Mobile DNAPub Date : 2025-07-16DOI: 10.1186/s13100-025-00365-w
Daniel A Murimi-Worstell, Irene B Murimi-Worstell, Farrah M Roy, Aidan Burn, Michael Freeman, Ralph B Puchalski, John M Coffin
{"title":"In-depth analysis of endogenous retrovirus expression in glioblastoma.","authors":"Daniel A Murimi-Worstell, Irene B Murimi-Worstell, Farrah M Roy, Aidan Burn, Michael Freeman, Ralph B Puchalski, John M Coffin","doi":"10.1186/s13100-025-00365-w","DOIUrl":"10.1186/s13100-025-00365-w","url":null,"abstract":"<p><strong>Background: </strong>Human endogenous retroviruses (HERVs) are remnants of ancient viral infections and comprise 6-8% of the human genome. Their biological functions in cancer remain poorly understood, especially in glioblastoma, the most common and deadly primary brain cancer in adults. Prior studies on HERV expression in glioblastoma have yielded conflicting results. Here, we employed orthogonal computational pipelines to address these limitations.</p><p><strong>Results: </strong>Locus-specific analysis revealed marked heterogeneity of transcription among HERVs within the same clade. We found that individual HERV proviruses are more than twice as likely to be underexpressed in glioblastoma than overexpressed and that most differentially expressed HERVs are exonized within transcripts. These HERVs are enriched in the 3'-terminal exons of transcripts, associated with alternative polyadenylation and contribute conserved polyadenylation signals. We identified HERV expression patterns associated with glioblastoma subtypes and anatomic features. We also identified three proviruses or proviral fragments of particular interest including one associated with survival and one exonized within a currently unannotated cancer-specific transcript. Among the most recently integrated clade of HERVs, excluding solo-LTRs, only the HML-2 provirus at 1q22 is overexpressed in glioblastoma. We report previously undescribed transcripts incorporating this provirus that may encode several proteins.</p><p><strong>Conclusions: </strong>This study represents the first systematic exploration of the heterogeneity of HERV expression between anatomic features of any cancer. It shows that exaptation of HERV polyadenylation signals and HERV-associated APA are widespread in the human transcriptome and identifies critical structural information regarding the HML-2 1q22 provirus transcript, which has been the focus of several recent analyses. Our findings underscore the importance of locus-specific and anatomic feature-specific HERV analysis and suggest structural and functional roles for HERVs in glioblastoma-associated transcripts.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"29"},"PeriodicalIF":4.7,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649847","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}
Mobile DNAPub Date : 2025-07-16DOI: 10.1186/s13100-025-00367-8
Hui Wen, Marcos Pérez-Losada, Lopa Mishra, Keith A Crandall
{"title":"Locus-specific HERV expression associated with hepatocellular carcinoma.","authors":"Hui Wen, Marcos Pérez-Losada, Lopa Mishra, Keith A Crandall","doi":"10.1186/s13100-025-00367-8","DOIUrl":"10.1186/s13100-025-00367-8","url":null,"abstract":"<p><strong>Background: </strong>Human endogenous retroviruses (HERVs) harbor accessory proteins that influence cellular processes and have been linked to a wide variety of diseases, including cancer. This study investigates locus-specific HERV expression and its association with gene dysregulation in hepatocellular carcinoma (HCC), a highly prevalent and deadly form of liver cancer worldwide.</p><p><strong>Methods: </strong>We analyzed RNASeq data from 424 HCC samples from The Cancer Genome Atlas (TCGA), which comprised 371 tumor and 50 matched normal tissues from a total of 371 hepatocellular carcinoma participants. We employed Telescope to identify and quantify HERV expression across the total RNA sequencing data.</p><p><strong>Results: </strong>The majority of differentially expressed HERVs exhibited reduced expression in tumor tissue (166 downregulated vs. 50 upregulated), suggesting a potential functional role of HERV expression patterns in shaping the pathophysiological landscape of HCC. Specifically, the suppression of HERV-H family members, which are known to regulate cellular differentiation, may contribute to tumor dedifferentiation, increased plasticity, and enhanced metastatic potential. This loss of differentiation control and increased adaptability may play a critical role in driving the progression of liver cancer.