Abstract Background Transposable elements drive genomic changes and are mobilized by specific nucleases. Among them are tyrosine recombinases (YRs), which mediate DNA cleavage and rejoining. YR-encoding elements, such as DIRS, Ngaro, Crypton, and Starships, occur in diverse eukaryotes and display characteristic terminal repeat structures that enable their mobility. Their activity in fungi results in large-scale chromosomal rearrangements, horizontal gene transfer, and the movement of genes for pathogenicity, symbiosis, and secondary metabolism. Other YR-elements underwent domestication giving rise to ZMYM transcriptional regulators in animals. Results We identify and characterize the fungal members of the CryptonA lineage of tyrosine recombinase-encoding transposons, which we name Glomhoppers. These elements encode a DUF3504 domain that retains the conserved catalytic residues characteristic of active YRs. In contrast, many domesticated animal DUF3504 homologs lack key catalytic residues, whereas active CryptonA transposon-derived DUF3504 elements have also been reported in animals. Structural modeling suggested the presence of a putative DNA-binding groove, and phylogenetic analyses placed Glomhoppers as a well-supported subclade within the CryptonA lineage, together with domesticated ZMYM-like derivatives. Across 72 Glomeromycota genomes, ~ 1,800 Glomhopper copies were identified, representing a subset of DUF3504-containing loci, mostly truncated or intronized, but ~ 25% lacked introns and maintained intact catalytic motifs, consistent with potential mobility. Genomic context analysis revealed their frequent localization within highly repetitive compartments, often alongside other transposon families. Expression data indicated that intronless variants respond to stress, reaching several-fold higher expression levels than intron-containing forms, especially in Gigaspora species. This is consistent with the possibility that a subset of Glomhoppers remains transcriptionally active and potentially mobilizable, although direct evidence of transposition is lacking. Conclusion Our findings establish Glomhoppers as a novel subfamily of DUF3504-encoding CryptonAs. The lineage-specific distribution, intron variation, and stress-responsive expression of Glomhoppers suggest divergent evolutionary trajectories, potentially including both mobility and domestication. These elements expand the known diversity of YR transposons and highlight DUF3504 as a candidate domain for further functional and evolutionary studies.
Domestic dogs, Canis lupus familiaris, have emerged as an important model system for studies of the genetic basis of phenotypes, patterns of genome variation and evolution, and for identifying loci relevant to human health and disease. The emergence of genome-scale sequencing data has revealed a disproportionate contribution of transposable elements to genetic variation in canines relative to humans, including insertions linked to traits and diseases. Insertions include LTR and non-LTR retrotransposons, such as Endogenous Retroviruses (ERVs), Long Interspersed Element-1 (LINE-1), and Short Interspersed Elements (SINEs). LINE-1 is an autonomous retroelement that encodes the proteins necessary for its retrotransposition and is currently active in canines. In addition, proteins encoded by LINE-1 s have mobilized SINEs and created gene retrocopies throughout the canine genome. In this review, we offer an overview of the classes of retrotransposons found in canine genomes and describe their contribution to traits and disease.
ONSEN is a Copia-type long terminal repeat (LTR) retrotransposon in Arabidopsis thaliana that serves as a powerful model for investigating host-transposon interactions. Its activation is directly coupled to the heat stress response via cis-acting elements within its LTRs, which recruit heat shock transcription factors. Under basal conditions, ONSEN is epigenetically silenced through DNA methylation and histone modifications. Heat stress partially relaxes this repression, yet productive mobilization remains limited by host countermeasures, including small RNAs, m6A RNA modification, and post-stress restoration of DNA methylation. These layered controls make ONSEN an ideal system for dissecting stress-responsive epigenetic regulation. Moreover, ONSEN insertions preferentially target euchromatic, gene-rich regions and can alter gene expression, splicing, and stress responsiveness. The conserved heat activation across plant retrotransposons further underscores its evolutionary relevance. Together, ONSEN offers a tractable framework for understanding how transposons and host genomes co-evolve and respond to environmental challenges. This review highlights how ONSEN provides insight into the dynamic balance between transposon activation and host genome defense.
