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Huang Y, Gao Y, Ly K, Lin L, Lambooij JP, King EG, Janssen A, Wei KHC, Lee YCG. Varying recombination landscapes between individuals are driven by polymorphic transposable elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613564. [PMID: 39345575 PMCID: PMC11429682 DOI: 10.1101/2024.09.17.613564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Meiotic recombination is a prominent force shaping genome evolution, and understanding the causes for varying recombination landscapes within and between species has remained a central, though challenging, question. Recombination rates are widely observed to negatively associate with the abundance of transposable elements (TEs), selfish genetic elements that move between genomic locations. While such associations are usually interpreted as recombination influencing the efficacy of selection at removing TEs, accumulating findings suggest that TEs could instead be the cause rather than the consequence. To test this prediction, we formally investigated the influence of polymorphic, putatively active TEs on recombination rates. We developed and benchmarked a novel approach that uses PacBio long-read sequencing to efficiently, accurately, and cost-effectively identify crossovers (COs), a key recombination product, among large numbers of pooled recombinant individuals. By applying this approach to Drosophila strains with distinct TE insertion profiles, we found that polymorphic TEs, especially RNA-based TEs and TEs with local enrichment of repressive marks, reduce the occurrence of COs. Such an effect leads to different CO frequencies between homologous sequences with and without TEs, contributing to varying CO maps between individuals. The suppressive effect of TEs on CO is further supported by two orthogonal approaches-analyzing the distributions of COs in panels of recombinant inbred lines in relation to TE polymorphism and applying marker-assisted estimations of CO frequencies to isogenic strains with and without transgenically inserted TEs. Our investigations reveal how the constantly changing mobilome can actively modify recombination landscapes, shaping genome evolution within and between species.
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2
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Lin L, Huang Y, McIntyre J, Chang CH, Colmenares S, Lee YCG. Prevalent Fast Evolution of Genes Involved in Heterochromatin Functions. Mol Biol Evol 2024; 41:msae181. [PMID: 39189646 PMCID: PMC11408610 DOI: 10.1093/molbev/msae181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 08/14/2024] [Accepted: 08/20/2024] [Indexed: 08/28/2024] Open
Abstract
Heterochromatin is a gene-poor and repeat-rich genomic compartment universally found in eukaryotes. Despite its low transcriptional activity, heterochromatin plays important roles in maintaining genome stability, organizing chromosomes, and suppressing transposable elements. Given the importance of these functions, it is expected that genes involved in heterochromatin regulation would be highly conserved. Yet, a handful of these genes were found to evolve rapidly. To investigate whether these previous findings are anecdotal or general to genes modulating heterochromatin, we compile an exhaustive list of 106 candidate genes involved in heterochromatin functions and investigate their evolution over short and long evolutionary time scales in Drosophila. Our analyses find that these genes exhibit significantly more frequent evolutionary changes, both in the forms of amino acid substitutions and gene copy number change, when compared to genes involved in Polycomb-based repressive chromatin. While positive selection drives amino acid changes within both structured domains with diverse functions and intrinsically disordered regions, purifying selection may have maintained the proportions of intrinsically disordered regions of these proteins. Together with the observed negative associations between the evolutionary rate of these genes and the genomic abundance of transposable elements, we propose an evolutionary model where the fast evolution of genes involved in heterochromatin functions is an inevitable outcome of the unique functional roles of heterochromatin, while the rapid evolution of transposable elements may be an effect rather than cause. Our study provides an important global view of the evolution of genes involved in this critical cellular domain and provides insights into the factors driving the distinctive evolution of heterochromatin.
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Affiliation(s)
- Leila Lin
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Jennifer McIntyre
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Ching-Ho Chang
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Serafin Colmenares
- Department of Cell and Molecular Biology, University of California, Berkeley, CA, USA
| | - Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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3
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Yi SV. Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms. Mol Biol Evol 2024; 41:msae170. [PMID: 39235767 PMCID: PMC11376073 DOI: 10.1093/molbev/msae170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 09/06/2024] Open
Abstract
Epigenetics research in evolutionary biology encompasses a variety of research areas, from regulation of gene expression to inheritance of environmentally mediated phenotypes. Such divergent research foci can occasionally render the umbrella term "epigenetics" ambiguous. Here I discuss several areas of contemporary epigenetics research in the context of evolutionary biology, aiming to provide balanced views across timescales and molecular mechanisms. The importance of epigenetics in development is now being assessed in many nonmodel species. These studies not only confirm the importance of epigenetic marks in developmental processes, but also highlight the significant diversity in epigenetic regulatory mechanisms across taxa. Further, these comparative epigenomic studies have begun to show promise toward enhancing our understanding of how regulatory programs evolve. A key property of epigenetic marks is that they can be inherited along mitotic cell lineages, and epigenetic differences that occur during early development can have lasting consequences on the organismal phenotypes. Thus, epigenetic marks may play roles in short-term (within an organism's lifetime or to the next generation) adaptation and phenotypic plasticity. However, the extent to which observed epigenetic variation occurs independently of genetic influences remains uncertain, due to the widespread impact of genetics on epigenetic variation and the limited availability of comprehensive (epi)genomic resources from most species. While epigenetic marks can be inherited independently of genetic sequences in some species, there is little evidence that such "transgenerational inheritance" is a general phenomenon. Rather, molecular mechanisms of epigenetic inheritance are highly variable between species.
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Affiliation(s)
- Soojin V Yi
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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4
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Del Toro-De León G, van Boven J, Santos-González J, Jiao WB, Peng H, Schneeberger K, Köhler C. Epigenetic and transcriptional consequences in the endosperm of chemically induced transposon mobilization in Arabidopsis. Nucleic Acids Res 2024; 52:8833-8848. [PMID: 38967011 PMCID: PMC11347142 DOI: 10.1093/nar/gkae572] [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: 03/13/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals-tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs-both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, revealing that chemically-induced epigenome changes can have long-term consequences on imprinted gene expression.
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Affiliation(s)
- Gerardo Del Toro-De León
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Joram van Boven
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
| | - Wen-Biao Jiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Haoran Peng
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany
- Faculty for Biology, LMU Munich, Planegg-Martinsried 82152, Germany
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf 40225, Germany
| | - Claudia Köhler
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Centre for Plant Biology, Uppsala 75007, Sweden
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5
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Betancourt AJ, Wei KHC, Huang Y, Lee YCG. Causes and Consequences of Varying Transposable Element Activity: An Evolutionary Perspective. Annu Rev Genomics Hum Genet 2024; 25:1-25. [PMID: 38603565 DOI: 10.1146/annurev-genom-120822-105708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Transposable elements (TEs) are genomic parasites found in nearly all eukaryotes, including humans. This evolutionary success of TEs is due to their replicative activity, involving insertion into new genomic locations. TE activity varies at multiple levels, from between taxa to within individuals. The rapidly accumulating evidence of the influence of TE activity on human health, as well as the rapid growth of new tools to study it, motivated an evaluation of what we know about TE activity thus far. Here, we discuss why TE activity varies, and the consequences of this variation, from an evolutionary perspective. By studying TE activity in nonhuman organisms in the context of evolutionary theories, we can shed light on the factors that affect TE activity. While the consequences of TE activity are usually deleterious, some have lasting evolutionary impacts by conferring benefits on the host or affecting other evolutionary processes.
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Affiliation(s)
- Andrea J Betancourt
- Institute of Infection, Veterinary, and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Kevin H-C Wei
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Yuh Chwen G Lee
- Center for Complex Biological Systems, University of California, Irvine, California, USA;
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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6
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Lin L, Huang Y, McIntyre J, Chang CH, Colmenares S, Lee YCG. Prevalent fast evolution of genes involved in heterochromatin functions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583199. [PMID: 38496614 PMCID: PMC10942301 DOI: 10.1101/2024.03.03.583199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Heterochromatin is a gene-poor and repeat-rich genomic compartment universally found in eukaryotes. Despite its low transcriptional activity, heterochromatin plays important roles in maintaining genome stability, organizing chromosomes, and suppressing transposable elements (TEs). Given the importance of these functions, it is expected that the genes involved in heterochromatin regulation would be highly conserved. Yet, a handful of these genes were found to evolve rapidly. To investigate whether these previous findings are anecdotal or general to genes modulating heterochromatin, we compile an exhaustive list of 106 candidate genes involved in heterochromatin functions and investigate their evolution over short and long evolutionary time scales in Drosophila. Our analyses find that these genes exhibit significantly more frequent evolutionary changes, both in the forms of amino acid substitutions and gene copy number change, when compared to genes involved in Polycomb-based repressive chromatin. While positive selection drives amino acid changes within both structured domains with diverse functions and intrinsically disordered regions (IDRs), purifying selection may have maintained the proportions of IDRs of these proteins. Together with the observed negative associations between evolutionary rates of these genes and genomic TE abundance, we propose an evolutionary model where the fast evolution of genes involved in heterochromatin functions is an inevitable outcome of the unique functional roles of heterochromatin, while the rapid evolution of TEs may be an effect rather than cause. Our study provides an important global view of the evolution of genes involved in this critical cellular domain and provides insights into the factors driving the distinctive evolution of heterochromatin.
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7
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Chernomas G, Griswold CK. Deleterious mutation/epimutation-selection balance with and without inbreeding: a population (epi)genetics model. Genetics 2024; 227:iyae080. [PMID: 38733620 PMCID: PMC11228854 DOI: 10.1093/genetics/iyae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Epigenetics in the form of DNA methylation and other processes is an established property of genotypes and a focus of empirical research. Yet, there remain fundamental gaps in the evolutionary theory of epigenetics. To support a comprehensive understanding of epigenetics, this paper investigates theoretically the combined effects of deleterious mutation and epimutation with and without inbreeding. Both spontaneous epimutation and paramutation are considered to cover a broader range of epigenetic phenomena. We find that inbreeding generally reduces the amount of segregating deleterious genetic and epigenetic variation at equilibrium, although interestingly inbreeding can also increase the amount of deleterious genetic or epigenetic variation. Furthermore, we also demonstrate that epimutation indirectly can cause increased or decreased deleterious genetic variation at equilibrium relative to classic expectations, which is particularly evident when paramutation is occurring. With the addition of deleterious epimutation, there may be significantly increased purging of deleterious variation in more inbred populations and a significantly increased amount of segregating deleterious variation in more outbred populations, with notable exceptions.
