Mobile DNA最新文献

{"title":"FoTeRs: a novel family of telomere-associated retrotransposons in Fusarium oxysporum.","authors":"Sahar Salimi, Mostafa Rahnama","doi":"10.1186/s13100-025-00385-6","DOIUrl":"10.1186/s13100-025-00385-6","url":null,"abstract":"<p><p>Transposable elements (TEs) are dynamic components of eukaryotic genomes, playing a crucial role in genome evolution and plasticity, particularly in unstable regions such as chromosome ends. In the globally significant fungal pathogen Fusarium oxysporum, we identified and characterized a novel family of non-LTR retrotransposons named FoTeRs (F. oxysporum Telomeric Retrotransposons). These elements are consistently and uniquely localized at chromosome ends, representing a rare example of site-specific TE integration. Phylogenetic analysis confirmed that FoTeRs form a distinct clade with other telomere-targeting retrotransposons, suggesting a shared evolutionary history and a convergent mechanism for telomeric integration. We found that individual FoTeR elements exhibit a duality in their evolutionary status. Putatively functional elements are under strong purifying selection, indicating that their protein-coding regions are highly conserved. This contrasts with the presence of other, non-functional copies that exhibit signs of mutational decay, a process accelerated by Repeat-Induced Point (RIP) mutations -a fungal-specific defense mechanism. The high density of upstream variable number tandem repeats (VNTRs) also contributes to their genomic plasticity. Furthermore, FoTeRs frequently co-localize with host Telomere-Linked Helicases (TLHs), suggesting a potential functional link in telomere maintenance. This study provides crucial insights into the role of TEs in shaping the genome architecture and adaptive potential of this important fungal pathogen.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":"5"},"PeriodicalIF":3.1,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12857005/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145596883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Plant MITEs: miniature transposable elements with major impacts.","authors":"Abirami Soundiramourtty, Marie Mirouze","doi":"10.1186/s13100-025-00375-8","DOIUrl":"10.1186/s13100-025-00375-8","url":null,"abstract":"<p><p>Miniature inverted repeat transposable elements (MITEs) are short, non-autonomous transposable elements that have attracted considerable attention over the years due to their ubiquitous presence and functional roles in plant genomes. A growing body of evidence points to a complex and multifaceted interplay between MITEs and host genomes. This review aims to elucidate the diverse roles of MITEs in shaping plant genome architecture, gene expression and adaptability to environmental stresses through different molecular mechanisms such as accommodation of regulatory sequences, promotion of alternative splicing, generation of epialleles and small RNAs, and mediation of structural variation. These examples highlight the functional importance of MITEs in plant genomes and provide directions for future research.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"43"},"PeriodicalIF":3.1,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12595863/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145471505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural and transduction patterns of human-specific polymorphic SVA insertions.","authors":"Ashley E Kirby, Mark Loftus, Emily C Golba, Miriam K Konkel","doi":"10.1186/s13100-025-00373-w","DOIUrl":"10.1186/s13100-025-00373-w","url":null,"abstract":"<p><strong>Background: </strong>SINE variable number tandem repeat Alu elements (SVAs) are a unique group of hominid-specific composite retrotransposons with highly variable internal structure. They represent the youngest TE family in humans and contribute to genetic diversity, evolution, and disease. Recent findings indicate that SVA mobilization rates may exceed previous estimates, and many SVAs exhibit insertion polymorphism. SVAs facilitate transduction (TD) events when transcription initiates upstream of a source element, or when their internal termination signal is bypassed, mobilizing adjacent 5' and/or 3' sequence. To investigate features of non-reference SVA elements currently polymorphic in the human genome, we analyzed a structural variant callset built upon 35 diverse human genomes generated by the Human Genome Structural Variation Consortium.</p><p><strong>Results: </strong>In our curated dataset of 543 polymorphic, non-reference SVAs, we identify insertions representing the three youngest subfamilies: D (7%), E (38%), and F (55%). Of the latter, we determine that at least 47% are actually SVA_F₁, a more recently discovered human-specific subfamily, indicating that F₁ is a major contributor to SVA expansion in the human population. We further uncover that 40% of non-reference SVAs carry a TD on their 5' and/or 3' ends. Of these, the majority (69%) harbor sequence originating in a gene, including 14 exonic events and the mobilization of a processed pseudogene, supporting the role of SVA in exon shuffling. In addition, we identified a so-called \"orphan\" TD, defined by the absence of SVA sequence at the insertion site. Leveraging TD origin coordinates, we identify 55 active source elements, including nine non-reference and 46 across GRCh38 and T2T-CHM13, giving rise to 84% of TD-carrying SVAs.