The global rise of multidrug resistant (MDR) ESKAPE pathogens represents a serious threat to antimicrobial therapy. While phage therapy has re-emerged as a promising alternative, its effectiveness may be compromised by bacterial defense systems, particularly those encoded on plasmids. Comprehensive surveillance of the distribution, diversity, and mobilome context of plasmid-encoded defense systems in ESKAPE pathogens remains key to the design of effective phage therapies. We analyzed 7,330 dereplicated plasmids from ESKAPE pathogens to characterize the prevalence, diversity, and co-occurrence of plasmid-encoded antiphage defense systems. Conjugative plasmids, especially from Enterobacter spp. and K. pneumoniae, harbored the highest prevalence and diversity of defense systems. Defense-positive plasmids showed larger sizes, higher GC content, and frequent co-occurrence of resistance genes, especially from β-lactam, aminoglycoside, and sulfonamide classes, along with transposable elements such as IS6, IS3, and Tn3. Random forest and correlation analyses confirmed TEs and ARGs as dominant predictors of defense system occurrence. Network analysis revealed structured and partially conserved interactions among defense genes, TEs, and ARGs. RM and CBASS systems were frequently linked to beta-lactam and aminoglycoside resistance genes, as well as TEs such as IS6 and IS3. Recurrent associations such as RM-IS6, RM–IS1380, CBASS-IS3 and RM-OXA suggest shared horizontal transfer mechanisms. Plasmid-encoded antiphage defense systems in ESKAPE pathogens are widespread, structured, and linked to ARGs and mobile genetic elements. These findings highlight the contribution of plasmids to the dissemination of phage-resistance traits, underscore the importance of the mobilome in shaping phage-resistance landscapes in multidrug-resistant pathogens, and support the incorporation of plasmid defense profiling into phage therapy design.
Methods for computational discovery of transposable elements (TEs) in DNA sequences are under continual development. Although many TE annotation pipelines have been published, differences in their methods are often opaque and can lead to inconsistent results. As new methods emerge, there is a growing need for an informative and reproducible strategy to evaluate pipeline performance. We developed TE_Bench, a user-friendly TE annotation benchmarking workflow that streamlines data generation and visualization for systematic comparison of annotation pipeline performance. TE_Bench can automate simulation of DNA sequences containing artificially evolved TEs from a database or accept user-provided real data to quantify how well test pipelines detect TEs relative to a reference annotation. To accommodate users with varying starting points, TE_Bench is housed as a Snakemake workflow with several options. The data it generates can be used to determine which TE annotation pipeline to use for a specific task, or to inform future improvements to pipelines by revealing shortcomings. We demonstrate the utility of TE_Bench in both contexts by benchmarking EDTA, RepeatModeler2, and Earl Grey using simulated and real DNA sequences. With simulated data, we assess the impact of variables including TE class and nested structure on annotation quality, and with real data, we consider whether read type and mapping method influence downstream annotation. In their default configurations, RepeatModeler2 and Earl Grey perform similarly, outperforming EDTA. TE_Bench is an extensible, open-source workflow that supports community-driven TE annotation benchmarking using simulated ground-truth or real genomes. TE_Bench can be accessed at https://gitub.com/hkania/TE_Bench.
Abstract Background Deer antlers represent one of the few mammalian organs capable of complete regeneration, yet the underlying genomic regulatory mechanisms remain incompletely understood. Transposable elements (TEs), as key drivers of genome evolution and gene regulation, may play pivotal roles in the evolution of complex traits. This study aimed to systematically investigate the evolutionary dynamics of TEs in sika deer genome and to elucidate their potential regulatory functions in the development of antler by integrating comparative and functional genomics approaches. Results Comparative genomics revealed a lineage-specific massive expansion of LINE retrotransposons (dominated by RTE-BovB and L1 subfamilies) in cervid genomes, particularly in sika deer and red deer, where they constitute over 29% of the genomic sequence. The peak of this expansion (~ 7.5 million years ago) coincides with the major cladogenesis events within Cervus . Expression analysis showed that approximately 8.88% of annotated TEs are transcriptionally active in antler mesenchyme, with LINE and LTR elements being predominant among the 1,191 TEs consistently highly expressed across all stages. We identified numerous stage-specifically expressed TEs (SETEs) and found positive correlations between SETEs and key antler development genes, such as the osteogenic master regulator RUNX2 , the extracellular matrix remodeling gene ANPEP , and the collagen synthesis gene P4HA3 . Enrichment analysis demonstrated that genes adjacent to these TEs are significantly involved in pathways crucial for regeneration and rapid growth, including Wnt signaling, Hippo signaling, regulation of the actin cytoskeleton, and protein digestion and absorption. Conclusions Our findings point to a potential role for cervid TEs expansion in driving genomic evolution and the acquisition of cervid-specific phenotypes, particularly antler growth and development. Through profiling TE expression in antler mesenchymal tissue across key development stages, the results suggest that dynamic TEs expression may be involved in the regulation of antler development, implicating a potential regulatory role for TEs in this rapid growth process. This study provides new insights into the molecular mechanisms underlying the rapid growth of antlers.
