Mobile DNA最新文献

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Transposable elements in the era of data science EMBO course: a call for open, accessible, and collaborative TE resources. 数据科学时代的转座元素EMBO课程:对开放、可访问和协作TE资源的呼吁。
IF 4.2 2区 生物学
Mobile DNA Pub Date : 2026-07-31 DOI: 10.1186/s13100-026-00412-0
Alexandre Rossi Paschoal, Fabiana Rodrigues de Goes, Wojciech Makałowski, Gökhan Karakülah, Rebecca V Berrens, Emmanuelle Lerat, Cristina Vieira, Shujun Ou, Anna-Sophie Fiston-Lavier, Marie-Anne Van Sluys, Romain Guyot
{"title":"Transposable elements in the era of data science EMBO course: a call for open, accessible, and collaborative TE resources.","authors":"Alexandre Rossi Paschoal, Fabiana Rodrigues de Goes, Wojciech Makałowski, Gökhan Karakülah, Rebecca V Berrens, Emmanuelle Lerat, Cristina Vieira, Shujun Ou, Anna-Sophie Fiston-Lavier, Marie-Anne Van Sluys, Romain Guyot","doi":"10.1186/s13100-026-00412-0","DOIUrl":"10.1186/s13100-026-00412-0","url":null,"abstract":"<p><p>This community letter represents a collective outcome from the EMBO Practical Course \"Transposable Elements in the Era of Data Science\" held at the Rosalind Franklin Institute from 12 to 16 May 2025, Didcot, United Kingdom ( https://meetings.embo.org/event/25-transposable-elements ). Written by course speakers together with an instructor representative, it reflects key discussions about the urgent need for open, accessible, and community-driven resources for transposable element (TE) research. This letter outlines key areas where collective action is imperative to accelerate our understanding of TEs and their profound impact on biological systems. In particular, the letter highlights limitations of existing databases, particularly Repbase, and calls for a new open-access platform that also supports non-model species and interoperates with large-scale genomic initiatives. It also underscores the crucial discussion on TE curation and the role of artificial intelligence (AI) in advancing TE research and advocates for a collaborative infrastructure to support the future of TE genomics. A central theme emerging from these discussions was the urgent need for enhanced open science practices, particularly concerning data sharing, tool development, and the establishment of robust, accessible community resources. To this end, we propose a set of strategic suggestions accompanied by practical actions to advance TE research. We hope this letter contributes to the community of TE researchers to discuss the latest advancements and persistent challenges in TE research in a sustainable and equitable manner.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"17 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13425858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148648926","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}
引用次数: 0
Interactions of antiphage defense systems in the ESKAPE pathogen plasmids. ESKAPE病原菌质粒中噬菌体防御系统的相互作用。
IF 4.2 2区 生物学
Mobile DNA Pub Date : 2026-07-16 DOI: 10.1186/s13100-026-00410-2
Adeel Farooq, Asma Rafique, Eunyoung Han, Soo-Min Park, Hye Seon Kim, Min Jung Kim, Asim Hussain, Muhammad Sheeraz Ahmad, Gisèle LaPointe
{"title":"Interactions of antiphage defense systems in the ESKAPE pathogen plasmids.","authors":"Adeel Farooq, Asma Rafique, Eunyoung Han, Soo-Min Park, Hye Seon Kim, Min Jung Kim, Asim Hussain, Muhammad Sheeraz Ahmad, Gisèle LaPointe","doi":"10.1186/s13100-026-00410-2","DOIUrl":"https://doi.org/10.1186/s13100-026-00410-2","url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148471959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
TE_Bench: a foundational benchmarking workflow for transposable element annotation pipelines. TE_Bench:可转置元素注释管道的基本基准测试工作流。
IF 4.2 2区 生物学
Mobile DNA Pub Date : 2026-07-16 DOI: 10.1186/s13100-026-00405-z
Hannah P Kania, Sierra A Seifert, Anne D Yoder
{"title":"TE_Bench: a foundational benchmarking workflow for transposable element annotation pipelines.","authors":"Hannah P Kania, Sierra A Seifert, Anne D Yoder","doi":"10.1186/s13100-026-00405-z","DOIUrl":"https://doi.org/10.1186/s13100-026-00405-z","url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transposable element dynamics and regulatory role in sika deer (Cervus nippon) antler development. 梅花鹿(Cervus nippon)鹿角发育中的转座因子动力学及调控作用。
IF 4.2 2区 生物学
Mobile DNA Pub Date : 2026-07-15 DOI: 10.1186/s13100-026-00411-1
Qianghui Wang, Haihua Xing, Yukai Ma, Zihui Sun, Ruobing Han, Heping Li
