Tandem repeat polymorphisms shape local adaptation

Trends in Ecology & Evolution, Год журнала: 2025, Номер 40(4), С. 331 - 334

Опубликована: Март 5, 2025

Язык: Английский

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BmNPV interacts with super-enhancer regions of the host chromatin to hijack cellular transcription machinery

Nucleic Acids Research, Год журнала: 2025, Номер 53(6)

Опубликована: Март 20, 2025

Abstract Effective transcriptional activation relies on the spatial interaction between specific DNA elements. interactions have also been observed viruses and their hosts, with limited understanding of involved details. Baculovirus is a representative species virus has reported to interact host genome in our previous study. However, biological significance baculovirus-host trans-species its underlying mechanisms remain elusive. Here, using Bombyx mori nucleopolyhedrovirus (BmNPV) as model virus, we combine epigenome, transcriptome, biochemical assays investigate interaction. Our data show that BmNPV hijacks regulatory capacity super-enhancers (SEs) by physically interacting these regions genome. This results usurpation activating an SE-binding transcription factor GATA thereby impairing SE-induced target antiviral genes. Moreover, hijacked spread through cis-interaction viral DNA, leading enhanced gene expression. Overall, provide novel insights into intricate interplay expression networks broaden vision exploitation cellular machinery.

Язык: Английский

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Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Melanoseris cyanea group

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Март 27, 2025

Melanoseris, a diverse genus in the Lactucinae subtribe, has 21 species China, with 13 being endemic. The high diversity of this presents taxonomic challenges, particularly M. cyanea group, where overlapping distributions and transitional morphological traits complicate classification. This study aims to analyze chloroplast genomes focus on explore structural differences phylogenetic relationships among these closely related species. We analyzed 16 Melanoseris samples, including 12 new from group. genome sizes ranged 152,255 152,558 bp exhibited typical quadripartite structure, an average GC content 37.7%. Each encodes 132 genes, 87 protein-coding 37 tRNAs, 8 rRNAs. Repeat analysis identified 89 105 dispersed repeats, 24 28 tandem 35 39 SSRs, mononucleotide A/T repeats most common. Sequence alignment revealed that variable regions were mainly concentrated single-copy regions. Nucleotide 0 0.00485, highlighting 10 mutation hotspot Phylogenetic showed limited differentiation within research enhances our understanding genetic laying foundation for future studies.

Язык: Английский

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DNA–Protein Binding is Dominated by Short Anchoring Elements

Advanced Science, Год журнала: 2025, Номер unknown

Опубликована: Март 26, 2025

Unveiling the complexities of gene expression regulation, study explores intricate DNA-binding mechanisms transcription factors (TFs). By employing KaScape method previously developed to measure both bound and unbound populations at thermodynamic equilibrium, "anchoring elements" (AEs), 3-4 base pair sequences, are identified in Arabidopsis WRKY human PU.1 TFs crucial for binding affinity. Building on BEESEM method, introduces AEEscape algorithm, which advances AE concept by creating a precise model position-specific k-mer energy landscape. This allows direct identification dominant role AEs from experimental data. Moreover, when integrated with genomic data, it reveals an energetic funnel around factor sites (TFBSs), is directly correlated density (AED). The findings not only offer fresh perspective TF-TFBS interactions but also highlight critical AED regulation. These insights can pave way innovative strategies manipulate expression.

Язык: Английский

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Aberrant Short Tandem Repeats: Pathogenicity, Mechanisms, Detection, and Roles in Neuropsychiatric Disorders

Genes, Год журнала: 2025, Номер 16(4), С. 406 - 406

Опубликована: Март 30, 2025

Short tandem repeat (STR) sequences are highly variable DNA segments that significantly contribute to human neurodegenerative disorders, highlighting their crucial role in neuropsychiatric conditions. This article examines the pathogenicity of abnormal STRs and classifies expansion disorders(TREDs), emphasizing genetic characteristics, mechanisms action, detection methods, associated animal models. STR expansions exhibit complex patterns affect age onset symptom severity. These disrupt gene function through such as silencing, toxic gain-of-function mutations leading RNA protein toxicity, generation peptides via repeat-associated non-AUG (RAN) translation. Advances sequencing technologies—from traditional PCR Southern blotting next-generation long-read sequencing—have enhanced accuracy variation detection. Research utilizing these technologies has linked a range including autism spectrum disorders schizophrenia, contribution disease risk phenotypic expression effects on genes involved neurodevelopment, synaptic function, neuronal signaling. Therefore, further investigation is essential elucidate intricate interplay between diseases, paving way for improved diagnostic therapeutic strategies.

Язык: Английский

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