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Affiliation(s)
- Gregory Chernomas
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Cortland K Griswold
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Baduel P, Sammarco I, Barrett R, Coronado‐Zamora M, Crespel A, Díez‐Rodríguez B, Fox J, Galanti D, González J, Jueterbock A, Wootton E, Harney E. The evolutionary consequences of interactions between the epigenome, the genome and the environment. Evol Appl 2024; 17:e13730. [PMID: 39050763 PMCID: PMC11266121 DOI: 10.1111/eva.13730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/30/2024] [Accepted: 05/22/2024] [Indexed: 07/27/2024] Open
Abstract
The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'Ecole Normale SupérieurePSL University, CNRSParisFrance
| | - Iris Sammarco
- Institute of Botany of the Czech Academy of SciencesPrůhoniceCzechia
| | - Rowan Barrett
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | | | | | | | - Janay Fox
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | - Dario Galanti
- Institute of Evolution and Ecology (EvE)University of TuebingenTübingenGermany
| | | | - Alexander Jueterbock
- Algal and Microbial Biotechnology Division, Faculty of Biosciences and AquacultureNord UniversityBodøNorway
| | - Eric Wootton
- Redpath Museum and Department of BiologyMcGill UniversityMontrealCanada
| | - Ewan Harney
- Institute of Evolutionary BiologyCSIC, UPFBarcelonaSpain
- School of BiosciencesUniversity of SheffieldSheffieldUK
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9
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Gluck-Thaler E, Vogan A. Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity. Nucleic Acids Res 2024; 52:5496-5513. [PMID: 38686785 PMCID: PMC11162782 DOI: 10.1093/nar/gkae327] [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: 10/24/2023] [Revised: 03/12/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Cargo-mobilizing mobile elements (CMEs) are genetic entities that faithfully transpose diverse protein coding sequences. Although common in bacteria, we know little about eukaryotic CMEs because no appropriate tools exist for their annotation. For example, Starships are giant fungal CMEs whose functions are largely unknown because they require time-intensive manual curation. To address this knowledge gap, we developed starfish, a computational workflow for high-throughput eukaryotic CME annotation. We applied starfish to 2 899 genomes of 1 649 fungal species and found that starfish recovers known Starships with 95% combined precision and recall while expanding the number of annotated elements ten-fold. Extant Starship diversity is partitioned into 11 families that differ in their enrichment patterns across fungal classes. Starship cargo changes rapidly such that elements from the same family differ substantially in their functional repertoires, which are predicted to contribute to diverse biological processes such as metabolism. Many elements have convergently evolved to insert into 5S rDNA and AT-rich sequence while others integrate into random locations, revealing both specialist and generalist strategies for persistence. Our work establishes a framework for advancing mobile element biology and provides the means to investigate an emerging dimension of eukaryotic genetic diversity, that of genomes within genomes.
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Affiliation(s)
- Emile Gluck-Thaler
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Neuchâtel 2000, Switzerland
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Wisconsin Institute for Discovery, Madison, WI 53706, USA
| | - Aaron A Vogan
- Systematic Biology, Department of Organismal Biology, Uppsala University, Uppsala, 752 36, Sweden
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Yu Z, Li J, Wang H, Ping B, Li X, Liu Z, Guo B, Yu Q, Zou Y, Sun Y, Ma F, Zhao T. Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation. HORTICULTURE RESEARCH 2024; 11:uhae118. [PMID: 38919560 PMCID: PMC11197308 DOI: 10.1093/hr/uhae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/17/2024] [Indexed: 06/27/2024]
Abstract
Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, Rubus idaeus showed a transposition rate twice as fast as Fragaria vesca, while Pyrus bretschneideri displayed significantly faster transposition compared with Crataegus pinnatifida. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in Malus domestica cv. 'Gala' and M. domestica (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.
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Affiliation(s)
- Ze Yu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiale Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hanyu Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Boya Ping
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinchu Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhiguang Liu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bocheng Guo
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiaoming Yu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yangjun Zou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yaqiang Sun
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tao Zhao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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11
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Huang Y, Lee YCG. Blessing or curse: how the epigenetic resolution of host-transposable element conflicts shapes their evolutionary dynamics. Proc Biol Sci 2024; 291:20232775. [PMID: 38593848 PMCID: PMC11003778 DOI: 10.1098/rspb.2023.2775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024] Open
Abstract
Transposable elements (TEs) are selfish genetic elements whose antagonistic interactions with hosts represent a common genetic conflict in eukaryotes. To resolve this conflict, hosts have widely adopted epigenetic silencing that deposits repressive marks at TEs. However, this mechanism is imperfect and fails to fully halt TE replication. Furthermore, TE epigenetic silencing can inadvertently spread repressive marks to adjacent functional sequences, a phenomenon considered a 'curse' of this conflict resolution. Here, we used forward simulations to explore how TE epigenetic silencing and its harmful side effects shape the evolutionary dynamics of TEs and their hosts. Our findings reveal that epigenetic silencing allows TEs and their hosts to stably coexist under a wide range of conditions, because the underlying molecular mechanisms give rise to copy-number dependency of the strength of TE silencing. Interestingly, contrary to intuitive expectations that TE epigenetic silencing should evolve to be as strong as possible, we found a selective benefit for modifier alleles that weaken TE silencing under biologically feasible conditions. These results reveal that the dual nature of TE epigenetic silencing, with both positive and negative effects, complicates its evolutionary trajectory and makes it challenging to determine whether TE epigenetic silencing is a 'blessing' or a 'curse'.
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Affiliation(s)
- Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
| | - Yuh Chwen G. Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, USA
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12
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Zheng W, Gojobori J, Suh A, Satta Y. Different Host-Endogenous Retrovirus Relationships between Mammals and Birds Reflected in Genome-Wide Evolutionary Interaction Patterns. Genome Biol Evol 2024; 16:evae065. [PMID: 38527852 PMCID: PMC11005779 DOI: 10.1093/gbe/evae065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/25/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024] Open
Abstract
Mammals and birds differ largely in their average endogenous retrovirus loads, namely the proportion of endogenous retrovirus in the genome. The host-endogenous retrovirus relationships, including conflict and co-option, have been hypothesized among the causes of this difference. However, there has not been studies about the genomic evolutionary signal of constant host-endogenous retrovirus interactions in a long-term scale and how such interactions could lead to the endogenous retrovirus load difference. Through a phylogeny-controlled correlation analysis on ∼5,000 genes between the dN/dS ratio of each gene and the load of endogenous retrovirus in 12 mammals and 21 birds, separately, we detected genes that may have evolved in association with endogenous retrovirus loads. Birds have a higher proportion of genes with strong correlation between dN/dS and the endogenous retrovirus load than mammals. Strong evidence of association is found between the dN/dS of the coding gene for leucine-rich repeat-containing protein 23 and endogenous retrovirus load in birds. Gene set enrichment analysis shows that gene silencing rather than immunity and DNA recombination may have a larger contribution to the association between dN/dS and the endogenous retrovirus load for both mammals and birds. The above results together showing different evolutionary patterns between bird and mammal genes can partially explain the apparently lower endogenous retrovirus loads of birds, while gene silencing may be a universal mechanism that plays a remarkable role in the evolutionary interaction between the host and endogenous retrovirus. In summary, our study presents signals that the host genes might have driven or responded to endogenous retrovirus load changes in long-term evolution.
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Affiliation(s)
- Wanjing Zheng
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jun Gojobori
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
- Research Center for Integrative Evolutionary Science, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
| | - Alexander Suh
- Department of Organismal Biology—Systematic Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala 75236, Sweden
- School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, School of Advanced Sciences, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
- Research Center for Integrative Evolutionary Science, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan
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13
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Wang M, Bissonnette N, Laterrière M, Dudemaine PL, Gagné D, Roy JP, Sirard MA, Ibeagha-Awemu EM. DNA methylation haplotype block signatures responding to Staphylococcus aureus subclinical mastitis and association with production and health traits. BMC Biol 2024; 22:65. [PMID: 38486242 PMCID: PMC10941392 DOI: 10.1186/s12915-024-01843-y] [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: 06/02/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND DNA methylation has been documented to play vital roles in diseases and biological processes. In bovine, little is known about the regulatory roles of DNA methylation alterations on production and health traits, including mastitis. RESULTS Here, we employed whole-genome DNA methylation sequencing to profile the DNA methylation patterns of milk somatic cells from sixteen cows with naturally occurring Staphylococcus aureus (S. aureus) subclinical mastitis and ten healthy control cows. We observed abundant DNA methylation alterations, including 3,356,456 differentially methylated cytosines and 153,783 differential methylation haplotype blocks (dMHBs). The DNA methylation in regulatory regions, including promoters, first exons and first introns, showed global significant negative correlations with gene expression status. We identified 6435 dMHBs located in the regulatory regions of differentially expressed genes and significantly correlated with their corresponding genes, revealing their potential effects on transcriptional activities. Genes harboring DNA methylation alterations were significantly enriched in multiple immune- and disease-related pathways, suggesting the involvement of DNA methylation in regulating host responses to S. aureus subclinical mastitis. In addition, we found nine discriminant signatures (differentiates cows with S. aureus subclinical mastitis from healthy cows) representing the majority of the DNA methylation variations related to S. aureus subclinical mastitis. Validation of seven dMHBs in 200 cows indicated significant associations with mammary gland health (SCC and SCS) and milk production performance (milk yield). CONCLUSIONS In conclusion, our findings revealed abundant DNA methylation alterations in milk somatic cells that may be involved in regulating mammary gland defense against S. aureus infection. Particularly noteworthy is the identification of seven dMHBs showing significant associations with mammary gland health, underscoring their potential as promising epigenetic biomarkers. Overall, our findings on DNA methylation alterations offer novel insights into the regulatory mechanisms of bovine subclinical mastitis, providing further avenues for the development of effective control measures.