</p><p><strong>Conclusions: </strong>Our analyses indicate that SVA_F₁ is more active than previously described and is a main driver of SVA expansion. We find two-fold more TD events compared to previous estimates, with an unexpected bias toward 3' events. Finally, we postulate that the discrepant SVA mobilization rate may be attributed to inter-individual variation in the presence/absence of source elements, a recent uptick in mobilization supported by overall low allele frequencies, and/or negative selection against deleterious insertions.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"42"},"PeriodicalIF":4.2,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12593883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145459283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A specialized bacterial group II intron is a highly efficient retrotransposon.","authors":"Lucie Gomes, Claire Toffano-Nioche, Daniel Gautheret, Maria Costa","doi":"10.1186/s13100-025-00380-x","DOIUrl":"10.1186/s13100-025-00380-x","url":null,"abstract":"<p><p>Mobile group II introns are site-specific retrotransposons composed of a large self-splicing ribozyme and an intron-encoded reverse transcriptase that are widespread in bacterial and organellar genomes. Sequence and structural variations of the ribozyme and the associated reverse transcriptase define several lineages of bacterial group II introns. Interestingly, some of these intron families evolved different mobility strategies while others colonize particular genetic contexts. Here, we have investigated the mobility activity of an Escherichia coli group II intron that is inserted into the stop codon of the stress-response gene groEL. Using mobility assays based on over-expression from a donor plasmid, we demonstrate that this intron is a highly efficient and site-specific retrotransposon, capable of colonizing the groEL gene of an E. coli host strain according to the insertion pattern observed in natural genomes. Furthermore, we provide evidence that a chromosomal copy of the full-length retrotransposon can be expressed from its native genetic locus to yield mobile retroelement particles. This intron constitutes a novel model system that could help reveal original mobility strategies used by some group II intron retrotransposons to colonize bacterial genomes.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"41"},"PeriodicalIF":3.1,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12584367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145445441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High interferon response signatures in SLE patient leukocytes are associated with increased transposable element expression in gene introns and intergenic regions.","authors":"Leo J Arteaga-Vazquez, Hugo Sepulveda, Bruno Villalobos Reveles, Kazumasa Suzuki, Kenneth C Kalunian, Ferhat Ay, Mark R Boothby, Anjana Rao","doi":"10.1186/s13100-025-00377-6","DOIUrl":"10.1186/s13100-025-00377-6","url":null,"abstract":"&lt;p&gt;&lt;p&gt;BACKGROUND: Systemic lupus erythematosus (SLE) is a spontaneous systemic auto-immune condition for which the inciting factors and genetic basis are generally unknown. Although heterogeneous in its manifestations and severity, SLE involves chronic inflammation along with sustained autoantibody production. The root causes and pathophysiology of the inflammation and breaches of tolerance are incompletely understood, but neutrophils are thought to be important elements of the pathophysiology. Type I interferons (IFN) in the bloodstream and an IFN-stimulated gene (ISG) signature in circulating leukocytes, including neutrophils, are common features in many patients. Earlier work has provided evidence of increased levels of transcripts derived from transposable elements (TEs) in peripheral blood cells of SLE patients. Using six leukocyte types, including neutrophils, we tested the correlation of TE expression with disease severity and explored the relationships between increased ISG and TE expression with attention to the genomic locations of the expressed TEs. RESULTS: We reanalysed previously published data from neutrophils and other leukocytes of SLE patients sub-divided into ISG-high (termed IFNpos, n = 12) and ISG-low (termed IFNneg, n = 11) patients in the original study, examining RNA-seq data from B and T lymphocytes, conventional and plasmacytoid dendritic cells (DC), monocytes and PMN of IFNpos and IFNneg SLE patients compared to healthy controls. SLE patients pre-stratified as IFNneg showed no significant increase in TE expression. All IFNpos cell types had similar amounts of total TE-encoded RNA, but among the 6 cell types, PMN had the highest number of differentially expressed TEs and ISGs in IFNpos SLE patients compared to healthy controls. There was a strong correlation between expression of several specific TE families and disease activity assessed at the time of the visit. Although most upregulated TEs (∼ 80%) were present in introns of upregulated genes, a substantial portion (∼ 20%) were