IF 3.1 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":"https://doi.org/10.1186/s13100-026-00401-3","url":null,"abstract":"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.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 3.1 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":"https://doi.org/10.1186/s13100-026-00402-2","url":null,"abstract":"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.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The extraordinary satellitome diversity of freshwater crayfish: a driver of genome evolution. 淡水小龙虾非凡的卫星组多样性：基因组进化的驱动力。

IF 3.1 2区生物学

Mobile DNA Pub Date : 2026-04-28 DOI: 10.1186/s13100-026-00399-8

Lena Bonassin, Ljudevit Luka Boštjančić, Christelle Rutz, Caterina Francesconi, Leonie Schardt, Damian Baranski, Carola Greve, Lucian Pârvulescu, Višnja Besendorfer, Jelena Mlinarec, Ivana Maguire, Kathrin Theissinger, Odile Lecompte

引用次数: 0

HERV-K HML-2 transcriptional profiling and splicing pattern unveiled by direct single-molecule long-read RNA sequencing. 直接单分子长读RNA测序揭示HERV-K HML-2转录谱和剪接模式。

IF 3.1 2区生物学

Mobile DNA Pub Date : 2026-04-23 DOI: 10.1186/s13100-026-00400-4

Mariana Polychronopoulou, Eleni Kyriakou, Filiana Sotiriadou, Magda Bletsa, Gkikas Magiorkinis

引用次数: 0

Centromeric retrotransposons shape chromosomal evolution beyond pericentromeric regions. 着丝粒反转录转座子影响着染色体的进化。

IF 3.1 2区生物学

Mobile DNA Pub Date : 2026-04-01 DOI: 10.1186/s13100-026-00398-9

Manuel Poretti, Terezie Mandáková, Rimjhim R Choudhury, Leo Wuetschert, Martin A Lysak, Christian Parisod

引用次数: 0

A phylogenetic estimate of canine retrotransposition rates based on genome assembly comparisons. 基于基因组组装比较的犬逆转录率的系统发育估计。

IF 3.1 2区生物学

Mobile DNA Pub Date : 2026-03-20 DOI: 10.1186/s13100-026-00397-w

Matthew S Blacksmith, Anthony K Nguyen, John V Moran, Jeffrey M Kidd

引用次数: 0

Massive proliferation of retrotransposons contributes to genome size expansion in species of the Pseudocercospora genus. 反转录转座子的大量增殖有助于伪尾孢属物种基因组大小的扩大。

IF 3.1 2区生物学

Mobile DNA Pub Date : 2026-02-26 DOI: 10.1186/s13100-026-00396-x

Sandra-Milena González Sáyer, Ibonne A Garcia, Cristian A Traslaviña, Alex Z Zaccaron, Ioannis Stergiopoulos, Fabio A Aristizabal, Ursula Oggenfuss, Daniel Croll

{"title":"Massive proliferation of retrotransposons contributes to genome size expansion in species of the Pseudocercospora genus.","authors":"Sandra-Milena González Sáyer, Ibonne A Garcia, Cristian A Traslaviña, Alex Z Zaccaron, Ioannis Stergiopoulos, Fabio A Aristizabal, Ursula Oggenfuss, Daniel Croll","doi":"10.1186/s13100-026-00396-x","DOIUrl":"10.1186/s13100-026-00396-x","url":null,"abstract":"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.","PeriodicalId":18854,"journal":{"name":"Mobile DNA","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2026-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13041039/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147307868","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

scTELL: a single-cell ATAC-seq tool for locus-specific transposable element identification in chromatin accessibility. scTELL：一种单细胞ATAC-seq工具，用于染色质可及性中位点特异性转座元件的鉴定。

IF 3.1 2区生物学

Mobile DNA Pub Date : 2026-02-24 DOI: 10.1186/s13100-026-00395-y

Kyeonghun Jeong, Hongseok Ha, Jinchuan Xing, Jinwook Choi, Kwangsoo Kim

引用次数: 0

Boundary-associated propagation of a processed pseudogene dissects pre-existing limitations of genome annotation in the T2T era. 处理过的假基因的边界相关繁殖剖析了T2T时代基因组注释的预先存在的局限性。

IF 3.1 2区生物学

Mobile DNA Pub Date : 2026-02-17 DOI: 10.1186/s13100-026-00394-z

Min-Gyu Lee

引用次数: 0

Tracing ancient viral footprints: a comprehensive study of endogenous viral elements in Bombus species. 追踪古代病毒足迹：Bombus种内源性病毒元素的综合研究。

IF 3.1 2区生物学

Mobile DNA Pub Date : 2026-02-05 DOI: 10.1186/s13100-026-00393-0

Lucas Barbosa de Amorim Conceição, João Pedro Nunes Santos, Lucas Yago Melo Ferreira, Gabriel Victor Pina Rodrigues, Marco Antônio Costa, Eric Roberto Guimarães Rocha Aguiar

引用次数: 0

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