Transposon–host arms race: a saga of genome evolution

Trends in Genetics, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

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A maternal-to-zygotic-transition gene block on the zebrafish sex chromosome

G3 Genes Genomes Genetics, Год журнала: 2024, Номер 14(5)

Опубликована: Март 11, 2024

Wild zebrafish (Danio rerio) have a ZZ/ZW chromosomal sex-determination system with the major sex locus on right arm of chromosome-4 (Chr4R) near largest heterochromatic block in genome, suggesting that Chr4R transcriptomics might differ from rest genome. To test this hypothesis, we conducted an RNA-seq analysis adult ZW ovaries and ZZ testes Nadia strain identified 4 regions Chr4 different gene expression profiles. Unique protein-coding genes 41.7 Mb section (Region-2) were expressed testis but silent ovary. The AB lab strain, which lacks chromosomes, verified result, showing testis-biased Region-2 depends gonad biology, not sex-determining mechanism. analyses female male brains livers validated reduced transcripts somatic cells, without specificity. corresponds to portion its content repetitive elements distinguishes it human orthologs; has zinc finger early zygotic genome activation; maternal 5S rRNA genes, spliceosome concentration tRNA distinct set elements. colocalization (1) silenced are (2) embryos briefly at onset (3) maternal-specific for translation machinery; (4) components; (5) adjacent encoding miR-430, mediates transcript degradation, suggest is maternal-to-zygotic-transition regulatory block.

Язык: Английский

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C2H2 proteins: Evolutionary aspects of domain architecture and diversification

BioEssays, Год журнала: 2024, Номер 46(8)

Опубликована: Июнь 14, 2024

The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2-type zinc finger domains that specifically bind to DNA. Few well-studied however, demonstrate their key role the control gene expression and chromosome architecture. Here we review features domain architecture proteins likely origin fingers. A comprehensive investigation proteomes for presence with multiple clustered has revealed a difference between groups organisms. Unlike plants, metazoans clusters typically separated by linker TGEKP consensus sequence. average size varies substantially, even genomes metazoans, tendency increase combination SCAN, especially KRAB domains, reflecting increasing complexity regulatory networks.

Язык: Английский

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Recurrent oncogenic ZC3H18 mutations stabilize endogenous retroviral RNA

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 14, 2025

Endogenous retroviral (ERV) RNA is highly expressed in cancer, although the molecular causes and consequences remain unknown. We found that ZC3H18 (Z18), a component of multiple nuclear surveillance complexes, has recurrent truncating mutations cancer. show Z18 trunc are oncogenic plays an evolutionarily conserved role ERV RNA. In zebrafish, expedited melanoma onset promoted specific accumulation mutant human cell lines from Cancer Cell Line Encyclopedia also higher levels engineered cells, enhanced more than loss one copy, indicating dominant negative activity. directly bound stabilized Notably, expression was sufficient to expedite oncogenesis zebrafish model, which first evidence we aware transcripts can play functional Our work illuminates mechanism for elevated cancer supports aberrant broadly oncogenic.

Язык: Английский

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Transposable element dynamics in Xenopus laevis embryogenesis: a tale of two coexisting subgenomes

Mobile DNA, Год журнала: 2025, Номер 16(1)

Опубликована: Апрель 9, 2025

Abstract The African clawed frog Xenopus laevis has an allotetraploid genome consisting of two subgenomes referred as L relating to the Long chromosomes and S Short chromosomes. While subgenome presents conserved synteny with X. tropicalis chromosomes, undergone rearrangements deletions leading differences in gene transposable element (TE) content between subgenomes. asymmetry evolution is also detectable expression levels TE mobility. TEs, known “jumping genes”, are mobile genetic elements having a key role regulation. However, due their potential deleterious effects, TEs controlled by host defense mechanisms such nucleosome remodeling deacetylase (NuRD) complex Argonaute proteins that mainly modify heterochromatin environment. In embryogenesis, can escape silencing during maternal-to-zygotic transition when transcriptionally permissive environment created. Moreover, further evidence highlighted reactivation early developmental stages not result this genome-wide reorganization chromatin but it class stage-specific, suggesting precise line these premises, we explored impact transcriptional contribution six . Overall, pattern entire set transcribed was constant across abundance genome. focusing on subgenome-specific our analyses revealed distinctive dominated LTR retroelements LINE attributable young copies. Interestingly, genes encoding involved maintaining repressive were active both highlighting controlling systems embryogenesis evolved symmetrically.

