Identification and Characterization of LINE and SINE Retrotransposons in the African Hedgehog (Atelerix albiventris, Erinaceidae) and Their Association with 3D Genome Organization and Gene Expression

Genes, Год журнала: 2025, Номер 16(4), С. 397 - 397

Опубликована: Март 29, 2025

Background: The African hedgehog (Atelerix albiventris) exhibits specialized skin differentiation leading to spine formation, yet its regulatory mechanisms remain unclear. Transposable elements (TEs), particularly LINEs (long interspersed nuclear elements) and SINEs (short elements), are known influence genome organization gene regulation. Objectives: Given the high proportion of in genome, this study aims characterize distribution, evolutionary dynamics, potential roles SINEs, focusing on their associations with chromatin architecture, DNA methylation, expression. Methods: We analyzed LINE SINE distribution using HiFi sequencing classified TE families through phylogenetic reconstruction. Hi-C data were used explore interactions while whole-genome 5mCpG methylation was inferred from PacBio reads muscle tissue a deep-learning-based approach. RNA-seq tissues assess expression genes linked development. Results: form distinct genomic blocks GC-rich highly methylated regions, whereas enriched AT-rich, hypomethylated regions. associated differently A/B compartments, euchromatin heterochromatin. Methylation analysis suggests that younger TEs tend have higher levels, indicates some differentially expressed may be involved epidermal skeletal Conclusions: This provides genome-wide perspective patterns, A. albiventris. While not establishing direct causal link, findings suggest development, offering basis for future functional studies.

Язык: Английский

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Insertion of short L1 sequences generates inter-strain histone acetylation differences in the mouse

Mobile DNA, Год журнала: 2024, Номер 15(1)

Опубликована: Май 10, 2024

Abstract Background Gene expression divergence between populations and individuals can emerge from genetic variations within the genes and/or in cis regulatory elements. Since epigenetic modifications regulate gene expression, it is conceivable that elements also be a source of divergence. Results In this study, we compared histone acetylation (namely, H3K9ac) profiles two mouse strains different subspecies origin, C57BL/6 J (B6) MSM/Ms (MSM), as well their F1 hybrids. This identified 319 regions strain-specific acetylation, about half which were observed alleles While allele-specific presence interferon factor 3 (IRF3) binding sequence was associated with revealed B6-specific insertions short 3′ fragment LINE-1 (L1) retrotransposon occur or proximal to MSM-specific acetylated regions. Furthermore, even hyperacetylated domains, flanking non-polymorphic L1 fragments hypoacetylated, suggesting general activity induce hypoacetylation. Indeed, confirmed region by three Krüppel-associated box domain-containing zinc finger proteins (KZFPs), interact deacetylases. These results suggest insertion would excluded gene- acetylation-rich natural selection. Finally, mRNA-seq analysis for hybrids carried out, disclosed link promoter/enhancer expression. Conclusions study number changes have changed levels during evolution subspecies, part changes. Insertions very decrease level neighboring thereby been counter-selected gene-rich regions, may explain long-standing mystery discrete genomic distribution LINEs SINEs.

Язык: Английский

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YY1 is a transcriptional activator of mouse LINE-1 Tf subfamily

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Янв. 4, 2024

Long interspersed element type 1 (LINE-1, L1) is an active autonomous transposable (TE) in the human genome. The first step of L1 replication transcription, which controlled by internal RNA polymerase II promoter 5' untranslated region (UTR) a full-length L1. It has been shown that transcription factor YY1 binds to conserved sequence motif at end 5'UTR and dictates where initiates but not level transcription. Putative YY1-binding motifs have predicted 5'UTRs two distinct mouse subfamilies, Tf Gf. Using site-directed mutagenesis, vitro binding, gene knockdown assays, we experimentally tested role Our results indicate Tf, Gf subfamily, harbors functional sites its monomers. In contrast L1, functions as transcriptional activator for subfamily. Furthermore, are solely responsible synergistic interaction between monomers, consistent with model wherein distant monomers act enhancers abundance elements also raise important implications regulation genomic level.

Язык: Английский

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Retrotransposon SINEs in Age-Related Diseases: Mechanisms and Therapeutic Implications

Ageing Research Reviews, Год журнала: 2024, Номер 101, С. 102539 - 102539

Опубликована: Окт. 11, 2024

Язык: Английский

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