Repbase and Dfam, the two foundational resources for transposable element annotation, are being unified into a single, fully open access framework, with Repbase released under CC-0 and its core curation team joining the Dfam project.
Abstract Transposable elements (TEs) contribute to genome expansions, gene duplications, and the evolution of gene regulatory networks. Recent work has highlighted the role of TE domestication in contributing to regulatory programs during animal development. Likewise, a role for TEs in regeneration has been proposed but remains understudied. Hydra vulgaris is a cnidarian polyp with astonishing regenerative ability. Approximately 60% of the Hydra genome is made up of transposable elements with a recent LINE/CR1 expansion potentially contributing to their speciation. Previous studies identified signatures of TE expression during Hydra regeneration, but the specific TEs involved, and their temporal expression patterns remain unknown. Here, I used publicly available RNA-sequencing data from a time course of Hydra head regeneration to characterize TE expression patterns. 262 TEs with dynamic temporal expression over regeneration were identified. This analysis also revealed TEs with expression patterns similar to genes involved in wound repair and tissue repatterning. Some dynamically expressed TEs were in close genomic proximity to genes involved in apoptosis, extracellular matrix remodeling, and proteins that interact with regeneration signaling pathways. This study provides a set of candidate TEs for future investigation into the mechanistic role of TEs in regeneration.
Transposable elements drive genomic changes and are mobilized by specific nucleases. Among them are tyrosine recombinases (YRs), which mediate DNA cleavage and rejoining. YR-encoding elements, such as DIRS, Ngaro, Crypton, and Starships, occur in diverse eukaryotes and display characteristic terminal repeat structures that enable their mobility. Their activity in fungi results in large-scale chromosomal rearrangements, horizontal gene transfer, and the movement of genes for pathogenicity, symbiosis, and secondary metabolism. Other YR-elements underwent domestication giving rise to ZMYM transcriptional regulators in animals. We identify and characterize the fungal members of the CryptonA lineage of tyrosine recombinase-encoding transposons, which we name Glomhoppers. These elements encode a DUF3504 domain that retains the conserved catalytic residues characteristic of active YRs. In contrast, many domesticated animal DUF3504 homologs lack key catalytic residues, whereas active CryptonA transposon-derived DUF3504 elements have also been reported in animals. Structural modeling suggested the presence of a putative DNA-binding groove, and phylogenetic analyses placed Glomhoppers as a well-supported subclade within the CryptonA lineage, together with domesticated ZMYM-like derivatives. Across 72 Glomeromycota genomes, 1,800 Glomhopper copies were identified, representing a subset of DUF3504-containing loci, mostly truncated or intronized, but 25
BACKGROUND: The evolution of human genome has been inextricably linked to germ cell infectivity and retrotransposition activity of endogenous retroviruses (ERVs). In result, 8% of the modern human DNA is occupied by human ERVs (HERVs), which although non-infectious and replication incompetent, are transcriptionally active in several cases (such as viral infections and cancer), and are able to produce functional mRNAs, non-coding RNAs and proteins, which on one hand are utilized for cell processes and on the other hand have been reported to be implicated in various pathologies. RESULTS: We used Nanopore Direct RNA Sequencing (DRS) technology to study the transcriptome of the transcriptionally active HERV family, HERV-K HML-2 (HK2) in a teratocarcinoma cell line. We developed a unique pipeline of HK2 DRS data analysis, which along with DRS itself, enabled us to investigate the true HK2 transcriptional profile on a single-molecule basis, unveiling alternative and non-canonical splicing patterns, length variants distribution and polyadenine tail length estimation. CONCLUSIONS: We uncovered a plethora of non-annotated HK2 transcriptional isoforms and read-through transcripts that utilized HK2 splicing sites, promoters and polyadenylation signals to assemble copies of the surrounding genes. This finding supports the observation that HERVs are involved in regulation of cellular transcription.