</p><p><strong>Discussion: </strong>Our study highlights a significant association of HERV expression with HCC, highlighting the differential regulation of specific HERV families in tumor tissue. For example, HERVH and ERVLE families showed consistent downregulation in tumor samples, while HERVE and HERV9 were more commonly upregulated. These shifts may reflect underlying changes in transcriptional regulation or chromatin structure between normal and malignant tissues. Rather than indicating a singular functional role, the observed expression patterns likely reflect a multifaceted relationship between HERVs and tumor biology. Further studies will be needed to determine whether these expression differences contribute to, or result from, tumor progression and to explore their potential as biomarkers or therapeutic targets.</p><p><strong>Clinical trial number: </strong>Not applicable.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"30"},"PeriodicalIF":4.7,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12265279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649848","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}
Mobile DNAPub Date : 2025-07-12DOI: 10.1186/s13100-025-00366-9
Ahlam Chaaban, Reem Sleem, Jana Santina, Mohamad Rima, José-Noel Ibrahim
{"title":"Exploring transposable elements: new horizons in cancer diagnostics and therapeutics.","authors":"Ahlam Chaaban, Reem Sleem, Jana Santina, Mohamad Rima, José-Noel Ibrahim","doi":"10.1186/s13100-025-00366-9","DOIUrl":"10.1186/s13100-025-00366-9","url":null,"abstract":"<p><p>Transposable elements (TE), also called transposons, are repetitive DNA sequences making up half of the human genome. Initially, TEs were described as \"junk DNA\" because they lack specific function. However, they have been recognized for their ability to replicate and integrate into different genomic locations; this \"jumping gene\" activity results in genomic instability, variation of the chromosomal architecture, and transcriptional dysregulation, all of which represent major hallmarks of cancer. In this respect, the involvement of TE in tumorigenesis was extensively studied and their role as diagnostic and therapeutic tools in cancer is now well-established. Transposons' products, including TE-derived cancer antigens, transcripts, and associated epigenetic modifications, mainly hypomethylation, were found to be promising biomarkers in several types of cancer ensuring early disease detection and prognosis. In addition, TE are currently used to design innovative approaches, with transposon-based systems, namely, Sleeping Beauty and PiggyBac, enabling precise genomic modifications and novel strategies for cancer therapy. Therefore, the aim of this review is to provide an overview on the dual application of TE as diagnostic and therapeutic tools in cancer, paving the way to improved clinical outcomes. CLINICAL TRIAL NUMBER: Not applicable.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"28"},"PeriodicalIF":4.7,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12255080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144619049","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}
Mobile DNAPub Date : 2025-07-05DOI: 10.1186/s13100-025-00361-0
Zsuzsanna Izsvák, Jin Ma, Manvendra Singh, Laurence D Hurst
{"title":"Co-option of an endogenous retrovirus (LTR7-HERVH) in early human embryogenesis: becoming useful and going unnoticed.","authors":"Zsuzsanna Izsvák, Jin Ma, Manvendra Singh, Laurence D Hurst","doi":"10.1186/s13100-025-00361-0","DOIUrl":"10.1186/s13100-025-00361-0","url":null,"abstract":"<p><p>While it is straightforward to understand why most mutations affecting functional sequence are harmful, how genomic changes result in new beneficial traits is harder to understand. Domestication of transposable elements (TEs) is an important source of both new genes and new regulatory systems as, for their own propagation, TEs need to have transcription factor binding sites and functional products that predispose to their recruitment. But are such predispositions to gain-of-function sufficient? Here we consider the case of the endogenous retrovirus, HERVH. Knockdown data supports HERVH having roles in pluripotency, self-renewal and defence against transpositionally-active retroelements in the early human embryo. We clarify the pluripotent cell types associated with HERVH expression and, in the process, note a key unresolved issue, framed by the unwanted transcript hypothesis: how can some cell types have 2% of their transcripts being HERVH-derived but survive the multiplicity of cellular devices that suppress foreign transcripts, be this by transcriptional repression or post-transcriptional filtering? We note a common coupling between novelty generation and suppression evasion. For example, pluripotency-associated KLF4 binding is thought to compete with transcriptional suppressor binding. Similarly, HERVH has a strong splice site enabling efficient novel chimeric transcript formation, the resulting exon-intron junctions enabling evasion of the unwanted transcript filters that recognize low or absent intron presence. We conclude that to better understand domestication, a focus on predispositions to avoidance of unwanted transcripts filters, as well as predispositions to gain of functions, is necessary. The same insights will be valuable for transgene design (eg for gene therapy) and instructive of gain-of-function in tumours, as HERVH is known to be involved in onco-exaptation events.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"27"},"PeriodicalIF":4.7,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12228294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144567578","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}
