Epigenetic Genome Defense Against Transposable Elements: Conserved Logic and Lineage-Specific Mechanisms

Transposable elements are controlled by layered genome-defense systems that limit their transcription, replication, mobilization, and insertional damage while permitting regulated activation and occasional co-option. Across eukaryotes, recurrent strategies include chromatin compaction, repressive histone modifications, DNA methylation where present, small-RNA-guided recognition, RNA surveillance, and developmental genome remodeling. However, these strategies do not arise from a single universal pathway: their molecular components, targeting rules, genomic contexts, and reversibility have been lost, replaced, or independently elaborated across lineages. Important questions remain concerning which mechanisms are ancestrally conserved, which reflect convergent evolution, and how genome-defense pathways influence development, immunity, genome architecture, and evolutionary innovation [Ste22b, Kab21, Sch19e]. This Research Topic aims to advance a comparative and mechanistic understanding of these processes across diverse eukaryotic systems.This Research Topic aims to investigate how plants, animals, fungi, and unicellular eukaryotes recognize and control transposable elements, and how comparative analysis can clarify the evolution of epigenetic regulation. It will consider how repeat recognition is translated into chromatin-mediated repression, RNA-based surveillance, sequence change, DNA elimination, immune activation, or functional co-option. Contributions may test hypotheses concerning the conservation, divergence, replacement, loss, or independent emergence of genome-defense mechanisms. Single-organism or single-pathway studies are welcome when they clearly address broader questions of mechanism, evolutionary function, biological consequence, or comparative significance.To gather further insights across eukaryotic genome-defense systems and their evolutionary diversification, we welcome articles addressing, but not limited to, the following themes:- Conserved and divergent silencing layers, including H3K9 and H3K27 methylation, DNA methylation, HP1 and functional analogues, chromatin remodelers, histone variants, and sequence-specific or sequence-agnostic targeting.- Small-RNA-guided genome defense, including animal piRNA pathways, plant Pol IV/Pol V-dependent RdDM, fungal quelling and MSUD, ciliate scan-RNA pathways, and related RNA-silencing systems.- Genetic–epigenetic interfaces, including repeat-induced point mutation, methylation-induced premeiotic silencing, meiotic surveillance, transposon excision, programmed DNA elimination, and reversible or heritable genome remodeling.- TE regulation during development, reproduction, meiosis, embryogenesis, imprinting, tissue differentiation, stress responses, cellular senescence, aging, and transgenerational inheritance.- TE-derived nucleic acids and host immunity, including RIG-I, MDA5, cGAS–STING, viral mimicry, autoimmune or age-associated inflammation, and mechanistically distinct plant and fungal defense systems.- TE co-option, chromatin architecture, and genome evolution, including regulatory elements, 3D genome organization, plant NLR regulation, transposase capture, RAG-related innovation, CENP-B-related proteins, syncytins, PiggyMac, and Tpb2.- Methods and resources for TE epigenomics, including multi-mapping read assignment, pangenomes, graph genomes, long-read sequencing, native DNA-methylation detection, single-cell profiling, allele-specific analysis, TE annotation, and computational benchmarking.- Comparative and evolutionary synthesis of TE-silencing components, pathway loss or replacement, subfunctionalization, convergent targeting logic, homology, and carefully bounded comparisons with prokaryotic genome-defense systems.- Functional interpretation of TE expression, particularly studies that resolve underlying epigenetic or genome-defense mechanisms, establish biological consequences, or test evolutionary co-option.Appendix: We welcome Original Research, Review, Mini Review, Perspective, Brief Research Report, Methods, Hypothesis and Theory, and Systematic Review articles, subject to the article types available in the selected specialty section. Relevant specialty sections may include Chromatin Epigenomics, Epigenetics and Metabolism, Epigenomic Tools, and Plant Epigenetics, with article-type availability determined at section level. Editorials are normally commissioned from the Research Topic editors rather than submitted as standard contributions. Topic editors: Mande Xue, Ling Wang, Nicolas Descostes Source: https://www.frontiersin.org/research-topics/86147/epigenetic-genome-defense-against-transposable-elements-conserved-logic-and-lineage-specific-mechanisms