Evolutionary dynamics between transposable elements and their host genomes: mechanisms of suppression and escape

Current Opinion in Genetics & Development, Год журнала: 2023, Номер 82, С. 102092 - 102092

Опубликована: Июль 28, 2023

Transposable elements (TEs) are ubiquitous among eukaryotic species. Their evolutionary persistence is likely due to a combination of tolerogenic, evasive/antagonistic, and cooperative interactions with their host genomes. Here, we focus on metazoan species review recent advances related the harmful effects TE insertions, including how epigenetic TE-derived RNAs can damage cells. We discuss new findings pathways that silence TEs, such as piRNA pathway APOBEC3 Kruppel-associated box zinc finger gene families. Finally, summarize novel strategies used by TEs evade silencing, Y chromosome permissive niche for mobilization counterdefense block silencing factors.

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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The emerging H3K9me3 chromatin landscape during zebrafish embryogenesis

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

Опубликована: Март 5, 2024

The structural organization of eukaryotic genomes is contingent upon the fractionation DNA into transcriptionally permissive euchromatin and repressive heterochromatin. However, we have a limited understanding how these distinct states are first established during animal embryogenesis. Histone 3 lysine 9 trimethylation (H3K9me3) critical to heterochromatin formation bulk establishment this mark thought help drive large-scale remodeling an initially naive chromatin state detailed process lacking. Here, leverage CUT&RUN define emerging H3K9me3 landscape zebrafish embryo with high sensitivity temporal resolution. Despite prevalence transposons in genome, found that LTR preferentially targeted for embryonic deposition, different families exhibiting timelines. High signal-to-noise ratios afforded by revealed new, sites low-amplitude initiated before major wave zygotic genome activation (ZGA). Early predominated at specific subsets were particularly enriched transposon sequences maternal piRNAs pericentromeric localization. Notably, number increased linearly across blastula development, while quantitative comparison >10-fold genome-wide increase signal over just 30 minutes onset ZGA. Continued maturation was observed beyond initial establishment.

Язык: Английский

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The emerging H3K9me3 chromatin landscape during zebrafish embryogenesis

Genetics, Год журнала: 2024, Номер 228(2)

Опубликована: Авг. 21, 2024

Abstract The structural organization of eukaryotic genomes is contingent upon the fractionation DNA into transcriptionally permissive euchromatin and repressive heterochromatin. However, we have a limited understanding how these distinct states are first established during animal embryogenesis. Histone 3 lysine 9 trimethylation (H3K9me3) critical to heterochromatin formation, bulk establishment this mark thought help drive large-scale remodeling an initially naive chromatin state detailed process lacking. Here, leverage CUT&RUN define emerging H3K9me3 landscape zebrafish embryo with high sensitivity temporal resolution. Despite prevalence transposons in genome, found that LTR preferentially targeted for embryonic deposition, different families exhibiting timelines. High signal-to-noise ratios afforded by revealed new, sites low-amplitude initiated before major wave zygotic genome activation (ZGA). Early predominated at specific subsets were particularly enriched transposon sequences maternal piRNAs pericentromeric localization. Notably, number increased linearly across blastula development, while quantitative comparison >10-fold genome-wide increase signal over just 30 min onset ZGA. Continued maturation was observed beyond initial establishment.

Язык: Английский

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Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish

PLoS Biology, Год журнала: 2024, Номер 22(12), С. e3002887 - e3002887

Опубликована: Дек. 5, 2024

Quality control of translation is crucial for maintaining cellular and organismal homeostasis. Obstacles in elongation induce ribosome collision, which monitored by multiple sensor mechanisms eukaryotes. The E3 ubiquitin ligase Znf598 recognizes collided ribosomes, triggering ribosome-associated quality (RQC) to rescue stalled ribosomes no-go decay (NGD) degrade stall-prone mRNAs. However, the impact RQC NGD on translational homeostasis endogenous mRNAs has remained unclear. In this study, we investigated substrate during maternal-to-zygotic transition (MZT) zebrafish development. RNA-Seq analysis znf598 mutant embryos revealed that down-regulates encoding C2H2-type zinc finger domain (C2H2-ZF) MZT. Reporter assays disome profiling indicated stall collide while translating tandem C2H2-ZFs, leading mRNA degradation Znf598. Our results suggest maintains translatome mitigating risk collision at abundantly present C2H2-ZF sequences vertebrate genome.