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Affiliation(s)
- Mengqi Wang
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Mario Laterrière
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Pier-Luc Dudemaine
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - David Gagné
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Jean-Philippe Roy
- Department of Clinical Sciences, Université de Montréal, St-Hyacinthe, QC, Canada
| | | | - Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada.
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14
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Abraham LN, Oggenfuss U, Croll D. Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen. mBio 2024; 15:e0284023. [PMID: 38349152 PMCID: PMC10936205 DOI: 10.1128/mbio.02840-23] [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: 10/20/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024] Open
Abstract
The rapid adaptive evolution of microbes is driven by strong selection pressure acting on genetic variation. How adaptive genetic variation is generated within species and how such variation influences phenotypic trait expression is often not well understood though. We focused on the recent activity of transposable elements (TEs) using deep population genomics and transcriptomics analyses of a fungal plant pathogen with a highly active content of TEs in the genome. Zymoseptoria tritici causes one of the most damaging diseases on wheat, with recent adaptation to the host and environment being facilitated by TE-associated mutations. We obtained genomic and RNA-sequencing data from 146 isolates collected from a single wheat field. We established a genome-wide map of TE insertion polymorphisms in the population by analyzing recent TE insertions among individuals. We quantified the locus-specific transcription of individual TE copies and found considerable population variation at individual TE loci in the population. About 20% of all TE copies show transcription in the genome suggesting that genomic defenses such as repressive epigenetic marks and repeat-induced polymorphisms are at least partially ineffective at preventing the proliferation of TEs in the genome. A quarter of recent TE insertions are associated with expression variation of neighboring genes providing broad potential to influence trait expression. We indeed found that TE insertions are likely responsible for variation in virulence on the host and potentially diverse components of secondary metabolite production. Our large-scale transcriptomics study emphasizes how TE-derived polymorphisms segregate even in individual microbial populations and can broadly underpin trait variation in pathogens.IMPORTANCEPathogens can rapidly adapt to new hosts, antimicrobials, or changes in the environment. Adaptation arises often from mutations in the genome; however, how such variation is generated remains poorly understood. We investigated the most dynamic regions of the genome of Zymoseptoria tritici, a major fungal pathogen of wheat. We focused on the transcription of transposable elements. A large proportion of the transposable elements not only show signatures of potential activity but are also variable within a single population of the pathogen. We find that this variation in activity is likely influencing many important traits of the pathogen. Hence, our work provides insights into how a microbial species can adapt over the shortest time periods based on the activity of transposable elements.
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Affiliation(s)
- Leen Nanchira Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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15
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Carpinteyro-Ponce J, Machado CA. The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes. Genome Biol Evol 2024; 16:evae047. [PMID: 38482945 PMCID: PMC10980976 DOI: 10.1093/gbe/evae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
Structural genomic variants are key drivers of phenotypic evolution. They can span hundreds to millions of base pairs and can thus affect large numbers of genetic elements. Although structural variation is quite common within and between species, its characterization depends upon the quality of genome assemblies and the proportion of repetitive elements. Using new high-quality genome assemblies, we report a complex and previously hidden landscape of structural divergence between the genomes of Drosophila persimilis and D. pseudoobscura, two classic species in speciation research, and study the relationships among structural variants, transposable elements, and gene expression divergence. The new assemblies confirm the already known fixed inversion differences between these species. Consistent with previous studies showing higher levels of nucleotide divergence between fixed inversions relative to collinear regions of the genome, we also find a significant overrepresentation of INDELs inside the inversions. We find that transposable elements accumulate in regions with low levels of recombination, and spatial correlation analyses reveal a strong association between transposable elements and structural variants. We also report a strong association between differentially expressed (DE) genes and structural variants and an overrepresentation of DE genes inside the fixed chromosomal inversions that separate this species pair. Interestingly, species-specific structural variants are overrepresented in DE genes involved in neural development, spermatogenesis, and oocyte-to-embryo transition. Overall, our results highlight the association of transposable elements with structural variants and their importance in driving evolutionary divergence.
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Affiliation(s)
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
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16
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Berdan EL, Aubier TG, Cozzolino S, Faria R, Feder JL, Giménez MD, Joron M, Searle JB, Mérot C. Structural Variants and Speciation: Multiple Processes at Play. Cold Spring Harb Perspect Biol 2024; 16:a041446. [PMID: 38052499 PMCID: PMC10910405 DOI: 10.1101/cshperspect.a041446] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.
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Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, Gothenburg University, Gothenburg 40530, Sweden
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Thomas G Aubier
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, 4485-661 Vairão, Portugal
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Claire Mérot
- CNRS, UMR 6553 Ecobio, OSUR, Université de Rennes, 35000 Rennes, France
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17
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Le Breton A, Bettencourt MP, Gendrel AV. Navigating the brain and aging: exploring the impact of transposable elements from health to disease. Front Cell Dev Biol 2024; 12:1357576. [PMID: 38476259 PMCID: PMC10927736 DOI: 10.3389/fcell.2024.1357576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that constitute on average 45% of mammalian genomes. Their presence and activity in genomes represent a major source of genetic variability. While this is an important driver of genome evolution, TEs can also have deleterious effects on their hosts. A growing number of studies have focused on the role of TEs in the brain, both in physiological and pathological contexts. In the brain, their activity is believed to be important for neuronal plasticity. In neurological and age-related disorders, aberrant activity of TEs may contribute to disease etiology, although this remains unclear. After providing a comprehensive overview of transposable elements and their interactions with the host, this review summarizes the current understanding of TE activity within the brain, during the aging process, and in the context of neurological and age-related conditions.
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Affiliation(s)
| | | | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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18
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Pugacheva EM, Bhatt DN, Rivero-Hinojosa S, Tajmul M, Fedida L, Price E, Ji Y, Loukinov D, Strunnikov AV, Ren B, Lobanenkov VV. BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites. Genome Biol 2024; 25:40. [PMID: 38297316 PMCID: PMC10832218 DOI: 10.1186/s13059-024-03175-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/15/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little is known regarding the mechanisms underpinning the activation of alternative promoters. RESULTS Here we describe how alternative cancer-testis-specific transcription is activated. We show that intergenic and intronic CTCF binding sites, which are transcriptionally inert in normal somatic cells, could be epigenetically reprogrammed into active de novo promoters in germ and cancer cells. BORIS/CTCFL, the testis-specific paralog of the ubiquitously expressed CTCF, triggers the epigenetic reprogramming of CTCF sites into units of active transcription. BORIS binding initiates the recruitment of the chromatin remodeling factor, SRCAP, followed by the replacement of H2A histone with H2A.Z, resulting in a more relaxed chromatin state in the nucleosomes flanking the CTCF binding sites. The relaxation of chromatin around CTCF binding sites facilitates the recruitment of multiple additional transcription factors, thereby activating transcription from a given binding site. We demonstrate that the epigenetically reprogrammed CTCF binding sites can drive the expression of cancer-testis genes, long noncoding RNAs, retro-pseudogenes, and dormant transposable elements. CONCLUSIONS Thus, BORIS functions as a transcription factor that epigenetically reprograms clustered CTCF binding sites into transcriptional start sites, promoting transcription from alternative promoters in both germ cells and cancer cells.
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Affiliation(s)
- Elena M Pugacheva
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Dharmendra Nath Bhatt
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Samuel Rivero-Hinojosa
- Center for Cancer and Immunology Research, Children's National Research Institute, Washington, DC, 20010, USA
| | - Md Tajmul
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Liron Fedida
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Emma Price
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yon Ji
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dmitri Loukinov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alexander V Strunnikov
- Guangzhou Institutes of Biomedicine and Health, Molecular Epigenetics Laboratory, 190 Kai Yuan Avenue, Science Park, Guangzhou, 510530, China
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, Center for Epigenomics, Moores Cancer Center and Institute of Genomic Medicine, University of California, San Diego School of Medicine, La Jolla, CA, 92093-0653, USA
| | - Victor V Lobanenkov
- Molecular Pathology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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19
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Gupta A, Nair S. Epigenetic Diversity Underlying Seasonal and Annual Variations in Brown Planthopper (BPH) Populations as Revealed by Methylation- sensitive Restriction Assay. Curr Genomics 2023; 24:354-367. [PMID: 38327650 PMCID: PMC10845068 DOI: 10.2174/0113892029276542231205065843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/10/2023] [Indexed: 02/09/2024] Open
Abstract
Background The brown planthopper (BPH) is a monophagous sap-sucking insect pest of rice that is responsible for massive yield loss. BPH populations, even when genetically homogenous, can display a vast range of phenotypes, and the development of effective pest-management strategies requires a good understanding of what generates this phenotypic variation. One potential source could be epigenetic differences. Methods With this premise, we explored epigenetic diversity, structure and differentiation in field populations of BPH collected across the rice-growing seasons over a period of two consecutive years. Using a modified methylation-sensitive restriction assay (MSRA) and CpG island amplification-representational difference analysis, site-specific cytosine methylation of five stress-responsive genes (CYP6AY1, CYP6ER1, Carboxylesterase, Endoglucanase, Tf2-transposon) was estimated, for identifying methylation-based epiallelic markers and epigenetic variation across BPH populations. Results Using a cost-effective and rapid protocol, our study, for the first time, revealed the epigenetic component of phenotypic variations in the wild populations of BPH. Besides, results showed that morphologically indistinguishable populations of BPH can be epigenetically distinct. Conclusion Screening field-collected BPH populations revealed the presence of previously unreported epigenetic polymorphisms and provided a platform for future studies aimed at investigating their significance for BPH. Furthermore, these findings can form the basis for understanding the contribution(s) of DNA methylation in providing phenotypic plasticity to BPH.