Mobile DNAPub Date : 2025-07-04DOI: 10.1186/s13100-025-00364-x
Bachir Boureima Abdou, Alicia Silvant, Chloé Le Roy, Jennifer Guiraud, Léa Bientz, Laure Béven, Véronique Dubois, Eric Baranowski, Cécile Bébéar, Sabine Pereyre
{"title":"Interaction with eukaryotic cells enhances the circularization and transcription of integrative and conjugative elements in Mycoplasma hominis.","authors":"Bachir Boureima Abdou, Alicia Silvant, Chloé Le Roy, Jennifer Guiraud, Léa Bientz, Laure Béven, Véronique Dubois, Eric Baranowski, Cécile Bébéar, Sabine Pereyre","doi":"10.1186/s13100-025-00364-x","DOIUrl":"10.1186/s13100-025-00364-x","url":null,"abstract":"<p><p>Mobile genetic elements drive bacterial evolution by promoting genetic plasticity and adaptation; among them, mycoplasma Integrative and Conjugative Elements (ICEs) challenge the notion that mycoplasmas evolved solely through genome reduction. However, they remain poorly characterized, particularly in Mycoplasma hominis, which is a human genital pathogen. In this study, we investigated the circularization, transcription, and protein expression of M. hominis 4788 ICE (ICEHo4788) under the following four environmental conditions: axenic growth, coculture with HeLa cells, mitomycin C exposure, and thermal stress. During axenic growth, ICEHo4788 circularization peaked at 12 h with a 9.4-fold increase in the number of circular forms. Mitomycin C and cold shock induced only a moderate increase in circularization (approximately 3-fold), whereas heat shock significantly reduced the number of circular forms. In coculture with HeLa cells, a strong increase in the number of circular forms was observed at 72 h and 7 days postinfection with 10- and 23-fold increases, respectively. Coculture also led to a 5- to 23-fold increase in transcription at 7 days, whereas axenic growth, mitomycin C exposure, and thermal stress did not differ. Proteomic analysis revealed that MhoH(a), CDS18, CDS17, and CDS11 were significantly overexpressed at 12 h. Neither mitomycin C nor cold shock induced changes in ICE-related proteins, but heat shock upregulated two M. hominis molecular chaperones and ICEHo4788 MhoH(a). In conclusion, environmental conditions modulate M. hominis ICE activity with strong stimulation in the presence of eukaryotic cells. These findings offer new insights into the regulation and environmental responses of M. hominis ICEs.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"26"},"PeriodicalIF":4.7,"publicationDate":"2025-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12228374/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564968","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}
Mobile DNAPub Date : 2025-06-14DOI: 10.1186/s13100-025-00360-1
Rachel N Behm, Barbara J Sharanowski
{"title":"The highly diverse repertoire of transposable elements within the genomes of parasitic wasps (Hymenoptera: Braconidae).","authors":"Rachel N Behm, Barbara J Sharanowski","doi":"10.1186/s13100-025-00360-1","DOIUrl":"10.1186/s13100-025-00360-1","url":null,"abstract":"<p><p>Transposable elements (TEs) are known to be major components of eukaryotic genomes and impact genome evolution and architecture, including in the speciose lineage of Insecta. Although new and increased efforts have allowed for more insect genomes to become available, our understanding of insect TE diversity across various lineages is poor. This lack of knowledge is especially true in the hyper-diverse Hymenoptera (including bees, ants, wasps, and sawflies) which includes some of the most beneficial insects, such as pollinators and parasitoid (parasitic) wasps. Here, we present the order-level TE composition and analyze its phylogenetic signal across the Braconidae (Hymenoptera), a very diverse lineage of parasitic wasps. Further we investigate the effect of TEs on genome size and note a positive relationship that has some distinct lineage specific differences. Despite phylogenetically conserved genome sizes within Braconidae, we found that TE abundance and diversity was not phylogenetically conserved and was highly variable across taxa, more so than what has been reported for other insect lineages. This represents the first comparative genomic analysis of TEs in a lineage of parasitic wasps and increases our understanding of the diversity of TE composition across related taxa.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"24"},"PeriodicalIF":4.7,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166591/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144294130","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}