not. Of the upregulated genes linked to upregulated TEs, approximately 1/3 were not ISGs whereas ∼ 67% were ISGs. By mapping expressed TEs in ISGs, we found that high intronic TE expression correlated strongly with increased ISG expression as well as with splicing alterations in annotated exons flanking expressed TEs. Consistent with autonomous TE expression, upregulated TEs were also observed at intergenic sites distant from annotated genes, perhaps due to weakening of heterochromatin integrity. CONCLUSIONS: Here we describe a strong association between increased TE expression and an ISG-based gene network signature in multiple types of leukocytes centrally involved in SLE pathogenesis. The subset of SLE patients with higher ISG expression also showed high TE expression, compared to healthy donors and SLE patients with low ISG expression. Our data do not offer mechanistic insights into how TE expression might be linked to SLE pathogenesis or IS","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"40"},"PeriodicalIF":4.2,"publicationDate":"2025-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12581288/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145438577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: A plan or pandemonium? The conundrum of retrotransposon activation in cancer.","authors":"Elina Zueva","doi":"10.1186/s13100-025-00379-4","DOIUrl":"10.1186/s13100-025-00379-4","url":null,"abstract":"","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"38"},"PeriodicalIF":4.2,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12539060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antagonistic regulation of LINE-1/Alu elements and their repressor APOBEC3B in cellular senescence.","authors":"Daksha Munot, Yueshuang Lu, Isabell Haußmann, Gregoire Najjar, Charlotte Baur, Manvendra Singh, Cagatay Günes, Daniel Sauter, Ankit Arora","doi":"10.1186/s13100-025-00378-5","DOIUrl":"10.1186/s13100-025-00378-5","url":null,"abstract":"<p><p>Long Interspersed Nuclear Elements-1 (LINE-1 or L1) make up approximately 21% of the human genome, with some L1 loci containing intact open reading frames (ORFs) that facilitate retrotransposition. Because retrotransposition can have deleterious effects leading to mutations and genomic instability, L1 activity is typically suppressed in somatic cells through transcriptional and post-transcriptional mechanisms. However, L1 elements are derepressed in senescent cells causing age-associated inflammation. Despite the recognition of L1 activity as a hallmark of aging, the underlying molecular mechanisms governing L1 derepression in these cells are not fully understood. In this study, we employed high throughput sequencing datasets and validated our findings through independent experiments to investigate the regulation of L1 elements in senescent cells. Our results reveal that both replicative and oncogene-induced senescence are associated with reduced expression of the cytidine deaminase APOBEC3B, a known suppressor of L1 retrotransposition. Consequently, senescent cells exhibited diminished levels of C-to-U editing of full-length L1 elements. Moreover, Ribo-seq profiling indicated that progression to senescence is not only associated with increased L1 transcription, but also translation of L1 ORFs. In summary, our results suggest that the depletion of APOBEC3B contributes to enhanced activity of L1 in senescent cells and promotion of L1-induced DNA damage and aging.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"39"},"PeriodicalIF":3.1,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12538936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Strict retroelement regulation is frequently lost following cancer transformation and generates a promising reservoir of cancer biomarkers.","authors":"Eric Russ, Sergey Iordanskiy","doi":"10.1186/s13100-025-00376-7","DOIUrl":"10.1186/s13100-025-00376-7","url":null,"abstract":"<p><strong>Background: </strong>Retroelements are repetitive sequences that comprise 42% of the human genome and are strictly regulated through various epigenetic mechanisms. Examining retroelement expression on a locus-specific level in relation to cancer can uncover distinct disease signatures.</p><p><strong>Results: </strong>Using over 5000 RNA-sequencing samples, we assessed retroelement transcription across 23 tissue systems, 159 cell types, 1019 cancer cell lines, and cells isolated from various stages of embryogenesis using the specialized software tool, Telescope. In healthy individuals, 11,388 retroelements were found to be actively transcribed and dynamically regulated in a tissue- and cell type-dependent manner. Using the adult human body as a reference, we observed that 94% of cancer cell lines displayed elevated transcription of at least one cancer-specific retroelement, providing a three-fold larger reservoir of cancer biomarkers (1182) than our comparable analysis of annotated protein-coding genes (338). The precise retroelements that were transcribed following tumorigenesis were influenced by the originating location, with cancers of the blood, lungs, and soft tissue displaying the highest origin-specific activation. Moreover, nearly half of the cancer-specific retroelement loci, mostly from the HERV-H family, were found to be expressed during early embryonic development.