Human Endogenous Retrovirus-K (HML-2)-Related Genetic Variation: Human Genome Diversity and Disease

Genes, Год журнала: 2023, Номер 14(12), С. 2150 - 2150

Опубликована: Ноя. 28, 2023

Human endogenous retroviruses (HERVs) comprise a significant portion of the human genome, making up roughly 8%, notable comparison to 2–3% represented by coding sequences. Numerous studies have underscored critical role and importance HERVs, highlighting their diverse extensive influence on evolution genome establishing complex correlation with various diseases. Among HERV-K (HML-2) subfamily has recently attracted attention, integrating into after divergence between humans chimpanzees. Its insertion in received considerable attention due its structural functional characteristics time insertion. Originating from ancient exogenous retroviruses, these elements succeeded infecting germ cells, enabling vertical transmission existing as proviruses within genome. Remarkably, sequences retained capacity form complete viral sequences, exhibiting activity transcription translation. The is subject active debate about potential positive or negative effects pathologies. This review summarizes variation, regulation, diseases arising (HML-2).

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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CRISPR deletion of a SINE-VNTR-Alu (SVA_67) retrotransposon demonstrates its ability to differentially modulate gene expression at the MAPT locus

Frontiers in Neurology, Год журнала: 2023, Номер 14

Опубликована: Сен. 29, 2023

SINE-VNTR-Alu (SVA) retrotransposons are hominid-specific elements which have been shown to play important roles in processes such as chromatin structure remodelling and regulation of gene expression demonstrating that these repetitive exert regulatory functions. We previously the presence or absence a specific SVA element, termed SVA_67, was associated with differential several genes at MAPT locus, locus Parkinson's Disease (PD) frontotemporal dementia. However, we were not able demonstrate causation directed by due lack functional validation.We performed CRISPR delete SVA_67 HEK293 cell line. Quantification target using qPCR assess effects on response deletion SVA_67. Differences between edit control lines analysed two-tailed t-test minimum 95% confidence interval determine statistical significance.In this study, provide data highlighting SVA-specific effect expression. hemizygous endogenous edited neurodegenerative diseases including KANSL1, LRRC37A.This is consistent our previous bioinformatic work analysis transcriptomic from Progression Markers Initiative (PPMI) cohort. As SVAs influences expression, insertion polymorphisms contribute interpersonal differences patterns, results highlight potential contribution complex potentially many genetic components, PD.

Язык: Английский

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Dynamic Evolution of Repetitive Elements and Chromatin States in Apis mellifera Subspecies

Genes, Год журнала: 2024, Номер 15(1), С. 89 - 89

Опубликована: Янв. 11, 2024

In this study, we elucidate the contribution of repetitive DNA sequences to establishment social structures in honeybees (Apis mellifera). Despite recent advancements understanding molecular mechanisms underlying formation honeybee castes, primarily associated with Notch signaling, comprehensive identification specific genomic cis-regulatory remains elusive. Our objective is characterize landscape within genomes two subspecies, namely A. m. mellifera and ligustica. An observed burst repeats highlights a notable distinction between subspecies. After that, transitioned identifying differentially expressed elements that may function as elements. Nevertheless, expression these showed minimal disparity transcriptome during caste differentiation, pivotal process eusocial organization. this, chromatin segmentation, facilitated by ATAC-seq, ChIP-seq, RNA-seq data, revealed distinct state repeats. Lastly, an analysis sequence divergence among indicates successive changes repeat states, correlating their respective time origin. Collectively, findings propose potential role acquiring novel regulatory functions.

Язык: Английский

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Conventional cytogenetics and microsatellite chromosomal distribution in social wasp Mischocyttarus cassununga (Ihering, 1903) (Vespidae, Polistinae, Mischocyttarini)

Genome, Год журнала: 2024, Номер 67(5), С. 151 - 157

Опубликована: Янв. 23, 2024

Cytogenetics has allowed the investigation of chromosomal diversity and repetitive genomic content in wasps. In this study, we characterized karyotype social wasp Mischocyttarus cassununga using conventional cytogenetics mapping sequences. This study was undertaken to extend our understanding organization DNA wasps is first molecular cytogenetic insight into genus Mischocyttarus. The M. had a chromosome number 2 n = 64 for females 32 males. Constitutive heterochromatin exhibited three distribution patterns: centromeric pericentromeric regions along smaller arms extending almost entire chromosome. major ribosomal sites were located on pair one Positive signals microsatellite probes (GA) (GAG) observed euchromatic all chromosomes. microsatellites, (CGG) , (TAT) (TTAGG) n, (TCAGG) not any region Our results contrast with those previously obtained Polybia fastidiosuscula, which showed that microsatellites are predominantly constitutive heterochromatin. suggests variations sequences genomes

Язык: Английский

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