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Affiliation(s)
- Ayushi Gupta
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Current Address: Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH 93BF, UK
| | - Suresh Nair
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India
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20
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Braz CU, Passamonti MM, Khatib H. Characterization of genomic regions escaping epigenetic reprogramming in sheep. ENVIRONMENTAL EPIGENETICS 2023; 10:dvad010. [PMID: 38496251 PMCID: PMC10944287 DOI: 10.1093/eep/dvad010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 03/19/2024]
Abstract
The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.
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Affiliation(s)
- Camila U Braz
- Department of Animal Sciences, University of Illinois Urbana–Champaign, Urbana, IL 61801, USA
| | - Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition, Universit’a Cattolica del Sacro Cuore, Piacenza, 29122, Italy
| | - Hasan Khatib
- Department of Animal and Dairy Sciences, University of Wisconsin–Madison, Madison, WI 53706, USA
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21
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Switzer CH. Non-canonical nitric oxide signalling and DNA methylation: Inflammation induced epigenetic alterations and potential drug targets. Br J Pharmacol 2023. [PMID: 38116806 DOI: 10.1111/bph.16302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/29/2023] [Accepted: 09/20/2023] [Indexed: 12/21/2023] Open
Abstract
DNA methylation controls DNA accessibility to transcription factors and other regulatory proteins, thereby affecting gene expression and hence cellular identity and function. As epigenetic modifications control the transcriptome, epigenetic dysfunction is strongly associated with pathological conditions and ageing. The development of pharmacological agents that modulate the activity of major epigenetic proteins are in pre-clinical development and clinical use. However, recent publications have identified novel redox-based signalling pathways, and therefore novel drug targets, that may exert epigenetic effects. This review will discuss the recent developments in nitric oxide (NO) signalling on DNA methylation as well as potential epigenetic drug targets that have emerged from the intersection of inflammation/redox biology and epigenetic regulation.
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Affiliation(s)
- Christopher H Switzer
- William Harvey Research Institute, Barts & The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
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22
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Cheatle Jarvela AM, Wexler JR. Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution. Dev Genes Evol 2023; 233:59-76. [PMID: 37982820 DOI: 10.1007/s00427-023-00712-y] [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: 06/16/2023] [Accepted: 11/05/2023] [Indexed: 11/21/2023]
Abstract
Current sequencing technology allows for the relatively affordable generation of highly contiguous genomes. Technological advances have made it possible for researchers to investigate the consequences of diverse sorts of genomic variants, such as gene gain and loss. With the extraordinary number of high-quality genomes now available, we take stock of how these genomic variants impact phenotypic evolution. We take care to point out that the identification of genomic variants of interest is only the first step in understanding their impact. Painstaking lab or fieldwork is still required to establish causal relationships between genomic variants and phenotypic evolution. We focus mostly on arthropod research, as this phylum has an impressive degree of phenotypic diversity and is also the subject of much evolutionary genetics research. This article is intended to both highlight recent advances in the field and also to be a primer for learning about evolutionary genetics and genomics.
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Affiliation(s)
- Alys M Cheatle Jarvela
- Department of Entomology, University of Maryland, College Park, MD, USA.
- HHMI Janelia Research Campus, Ashburn, VA, USA.
| | - Judith R Wexler
- Department of Ecology, Evolution, and Behavior, The Hebrew University in Jerusalem, Jerusalem, Israel.
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23
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Bhadra S, Leitch IJ, Onstein RE. From genome size to trait evolution during angiosperm radiation. Trends Genet 2023; 39:728-735. [PMID: 37582671 DOI: 10.1016/j.tig.2023.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/17/2023]
Abstract
Angiosperm diversity arises from trait flexibility and repeated evolutionary radiations, but the role of genomic characters in these radiations remains unclear. In this opinion article, we discuss how genome size can influence angiosperm diversification via its intricate link with cell size, tissue packing, and physiological processes which, in turn, influence the macroevolution of functional traits. We propose that integrating genome size, functional traits, and phylogenetic data across a wide range of lineages allows us to test whether genome size decrease consistently leads to increased trait flexibility, while genome size increase constrains trait evolution. Combining theories from molecular biology, functional ecology and macroevolution, we provide a framework to better understand the role of genome size in trait evolution, evolutionary radiations, and the global distribution of angiosperms.
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Affiliation(s)
- Sreetama Bhadra
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, D-04103, Leipzig, Germany; Leipzig University, Ritterstraße 26, 04109 Leipzig, Germany.
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Kew Green, Richmond TW9 3AE, UK
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, D-04103, Leipzig, Germany; Leipzig University, Ritterstraße 26, 04109 Leipzig, Germany; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
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24
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Lawlor MA, Ellison CE. Evolutionary dynamics between transposable elements and their host genomes: mechanisms of suppression and escape. Curr Opin Genet Dev 2023; 82:102092. [PMID: 37517354 PMCID: PMC10530431 DOI: 10.1016/j.gde.2023.102092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/27/2023] [Accepted: 07/02/2023] [Indexed: 08/01/2023]
Abstract
Transposable elements (TEs) are ubiquitous among eukaryotic species. Their evolutionary persistence is likely due to a combination of tolerogenic, evasive/antagonistic, and cooperative interactions with their host genomes. Here, we focus on metazoan species and review recent advances related to the harmful effects of TE insertions, including how epigenetic effects and TE-derived RNAs can damage host cells. We discuss new findings related to host pathways that silence TEs, such as the piRNA pathway and the APOBEC3 and Kruppel-associated box zinc finger gene families. Finally, we summarize novel strategies used by TEs to evade host silencing, including the Y chromosome as a permissive niche for TE mobilization and TE counterdefense strategies to block host silencing factors.
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25
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Orozco-Arias S, Lopez-Murillo LH, Piña JS, Valencia-Castrillon E, Tabares-Soto R, Castillo-Ossa L, Isaza G, Guyot R. Genomic object detection: An improved approach for transposable elements detection and classification using convolutional neural networks. PLoS One 2023; 18:e0291925. [PMID: 37733731 PMCID: PMC10513252 DOI: 10.1371/journal.pone.0291925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023] Open
Abstract
Analysis of eukaryotic genomes requires the detection and classification of transposable elements (TEs), a crucial but complex and time-consuming task. To improve the performance of tools that accomplish these tasks, Machine Learning approaches (ML) that leverage computer resources, such as GPUs (Graphical Processing Unit) and multiple CPU (Central Processing Unit) cores, have been adopted. However, until now, the use of ML techniques has mostly been limited to classification of TEs. Herein, a detection-classification strategy (named YORO) based on convolutional neural networks is adapted from computer vision (YOLO) to genomics. This approach enables the detection of genomic objects through the prediction of the position, length, and classification in large DNA sequences such as fully sequenced genomes. As a proof of concept, the internal protein-coding domains of LTR-retrotransposons are used to train the proposed neural network. Precision, recall, accuracy, F1-score, execution times and time ratios, as well as several graphical representations were used as metrics to measure performance. These promising results open the door for a new generation of Deep Learning tools for genomics. YORO architecture is available at https://github.com/simonorozcoarias/YORO.
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Affiliation(s)
- Simon Orozco-Arias
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Colombia
- Center for Technology Development Bioprocess and Agroindustry Plant, Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia
| | | | - Johan S. Piña
- Department of Computer Science, Universidad Autónoma de Manizales, Manizales, Colombia
| | | | - Reinel Tabares-Soto
- Center for Technology Development Bioprocess and Agroindustry Plant, Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Luis Castillo-Ossa
- Center for Technology Development Bioprocess and Agroindustry Plant, Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia
| | - Gustavo Isaza
- Center for Technology Development Bioprocess and Agroindustry Plant, Department of Systems and Informatics, Universidad de Caldas, Manizales, Colombia
| | - Romain Guyot
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
- Institut de Recherche pour le Développement, CIRAD, Univ. Montpellier, Montpellier, France
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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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Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Curr Opin Genet Dev 2023; 81:102087. [PMID: 37441873 DOI: 10.1016/j.gde.2023.102087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023]
Abstract
Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations.
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Affiliation(s)
| | - Amy Briffa
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Martin Howard
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Daniel Zilberman
- Institute of Science and Technology, 3400 Klosterneuburg, Austria.
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28
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Yang LL, Zhang XY, Wang LY, Li YG, Li XT, Yang Y, Su Q, Chen N, Zhang YL, Li N, Deng CL, Li SF, Gao WJ. Lineage-specific amplification and epigenetic regulation of LTR-retrotransposons contribute to the structure, evolution, and function of Fabaceae species. BMC Genomics 2023; 24:423. [PMID: 37501164 PMCID: PMC10373317 DOI: 10.1186/s12864-023-09530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/22/2023] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND Long terminal repeat (LTR)-retrotransposons (LTR-RTs) are ubiquitous and make up the majority of nearly all sequenced plant genomes, whereas their pivotal roles in genome evolution, gene expression regulation as well as their epigenetic regulation are still not well understood, especially in a large number of closely related species. RESULTS Here, we analyzed the abundance and dynamic evolution of LTR-RTs in 54 species from an economically and agronomically important family, Fabaceae, and also selected two representative species for further analysis in expression of associated genes, transcriptional activity and DNA methylation patterns of LTR-RTs. Annotation results revealed highly varied proportions of LTR-RTs in these genomes (5.1%~68.4%) and their correlation with genome size was highly positive, and they were significantly contributed to the variance in genome size through species-specific unique amplifications. Almost all of the intact LTR-RTs were inserted into the genomes 4 Mya (million years ago), and more than 50% of them were inserted in the last 0.5 million years, suggesting that recent amplifications of LTR-RTs were an important force driving genome evolution. In addition, expression levels of genes with intronic, promoter, and downstream LTR-RT insertions of Glycine max and Vigna radiata, two agronomically important crops in Fabaceae, showed that the LTR-RTs located in promoter or downstream regions suppressed associated gene expression. However, the LTR-RTs within introns promoted gene expression or had no contribution to gene expression. Additionally, shorter and younger LTR-RTs maintained higher mobility and transpositional potential. Compared with the transcriptionally silent LTR-RTs, the active elements showed significantly lower DNA methylation levels in all three contexts. The distributions of transcriptionally active and silent LTR-RT methylation varied across different lineages due to the position of LTR-RTs located or potentially epigenetic regulation. CONCLUSION Lineage-specific amplification patterns were observed and higher methylation level may repress the activity of LTR-RTs, further influence evolution in Fabaceae species. This study offers valuable clues into the evolution, function, transcriptional activity and epigenetic regulation of LTR-RTs in Fabaceae genomes.
