Gene capture by transposable elements leads to epigenetic conflict in maize

Muyle, Aline; Seymour, Danelle K.; Darzentas, Nikos; Primetis, Elias; Gaut, Brandon S.; Bousios, Alexandros

doi:10.1016/j.molp.2020.11.003

Cited by 19 publications

(14 citation statements)

References 71 publications

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“…Pack-TYPE TEs can potentially generate conflicts in the epigenetic regulation of the DNA portion with homology to genes because small RNAs produced to silence TEs can target similar sequences found in actively expressed genes (37–39). This phenomenon can lead to the fast pseudogenisation of less-constrained genes and rapid divergence of DNA sequences shared by functional genes and TEs (39), reducing the probability of significant blast hits. Therefore, BLAST approaches may only efficiently identify relatively recent acquisition events of protein coding DNA.…”

Section: Discussionmentioning

confidence: 99%

The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution

Gisby

Catoni

2021

Preprint

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Pack-TYPE transposable elements (TEs) are a group of non-autonomous DNA transposons found in plants. These elements can efficiently capture and shuffle coding DNA across the host genome, accelerating the evolution of genes. Despite their relevance for plant genome plasticity, the detection and study of Pack-TYPE TEs are challenging due to the high similarity these elements have with genes. Here, we produced an automated annotation procedure designed to study Pack-TYPE elements and used it to successfully annotate and analyse more than 4000 new Pack-TYPE TEs in the rice and maize genomes. Our analysis indicates that Pack-TYPE TEs are an abundant and heterogeneous group of elements. We found that these elements are associated with all main superfamilies of Class II DNA transposons in plants and likely share a similar mechanism to capture new chromosomal DNA sequences. Furthermore, we report examples of the direct contribution of these TEs to coding genes, suggesting a generalised and extensive role of Pack-TYPE TEs in plant genome evolution.

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Section: Discussionmentioning

confidence: 99%

The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution

Gisby

Catoni

2021

Preprint

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“…Finally, the epigenetic state of over a thousand transduplicated genes was analyzed in the maize genome [ 215 ]. Remarkably, the level of DNA methylation and siRNAs was higher at donor genes than at genes with no evidence of transduplication capture.…”

Section: Exaptation Of Te Coding Regionsmentioning

confidence: 99%

“…Furthermore, Pack-TEs mapped fewer siRNAs and were slightly less methylated than related TEs without captured fragments. All together, these observations could reflect some epigenetic conflicts between Pack-TEs and their relative, as well as between donor and transduplicated genes [ 215 ]. This undoubtedly depicts the complex interaction between TEs and host genomes.…”

Section: Exaptation Of Te Coding Regionsmentioning

confidence: 99%

“…In maize, captures of gene fragments by TEs can lead to evolutionary conflicts [ 215 ]. SiRNA crosstalk can occur between donor genes and TEs carrying the gene fragments, making donor genes more prone to accumulating siRNAs, to be DNA methylated and transcriptionally repressed.…”

Section: Exaptation Of Te-derived Non-coding Regionsmentioning

confidence: 99%

“…SiRNA crosstalk can occur between donor genes and TEs carrying the gene fragments, making donor genes more prone to accumulating siRNAs, to be DNA methylated and transcriptionally repressed. While this would be particularly true for translocated donor genes that are under low selective pressure, it is not the case for donor genes with important function that maintain high expression level with lower DNA methylation/siRNA levels, suggesting that capture of gene fragments could provide selective advantage to TEs [ 215 ]. Finally, in bread wheat ( Triticum aestivum L.), a recent study showed that class II MITE and Mariner TEs are important sources of miRNAs with a potential role in plant immunity [ 257 ].…”

Section: Exaptation Of Te-derived Non-coding Regionsmentioning

confidence: 99%

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The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

Nicolau

Picault

Moissiard

2021

Cells

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Transposable elements (TEs) are self-replicating DNA elements that constitute major fractions of eukaryote genomes. Their ability to transpose can modify the genome structure with potentially deleterious effects. To repress TE activity, host cells have developed numerous strategies, including epigenetic pathways, such as DNA methylation or histone modifications. Although TE neo-insertions are mostly deleterious or neutral, they can become advantageous for the host under specific circumstances. The phenomenon leading to the appropriation of TE-derived sequences by the host is known as TE exaptation or co-option. TE exaptation can be of different natures, through the production of coding or non-coding DNA sequences with ultimately an adaptive benefit for the host. In this review, we first give new insights into the silencing pathways controlling TE activity. We then discuss a model to explain how, under specific environmental conditions, TEs are unleashed, leading to a TE burst and neo-insertions, with potential benefits for the host. Finally, we review our current knowledge of coding and non-coding TE exaptation by providing several examples in various organisms and describing a method to identify TE co-option events.

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The role of epigenetics in phenotypic evolution: lessons from the genomic response to stresses, genetic conflicts and developmental plasticity in Drosophila

Chatterjee

2024

Nucleus

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Gene capture by transposable elements leads to epigenetic conflict in maize

Cited by 19 publications

References 71 publications

The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution

The widespread nature of Pack-TYPE transposons reveals their importance for plant genome evolution

The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

The role of epigenetics in phenotypic evolution: lessons from the genomic response to stresses, genetic conflicts and developmental plasticity in Drosophila

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