ArticleGenome biology2016
DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- Proteomic Characterization of Virulence Factors and Related Proteins inInternational journal of molecular sciences · 2022Article
- Maize DNA Methylation in Response to Drought Stress Is Involved in Target Gene Expression and Alternative Splicing.International journal of molecular sciences · 2021Article
- Proteomic Characterization of Antibiotic Resistance inInternational journal of molecular sciences · 2021Article
- Epigenomic landscape and epigenetic regulation in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- CsMYB60 is a key regulator of flavonols and proanthocyanidans that determine the colour of fruit spines in cucumber.Journal of experimental botany · 2019Article
- The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum.Nucleic acids research · 2018Article
- Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.Nature genetics · 2018Article
- Expression dynamics and relations with nearby genes of rat transposable elements across 11 organs, 4 developmental stages and both sexes.BMC genomics · 2017Article
- Domestication of rice has reduced the occurrence of transposable elements within gene coding regions.BMC genomics · 2017Article
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMutator-like transposable elements, a class of DNA transposons, exist pervasively in both prokaryotic and eukaryotic genomes, with more than 10,000 copies identified in the rice genome. These elements can capture ectopic genomic sequences that lead to the formation of new gene structures. Here, based on whole-genome comparative analyses, we comprehensively investigated processes and mechanisms of the evolution of putative genes derived from Mutator-like transposable elements in ten Oryza species and the outgroup Leersia perieri, bridging ~20 million years of evolutionary history.
resultsOur analysis identified thousands of putative genes in each of the Oryza species, a large proportion of which have evidence of expression and contain chimeric structures. Consistent with previous reports, we observe that the putative Mutator-like transposable element-derived genes are generally GC-rich and mainly derive from GC-rich parental sequences. Furthermore, we determine that Mutator-like transposable elements capture parental sequences preferentially from genomic regions with low methylation levels and high recombination rates. We explicitly show that methylation levels in the internal and terminated inverted repeat regions of these elements, which might be directed by the 24-nucleotide small RNA-mediated pathway, are different and change dynamically over evolutionary time. Lastly, we demonstrate that putative genes derived from Mutator-like transposable elements tend to be expressed in mature pollen, which have undergone de-methylation programming, thereby providing a permissive expression environment for newly formed/transposable element-derived genes.
conclusionsOur results suggest that DNA methylation may be a primary mechanism to facilitate the origination, survival, and regulation of genes derived from Mutator-like transposable elements, thus contributing to the evolution of gene innovation and novelty in plant genomes.
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