{"title":"Transposable element dynamics and regulatory role in sika deer (Cervus nippon) antler development.","authors":"Qianghui Wang, Haihua Xing, Yukai Ma, Zihui Sun, Ruobing Han, Heping Li","doi":"10.1186/s13100-026-00411-1","DOIUrl":"10.1186/s13100-026-00411-1","url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusions: </strong>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.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13445738/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148456502","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}
引用次数: 0
Unifying Repbase and Dfam: a new open foundation for transposable element research. 统一Repbase和Dfam:转座元件研究的一个新的开放基础。
IF 4.2 2区 生物学
Mobile DNA Pub Date : 2026-06-25 DOI: 10.1186/s13100-026-00409-9
Kenji K Kojima, Arian F A Smit, Weidong Bao, Oleksiy Kohany, Noriko F Kojima, Timothy Jurka, Robert Hubley, Travis J Wheeler
{"title":"Unifying Repbase and Dfam: a new open foundation for transposable element research.","authors":"Kenji K Kojima, Arian F A Smit, Weidong Bao, Oleksiy Kohany, Noriko F Kojima, Timothy Jurka, Robert Hubley, Travis J Wheeler","doi":"10.1186/s13100-026-00409-9","DOIUrl":"10.1186/s13100-026-00409-9","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"17 1","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13296103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148318109","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}
引用次数: 0
Dynamic transposable element expression during Hydra head regeneration. 九头蛇再生过程中动态转座因子的表达。
IF 4.2 2区 生物学
Mobile DNA Pub Date : 2026-06-08 DOI: 10.1186/s13100-026-00406-y
Aide Macias-Muñoz
{"title":"Dynamic transposable element expression during Hydra head regeneration.","authors":"Aide Macias-Muñoz","doi":"10.1186/s13100-026-00406-y","DOIUrl":"10.1186/s13100-026-00406-y","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13465017/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148199545","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}
引用次数: 0
Glomhopper-a subfamily of DUF3504-encoding CryptonA elements in Glomeromycota. glomhopper -一个duf3504亚家族,在肾小球菌科中编码隐体因子。
IF 4.2 2区 生物学
Mobile DNA Pub Date : 2026-06-06 DOI: 10.1186/s13100-026-00404-0
Marianna Krysińska, Drishtee Barua, Anna Muszewska
{"title":"Glomhopper-a subfamily of DUF3504-encoding CryptonA elements in Glomeromycota.","authors":"Marianna Krysińska, Drishtee Barua, Anna Muszewska","doi":"10.1186/s13100-026-00404-0","DOIUrl":"10.1186/s13100-026-00404-0","url":null,"abstract":"<p><strong>Background: </strong>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.</p><p><strong>Results: </strong>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.</p><p><strong>Conclusion: </strong>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.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13465315/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148194820","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}
引用次数: 0
Stones in genomic storms: transposable element-driven variation in Prunus fruit trees. 基因组风暴中的石头:李果树转座因子驱动的变异。
IF 4.2 2区 生物学
Mobile DNA Pub Date : 2026-05-12 DOI: 10.1186/s13100-026-00403-1
Attila Hegedűs, Beti Ivanovska, Júlia Halász
{"title":"Stones in genomic storms: transposable element-driven variation in Prunus fruit trees.","authors":"Attila Hegedűs, Beti Ivanovska, Júlia Halász","doi":"10.1186/s13100-026-00403-1","DOIUrl":"10.1186/s13100-026-00403-1","url":null,"abstract":"<p><p>Transposable elements (TEs) are major components of plant genomes and drivers of structural and functional diversification. In Prunus species, including peach, almond, apricot, cherry, and plum, TEs constitute more than half of the genome and shape evolutionary trajectories and phenotypic traits. This review synthesizes knowledge on TE composition, evolutionary dynamics and functional impacts in Prunus, highlighting advances enabled by long-read sequencing and structure-aware annotation pipelines. Both class I retrotransposons and class II DNA transposons contribute to genome expansion, gene duplication, regulatory innovation, and lineage-specific evolutionary shifts. TE insertions influence traits such as flowering time, fruit firmness, pigmentation, and the breakdown of self-incompatibility through mechanisms including promoter modulation, methylation changes, and exon disruption. We examine TE-derived small RNAs in epigenetic regulation and summarize evidence for recent TE bursts linked to hybridization, demographic bottlenecks, polyploidization, and local adaptation, collectively contributing to the diversification of Prunus genomes. Beyond their biological roles, TE insertion polymorphisms serve as powerful molecular markers for diversity assessment, phylogenetics, and breeding with both retrotransposon- and MITE-based systems showing high discriminatory power across Prunus germplasm. Integration of high-resolution TE mapping with functional genomics and epigenetic profiling promises deeper understanding of TE-mediated regulatory networks and their potential exploitation for crop improvement.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13359793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147931553","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}