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Affiliation(s)
- Long-Long Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Xin-Yu Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Li-Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Yan-Ge Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Xiao-Ting Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Yi Yang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Qing Su
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Ning Chen
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Yu-Lan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China
| | - Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, P. R. China.
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29
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Hara Y, Kuraku S. The impact of local genomic properties on the evolutionary fate of genes. eLife 2023; 12:82290. [PMID: 37223962 DOI: 10.7554/elife.82290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 04/25/2023] [Indexed: 05/25/2023] Open
Abstract
Functionally indispensable genes are likely to be retained and otherwise to be lost during evolution. This evolutionary fate of a gene can also be affected by factors independent of gene dispensability, including the mutability of genomic positions, but such features have not been examined well. To uncover the genomic features associated with gene loss, we investigated the characteristics of genomic regions where genes have been independently lost in multiple lineages. With a comprehensive scan of gene phylogenies of vertebrates with a careful inspection of evolutionary gene losses, we identified 813 human genes whose orthologs were lost in multiple mammalian lineages: designated 'elusive genes.' These elusive genes were located in genomic regions with rapid nucleotide substitution, high GC content, and high gene density. A comparison of the orthologous regions of such elusive genes across vertebrates revealed that these features had been established before the radiation of the extant vertebrates approximately 500 million years ago. The association of human elusive genes with transcriptomic and epigenomic characteristics illuminated that the genomic regions containing such genes were subject to repressive transcriptional regulation. Thus, the heterogeneous genomic features driving gene fates toward loss have been in place and may sometimes have relaxed the functional indispensability of such genes. This study sheds light on the complex interplay between gene function and local genomic properties in shaping gene evolution that has persisted since the vertebrate ancestor.
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Affiliation(s)
- Yuichiro Hara
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
- Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
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30
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Miller DE, Dorador AP, Van Vaerenberghe K, Li A, Grantham EK, Cerbin S, Cummings C, Barragan M, Egidy RR, Scott AR, Hall KE, Perera A, Gilliland WD, Hawley RS, Blumenstiel JP. Off-target piRNA gene silencing in Drosophila melanogaster rescued by a transposable element insertion. PLoS Genet 2023; 19:e1010598. [PMID: 36809339 PMCID: PMC9983838 DOI: 10.1371/journal.pgen.1010598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/03/2023] [Accepted: 01/04/2023] [Indexed: 02/23/2023] Open
Abstract
Transposable elements (TE) are selfish genetic elements that can cause harmful mutations. In Drosophila, it has been estimated that half of all spontaneous visible marker phenotypes are mutations caused by TE insertions. Several factors likely limit the accumulation of exponentially amplifying TEs within genomes. First, synergistic interactions between TEs that amplify their harm with increasing copy number are proposed to limit TE copy number. However, the nature of this synergy is poorly understood. Second, because of the harm posed by TEs, eukaryotes have evolved systems of small RNA-based genome defense to limit transposition. However, as in all immune systems, there is a cost of autoimmunity and small RNA-based systems that silence TEs can inadvertently silence genes flanking TE insertions. In a screen for essential meiotic genes in Drosophila melanogaster, a truncated Doc retrotransposon within a neighboring gene was found to trigger the germline silencing of ald, the Drosophila Mps1 homolog, a gene essential for proper chromosome segregation in meiosis. A subsequent screen for suppressors of this silencing identified a new insertion of a Hobo DNA transposon in the same neighboring gene. Here we describe how the original Doc insertion triggers flanking piRNA biogenesis and local gene silencing. We show that this local gene silencing occurs in cis and is dependent on deadlock, a component of the Rhino-Deadlock-Cutoff (RDC) complex, to trigger dual-strand piRNA biogenesis at TE insertions. We further show how the additional Hobo insertion leads to de-silencing by reducing flanking piRNA biogenesis triggered by the original Doc insertion. These results support a model of TE-mediated gene silencing by piRNA biogenesis in cis that depends on local determinants of transcription. This may explain complex patterns of off-target gene silencing triggered by TEs within populations and in the laboratory. It also provides a mechanism of sign epistasis among TE insertions, illuminates the complex nature of their interactions and supports a model in which off-target gene silencing shapes the evolution of the RDC complex.
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Affiliation(s)
- Danny E. Miller
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, Washington, United States of America
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Ana P. Dorador
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Kelley Van Vaerenberghe
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Angela Li
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Emily K. Grantham
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Stefan Cerbin
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Celeste Cummings
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Marilyn Barragan
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Rhonda R. Egidy
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Allison R. Scott
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Kate E. Hall
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Anoja Perera
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - William D. Gilliland
- Department of Biological Sciences, DePaul University, Chicago, Illinois, United States of America
| | - R. Scott Hawley
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Justin P. Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
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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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32
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Fraser CJ, Whitehall SK. Heterochromatin in the fungal plant pathogen, Zymoseptoria tritici: Control of transposable elements, genome plasticity and virulence. Front Genet 2022; 13:1058741. [DOI: 10.3389/fgene.2022.1058741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
Heterochromatin is a repressive chromatin state that plays key roles in the functional organisation of eukaryotic genomes. In fungal plant pathogens, effector genes that are required for host colonization tend to be associated with heterochromatic regions of the genome that are enriched with transposable elements. It has been proposed that the heterochromatin environment silences effector genes in the absence of host and dynamic chromatin remodelling facilitates their expression during infection. Here we discuss this model in the context of the key wheat pathogen, Zymoseptoria tritici. We cover progress in understanding the deposition and recognition of heterochromatic histone post translational modifications in Z. tritici and the role that heterochromatin plays in control of genome plasticity and virulence.
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33
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Cerbin S, Ou S, Li Y, Sun Y, Jiang N. Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:172-192. [PMID: 35959634 PMCID: PMC9804982 DOI: 10.1111/tpj.15938] [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] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Sacred lotus (Nelumbo nucifera Gaertn.) is a basal eudicot plant with a unique lifestyle, physiological features, and evolutionary characteristics. Here we report the unique profile of transposable elements (TEs) in the genome, using a manually curated repeat library. TEs account for 59% of the genome, and hAT (Ac/Ds) elements alone represent 8%, more than in any other known plant genome. About 18% of the lotus genome is comprised of Copia LTR retrotransposons, and over 25% of them are associated with non-canonical termini (non-TGCA). Such high abundance of non-canonical LTR retrotransposons has not been reported for any other organism. TEs are very abundant in genic regions, with retrotransposons enriched in introns and DNA transposons primarily in flanking regions of genes. The recent insertion of TEs in introns has led to significant intron size expansion, with a total of 200 Mb in the 28 455 genes. This is accompanied by declining TE activity in intergenic regions, suggesting distinct control efficacy of TE amplification in different genomic compartments. Despite the prevalence of TEs in genic regions, some genes are associated with fewer TEs, such as those involved in fruit ripening and stress responses. Other genes are enriched with TEs, and genes in epigenetic pathways are the most associated with TEs in introns, indicating a dynamic interaction between TEs and the host surveillance machinery. The dramatic differential abundance of TEs with genes involved in different biological processes as well as the variation of target preference of different TEs suggests the composition and activity of TEs influence the path of evolution.
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Affiliation(s)
- Stefan Cerbin
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Ecology & Evolutionary BiologyUniversity of Kansas1200 Sunnyside AvenueLawrenceKS66045USA
| | - Shujun Ou
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
- Present address:
Department of Computer ScienceJohns Hopkins UniversityBaltimoreMD21218USA
| | - Yang Li
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Yanni Sun
- Department of Electrical EngineeringCity University of Hong KongKowloonHong Kong SARChina
| | - Ning Jiang
- Department of HorticultureMichigan State University1066 Bogue StreetEast LansingMI48824USA
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Trabuco Amaral D, Mitani Y, Aparecida Silva Bonatelli I, Cerri R, Ohmiya Y, Viviani V. Genome analysis of Phrixothrix hirtus (Phengodidae) railroad worm shows the expansion of odorant-binding gene families and positive selection on morphogenesis and sex determination genes. Gene X 2022; 850:146917. [PMID: 36174905 DOI: 10.1016/j.gene.2022.146917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 10/14/2022] Open
Abstract
Among bioluminescent beetles of the Elateroidea superfamily, Phengodidae is the third largest family, with 244 bioluminescent species distributed only in the Americas, but is still the least studied from the phylogenetic and evolutionary points of view. The railroad worm Phrixothrix hirtus is an essential biological model and symbolic species due to its bicolor bioluminescence, being the only organism that produces true red light among bioluminescent terrestrial species. Here, we performed partial genome assembly of P. hirtus, combining short and long reads generated with Illumina sequencing, providing the first source of genomic information and a framework for comparative analyses of the bioluminescent system in Elateroidea. This is the largest genome described in the Elateroidea superfamily, with an estimated size of ∼3.4 Gb, displaying 32 % GC content, and 67 % transposable elements. Comparative genomic analyses showed a positive selection of genes and gene family expansion events of growths and morphogenesis gene products, which could be associated with the atypical anatomical development and morphogenesis found in paedomorphic females and underdeveloped males. We also observed gene family expansion among distinct odorant-binding receptors, which could be associated with the pheromone communication system typical of these beetles, and retrotransposable elements. Common genes putatively regulating bioluminescence production and control, including two luciferase genes corresponding to lateral lanterns green-emitting and head lanterns red-emitting luciferases with 7 exons and 6 introns, and genes potentially involved in luciferin biosynthesis were found, indicating that there are no clear differences about the presence or absence of gene families associated with bioluminescence in Elateroidea.
