The GC-content at the 5′ ends of human protein-coding genes is undergoing mutational decay

Genome biology, Journal Year: 2024, Volume and Issue: 25(1)

Published: Aug. 13, 2024

Abstract Background In vertebrates, most protein-coding genes have a peak of GC-content near their 5′ transcriptional start site (TSS). This feature promotes both the efficient nuclear export and translation mRNAs. Despite importance for RNA metabolism, its general features, origin, maintenance remain mysterious. We investigate evolutionary forces shaping at (TSS) through comparative genomic analysis nucleotide substitution rates between different species by examining human de novo mutations. Results Our data suggests that GC-peaks TSSs were present in last common ancestor amniotes, likely vertebrates. observe apes rodents, where recombination is directed away from PRDM9, end gene currently undergoing mutational decay. canids, which lack PRDM9 perform TSSs, increasing. show these patterns extend into open reading frame, thus impacting synonymous codon position choices. Conclusions results indicate dynamics this GC-peak amniotes largely shaped historic recombination. Since decay towards mutation rate equilibrium default state non-functional DNA, observed decrease rodents indicates not being maintained selection on those species.

Language: Английский

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Diversity in Recombination Hotspot Characteristics and Gene Structure Shape Fine-Scale Recombination Patterns in Plant Genomes

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(9)

Published: Sept. 1, 2024

During the meiosis of many eukaryote species, crossovers tend to occur within narrow regions called recombination hotspots. In plants, it is generally thought that gene regulatory sequences, especially promoters and 5' 3' untranslated regions, are enriched in hotspots, but this has been characterized a handful species only. We also lack clear description fine-scale variation rates genic little known about hotspot position intensity plants. To address question, we constructed maps from genetic polymorphism data inferred hotspots 11 plant species. detected gradients most yet varied shape depending on specific locations structure. further characterize gradients, decomposed them according structure by rank number exons. generalized previously observed pattern organized around boundaries coding promoters. However, our results provided new insight into relative importance end genes some possible location away Variation among seemed driven more than differences size or Our shed light at very fine scale, revealing diversity complexity emerging interaction between

Language: Английский

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Conservation of mutation and recombination parameters between mammals and zebra finch

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 5, 2024

Most of our understanding the fundamental processes mutation and recombination stems from a handful disparate model organisms pedigree studies mammals, with little known about other vertebrates. To gain broader comparative perspective, we focused on zebra finch (

Language: Английский

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Multiple losses of aKRAB from PRDM9 coincide with a teleost-specific intron size distribution

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Nov. 27, 2024

Abstract Background Primary transcripts are largely comprised of intronic sequences that excised and discarded shortly after synthesis. In vertebrates, the shape intron size distribution is constant; however, most teleost fish have a diverged log-bimodal ‘teleost distribution’ (TD) seen only in teleosts. How TD evolved to what extent this was affected by adaptative or non-adaptive mechanisms unknown. Results Here, we show has independently at least six times its appearance linked loss aKRAB domain from PRDM9. We determined distributions identified PRDM9 orthologues annotated genomes addition scanning 1193 assemblies for domain. form ( $$\beta$$ β ) predominant teleosts whereas $$\alpha$$ α version absent species. Only subset PRDM9- proteins contain aKRAB, hence, it present small number lineages. Almost all lineages lacking (but no species with) had TDs. Conclusions mammals, defines sites meiotic recombination through mechanism increases structural variance depends on aKRAB. The likely shifted locations both hotspots. Our observations suggest as side-effect these changes link evolution illustrating how genome architectures can evolve absence selection.

Language: Английский

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Ubiquitous recombination gradients within plant genic regions shaped by recombination hotspots

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 13, 2023

Abstract During the meiosis of many eukaryote species, crossovers tend to occur within narrow regions called recombination hotspots. In plants, it is generally thought that gene regulatory sequences, especially promoters and 5’-3’ untranslated regions, are enriched in hotspots, but this has been characterized a handful species only. We also lack clear description fine-scale variation rates genic little known about hotspot position intensity plants. To address question we constructed maps from genetic polymorphism data inferred hotspots eleven plant species. detected gradients both 5’ 3’ most yet varied shape depending on specific locations structure. further characterize gradients, decomposed them according structure by rank number exons. generalized previously observed pattern organized around boundaries coding promoters. However, our results provided new insight into relative importance end genes some possible location away Variation among seemed driven more than differences size or Our shed light at very fine scale, detailed whole genome averaged estimates used so far, revealing diversity complexity emerging interaction between

Language: Английский

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