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Barro-Trastoy D, Köhler C. Helitrons: genomic parasites that generate developmental novelties. Trends Genet 2024; 40:437-448. [PMID: 38429198 DOI: 10.1016/j.tig.2024.02.002] [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: 12/29/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as 'peel-and-paste elements'. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for host genomes. This review discusses the current understanding of Helitrons, exploring their origins, transposition mechanism, and the extensive repercussions of their activity on genome structure and function. We also explore the evolutionary conflicts stemming from Helitron-transposed gene fragments and elucidate their domestication for regulating responses to environmental challenges. Looking ahead, further research in this evolving field promises to bring interesting discoveries on the role of Helitrons in shaping genomic landscapes.
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Affiliation(s)
- Daniela Barro-Trastoy
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Claudia Köhler
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden.
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Samelak-Czajka A, Wojciechowski P, Marszalek-Zenczak M, Figlerowicz M, Zmienko A. Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes. Funct Integr Genomics 2023; 23:120. [PMID: 37036577 PMCID: PMC10085913 DOI: 10.1007/s10142-023-01043-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 04/11/2023]
Abstract
MicroRNAs (miRNAs) regulate gene expression by RNA interference mechanism. In plants, miRNA genes (MIRs) which are grouped into conserved families, i.e. they are present among the different plant taxa, are involved in the regulation of many developmental and physiological processes. The roles of the nonconserved MIRs-which are MIRs restricted to one plant family, genus, or even species-are less recognized; however, many of them participate in the responses to biotic and abiotic stresses. Both over- and underproduction of miRNAs may influence various biological processes. Consequently, maintaining intracellular miRNA homeostasis seems to be crucial for the organism. Deletions and duplications in the genomic sequence may alter gene dosage and/or activity. We evaluated the extent of copy number variations (CNVs) among Arabidopsis thaliana (Arabidopsis) MIRs in over 1000 natural accessions, using population-based analysis of the short-read sequencing data. We showed that the conserved MIRs were unlikely to display CNVs and their deletions were extremely rare, whereas nonconserved MIRs presented moderate variation. Transposon-derived MIRs displayed exceptionally high diversity. Conversely, MIRs involved in the epigenetic control of transposons reactivated during development were mostly invariable. MIR overlap with the protein-coding genes also limited their variability. At the expression level, a higher rate of nonvariable, nonconserved miRNAs was detectable in Col-0 leaves, inflorescence, and siliques compared to nonconserved variable miRNAs, although the expression of both groups was much lower than that of the conserved MIRs. Our data indicate that CNV rate of Arabidopsis MIRs is related with their age, function, and genomic localization.
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Affiliation(s)
- Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
- Institute of Computing Science, Faculty of Computing and Telecommunications, Poznan University of Technology, 60-965, Poznan, Poland
| | | | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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Chellapan BV, van Dam P, Rep M, Cornelissen BJC, Fokkens L. Non-canonical Helitrons in Fusarium oxysporum. Mob DNA 2016; 7:27. [PMID: 27990178 PMCID: PMC5148889 DOI: 10.1186/s13100-016-0083-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/03/2016] [Indexed: 01/18/2023] Open
Abstract
Background Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi. Results Here, we comprehensively survey Helitrons in several completely sequenced genomes representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex. FOSC Helitrons resemble members of the Helitron2 variant that includes Helentrons and DINEs. The fact that some Helitrons appeared to be still active in FOSC provided the opportunity to determine whether Helitrons occur as a circular intermediate in FOSC. We present experimental evidence suggesting that at least one Helitron subgroup occurs with joined ends, suggesting a circular intermediate. We extend our analyses to other Pezizomycotina and find that most fungal Helitrons we identified group phylogenetically with Helitron2 and probably have similar characteristics. Conclusions FOSC genomes harbour non-canonical Helitrons that are characterized by asymmetric terminal inverted repeats, show hallmarks of recent activity and likely transpose via a circular intermediate. Bioinformatic analyses indicate that they are representative of a large reservoir of fungal Helitrons that thus far has not been characterized. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0083-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Biju Vadakkemukadiyil Chellapan
- Department of Computational Biology and Bioinformatics, University of Kerala, Karyavattom Campus, Karyavattom PO, Trivandrum, Kerala India ; Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands
| | - Peter van Dam
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands
| | - Ben J C Cornelissen
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, P.O. Box 94215, 1090 Amsterdam, GE The Netherlands
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Abstract
Helitrons, the eukaryotic rolling-circle transposable elements, are widespread but most prevalent among plant and animal genomes. Recent studies have identified three additional coding and structural variants of Helitrons called Helentrons, Proto-Helentron, and Helitron2. Helitrons and Helentrons make up a substantial fraction of many genomes where nonautonomous elements frequently outnumber the putative autonomous partner. This includes the previously ambiguously classified DINE-1-like repeats, which are highly abundant in Drosophila and many other animal genomes. The purpose of this review is to summarize what we have learned about Helitrons in the decade since their discovery. First, we describe the history of autonomous Helitrons, and their variants. Second, we explain the common coding features and difference in structure of canonical Helitrons versus the endonuclease-encoding Helentrons. Third, we review how Helitrons and Helentrons are classified and discuss why the system used for other transposable element families is not applicable. We also touch upon how genome-wide identification of candidate Helitrons is carried out and how to validate candidate Helitrons. We then shift our focus to a model of transposition and the report of an excision event. We discuss the different proposed models for the mechanism of gene capture. Finally, we will talk about where Helitrons are found, including discussions of vertical versus horizontal transfer, the propensity of Helitrons and Helentrons to capture and shuffle genes and how they impact the genome. We will end the review with a summary of open questions concerning the biology of this intriguing group of transposable elements.