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Affiliation(s)
- Danilo Trabuco Amaral
- Programa de Pós-Graduação em Biotecnociência, Centro de Ciências Naturais e Humanas. Universidade Federal do ABC (UFABC), Santo André, Brazil
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | | | - Ricardo Cerri
- Department of Computational Science, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, AIST, Ikeda-Osaka, Japan; Osaka Institute of Technology, OIT, Osaka, Japan
| | - Vadim Viviani
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, Brazil; Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Sorocaba, Brazil.
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35
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Huang Y, Shukla H, Lee YCG. Species-specific chromatin landscape determines how transposable elements shape genome evolution. eLife 2022; 11:81567. [PMID: 35997258 PMCID: PMC9398452 DOI: 10.7554/elife.81567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic parasites that increase their copy number at the expense of host fitness. The ‘success’, or genome-wide abundance, of TEs differs widely between species. Deciphering the causes for this large variety in TE abundance has remained a central question in evolutionary genomics. We previously proposed that species-specific TE abundance could be driven by the inadvertent consequences of host-direct epigenetic silencing of TEs—the spreading of repressive epigenetic marks from silenced TEs into adjacent sequences. Here, we compared this TE-mediated local enrichment of repressive marks, or ‘the epigenetic effect of TEs’, in six species in the Drosophila melanogaster subgroup to dissect step-by-step the role of such effect in determining genomic TE abundance. We found that TE-mediated local enrichment of repressive marks is prevalent and substantially varies across and even within species. While this TE-mediated effect alters the epigenetic states of adjacent genes, we surprisingly discovered that the transcription of neighboring genes could reciprocally impact this spreading. Importantly, our multi-species analysis provides the power and appropriate phylogenetic resolution to connect species-specific host chromatin regulation, TE-mediated epigenetic effects, the strength of natural selection against TEs, and genomic TE abundance unique to individual species. Our findings point toward the importance of host chromatin landscapes in shaping genome evolution through the epigenetic effects of a selfish genetic parasite. All the instructions required for life are encoded in the set of DNA present in a cell. It therefore seems natural to think that every bit of this genetic information should serve the organism. And yet most species carry parasitic ‘transposable’ sequences, or transposons, whose only purpose is to multiply and insert themselves at other positions in the genome. It is possible for cells to suppress these selfish elements. Chemical marks can be deposited onto the DNA to temporarily ‘silence’ transposons and prevent them from being able to move and replicate. However, this sometimes comes at a cost: the repressive chemical modifications can spread to nearby genes that are essential for the organism and perturb their function. Strangely, the prevalence of transposons varies widely across the tree of life. These sequences form the majority of the genome of certain species – in fact, they represent about half of the human genetic information. But their abundance is much lower in other organisms, forming a measly 6% of the genome of puffer fish for instance. Even amongst fruit fly species, the prevalence of transposable elements can range between 2% and 25%. What explains such differences? Huang et al. set out to examine this question through the lens of transposon silencing, systematically comparing how this process impacts nearby regions in six species of fruit flies. This revealed variations in the strength of the side effects associated with transposon silencing, resulting in different levels of perturbation on neighbouring genes. A stronger impact was associated with the species having fewer transposons in its genome, suggesting that an evolutionary pressure is at work to keep the abundance of transposons at a low level in these species. Further analyses showed that the genes which determine how silencing marks are distributed may also be responsible for the variations in the impact of transposon silencing. They could therefore be the ones driving differences in the abundance of transposons between species. Overall, this work sheds light on the complex mechanisms shaping the evolution of genomes, and it may help to better understand how transposons are linked to processes such as aging and cancer.
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Affiliation(s)
- Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Harsh Shukla
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
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Understanding the Role of PIN Auxin Carrier Genes under Biotic and Abiotic Stresses in Olea europaea L. BIOLOGY 2022; 11:biology11071040. [PMID: 36101418 PMCID: PMC9312197 DOI: 10.3390/biology11071040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/19/2022] [Accepted: 06/19/2022] [Indexed: 11/16/2022]
Abstract
The PIN-FORMED (PIN) proteins represent the most important polar auxin transporters in plants. Here, we characterized the PIN gene family in two olive genotypes, the Olea europaea subsp. europaea var. sylvestris and the var. europaea (cv. ‘Farga’). Twelve and 17 PIN genes were identified for vars. sylvestris and europaea, respectively, being distributed across 6 subfamilies. Genes encoding canonical OePINs consist of six exons, while genes encoding non-canonical OePINs are composed of five exons, with implications at protein specificities and functionality. A copia-LTR retrotransposon located in intron 4 of OePIN2b of var. europaea and the exaptation of partial sequences of that element as exons of the OePIN2b of var. sylvestris reveals such kind of event as a driving force in the olive PIN evolution. RNA-seq data showed that members from the subfamilies 1, 2, and 3 responded to abiotic and biotic stress factors. Co-expression of OePINs with genes involved in stress signaling and oxidative stress homeostasis were identified. This study highlights the importance of PIN genes on stress responses, contributing for a holistic understanding of the role of auxins in plants.
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DeRosa H, Richter T, Wilkinson C, Hunter RG. Bridging the Gap Between Environmental Adversity and Neuropsychiatric Disorders: The Role of Transposable Elements. Front Genet 2022; 13:813510. [PMID: 35711940 PMCID: PMC9196244 DOI: 10.3389/fgene.2022.813510] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/13/2022] [Indexed: 12/21/2022] Open
Abstract
Long regarded as “junk DNA,” transposable elements (TEs) have recently garnered much attention for their role in promoting genetic diversity and plasticity. While many processes involved in mammalian development require TE activity, deleterious TE insertions are a hallmark of several psychiatric disorders. Moreover, stressful events including exposure to gestational infection and trauma, are major risk factors for developing psychiatric illnesses. Here, we will provide evidence demonstrating the intersection of stressful events, atypical TE expression, and their epigenetic regulation, which may explain how neuropsychiatric phenotypes manifest. In this way, TEs may be the “bridge” between environmental perturbations and psychopathology.
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Affiliation(s)
- Holly DeRosa
- Psychology Department, Developmental Brain Sciences Program, College of Liberal Arts, University of Massachusetts Boston, Boston, MA, United States
| | - Troy Richter
- Psychology Department, Developmental Brain Sciences Program, College of Liberal Arts, University of Massachusetts Boston, Boston, MA, United States
| | - Cooper Wilkinson
- Psychology Department, Developmental Brain Sciences Program, College of Liberal Arts, University of Massachusetts Boston, Boston, MA, United States
| | - Richard G Hunter
- Psychology Department, Developmental Brain Sciences Program, College of Liberal Arts, University of Massachusetts Boston, Boston, MA, United States
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38
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Inadvertent Transfer of Murine VL30 Retrotransposons to CAR-T Cells. ADVANCES IN CELL AND GENE THERAPY 2022; 2022. [PMID: 36081760 PMCID: PMC9450689 DOI: 10.1155/2022/6435077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
For more than a decade, genetically engineered autologous T-cells have been successfully employed as immunotherapy drugs for patients with incurable blood cancers. The active components in some of these game-changing medicines are autologous T-cells that express viral vector-delivered chimeric antigen receptors (CARs), which specifically target proteins that are preferentially expressed on cancer cells. Some of these therapeutic CAR expressing T-cells (CAR-Ts) are engineered via transduction with
-retroviral vectors (
-RVVs) produced in a stable producer cell line that was derived from murine PG13 packaging cells (ATCC CRL-10686). Earlier studies reported on the copackaging of murine virus-like 30S RNA (VL30) genomes with
-retroviral vectors generated in murine stable packaging cells. In an earlier study, VL30 mRNA was found to enhance the metastatic potential of human melanoma cells. These findings raise biosafety concerns regarding the possibility that therapeutic CAR-Ts have been inadvertently contaminated with potentially oncogenic VL30 retrotransposons. In this study, we demonstrated the presence of infectious VL30 particles in PG13 cell-conditioned media and observed the ability of these particles to deliver transcriptionally active VL30 genomes to human cells. Notably, VL30 genomes packaged by HIV-1-based vector particles transduced naïve human cells in culture. Furthermore, we detected the transfer and expression of VL30 genomes in clinical-grade CAR-T cells generated by transduction with PG13 cell-derived
-retroviral vectors. Our findings raise biosafety concerns regarding the use of murine packaging cell lines in ongoing clinical applications.
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39
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Chen TH, Winefield C. Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants. Mob DNA 2022; 13:16. [PMID: 35549762 PMCID: PMC9097378 DOI: 10.1186/s13100-022-00271-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/13/2022] [Indexed: 11/29/2022] Open
Abstract
Background Transposable element (TE) transcription is a precursor to its mobilisation in host genomes. However, the characteristics of expressed TE loci, the identification of self-competent transposon loci contributing to new insertions, and the genomic conditions permitting their mobilisation remain largely unknown. Results Using Vitis vinifera embryogenic callus, we explored the impact of biotic stressors on transposon transcription through the exposure of the callus to live cultures of an endemic grapevine yeast, Hanseniaspora uvarum. We found that only 1.7–2.5% of total annotated TE loci were transcribed, of which 5–10% of these were full-length, and the expressed TE loci exhibited a strong location bias towards expressed genes. These trends in transposon transcription were also observed in RNA-seq data from Arabidopsis thaliana wild-type plants but not in epigenetically compromised Arabidopsis ddm1 mutants. Moreover, differentially expressed TE loci in the grapevine tended to share expression patterns with co-localised differentially expressed genes. Utilising nanopore cDNA sequencing, we found a strong correlation between the inclusion of intronic TEs in gene transcripts and the presence of premature termination codons in these transcripts. Finally, we identified low levels of full-length transcripts deriving from structurally intact TE loci in the grapevine model. Conclusion Our observations in two disparate plant models representing clonally and seed propagated plant species reveal a closely connected transcriptional relationship between TEs and co-localised genes, particularly when epigenetic silencing is not compromised. We found that the stress treatment alone was insufficient to induce large-scale full-length transcription from structurally intact TE loci, a necessity for non-autonomous and autonomous mobilisation. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00271-5.
