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The Role of Small RNA-Based Epigenetic Silencing for Purifying Selection on Transposable Elements in Capsella grandiflora
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).ORCID-id: 0000-0002-3221-8835
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik. Stockholms universitet, Science for Life Laboratory (SciLifeLab).ORCID-id: 0000-0001-6020-5102
2017 (engelsk)Inngår i: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, nr 10, s. 2911-2920Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

To avoid negative effects of transposable element (TE) proliferation, plants epigenetically silence TEs using a number of mechanisms, including RNA-directed DNA methylation. These epigenetic modifications can extend outside the boundaries of TE insertions and lead to silencing of nearby genes, resulting in a trade-off between TE silencing and interference with nearby gene regulation. Therefore, purifying selection is expected to remove silenced TE insertions near genes more efficiently and prevent their accumulation within a population. To explore how effects of TE silencing on gene regulation shapes purifying selection on TEs, we analyzed whole genome sequencing data from 166 individuals of a large population of the outcrossing species Capsella grandiflora. We found that most TEs are rare, and in chromosome arms, silenced TEs are exposed to stronger purifying selection than those that are not silenced by 24-nucleotide small RNAs, especially with increasing proximity to genes. An age-of-allele test of neutrality on a subset of TEs supports our inference of purifying selection on silenced TEs, suggesting that our results are robust to varying transposition rates. Our results provide new insights into the processes affecting the accumulation of TEs in an outcrossing species and support the view that epigenetic silencing of TEs results in a trade-off between preventing TE proliferation and interference with nearby gene regulation. We also suggest that in the centromeric and pericentromeric regions, the negative aspects of epigenetic TE silencing are missing.

sted, utgiver, år, opplag, sider
2017. Vol. 9, nr 10, s. 2911-2920
Emneord [en]
transposable elements, methylation, purifying selection, gene expression, epigenetic silencing, Capsella
HSV kategori
Forskningsprogram
evolutionär genetik
Identifikatorer
URN: urn:nbn:se:su:diva-151594DOI: 10.1093/gbe/evx206OAI: oai:DiVA.org:su-151594DiVA, id: diva2:1174572
Tilgjengelig fra: 2018-01-16 Laget: 2018-01-16 Sist oppdatert: 2018-05-18bibliografisk kontrollert

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