引用次数: 0
Transposable elements in hematopoietic stem cells upon aging and myeloid malignancies. 衰老和髓系恶性肿瘤中造血干细胞的转座因子。
IF 4.2 2区 生物学
Mobile DNA Pub Date : 2026-05-05 DOI: 10.1186/s13100-026-00401-3
Emilie Elvira-Matelot, Françoise Porteu
{"title":"Transposable elements in hematopoietic stem cells upon aging and myeloid malignancies.","authors":"Emilie Elvira-Matelot, Françoise Porteu","doi":"10.1186/s13100-026-00401-3","DOIUrl":"10.1186/s13100-026-00401-3","url":null,"abstract":"<p><p>Transposable elements (TEs) constitute nearly half of the human genome and profoundly influence hematopoietic stem cell (HSC) biology. In this review, we synthesize current evidence demonstrating that TEs exert dual and context-dependent roles in HSCs during steady-state hematopoiesis, stress responses, aging, and leukemogenesis. Under basal conditions, tightly controlled TE activity can be beneficial for HSC biology, through the induction of intrinsic type I interferon signaling and a fine-tuned control of gene expression. However, dysregulated TE activation upon stresses and aging can undermine HSC self-renewal, impair genomic integrity, and drive age-associated hematopoietic decline. TEs also play a dual role in leukemogenesis. Derepression of transcription factor motifs within TEs can activate oncogenic programs, while TE-derived nucleic acids can simultaneously elicit antiviral and DNA damage responses that trigger anti-tumoral p53- or interferon-dependent growth arrest or apoptosis. The balance between these pro- and anti-tumoral effects remains an open question, likely shaped by cellular context, TE subtypes, and the magnitude of TE expression. Finally, we discuss the potential to therapeutically modulate TE activity. Understanding TE dynamics in HSCs offers new opportunities for mechanistic insight and clinical innovation in myeloid malignancies.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13312697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147840596","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}
引用次数: 0
Howler monkey Platy-1 and Alu SINEs: a resource for Alouatta genomics. 吼猴Platy-1和Alu sin: Alouatta基因组学资源。
IF 4.2 2区 生物学
Mobile DNA Pub Date : 2026-04-29 DOI: 10.1186/s13100-026-00402-2
Jerilyn A Walker, Jessica M Storer, Sarah O Massey, Thomas O Beckstrom, David A Ray, Mark A Batzer
{"title":"Howler monkey Platy-1 and Alu SINEs: a resource for Alouatta genomics.","authors":"Jerilyn A Walker, Jessica M Storer, Sarah O Massey, Thomas O Beckstrom, David A Ray, Mark A Batzer","doi":"10.1186/s13100-026-00402-2","DOIUrl":"10.1186/s13100-026-00402-2","url":null,"abstract":"<p><p>Recent discovery of two lineage-specific Platy-1 SINE (Short INterspersed Element) subfamilies, active within the genome of mantled howler monkey (Alouatta palliata) [AloPal_v1], prompted analyses by polymerase chain reaction (PCR) to evaluate their utility for population genetics. A polymorphism rate of 30% was detected by comparison to DNA from a cis-Andean species, A. sara. Concurrently, six new genome assemblies were released for Alouatta species from the cis-Andean clade for comparison. A. palliata also has a more robust amplification of young Alu SINEs, as compared to other Atelidae species, including a limited number of pre-AluTa15 derived insertions. While Alu mobile element insertions (MEIs), have been widely used to study primate phylogenetics, SINEs have not yet been utilized in the study of howler monkey (Alouatta) relationships. This study reports phylogenetically informative presence / absence data and candidate oligonucleotides for locus-specific PCR for 335 young Alu elements from A. palliata as well as over 600 Platy-1 MEIs representing A. palliata, A. caraya, A. belzebul, A. discolor, A. seniculus puruensis, A. s. juara and A. macconnelli. These datasets provide a valuable resource of 'identical by descent' MEIs for the study of howler monkey phylogenetics, population genetics and conservation strategies for application to wild populations.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13274081/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147776776","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}
引用次数: 0
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