Conflict--Final--MolecularPlant_accepted.pdf (6.91 MB)
Gene capture by transposable elements leads to epigenetic conflict in maize
journal contribution
posted on 2023-06-09, 22:36 authored by Aline Muyle, Danelle Seymour, Nikos Darzentas, Elias PrimetisElias Primetis, Brandon S Gaut, Alexandros BousiosAlexandros BousiosTransposable elements (TEs) regularly capture fragments of genes. When the host silences these TEs, siRNAs homologous to the captured regions may also target the genes. This epigenetic crosstalk establishes an intragenomic conflict: silencing the TEs has the cost of silencing the genes. If genes are important, however, natural selection may maintain function by moderating the silencing response, which may also advantage the TEs. In this study, we examined this model by focusing on Helitrons, Pack-MULEs, and Sirevirus LTR retrotransposons in the maize genome. We documented 1263 TEs containing exon fragments from 1629 donor genes. Consistent with epigenetic conflict, donor genes mapped more siRNAs and were more methylated than genes with no evidence of capture. However, these patterns differed between syntelog versus translocated donor genes. Syntelogs appeared to maintain function, as measured by gene expression, consistent with moderation of silencing for functionally important genes. Epigenetic marks did not spread beyond their captured regions and 24nt crosstalk siRNAs were linked with CHH methylation. Translocated genes, in contrast, bore the signature of silencing. They were highly methylated and less expressed, but also overrepresented among donor genes and located away from chromosomal arms, which suggests a link between capture and gene movement. Splitting genes into potential functional categories based on evolutionary constraint supported the synteny-based findings. TE families captured genes in different ways, but the evidence for their advantage was generally less obvious; nevertheless, TEs with captured fragments were older, mapped fewer siRNAs, and were slightly less methylated than TEs without captured fragments. Collectively, our results argue that TE capture triggers an intragenomic conflict that may not affect the function of important genes but may lead to the pseudogenization of less-constrained genes.
Funding
Silencing, rewiring, escaping: the epigenetic and evolutionary interactions between plant transposable elements and their host genomes; G2272; ROYAL SOCIETY; UF 160222
Structural and functional aspects of the RNAi recognition and regulatory exaptation of TE cis-regions by plant hosts; G2381; ROYAL SOCIETY; RGF\R1\180006
History
Publication status
- Published
File Version
- Accepted version
Journal
Molecular plantISSN
1752-9867Publisher
ElsevierExternal DOI
Volume
14Page range
1-16Department affiliated with
- Evolution, Behaviour and Environment Publications
Full text available
- Yes
Peer reviewed?
- Yes
Legacy Posted Date
2021-01-04First Open Access (FOA) Date
2021-11-08First Compliant Deposit (FCD) Date
2020-12-30Usage metrics
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