Язык: Английский

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Rise and SINE: roles of transcription factors and retrotransposons in zygotic genome activation

Nature Reviews Molecular Cell Biology, Год журнала: 2024, Номер unknown

Опубликована: Окт. 2, 2024

Язык: Английский

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Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

Genome biology, Год журнала: 2025, Номер 26(1)

Опубликована: Янв. 22, 2025

Abstract Background East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of phenotypic diversity these remains largely unknown. Although transposable elements (TEs) been associated with variation cichlids, little is known about their transcriptional activity and epigenetic silencing. We set out to bridge this gap understand interactions between TEs hosts. Results Here, we describe dynamic patterns TE expression gonads during early development. Orthology inference revealed strong conservation silencing factors expansion piwil1 genes Lake Malawi likely driven by PiggyBac TEs. The expanded copies signatures positive selection retain amino acid residues essential for catalytic activity. Furthermore, cichlids express a Piwi-interacting RNA (piRNA) pathway that targets define genomic sites piRNA production find divergence closely related species, line fast evolution piRNA-producing loci. Conclusions Our findings suggest co-evolution host pathways radiations. propose has contributed diversity.

Язык: Английский

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CUT&Tag Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Фев. 5, 2025

Summary Determining the genomic localization of chromatin features is an essential aspect investigating gene expression control, and ChIP-Seq has long been gold standard technique for interrogating landscapes. Recently, development alternative methods, such as CUT&Tag, have provided researchers with strategies that eliminate need purification, allow in situ investigation histone modifications bound factors. Mindful technical differences, we set out to investigate whether distinct were equally compatible these different interrogation techniques. We found CUT&Tag performed similarly known reside at regulatory regions, promoters enhancers, but major differences observed when assessed enrichment over heterochromatin-associated loci. Unlike ChIP-Seq, detects robust levels H3K9me3 a substantial number repetitive elements, especially high sensitivity evolutionarily young retrotransposons. IAPEz-int elements example, exhibited underrepresentation mouse datasets strong using CUT&Tag. Additionally, identified several euchromatin-associated proteins co-purify loci are depleted applying ChIP-based methods. This study reveals our current knowledge states across heterochromatin portions mammalian genome extensively incomplete, largely due limitations ChIP-Seq. also demonstrate newer fragmentation-based techniques, CUT&RUN, more suitable studying Highlights In fragmentation overcomes biases produced by Heterochromatic regions lost insoluble pellet during allows mapping elements. Euchromatin-associated factors heterochromatin.

Язык: Английский

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Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

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

Опубликована: Апрель 1, 2024

Abstract East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of phenotypic diversity these remains largely unknown. Although transposable elements (TEs) been associated with variation cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns TE expression gonads during early development. Orthology inference revealed expansion piwil1 genes Lake Malawi likely driven by PiggyBac TEs. The expanded copies signatures positive selection retain amino acid residues essential for catalytic activity. Furthermore, cichlids express a Piwi-interacting RNA (piRNA) pathway that target We define genomic sites piRNA production find divergence closely related species, line fast evolution piRNA-producing loci. Our findings suggest co-evolution TEs host silencing pathways radiations. propose this has contributed to diversity.

Язык: Английский

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Syntenic lncRNAs exhibit DNA regulatory functions with sequence evolution

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

Опубликована: Апрель 26, 2024

Abstract Syntenic long non-coding RNAs (lncRNAs) often show limited sequence conservation across species, prompting concern in the field. This study delves into functional signatures of syntenic lncRNAs between humans and zebrafish. have high expression zebrafish ∼90% near protein-coding genes sense or antisense orientation. During early development human embryonic stem cells (H1-hESC), are enriched with cis-regulatory repressor signatures, influencing development-associated genes. In later developmental stages specific cell lines, these serve as enhancers transcription-start-sites(TSS) for protein-coding. Analysis Transposable Elements (TEs) lncRNA divergence unveils intriguing patterns, enrichment simple repeat elements, while counterparts exhibit LTR element enrichment. evolution, possibly stemming from post-rearrangement mutations, enhances DNA elements functions. It may also contribute to vertebrate innovation by creating novel TF binding sites within locus. sheds light on conserved functionality through emphasizing their role species despite divergence.

Язык: Английский

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