Mobile DNAPub Date : 2025-06-14DOI: 10.1186/s13100-025-00363-y
Landen Gozashti, Russell Corbett-Detig
{"title":"Double-stranded DNA viruses may serve as vectors for horizontal transfer of intron-generating transposons.","authors":"Landen Gozashti, Russell Corbett-Detig","doi":"10.1186/s13100-025-00363-y","DOIUrl":"10.1186/s13100-025-00363-y","url":null,"abstract":"<p><p>Specialized transposable elements capable of generating introns, termed introners, are one of the major drivers of intron gain in eukaryotes. Horizontal transfer of transposable elements (HTT) is thought to play an important role in shaping introner distributions. Viruses could function as vehicles of introner HTT since they often integrate into host genomes and have been implicated in widespread HTT in eukaryotes. We annotated integrated viral elements in diverse dinoflagellate genomes with active introners and queried viral elements for introner sequences. We find that 25% of viral elements contain introners. The vast majority of viral elements represent maverick-polinton-like double-stranded DNA (dsDNA) viruses in the family eupolintoviridae as well as giant dsDNA viruses. By querying a previously annotated set of eupolintoviral proviruses, we show that introners populate full-length elements with machinery required for transposition as well as viral infection. Introners in the vast majority of viral elements are younger than or similar in age to others in their host genome, suggesting that most viral elements acquired introners after integration. However, a subset of viral elements shows the opposite pattern wherein viral introners are significantly older than other introners, possibly consistent with virus-to-host horizontal transfer. Together, our results suggest that dsDNA viruses may serve as vectors for HTT of introners between individuals and species, resulting in the introduction of intron-generating transposons to new lineages.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"25"},"PeriodicalIF":4.7,"publicationDate":"2025-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12166617/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144294129","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}
Mobile DNAPub Date : 2025-05-31DOI: 10.1186/s13100-025-00362-z
José Cerca, Patricia Jaramillo Díaz, Clément Goubert, Heidi Yang, Vanessa C Bieker, Mario Fernández-Mazuecos, Pablo Vargas, Rowan Schley, Siyu Li, Juan Ernesto Guevara-Andino, Bent Petersen, Gitte Petersen, Neelima R Sinha, Lene R Nielsen, James H Leebens-Mack, Gonzalo Rivas-Torres, Loren H Rieseberg, Michael D Martin
{"title":"No evidence of transposable element bursts in the Galápagos Scalesia adaptive radiation despite hybridization, diversification and ecological niche shifts.","authors":"José Cerca, Patricia Jaramillo Díaz, Clément Goubert, Heidi Yang, Vanessa C Bieker, Mario Fernández-Mazuecos, Pablo Vargas, Rowan Schley, Siyu Li, Juan Ernesto Guevara-Andino, Bent Petersen, Gitte Petersen, Neelima R Sinha, Lene R Nielsen, James H Leebens-Mack, Gonzalo Rivas-Torres, Loren H Rieseberg, Michael D Martin","doi":"10.1186/s13100-025-00362-z","DOIUrl":"10.1186/s13100-025-00362-z","url":null,"abstract":"<p><p>Transposable elements (TEs) have been hypothesized to play a pivotal role in driving diversification by facilitating the emergence of novel phenotypes and the accumulation of divergence between species. Hybridization and adaptation to novel niches have been proposed to destabilize mechanisms constraining TE proliferation, potentially inducing a 'TE burst' that promotes TE accumulation on the genome. The rapid speciation and ecological diversification characteristic of adaptive radiations offer a unique opportunity to examine the link between TE accumulation and speciation, diversification, hybridization and adaptation. Here, focusing on all 15 species of the genus Scalesia (Asteraceae), a radiation endemic to the Galápagos Islands, we test whether diversification, hybridization, or shifts in ecological niche are associated with changes in TE accumulation in genomes. Our analyses reveal little to no variation in TE accumulation among Scalesia species nor its hybrid populations. Shifts in ecological niches, linked to climatic variation, did not result in discernible changes in TE accumulation, a surprising finding given the anticipated selective pressure imposed by aridity, a factor often linked to genome size reduction. We found no distinct patterns in the temporal accumulation of TEs, and no effects at the class or superfamily level. Our findings suggest that while TEs may play a key role in evolution at the locus level, their macroevolutionary association with diversification or speciation appears weak. Rather than actively driving evolutionary diversification, TEs may simply be'along for the ride.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"23"},"PeriodicalIF":4.7,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12125827/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144192029","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}
