Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression.

By Jesse D. Hollister, Brandon S. Gaut. Genome Research, 2009

636 citations recorded by the source corpus.

Transposable elements (TEs) are ubiquitous genomic parasites. The deleterious consequences of the presence and activity of TEs have fueled debate about the evolutionary forces countering their expansion. Purifying selection is thought to purge TE insertions from the genome, and TE sequences are targeted by hosts for epigenetic silencing. However, the interplay between epigenetic and evolutionary forces countering TE expansion remains unexplored. Here we analyze genomic, epigenetic, and population genetic data from Arabidopsis thaliana to yield three observations. First, gene expression is negatively correlated with the density of methylated TEs. Second, the signature of purifying selection is detectable for methylated TEs near genes but not for unmethylated TEs or for TEs far from genes. Third, TE insertions are distributed by age and methylation status, such that older, methylated TEs are farther from genes. Based on these observations, we present a model in which host silencing of TEs near genes has deleterious effects on neighboring gene expression, resulting in the preferential loss of methylated TEs from gene-rich chromosomal regions. This mechanism implies an evolutionary tradeoff in which the benefit of TE silencing imposes a fitness cost via deleterious effects on the expression of nearby genes.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/1b096d95db46ed9eb5ede465d0572dc9c2bb02c5

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In Plant Science

1. C. Grover
2. Shujun Ou
3. Ning Jiang
4. J. Wendel
5. Guillaume Le Blanc
6. Kenneth H. Wolfe
7. R. Cronn
8. D. Soltis

Citations in the corpus

• LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons1[OPEN] (2017, background): “…shaped genome landscapes, such as genome organization (Ammiraju et al., 2007, 2010) and epigenetic status of the insertion sites (Fedoroff, 2012), thereby affecting the expression of adjacent genes (Hollister and Gaut, 2009; Hollister et al., 2011; Vonholdt et al., 2012; Makarevitch et al., 2015).”
• Transposable elements contribute to activation of maize genes in response to abiotic stress (2014, background): “TE insertions near genes may influence gene expression through several potential mechanisms, including inserting within cis-regulatory regions, contributing an outward reading promoter from the TE into the gene [12]-[15], or providing novel cis-regulatory sequences that can act as enhancers/ repress”
• Recent Insights into Mechanisms of Genome Size Change in Plants (2010, background): “Recent work in Arabidopsis hints at a possible explanation for these periodic releases from suppression, while also underscoring the role that epigenetics plays with respect to TE deletion [60].”
• Genome evolution in fungal plant pathogens: looking beyond the two-speed genome model (2020, neutral): “…of the effector (Chuong et al. , 2016; Omrane et al. , 2017), through disturbance through by ectopic recombination (Devos et al. , 2002), by leaking of silencing (Hollister and Gaut, 2009), or even by creating effector genes de novo (Nottensteiner et al. , 2018; Sabelleck and Panstruga, 2018).”
• The “Polyploid Hop”: Shifting Challenges and Opportunities Over the Evolutionary Lifespan of Genome Duplications (2018, background): “First, TE insertions close to genes are known to have an impact, mostly negative (Hollister and Gaut, 2009) but sometimes positive (Quadrana et al.”