Background Transposable elements (TEs) play a key role in shaping chromosomal evolution and are particularly abundant in regions with high sequence turnover, such as centromeres. However, the factors driving the distribution of centromeric TEs remain largely unknown. This knowledge gap limits our understanding of TE biology and their functional role within host genomes. In this study, we analyse newly assembled chromosome-scale genomes of four closely related Biscutella species. Results Despite substantial synteny, we observe considerable variability in the centromeric and flanking pericentromeric regions among species. By comparing the distribution of centromeric TEs in space and time, we identify specialized CRM elements that target active centromeres, surrounded by Athila copies. Beyond such TE dynamics shaping all chromosomes, arms bearing distal nucleolus organizer regions further show expansion of these centromeric TEs being associated with increased DNA methylation and reduced gene expression. Conclusions Offering fresh insights into the evolutionary mechanisms shaping chromosome organization, this study highlights how the recurrent activity of centromeric TEs significantly impacts functionality and stability of adjacent chromosome regions, underscoring broader implications for understanding genome evolution.
Background Transposable elements (TEs) constitute a substantial fraction of the human genome and contribute to gene regulatory programs. However, systematic analysis of TEs at the individual locus level remains technically challenging, particularly in single-cell contexts. While single-cell technologies have advanced the study of cellular heterogeneity, most analytical frameworks remain gene-centric. Existing TE-focused approaches are largely restricted to transcriptional profiling using scRNA-seq data, while analyses of single-cell chromatin accessibility have focused primarily on aggregate or family-level TE signals rather than individual loci. Consequently, no dedicated computational framework exists for quantifying chromatin accessibility at individual TE loci from scATAC-seq data, limiting investigation of locus-specific TE regulatory activity at single-cell resolution. Results scTELL (single-cell Transposable Element Locus-Level analysis) is a computational framework that quantifies TE accessibility at individual loci from scATAC-seq data using a distance-weighted scoring scheme. We applied scTELL to diverse biological systems, including healthy peripheral blood mononuclear cells (PBMCs), clear cell renal cell carcinoma (ccRCC), and breast cancer (BC). In PBMCs, scTELL identified distinct cell-type-specific TE accessibility patterns with clustering performance comparable to established gene activity scoring approaches, and validated key TE accessibility patterns using bulk ATAC-seq data from sorted immune cell populations. Motif enrichment analyses of TE-associated accessible regions revealed distinct TF motif landscapes, including family-level motif signatures, within-family locus heterogeneity across cell types, and motifs enriched in TE-associated regions relative to gene promoters. In cancer contexts, scTELL identified heterogeneity-associated TE loci and observed clinically associated accessibility patterns, including an L1PA2 locus in ccRCC associated with progression-free interval, and survival-associated TE loci in BC. Conclusions scTELL provides a much-needed and robust tool to investigate the locus-specific regulatory landscape of TEs at single-cell resolution. Our findings demonstrate that this approach can uncover previously unrecognized cell-type-specific and disease-associated TE accessibility. The scTELL framework offers a new layer of biological insight, complementing existing single-cell analysis protocols and enabling the discovery of candidate biomarkers from a vast, understudied portion of the genome. While these associations are reproducible across datasets, prospective validation and functional studies will be required to establish clinical utility and to determine whether any locus has a causal role or therapeutic relevance.
Processed pseudogenes and retrogenes are defined by their RNA-mediated origin and, by virtue of this origin-based definition, are often interpreted as discrete genomic insertions. The completion of telomere-to-telomere (T2T) reference assemblies has substantially improved the resolution of segmental duplication architectures and centromeric satellite sequences that were previously inaccessible, allowing genomic structural contexts that were effectively invisible in earlier references to be directly examined. Using the SEPTIN14P-CICP locus family as a case study, chain-based comparative analyses showed that a genomic window spanning the SEPTIN14 3′ terminal exon and the adjacent processed pseudogene CICP12 is dispersed into multiple segmental duplication-associated units across great apes, rather than being maintained as a single orthologous locus. Genome-wide analyses further indicated that annotated CICP loci preferentially localize within segmental duplication blocks and accumulate near pericentromeric or subtelomeric regions. Despite this duplication-associated dispersion, codon-based selection analyses revealed pervasive purifying selection acting on the full-length SEPTIN14 coding sequence and its 3′ terminal exon, arguing against a model in which the terminal exon was newly formed through segmental duplication. Together, these results show that when highly conserved, strongly constrained coding regions are embedded within segmental duplication-rich regions, co-dispersed processed pseudogene copies can be interpreted as distinct from independently generated LINE-1-mediated insertions and as reflecting secondary structural propagation. When considered in light of origin-based definitions of processed pseudogenes and retrogenes, and specifically within duplication-rich and structurally unstable genomic regions resolved by T2T-level assemblies, these results suggest that multiple annotated loci can arise through secondary propagation of a single RNA-derived insertion. Under such contexts, incorporation of selective constraint and cross-species conservation enables more reliable distinction between source insertions and their secondarily propagated copies. This case study highlights a limitation of current annotation frameworks and demonstrates the need for more precise annotation that incorporates evolutionary and structural context in the T2T era.