Mobile DNAPub Date : 2025-05-09DOI: 10.1186/s13100-025-00358-9
Mirko Ronzio, Andrea Bernardini, Alberto Gallo, Roberto Mantovani, Diletta Dolfini
{"title":"Binding of NF-Y to transposable elements in mouse and human cells.","authors":"Mirko Ronzio, Andrea Bernardini, Alberto Gallo, Roberto Mantovani, Diletta Dolfini","doi":"10.1186/s13100-025-00358-9","DOIUrl":"https://doi.org/10.1186/s13100-025-00358-9","url":null,"abstract":"<p><strong>Background: </strong>Transposable Elements (TEs) represent a sizeable amount of mammalian genomes, providing regulatory sequences involved in shaping gene expression patterns. NF-Y is a Transcription factor -TF- trimer that binds to the CCAAT box, belonging to a selected group implicated in determining initiation of coding and noncoding RNAs.</p><p><strong>Results: </strong>We focus on NF-Y TE locations in 8 human and 8 mouse cells. Binding is exclusive for retroviral LTR12, MLT1 and MER in human and RLTR10 and IAPLTR in mouse cells. Cobinding and analysis of the DNA matrices signal enrichment of distinct TFs neighboring CCAAT in the three TE classes: MAFK/F/G in LTR12 and USF1/2 in MLT1 with precise alignment of sites, PKNOX1, MEIS2, PBX2/3 TALE TFs in MER57. The presence of \"epigenetic\" marks in human cells indicate prevalent co-association with open chromatin in MER, closed in LTR12 and mixed in MLT1. Based on chromatin features, these locations are mostly marked as enhancers, as confirmed by analysis of loci predicted to generate eRNAs.</p><p><strong>Conclusions: </strong>These results are discussed in the context of functional data, suggesting a complex -positive and potentially-negative role of NF-Y on distinct classes of repetitive sequences.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"22"},"PeriodicalIF":4.7,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12065363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144019778","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}
Mobile DNAPub Date : 2025-05-07DOI: 10.1186/s13100-025-00359-8
Eleni Kyriakou, Gkikas Magiorkinis
{"title":"Compilation of all known HERV-K HML-2 proviral integrations.","authors":"Eleni Kyriakou, Gkikas Magiorkinis","doi":"10.1186/s13100-025-00359-8","DOIUrl":"https://doi.org/10.1186/s13100-025-00359-8","url":null,"abstract":"<p><p>Human endogenous retroviruses (HERVs) occupy 8% of the human genome. Although most HERV integrations are severely degenerated by mutations, the most recently integrated proviruses, such as members of the HERV-K HML-2 subfamily, partially retain regulatory and protein-coding capacity. The precise number of HML-2 proviral copies in the modern human population is constantly changing in literature, as new integrations are being uncovered. The first comprehensive list of HML-2 proviral loci was compiled in 2011, including a total of 91 proviruses. Since then, multiple articles published additions and modifications to that list, mainly in the form of new polymorphic proviral sites, updated chromosomal band characterizations or the correspondence of coordinates in the new version of the published human reference genome. In the present study, we systematically searched the literature for lists of HML-2 proviruses and their coordinates and cross-examined every proviral locus information, also against the human genome. We gathered all available data about all HML-2 proviral integrations identified to date and updated, corrected and refined the coordinates in both human genome assemblies currently used in research, to incorporate the whole provirus in each case. Thereby we present an exhaustive (to date) catalogue of all known HML-2 proviruses and their respective coordinates, as a powerful tool for studies aiming to decipher HERV role in health and disease, especially for high-throughput data analyses, which could lead to the discovery of links between specific HERV integrations and biological mechanisms or medical disorders.</p>","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":"16 1","pages":"21"},"PeriodicalIF":4.7,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12057132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144018359","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}