The Human Silencing Hub (HUSH) complex is an epigenetic regulator that maintains transcriptional repression of transposable elements and other genomic loci though deposition of the repressive histone mark H3K9 trimethylation. Composed of core scaffold proteins TASOR, MPP8, and PPHLN1, and associated effectors including SETDB1, MORC2, and ZNF638, the HUSH complex enforces epigenetic silencing that limits expression of endogenous retroelements and suppresses innate immune activation. Disruption of this pathway induces viral mimicry though accumulation of double-stransded RNA (dsRNA), activating interferon signaling, enhancing antigen presentation, and promoting antitumor immunity. Consequently, pharmacologic inhibition of HUSH components represents a promising strategy to overcome tumor immune evasion and improve response to immunotherapy. This systematic review evaluates translational efforts targeting HUSH associated proteins, analyzing 26 original research studies identified though PRISMA-guided screening. These studies investigated 23 small molecules and 3 RNA-based therapeutics across 37 cancer types, with the majority targeting the catalytic methyltransferase SETDB1. Therapeutic strategies targeting HUSH-associated silencing include FDA-approved agents, repurposed targeted therapies, novel small-molecule inhibitors, and RNA-based modalities. These therapeutic strategies disrupt epigenetic repression though mechanisms such as transcriptional modulation, interference with chromatin-binding domains, and post-transcriptional regulation of HUSH components. Collectively, these findings identify emerging pharmacologic strategies for disrupting HUSH-associated silencing, although the available evidence remains predominantly preclinical and is heavily concentrated on SETDB1. Further development and validation of selective inhibitors, including evaluation in combination with immune checkpoint blockade and radiotherapy, will be necessary to determine the therapeutic potential and clinical feasibility of targeting HUSH-associated pathways.
P elements are a crucial component of DNA transposons, playing a vital role in shaping the evolution of eukaryotic genomes, yet their evolutionary profiles remain largely unknown. Here, we identified 1,801 P elements across 678 species, predominantly in Arthropods (578 species). Phylogenetic analysis revealed nine distinct families (Bus, Cab, Car, Gig, Taxi, Rook, Dive, Che, and Coach), each exhibiting distinct evolutionary trajectories. Despite considerable variation in transposon length, terminal inverted repeats, and flanking sequences, all families retain a highly conserved six-domain transposase architecture comprising the THAP DNA-binding domain (Thap), leucine zipper dimerization domain (LZDD), helix-turn-helix domain (HTH), RNase H-like catalytic domain (DDE), GTP-binding domain (GBD), and C-terminal domain (CTD), consistent with a “constrained core, variable periphery” evolutionary model. Kimura divergence analysis revealed contrasting evolutionary dynamics: the Bus, Coach, Car, and Dive families showed near-zero divergence peaks indicative of recent or ongoing transposition, whereas the Cab, Gig, and Taxi families represented remnants of ancient invasions, and the Che and Rook families exhibited multiple invasion waves. We further detected signatures of horizontal transfer in six families, including a striking cross-phylum transfer, indicating that horizontal transfer has repeatedly complemented vertical inheritance in the spread of P elements. Furthermore, we demonstrated that vertebrate Thap9 genes originated from a single domestication event of Che family transposases early in vertebrate evolution under strong purifying selection. Our findings establish a comprehensive classification framework for the P transposon superfamily, reveal family-specific evolutionary dynamics shaped by both vertical inheritance and horizontal transfer, and trace the origin of Thap9 domestication, providing new insights into the diversification, activity, and co-option of this major transposon lineage.
Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that became permanently integrated into host germline genomes. Although most ERV sequences accumulate mutations and lose coding potential over evolutionary time, some have been co-opted by the host for important physiological functions, particularly in placental development and antiviral defense. Despite the availability of high-quality genome assemblies, the genomes of elephants have not been systematically screened for conserved ERV envelope (env) genes. Here, we performed a comprehensive computational and evolutionary analysis to identify intact retroviral env open reading frames (ORFs) in elephant genomes and investigate their conservation across Afrotheria. A genome-wide screen of the African elephant (Loxodonta africana) and Asian elephant (Elephas maximus) identified 59 independently acquired intact retroviral env ORFs. Most represented recent lineage-specific integrations; however, one env gene, termed AFRenv, was conserved at the same orthologous genomic position across multiple Afrotherian orders, including Proboscidea, Sirenia, and Afrosoricida, indicating that the progenitor retrovirus became fixed in the common ancestor of extant Afrotherians at least 79 million years ago. AFRenv retains a full-length ORF in several Afrotherian lineages and preserves key structural features characteristic of gamma-type retroviral Env proteins, including a signal peptide, furin cleavage site, conserved cysteine motif, and transmembrane domain. Simulations of neutral sequence evolution demonstrated that long-term preservation of the AFRenv ORF is highly unlikely in the absence of selective pressure. Codon-based maximum likelihood analyses confirmed that AFRenv has evolved under purifying selection, with a substantial proportion of codons under negative selection and no evidence of diversifying selection. Transcriptomic analysis further revealed that AFRenv is transcriptionally active in elephants and exhibits placenta-enriched expression in the African elephant. Our findings identify AFRenv as one of the oldest intact retroviral env genes described in placental mammals. The remarkable preservation of its coding capacity, structural motifs in multiple lineages, and its placenta-enriched expression in the African elephant suggest that AFRenv has been maintained to fulfill a host physiological function in Afrotheria. These findings provide new insight into the long-term evolutionary impact of ancient retroviral integrations on mammalian genome evolution.
Abstract Plant genomes are filled with retrotransposons and their derivatives, constantly undergoing sequence diversification and structural rearrangement. Among them, short, non-autonomous retrotransposons lack full coding capacity and often form subfamilies. As a result, non-autonomous retrotransposons are incompletely identified in most to all genome assemblies. Here, we capitalize on our comprehensive understanding of the transposable element (TE) landscape in sugar beet ( Beta vulgaris ) to assess the extent of the blind spot for non-autonomous long terminal repeat (LTR) retrotransposons. This use case serves to answer if all of these sequences are derivatives of easier-to-identify full-length elements or if there is more variability that is currently overlooked. For this we applied a semi-automated structural discovery workflow followed by in-depth manual verification to characterize non-autonomous LTR retrotransposons in sugar beet. We retrieve more than 100 non-autonomous LTR retrotransposon families that lack complete autonomous coding capacity, including canonical terminal-repeat retrotransposons in miniature (TRIMs), elongated non-coding derivatives and families retaining fragmented coding remnants. The identified families span a broad range, including elements exceeding 15,000 bp in length and display evidence for reshuffling and modular evolution. Only a subset of families could be confidently linked to autonomous retrotransposons, showing sequence diversification within the non-autonomous LTR retrotransposon fraction beyond the autonomous genomic templates. We highlight that a large fraction of non-autonomous LTR retrotransposons is incompletely recovered with the current TE identification workflows, even if the output is well-curated and condensed into TE libraries and suggest procedures to remedy this gap. This study gives a genome-wide view into the non-autonomous LTR retrotransposon landscape of a single plant genome and highlights the importance of structure-based approaches for their identification and classification.
Abstract Background 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. Results 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. Conclusion 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.