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Affiliation(s)
- Ting-Hsuan Chen
- Department of Wine, Food, and Molecular Biosciences, Lincoln University, Lincoln, 7647, New Zealand.,Present address: The New Zealand Institute for Plant and Food Research Ltd, Lincoln, 7608, New Zealand
| | - Christopher Winefield
- Department of Wine, Food, and Molecular Biosciences, Lincoln University, Lincoln, 7647, New Zealand.
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40
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Wei KHC, Mai D, Chatla K, Bachtrog D. Dynamics and Impacts of Transposable Element Proliferation in the Drosophila nasuta Species Group Radiation. Mol Biol Evol 2022; 39:msac080. [PMID: 35485457 PMCID: PMC9075770 DOI: 10.1093/molbev/msac080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transposable element (TE) mobilization is a constant threat to genome integrity. Eukaryotic organisms have evolved robust defensive mechanisms to suppress their activity, yet TEs can escape suppression and proliferate, creating strong selective pressure for host defense to adapt. This genomic conflict fuels a never-ending arms race that drives the rapid evolution of TEs and recurrent positive selection of genes involved in host defense; the latter has been shown to contribute to postzygotic hybrid incompatibility. However, how TE proliferation impacts genome and regulatory divergence remains poorly understood. Here, we report the highly complete and contiguous (N50 = 33.8-38.0 Mb) genome assemblies of seven closely related Drosophila species that belong to the nasuta species group-a poorly studied group of flies that radiated in the last 2 My. We constructed a high-quality de novo TE library and gathered germline RNA-seq data, which allowed us to comprehensively annotate and compare TE insertion patterns between the species, and infer the evolutionary forces controlling their spread. We find a strong negative association between TE insertion frequency and expression of genes nearby; this likely reflects survivor bias from reduced fitness impact of TEs inserting near lowly expressed, nonessential genes, with limited TE-induced epigenetic silencing. Phylogenetic analyses of insertions of 147 TE families reveal that 53% of them show recent amplification in at least one species. The most highly amplified TE is a nonautonomous DNA element (Drosophila INterspersed Element; DINE) which has gone through multiple bouts of expansions with thousands of full-length copies littered throughout each genome. Across all TEs, we find that TEs expansions are significantly associated with high expression in the expanded species consistent with suppression escape. Thus, whereas horizontal transfer followed by the invasion of a naïve genome has been highlighted to explain the long-term survival of TEs, our analysis suggests that evasion of host suppression of resident TEs is a major strategy to persist over evolutionary times. Altogether, our results shed light on the heterogenous and context-dependent nature in which TEs affect gene regulation and the dynamics of rampant TE proliferation amidst a recently radiated species group.
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Affiliation(s)
- Kevin H.-C. Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dat Mai
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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41
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Sork VL, Cokus SJ, Fitz-Gibbon ST, Zimin AV, Puiu D, Garcia JA, Gugger PF, Henriquez CL, Zhen Y, Lohmueller KE, Pellegrini M, Salzberg SL. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. Nat Commun 2022; 13:2047. [PMID: 35440538 PMCID: PMC9018854 DOI: 10.1038/s41467-022-29584-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
The genus Quercus, which emerged ∼55 million years ago during globally warm temperatures, diversified into ∼450 extant species. We present a high-quality de novo genome assembly of a California endemic oak, Quercus lobata, revealing features consistent with oak evolutionary success. Effective population size remained large throughout history despite declining since early Miocene. Analysis of 39,373 mapped protein-coding genes outlined copious duplications consistent with genetic and phenotypic diversity, both by retention of genes created during the ancient γ whole genome hexaploid duplication event and by tandem duplication within families, including numerous resistance genes and a very large block of duplicated DUF247 genes, which have been found to be associated with self-incompatibility in grasses. An additional surprising finding is that subcontext-specific patterns of DNA methylation associated with transposable elements reveal broadly-distributed heterochromatin in intergenic regions, similar to grasses. Collectively, these features promote genetic and phenotypic variation that would facilitate adaptability to changing environments.
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Affiliation(s)
- Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA.
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.
| | - Shawn J Cokus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Sorel T Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Aleksey V Zimin
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Daniela Puiu
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jesse A Garcia
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Ying Zhen
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Steven L Salzberg
- Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21218, USA
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42
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Colonna Romano N, Fanti L. Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns. Cells 2022; 11:cells11061048. [PMID: 35326499 PMCID: PMC8947103 DOI: 10.3390/cells11061048] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome to another, in all organisms. For this reason, on the one hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality in individuals. On the other hand, TEs can increase genetic variability, making populations better equipped to respond adaptively to environmental change. To counteract the deleterious effects of TEs, organisms have evolved strategies to avoid their activation. However, their mobilization does occur. Usually, TEs are maintained silent through several mechanisms, but they can be reactivated during certain developmental windows. Moreover, TEs can become de-repressed because of drastic changes in the external environment. Here, we describe the ‘double life’ of TEs, being both ‘parasites’ and ‘symbionts’ of the genome. We also argue that the transposition of TEs contributes to two important evolutionary processes: the temporal dynamic of evolution and the induction of genetic variability. Finally, we discuss how the interplay between two TE-dependent phenomena, insertional mutagenesis and epigenetic plasticity, plays a role in the process of evolution.
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43
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Muyle AM, Seymour DK, Lv Y, Huettel B, Gaut BS. Gene-body methylation in plants: mechanisms, functions and important implications for understanding evolutionary processes. Genome Biol Evol 2022; 14:6550137. [PMID: 35298639 PMCID: PMC8995044 DOI: 10.1093/gbe/evac038] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Gene body methylation (gbM) is an epigenetic mark where gene exons are methylated in the CG context only, as opposed to CHG and CHH contexts (where H stands for A, C, or T). CG methylation is transmitted transgenerationally in plants, opening the possibility that gbM may be shaped by adaptation. This presupposes, however, that gbM has a function that affects phenotype, which has been a topic of debate in the literature. Here, we review our current knowledge of gbM in plants. We start by presenting the well-elucidated mechanisms of plant gbM establishment and maintenance. We then review more controversial topics: the evolution of gbM and the potential selective pressures that act on it. Finally, we discuss the potential functions of gbM that may affect organismal phenotypes: gene expression stabilization and upregulation, inhibition of aberrant transcription (reverse and internal), prevention of aberrant intron retention, and protection against TE insertions. To bolster the review of these topics, we include novel analyses to assess the effect of gbM on transcripts. Overall, a growing body of literature finds that gbM correlates with levels and patterns of gene expression. It is not clear, however, if this is a causal relationship. Altogether, functional work suggests that the effects of gbM, if any, must be relatively small, but there is nonetheless evidence that it is shaped by natural selection. We conclude by discussing the potential adaptive character of gbM and its implications for an updated view of the mechanisms of adaptation in plants.
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Affiliation(s)
| | | | - Yuanda Lv
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding, Cologne, Germany
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44
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Warmuth VM, Weissensteiner MH, Wolf J. Ineffective silencing of transposable elements on an avian W Chromosome. Genome Res 2022; 32:671-681. [PMID: 35149543 PMCID: PMC8997356 DOI: 10.1101/gr.275465.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 02/08/2022] [Indexed: 11/24/2022]
Abstract
One of the defining features of transposable elements (TEs) is their ability to move to new locations in the host genome. To minimise the potentially deleterious effects of de novo TE insertions, hosts have evolved several mechanisms to control TE activity, including recombination-mediated removal and epigenetic silencing; however, increasing evidence suggests that silencing of TEs is often incomplete. The crow family experienced a recent radiation of LTR retrotransposons (LTRs), offering an opportunity to gain insight into the regulatory control of young, potentially still active TEs. We quantified the abundance of TE-derived transcripts across several tissues in 15 Eurasian crows (Corvus (corone) spp.) raised under common garden conditions and find evidence for ineffective TE suppression on the female-specific W Chromosome. Using RNA-seq data, we show that ~ 9.5% of all transcribed TEs had considerably greater (average: 16-fold) transcript abundance in female crows, and that more than 85% of these female-biased TEs originated on the W Chromosome. After accounting for differences in TE density among chromosomal classes, W-linked TEs were significantly more highly expressed than TEs residing on other chromosomes, consistent with ineffective silencing on the former. Together, our results suggest that the crow W Chromosome acts as a source of transcriptionally active TEs, with possible negative fitness consequences for female birds analogous to Drosophila (an X/Y system), where overexpression of Y-linked TEs is associated with male-specific aging and fitness loss ('toxic Y').
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45
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Lee YCG. Synergistic epistasis of the deleterious effects of transposable elements. Genetics 2022; 220:iyab211. [PMID: 34888644 PMCID: PMC9097265 DOI: 10.1093/genetics/iyab211] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 11/12/2022] Open
Abstract
The replicative nature and generally deleterious effects of transposable elements (TEs) raise an outstanding question about how TE copy number is stably contained in host populations. Classic theoretical analyses predict that, when the decline in fitness due to each additional TE insertion is greater than linear, or when there is synergistic epistasis, selection against TEs can result in a stable equilibrium of TE copy number. While several mechanisms are predicted to yield synergistic deleterious effects of TEs, we lack empirical investigations of the presence of such epistatic interactions. Purifying selection with synergistic epistasis generates repulsion linkage between deleterious alleles. We investigated this population genetic signal in the likely ancestral Drosophila melanogaster population and found evidence supporting the presence of synergistic epistasis among TE insertions, especially TEs expected to exert large fitness impacts. Even though synergistic epistasis of TEs has been predicted to arise through ectopic recombination and TE-mediated epigenetic silencing mechanisms, we only found mixed support for the associated predictions. We observed signals of synergistic epistasis for a large number of TE families, which is consistent with the expectation that such epistatic interaction mainly happens among copies of the same family. Curiously, significant repulsion linkage was also found among TE insertions from different families, suggesting the possibility that synergism of TEs' deleterious fitness effects could arise above the family level and through mechanisms similar to those of simple mutations. Our findings set the stage for investigating the prevalence and importance of epistatic interactions in the evolutionary dynamics of TEs.