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Differential pre-mRNA Splicing Alters the Transcript Diversity of Helitrons Between the Maize Inbred Lines. G3-GENES GENOMES GENETICS 2015; 5:1703-11. [PMID: 26070844 PMCID: PMC4528327 DOI: 10.1534/g3.115.018630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The propensity to capture and mobilize gene fragments by the highly abundant Helitron family of transposable elements likely impacts the evolution of genes in Zea mays. These elements provide a substrate for natural selection by giving birth to chimeric transcripts by intertwining exons of disparate genes. They also capture flanking exons by read-through transcription. Here, we describe the expression of selected Helitrons in different maize inbred lines. We recently reported that these Helitrons produce multiple isoforms of transcripts in inbred B73 via alternative splicing. Despite sharing high degrees of sequence similarity, the splicing profile of Helitrons differed among various maize inbred lines. The comparison of Helitron sequences identified unique polymorphisms in inbred B73, which potentially give rise to the alternatively spliced sites utilized by transcript isoforms. Some alterations in splicing, however, do not have obvious explanations. These observations not only add another level to the creation of transcript diversity by Helitrons among inbred lines but also provide novel insights into the cis-acting elements governing splice-site selection during pre-mRNA processing.
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Castanera R, Pérez G, López L, Sancho R, Santoyo F, Alfaro M, Gabaldón T, Pisabarro AG, Oguiza JA, Ramírez L. Highly expressed captured genes and cross-kingdom domains present in Helitrons create novel diversity in Pleurotus ostreatus and other fungi. BMC Genomics 2014; 15:1071. [PMID: 25480150 PMCID: PMC4289320 DOI: 10.1186/1471-2164-15-1071] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Helitrons are class-II eukaryotic transposons that transpose via a rolling circle mechanism. Due to their ability to capture and mobilize gene fragments, they play an important role in the evolution of their host genomes. We have used a bioinformatics approach for the identification of helitrons in two Pleurotus ostreatus genomes using de novo detection and homology-based searching. We have analyzed the presence of helitron-captured genes as well as the expansion of helitron-specific helicases in fungi and performed a phylogenetic analysis of their conserved domains with other representative eukaryotic species. RESULTS Our results show the presence of two helitron families in P. ostreatus that disrupt gene colinearity and cause a lack of synteny between their genomes. Both putative autonomous and non-autonomous helitrons were transcriptionally active, and some of them carried highly expressed captured genes of unknown origin and function. In addition, both families contained eukaryotic, bacterial and viral domains within the helitron's boundaries. A phylogenetic reconstruction of RepHel helicases using the Helitron-like and PIF1-like helicase conserved domains revealed a polyphyletic origin for eukaryotic helitrons. CONCLUSION P. ostreatus helitrons display features similar to other eukaryotic helitrons and do not tend to capture host genes or gene fragments. The occurrence of genes probably captured from other hosts inside the helitrons boundaries pose the hypothesis that an ancient horizontal transfer mechanism could have taken place. The viral domains found in some of these genes and the polyphyletic origin of RepHel helicases in the eukaryotic kingdom suggests that virus could have played a role in a putative lateral transfer of helitrons within the eukaryotic kingdom. The high similarity of some helitrons, along with the transcriptional activity of its RepHel helicases indicates that these elements are still active in the genome of P. ostreatus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Lucía Ramírez
- Department of Agrarian Production, Genetics and Microbiology Research Group, Public University of Navarre, 31006 Pamplona, Navarre, Spain.
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Marroni F, Pinosio S, Morgante M. Structural variation and genome complexity: is dispensable really dispensable? CURRENT OPINION IN PLANT BIOLOGY 2014; 18:31-6. [PMID: 24548794 DOI: 10.1016/j.pbi.2014.01.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/08/2014] [Accepted: 01/26/2014] [Indexed: 05/18/2023]
Abstract
Structural variants (SVs) such as copy number variants (CNVs) and presence/absence variants (PAVs) substantially contribute to genetic variation and have an important effect on phenotypic diversity. Since unbalanced SVs are by definition sequences present only in some individuals, they have therefore been referred to as dispensable genome and are not necessary for survival, even though they may provide an important contribution to phenotypic diversity within the species. However, some multi-copy sequences of the dispensable genomes (e.g., multigene families) may be needed in a given proportion by each individual, thus belonging to a conditionally dispensable portion of the pan-genome. Another interesting aspect reported by recent studies is that the rate at which SVs are formed might be influenced by the mating system and by common environmental stresses. In conclusion the dispensable genome plays an important role in genome evolution and in the complex interplay between the genome and the environment.
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Affiliation(s)
- Fabio Marroni
- Dipartimento di Scienze Agrarie e Ambientali, Università di Udine, 33100 Udine, Italy; Istituto di Genomica Applicata (IGA), 33100 Udine, Italy
| | - Sara Pinosio
- Institute of Biosciences and Bioresources, National Research Council, Via Madonna del Piano 10, 50019 Sesto Fiorentino (Firenze), Italy; Istituto di Genomica Applicata (IGA), 33100 Udine, Italy
| | - Michele Morgante
- Dipartimento di Scienze Agrarie e Ambientali, Università di Udine, 33100 Udine, Italy; Istituto di Genomica Applicata (IGA), 33100 Udine, Italy.
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