumors and of GBM derived cells, at both the mRNA and the protein levels. We identify a new, small SETMAR protein (so called SETMAR-1200), enriched in GBMs and GBM stem cells as compared to the regular enzyme (SETMAR-2100). We show that SETMAR-1200 is able to increase DNA repair by non-homologous end-joining, albeit with a lower efficiency than the regular SETMAR protein. Interestingly, the regular/small ratio of SETMAR in GBM cells changes depending on cell type, providing evidence that SETMAR expression is regulated by alternative splicing. We also demonstrate that SETMAR expression can be regulated by the use of an alternative ATG. In conclusion, various SETMAR proteins can be synthesized in human GBM that may each have specific biophysical and/or biochemical properties and characteristics. Among them, the small SETMAR may play a role in GBMs biogenesis. On this basis, we would like to consider SETMAR-1200 as a new potential therapeutic target to investigate, in addition to the regular SETMAR protein already considered by others.
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Affiliation(s)
| | - Jérôme Jaillet
- EA 6306 IGC, University François Rabelais, 37200 Tours, France
| | - Laetitia Babin
- EA 6306 IGC, University François Rabelais, 37200 Tours, France
- UMR CNRS 7292 GICC, University François Rabelais, 37000 Tours, France
| | - Pierre Verrelle
- EA 7283 CREaT, Université d′Auvergne, BP 10448, 63000 Clermont-Ferrand, France
- Institut Curie, Dpt d'Oncologie Radiothérapique, 75005 Paris, France
- Centre Jean Perrin, Service Radiothérapie, Laboratoire de Radio-Oncologie Expérimentale, 63000 Clermont-Ferrand, France
| | - Lucie Karayan-Tapon
- INSERM U1084, Laboratoire de Neurosciences Expérimentales et Cliniques, F-86021 Poitiers, France
- University of Poitiers, F-86022 Poitiers, France
- CHU of Poitiers, Laboratoire de Cancérologie Biologique, F-86021 Poitiers, France
| | | | | | - Ilyess Zemmoura
- INSERM U930 Imagerie & Cerveau, University François Rabelais, 37000 Tours, France
- CHRU of Tours, Service de Neurochirurgie, 37000 Tours, France
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Bouallègue M, Rouault JD, Hua-Van A, Makni M, Capy P. Molecular Evolution of piggyBac Superfamily: From Selfishness to Domestication. Genome Biol Evol 2017; 9:323-339. [PMID: 28082605 PMCID: PMC5381638 DOI: 10.1093/gbe/evw292] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2016] [Indexed: 12/19/2022] Open
Abstract
The piggyBac transposable element was originally isolated from the cabbage looper moth, Trichoplusia ni, in the 1980s. Despite its early discovery and specificity compared to the other Class II elements, the diversity and evolution of this superfamily have been only partially analyzed. Two main types of elements can be distinguished: the piggyBac-like elements (PBLE) with terminal inverted repeats, untranslated region, and an open reading frame encoding a transposase, and the piggyBac-derived sequences (PGBD), containing a sequence derived from a piggyBac transposase, and which correspond to domesticated elements. To define the distribution, their structural diversity and phylogenetic relationships, analyses were conducted using known PBLE and PGBD sequences to scan databases. From this data mining, numerous new sequences were characterized (50 for PBLE and 396 for PGBD). Structural analyses suggest that four groups of PBLE can be defined according to the presence/absence of sub-terminal repeats. The transposase is characterized by highly variable catalytic domain and C-terminal region. There is no relationship between the structural groups and the phylogeny of these PBLE elements. The PGBD are clearly structured into nine main groups. A new group of domesticated elements is suspected in Neopterygii and the remaining eight previously described elements have been investigated in more detail. In all cases, these sequences are no longer transposable elements, the catalytic domain of the ancestral transposase is not always conserved, but they are under strong purifying selection. The phylogeny of both PBLE and PGBD suggests multiple and independent domestication events of PGBD from different PBLE ancestors.
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Affiliation(s)
- Maryem Bouallègue
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
- Université de Tunis El Manar, Faculté des Sciences de Tunis, UR11ES10 Génomique des Insectes Ravageurs de Cultures, Tunis, Tunisie
| | - Jacques-Deric Rouault
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélie Hua-Van
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mohamed Makni
- Université de Tunis El Manar, Faculté des Sciences de Tunis, UR11ES10 Génomique des Insectes Ravageurs de Cultures, Tunis, Tunisie
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
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49
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Abstract
DNA transposons are defined segments of DNA that are able to move from one genomic location to another. Movement is facilitated by one or more proteins, called the transposase, typically encoded by the mobile element itself. Here, we first provide an overview of the classification of such mobile elements in a variety of organisms. From a mechanistic perspective, we have focused on one particular group of DNA transposons that encode a transposase with a DD(E/D) catalytic domain that is topologically similar to RNase H. For these, a number of three-dimensional structures of transpososomes (transposase-nucleic acid complexes) are available, and we use these to describe the basics of their mechanisms. The DD(E/D) group, in addition to being the largest and most common among all DNA transposases, is the one whose members have been used for a wide variety of genomic applications. Therefore, a second focus of the article is to provide a nonexhaustive overview of transposon applications. Although several non-transposon-based approaches to site-directed genome modifications have emerged in the past decade, transposon-based applications are highly relevant when integration specificity is not sought. In fact, for many applications, the almost-perfect randomness and high frequency of integration make transposon-based approaches indispensable.
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Affiliation(s)
- Alison B. Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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50
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Warren IA, Naville M, Chalopin D, Levin P, Berger CS, Galiana D, Volff JN. Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates. Chromosome Res 2016; 23:505-31. [PMID: 26395902 DOI: 10.1007/s10577-015-9493-5] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.
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Affiliation(s)
- Ian A Warren
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.,Department of Genetics, University of Georgia, Athens, Georgia, 30602, USA
| | - Perrine Levin
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Chloé Suzanne Berger
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Delphine Galiana
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France.
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