</p><p><strong>Conclusions: </strong>Our data demonstrate that elevated transcription of certain tissue-specific and embryonic retroelements can be considered as a hallmark of tumorigenesis.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"37"},"PeriodicalIF":3.1,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12495673/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145225481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene and transposable element expression in response to stress in temperate and tropical populations of Drosophila.","authors":"Miriam Merenciano, Daniel S Oliveira, Judit Salces-Ortiz, Rita Rebollo, Bianca Manfré, Bianca Menezes, Gabriel Krasovec, Camille Simonet, Sonia Janillon, Nelly Burlet, Claudia M A Carareto, Cristina Vieira, Marie Fablet","doi":"10.1186/s13100-025-00372-x","DOIUrl":"10.1186/s13100-025-00372-x","url":null,"abstract":"<p><strong>Background: </strong>The study of stress response in natural populations is crucial for understanding species local adaptation and evolution. In Drosophila, significant genetic diversity across populations from different geographical origins has been observed, emphasizing the influence of local environments.</p><p><strong>Results: </strong>In this study, we explored the impact of starvation and cold stress on the phenotypic and transcriptomic response of two natural populations of D. melanogaster and D. simulans from temperate and tropical regions. Additionally, we investigated the behavior and influence of transposable elements (TEs) in these types of stress, combining RNA-seq and ChIP-seq experiments, with high-quality long-read genome assemblies of all the strains. Our findings in D. melanogaster revealed that the transcriptomic response to stress is similar across geographical origins, whereas in D. simulans there is more variability. Notably, neither starvation nor cold induced a general activation of TEs in D. melanogaster or D. simulans, at least in the tissue and strains analysed in this study. Finally, we found three polymorphic TEs producing TE-chimeric transcripts associated with changes in nearby gene expression levels after stress.</p><p><strong>Conclusions: </strong>Overall, this study highlights the complexity of stress-TE interactions and their potential impact on adaptation. Understanding these dynamics contributes to the broader knowledge of how genetic and environmental factors interact to modulate gene expression, shaping an organism's ability to adapt to varying conditions.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"35"},"PeriodicalIF":3.1,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487357/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Type I interferons increase expression of endogenous retrovirus K102 and envelope protein in myeloid cells from patients with autoimmune disease.","authors":"Ethan Le, Fatemeh Moadab, Xiaoxing Wang, Rayan Najjar, Alison Bays, Kathryn M Hastie, Jeremy Shek, Erica Ollmann Saphire, Tomas Mustelin","doi":"10.1186/s13100-025-00371-y","DOIUrl":"10.1186/s13100-025-00371-y","url":null,"abstract":"<p><strong>Background: </strong>Autoantibodies against envelope (Env) protein encoded by human endogenous retrovirus group K (HERV-K) are prevalent in rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE), but it remains unclear which proviruses are responsible for this autoantigen. It also remains poorly understood how the transcription of HERV-K loci is regulated in cells that can produce Env.</p><p><strong>Results: </strong>We aligned our neutrophil RNA sequencing data to the new telomere-to-telomere reference genome and found uniquely mapping transcripts from HERV-K101, K102, K104, K108, K109, K117 and ERVK5, of which only K102, K108, and K109 encode an intact Env. Expression of K102 and K108 were higher in SLE than in healthy donors or RA (p_adj < 0.05). Transcripts from these proviruses increased in response to interferon-α in monocytes and neutrophils from RA patients and healthy donors, but not in SLE, presumably because they have chronically elevated type I interferons in vivo. Indeed, HERV-K expression was significantly higher in SLE patients with high type I interferon gene signature. Tumor necrosis factor-α and other cytokines and TLR ligands also induced HERV-K102 and K108 transcripts. Interferon-α also increased detectable Env protein in monocytes, macrophages, and neutrophils from RA patients. Among the genes for epigenetic silencers of HERV-K, only TRIM28 was significantly decreased in SLE patients with high interferons (p_adj = 0.00024).</p><p><strong>Conclusions: </strong>Our data establish a role for interferons in maintaining increased HERV-K expression in SLE and suggest that interferons or other cytokines can upregulate HERV-K to similar levels in RA. A transient increase may also accompany normal immune responses, suggesting that endogenous retroviruses may have been co-opted for efficient immune responses.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"36"},"PeriodicalIF":3.1,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12486725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}