Язык: Английский

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

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 8, 2023

ABSTRACT Wild zebrafish ( Danio rerio ) have a ZZ/ZW chromosomal sex determination system with the major locus on right arm of chromosome-4 (Chr4R) near largest heterochromatic block in genome, suggesting hypothesis that Chr4R transcriptome might be different from rest genome. We conducted an RNA-seq analysis adult ZW ovaries and ZZ testes identified four regions Chr4 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 this result, showing testis-biased Region-2 depends gonad biology, not sex-determining mechanism. analyses female male brain liver validated few transcripts somatic cells, without sex-specificity. corresponds to portion its content repetitive elements distinguishes it In Region-2, lack 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; adjacent encoding miR-430, mediates transcript degradation, suggest is Maternal-to-Zygotic-Transition Gene Regulatory Block. ARTICLE SUMMARY wild chromosome region, unique contains transiently embryo as begins express own genes. This region also protein-synthesis machinery used specifically by developing embryos, molecules target degradation messenger RNAs mother stored her eggs. defines maternal-to-zygotic-transition block.

Язык: Английский

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The genomic study of repetitive elements in Solea senegalensis reveals multiple impacts of transposable elements in the evolution and architecture of Pleuronectiformes chromosomes

Frontiers in Marine Science, Год журнала: 2024, Номер 11

Опубликована: Фев. 28, 2024

Pleuronectiformes are flatfishes with high commercial value and a prominent example of successful marine adaptation through chromosomal evolution. Hence, the aim this study was to analyze 14 relative abundance repetitive elements (satellite DNA transposable (TE)) in 15 genome 10 fish species (8 flatfish) delving into special relevance, 16 Senegalese sole, Solea senegalensis. The results showed differences elements, S. senegalensis exhibiting highest frequency coverage these reaching 40% not at random distribution. It is noteworthy presence relevant peaks Helitrons centromeric/pericentromeric positions mainly bi-armed chromosomes 1, 2, 4, 6, 7, 9. position centromeres determined genomic localization family satellite PvuII , other sequences obtained de novo . This allowed us know 19 out 21 an accumulation tandem copies pericentromeric 1 occupying region, first case, 600Kb repeats. That has only been previously described mammals plants. Divergence copy number studies indicated active families species’ existence two important events transposon activity (burst) senegalensis, accentuated Helitrons. that transposons exhibited landscape symmetrical bell-shaped phylogenetic analysis Helitron revealed large groups four heterogeneous distribution among chromosomes. Finally, phylogenomic 8615 belonging insertions from 5 flatfish external species, classify nine different levels divergence clusters, including some branches distant phylogenetically species. implications will help expand knowledge chromosome structure evolution

Язык: Английский

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A retrospective case-control study for Clinical Validation of mutated ZNF208 as a novel biomarker of fatal blast crisis in Chronic Myeloid Leukemia