Endogenous Viral Elements (EVEs) are viral sequences integrated into the host germline and passed to offspring. Most virus types can integrate, often with the help of host retroelements, especially for non-retroviral RNA viruses. It is known that EVEs are widespread across insect species and related to an extensive range of virus taxa, many of which might share similar evolutionary origins. Bombus bees are essential pollinators that have been experiencing worldwide colony declines in recent decades. Therefore, uncovering genetic elements and pathways to better understand host–pathogen interactions is crucial in conserving biodiversity. Non-retroviral Integrated RNA Virus Sequences (NIRVS) were widespread in Bombus genomes, without a clear correlation between genome size and the number of EVEs. Most of the EVEs were single-copy, ranging from 111 to 3,729 bp with an average of 504 bp. Most of them share similarities with unclassified viruses and known viruses belonging to the families Partitiviridae and Virgaviridae, as well as the order Martellivirales. We observed that over 25
Spermatogenesis is a highly temperature sensitive process, which occurs 2–6 °C below core body temperature. Testicular hyperthermia rapidly affects male precursor cells, including spermatocytes and round spermatids, leading to elevated DNA damage. To understand the immediate transcriptional response of these cell types, we subjected mice to testicular hyperthermia and performed whole transcriptome sequencing on round spermatids following testicular hyperthermia. Analysis of sequencing data revealed that 93
How endogenous retroviral elements (ERVs), a family of transposable elements, may promote tumor progression is not well understood. Tripartite motif-containing 28 (TRIM28/TIF1b/KAP1) is a key transcriptional co-repressor protein that represses ERV expression in many cell types including embryonic stem cells, neural progenitor cells, differentiated adult cells, and cancer cells. In this study, we investigated the effect of Trim28 deletion on the expression of ERVs using an immune competent genetically engineered mouse model for prostate cancer. We found Trim28 deletion in prostate tumors led to the expression of ERVs in prostates from both hormonally intact and castrated mice. ERVs can regulate the expression of neighboring genes, and we detected increased expression of several protein-coding genes near overexpressed ERVs. Our data suggest that Trim28 deletion in prostate tumor epithelial cells may promote an innate immune response. However, Trim28 deletion also led to excessive deposition of tumor extracellular matrix (ECM). Our findings suggest that ECM alterations downstream of ERV derepression could affect immune cells in the tumor microenvironment and may promote tumor progression.
Genome size expansions are common among eukaryotic lineages. Enlarged genomes can be bioenergetically demanding, and active mobile elements can trigger chromosomal rearrangements and loss of gene function. What triggers genome size expansions remains largely unexplored in many biological clades, particularly within the fungal kingdom. Activation of large transposable elements (TEs), such as long-terminal repeats (LTRs), is a common contributor. Yet the mechanisms of LTR activation remain poorly understood. Here, we focus on the fungal genus Pseudocercospora and closely related species with known variation in genome size. In using an assembly-free approach, we found that TE content is highly variable among species, with species-specific retrotransposon families being the main drivers of independent genome expansions. We further focused on the two species with the most expanded genomes and reference-quality genomes, P. fijiensis and P. ulei. We found that the P. ulei genome is compartmentalized, with highly variable TE densities among chromosomal regions, and a striking reduction in pathogenicity-associated genes. Overall, our study indicates that species of Pseudocercospora originally had reduced genome sizes, and genome expansions are species-specific, driven by heterogeneous sets of TE families. We discuss what might have caused TE activation and subsequent proliferation in the genus, including stress conditions and host adaptation. Surveys of clades with highly dynamic genome sizes are crucial for the investigation of causal factors driving long-term TE dynamics.
The sixth Japanese meeting on host–transposon interactions, titled “Biological Function and Evolution through Interactions between Hosts and Transposable Elements,” was held on August 24th and 25th, 2023, at the National Institute of Genetics as well as online. This meeting was supported by the National Institute of Genetics and aimed to bring together researchers studying the diverse roles of TEs in genome function and evolution, as well as host defense systems against TE mobility, TE bursts during evolution, and intron mobility in mammals, insects, land plants, yeast, protozoa, and bacteria. Here, we have presented the highlights of the discussion. Organizers: Kenji Ichiyanagi, Yoko Ikeda, and Kuniaki Saito.