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Affiliation(s)
- Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
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46
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Catlin NS, Josephs EB. The important contribution of transposable elements to phenotypic variation and evolution. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102140. [PMID: 34883307 DOI: 10.1016/j.pbi.2021.102140] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/04/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Transposable elements (TEs) are responsible for significant genomic variation in plants. Our understanding of the evolutionary forces shaping TE polymorphism has lagged behind other mutations because of the difficulty of accurately identifying TE polymorphism in short-read population genomic data. However, new approaches allow us to quantify TE polymorphisms in population datasets and address fundamental questions about the evolution of these polymorphisms. Here, we discuss how insertional biases shape where, when, and how often TEs insert throughout the genome. Next, we examine mechanisms by which TEs can affect phenotype. Finally, we evaluate current evidence for selection on TE polymorphisms. All together, it is clear that TEs are important, but underappreciated, contributors to intraspecific phenotypic variation, and that understanding the dynamics governing TE polymorphism is crucial for evolutionary biologists interested in the maintenance of variation.
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Affiliation(s)
- Nathan S Catlin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
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47
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Ying H, Hayward DC, Klimovich A, Bosch TCG, Baldassarre L, Neeman T, Forêt S, Huttley G, Reitzel AM, Fraune S, Ball EE, Miller DJ. The role of DNA methylation in genome defense in Cnidaria and other invertebrates. Mol Biol Evol 2022; 39:6516040. [PMID: 35084499 PMCID: PMC8857917 DOI: 10.1093/molbev/msac018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Considerable attention has recently been focused on the potential involvement of DNA methylation in regulating gene expression in cnidarians. Much of this work has been centered on corals, in the context of changes in methylation perhaps facilitating adaptation to higher seawater temperatures and other stressful conditions. Although first proposed more than 30 years ago, the possibility that DNA methylation systems function in protecting animal genomes against the harmful effects of transposon activity has largely been ignored since that time. Here, we show that transposons are specifically targeted by the DNA methylation system in cnidarians, and that the youngest transposons (i.e., those most likely to be active) are most highly methylated. Transposons in longer and highly active genes were preferentially methylated and, as transposons aged, methylation levels declined, reducing the potentially harmful side effects of CpG methylation. In Cnidaria and a range of other invertebrates, correlation between the overall extent of methylation and transposon content was strongly supported. Present transposon burden is the dominant factor in determining overall level of genomic methylation in a range of animals that diverged in or before the early Cambrian, suggesting that genome defense represents the ancestral role of CpG methylation.
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Affiliation(s)
- Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David C Hayward
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University, Kiel, Germany.,Collaborative Research Center for the Origin and Function of Metaorganisms, Christian Albrechts University, Kiel, Germany
| | - Laura Baldassarre
- Department of Zoology and Organismal Interactions, Heinrich-Heine-University Düsseldorf, Germany
| | - Teresa Neeman
- Biological Data Institute, Australian National University, Canberra, ACT, Australia
| | - Sylvain Forêt
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - Gavin Huttley
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina, Charlotte, USA
| | - Sebastian Fraune
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Eldon E Ball
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.,Marine Climate Change Unit, Okinawa Institute of Science and Technology, Japan
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48
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Deneweth J, Van de Peer Y, Vermeirssen V. Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum. BMC Genomics 2022; 23:18. [PMID: 34983397 PMCID: PMC8725346 DOI: 10.1186/s12864-021-08215-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 11/09/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Transposable elements (TE) make up a large portion of many plant genomes and are playing innovative roles in genome evolution. Several TEs can contribute to gene regulation by influencing expression of nearby genes as stress-responsive regulatory motifs. To delineate TE-mediated plant stress regulatory networks, we took a 2-step computational approach consisting of identifying TEs in the proximity of stress-responsive genes, followed by searching for cis-regulatory motifs in these TE sequences and linking them to known regulatory factors. Through a systematic meta-analysis of RNA-seq expression profiles and genome annotations, we investigated the relation between the presence of TE superfamilies upstream, downstream or within introns of nearby genes and the differential expression of these genes in various stress conditions in the TE-poor Arabidopsis thaliana and the TE-rich Solanum lycopersicum. RESULTS We found that stress conditions frequently expressed genes having members of various TE superfamilies in their genomic proximity, such as SINE upon proteotoxic stress and Copia and Gypsy upon heat stress in A. thaliana, and EPRV and hAT upon infection, and Harbinger, LINE and Retrotransposon upon light stress in S. lycopersicum. These stress-specific gene-proximal TEs were mostly located within introns and more detected near upregulated than downregulated genes. Similar stress conditions were often related to the same TE superfamily. Additionally, we detected both novel and known motifs in the sequences of those TEs pointing to regulatory cooption of these TEs upon stress. Next, we constructed the regulatory network of TFs that act through binding these TEs to their target genes upon stress and discovered TE-mediated regulons targeted by TFs such as BRB/BPC, HD, HSF, GATA, NAC, DREB/CBF and MYB factors in Arabidopsis and AP2/ERF/B3, NAC, NF-Y, MYB, CXC and HD factors in tomato. CONCLUSIONS Overall, we map TE-mediated plant stress regulatory networks using numerous stress expression profile studies for two contrasting plant species to study the regulatory role TEs play in the response to stress. As TE-mediated gene regulation allows plants to adapt more rapidly to new environmental conditions, this study contributes to the future development of climate-resilient plants.
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Affiliation(s)
- Jan Deneweth
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Vanessa Vermeirssen
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium. .,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. .,Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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49
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Zangarelli C, Arnaiz O, Bourge M, Gorrichon K, Jaszczyszyn Y, Mathy N, Escoriza L, Bétermier M, Régnier V. Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics. Genome Res 2022; 32:2028-2042. [PMID: 36418061 PMCID: PMC9808624 DOI: 10.1101/gr.277027.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022]
Abstract
With its nuclear dualism, the ciliate Paramecium constitutes a unique model to study how host genomes cope with transposable elements (TEs). P. tetraurelia harbors two germline micronuclei (MICs) and a polyploid somatic macronucleus (MAC) that develops from one MIC at each sexual cycle. Throughout evolution, the MIC genome has been continuously colonized by TEs and related sequences that are removed from the somatic genome during MAC development. Whereas TE elimination is generally imprecise, excision of approximately 45,000 TE-derived internal eliminated sequences (IESs) is precise, allowing for functional gene assembly. Programmed DNA elimination is concomitant with genome amplification. It is guided by noncoding RNAs and repressive chromatin marks. A subset of IESs is excised independently of this epigenetic control, raising the question of how IESs are targeted for elimination. To gain insight into the determinants of IES excision, we established the developmental timing of DNA elimination genome-wide by combining fluorescence-assisted nuclear sorting with high-throughput sequencing. Essentially all IESs are excised within only one endoreplication round (32C to 64C), whereas TEs are eliminated at a later stage. We show that DNA elimination proceeds independently of replication. We defined four IES classes according to excision timing. The earliest excised IESs tend to be independent of epigenetic factors, display strong sequence signals at their ends, and originate from the most ancient integration events. We conclude that old IESs have been optimized during evolution for early and accurate excision by acquiring stronger sequence determinants and escaping epigenetic control.
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Affiliation(s)
- Coralie Zangarelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Olivier Arnaiz
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Mickaël Bourge
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Kevin Gorrichon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Nathalie Mathy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Loïc Escoriza
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Mireille Bétermier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Vinciane Régnier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France;,Université Paris Cité, UFR Sciences du Vivant, 75205 Paris Cedex 13, France
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Hassanaly-Goulamhoussen R, De Carvalho Augusto R, Marteu-Garello N, Péré A, Favery B, Da Rocha M, Danchin EGJ, Abad P, Grunau C, Perfus-Barbeoch L. Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita. Front Cell Dev Biol 2021; 9:765690. [PMID: 34938734 PMCID: PMC8685519 DOI: 10.3389/fcell.2021.765690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
In model organisms, epigenome dynamics underlies a plethora of biological processes. The role of epigenetic modifications in development and parasitism in nematode pests remains unknown. The root-knot nematode Meloidogyne incognita adapts rapidly to unfavorable conditions, despite its asexual reproduction. However, the mechanisms underlying this remarkable plasticity and their potential impact on gene expression remain unknown. This study provides the first insight into contribution of epigenetic mechanisms to this plasticity, by studying histone modifications in M. incognita. The distribution of five histone modifications revealed the existence of strong epigenetic signatures, similar to those found in the model nematode Caenorhabditis elegans. We investigated their impact on chromatin structure and their distribution relative to transposable elements (TE) loci. We assessed the influence of the chromatin landscape on gene expression at two developmental stages: eggs, and pre-parasitic juveniles. H3K4me3 histone modification was strongly correlated with high levels of expression for protein-coding genes implicated in stage-specific processes during M. incognita development. We provided new insights in the dynamic regulation of parasitism genes kept under histone modifications silencing. In this pioneering study, we establish a comprehensive framework for the importance of epigenetic mechanisms in the regulation of the genome expression and its stability in plant-parasitic nematodes.
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Affiliation(s)
| | - Ronaldo De Carvalho Augusto
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, France.,Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | | | - Arthur Péré
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Bruno Favery
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Martine Da Rocha
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | | | - Pierre Abad
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Christoph Grunau
- IHPE, Univ Perpignan Via Domitia, CNRS, IFREMER, Univ Montpellier, Perpignan, France
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