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

Опубликована: Март 15, 2024

Abstract The hallmark of Chronic Myeloid Leukemia (CML) is Philadelphia chromosome t(9:22), which leads to formation BCR-ABL1 fusion oncogene. induces genetic instability, causing the progression chronic myeloid leukemia from manageable Phase (CP-CML) accelerated phase (AP-CML) and ultimately lethal blast crisis (BC-CML). precise mechanism responsible for CML are not well comprehended, there a lack specific molecular biomarkers advanced CML. Mutations in transcription factors (TFs) have significant role cancer initiation, relapses, invasion, metastasis, resistance anti-cancer drugs. Recently, our group reported association novel factor, ZNF208, with was dire need clinical validation this biomarker. Therefore, aim study clinically validate mutated ZNF208 as biomarker larger cohort AP- BC-CML patients using control-case studies. A total 73 (N=73) King Saud University Medical City Riyadh Abdulaziz National Guard Hospital, Al-Ahsa, Saudi Arabia were enrolled (2020-2023), experimental (cases) consisting AP-CML (n=20) (n=12). controls consisted age/sex matched CP-CML (n=41). approved by Research Ethics Committees participating institutes all provided informed consent study. Clinical evaluations conducted according guidelines established European LeukemiaNet 2020. Targeted resequencing ZNF 208 employed Illumina NextSeq500 instrument (Illumina, San Diego, CA, USA) mutations confirmed Sanger sequencing. Both next generation sequencing identified missense mutation (c.64G>A) ZNF208. 56 (93.3) and12 (100) CP-, respectively, while none (0%) or healthy genomic databases (p=0.0001). studies show that very AP-and patients. other such proteins may cause carcinogenesis interacting KAP-1 repressor silence many target genes thus prove be drug targets well. we recommend carrying out prospective trials further its utilization decision, investigating pathogenesis investigate potential Simple Summary type blood caused oncogene, leading instability changes. This results advancement (CP) an (AP) finally (BC). development known, dearth dependable shared indicators. Transcription class molecules that, when altered, significantly contribute cancer, including has been factor gene associated BC-CML. Here, carried targeted resequencing. detected 0 (0%), respectively (p=0.0001) demonstrating high specificity shows progression. We

Язык: Английский

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Comprehensive Annotation and Expression Profiling of C2H2 Zinc Finger Transcription Factors across Chicken Tissues

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(19), С. 10525 - 10525

Опубликована: Сен. 30, 2024

As the most abundant class of transcription factors in eukaryotes, C2H2-type zinc finger proteins (C2H2-ZFPs) play critical roles various biological processes. Despite being extensively studied mammals, C2H2-ZFPs remain poorly characterized birds. Recent accumulation multi-omics data for chicken enables genome-wide investigation The purpose this study is to reveal genomic occurrence and evolutionary signature C2H2-ZFPs, further depict their expression profiles across diverse tissues. Here, we annotated 301 genome, which are associated with different effector domains, including KRAB, BTB, HOMEO, PHD, SCAN, SET. Among them, KRAB-ZFPs lack orthologues mammals tend form clusters by duplication, supporting fast evolution chicken. We also a unique previously unidentified SCAN-ZFP, lineage-specific highly expressed ovary testis. By integrating 101 RNA-seq datasets 32 tissues, found that have tissue-specific expression. Particularly, 74 C2H2-ZFPs—including 27 KRAB-ZFPs—show blastoderm-enriched expression, indicating association early embryo development. Overall, performs comprehensive annotation profiling C2H2 ZFPs gives new insights into potential function avian species.

Язык: Английский

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Evolutionarily recent transcription factors partake in human cell cycle regulation

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

Опубликована: Ноя. 6, 2024

Abstract The cell cycle is a fundamental process in eukaryotic biology and accordingly controlled by highly conserved core signaling cascade. However, whether recently evolved proteins also influence this unclear. Here, we systematically map the of evolutionarily recent transcription factors (TFs) on human progression. We find that genomic targets select young TFs, many which belong to rapidly evolving Krüppel-associated box (KRAB) zinc-finger (KZFP) family, exhibit synchronized expression. Systematic perturbation studies reveal silencing TFs disrupts normal progression, experimentally confirm for ZNF519, simian-restricted KZFP. Further, show therian-specific KZFP ZNF274 sets expression replication timing hundreds clustered genes. These findings highlight an underappreciated level lineage specificity regulation.

Язык: Английский

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