Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

By Mary Gehring, K. Bubb, Steven Henikoff. Science, 2009

599 citations recorded by the source corpus.

Dynamic Imprinting Gene imprinting—the silencing of either a maternally derived or paternally derived gene allele—is controlled in large part by DNA methylation. In plants, imprinting occurs in the endosperm, which nourishes the embryonic plant. Gehring et al. (p. 1447) and Hsieh et al. (p. 1451) analyzed the dynamics of DNA methylation in the endosperm and embryo of Arabidopsis and found extensive demethylation in the endosperm, suggesting that many imprinted genes are likely to exist. Gehring et al. characterized five imprinted genes in detail. Four of the 10 known imprinted genes are related homeodomain transcription factors. Furthermore, 5′ sequences demethylated in several of the genes were found to be derived from transposable elements, which supports the idea that imprinting arose as a by-product of silencing invading DNA. Gene function in Arabidopsis endosperm depends on whether a gene is maternally or paternally inherited. DNA methylation is an epigenetic mark associated with transposable element silencing and gene imprinting in flowering plants and mammals. In plants, imprinting occurs in the endosperm, which nourishes the embryo during seed development. We have profiled Arabidopsis DNA methylation genome-wide in the embryo and endosperm and found that large-scale methylation changes accompany endosperm development and endosperm-specific gene expression. Transposable element fragments are extensively demethylated in the endosperm. We discovered new imprinted genes by the identification of candidates associated with regions of reduced endosperm methylation and preferential expression in endosperm relative to other parts of the plant. These data suggest that imprinting in plants evolved from targeted methylation of transposable element insertions near genic regulatory elements followed by positive selection when the resulting expression change was advantageous.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/3ac0b0c6fc3e20d07b35ec8e6765b1954675de56

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Citations in the corpus

Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, unknown): “thaliana (Gehring et al., 2009; Wolff et al., 2011), however, the presence of DMRs seems rather rare in maize (Waters et al.”
Establishing, maintaining and modifying DNA methylation patterns in plants and animals (2010, background): “thaliana , these changes may reinforce transposon silencing in the sperm and egg cell”
Widespread dynamic DNA methylation in response to biotic stress (2012, background): “In the seed, hypermethylation of transposable elements (TEs) in the embryo genome, along with pervasive demethylation of the embryo-nourishing endosperm genome by DME, function to silence TEs and coordinate gene imprinting, respectively, and are hallmarks of early development (7, 8).”
Transgenerational Epigenetic Inheritance: myths and mechanisms (2014, unknown): “In both plants and animals, epigenetic inheritance of genes controlled by transposons may reflect a predisposition of transposons to DNA methylation and a resistance of transposons to reprogramming, leading to transgenerational epigenetic effects—and, in some cases, parent-of-origin effects—providin”
Active DNA demethylation: many roads lead to Rome (2010, background): “In vivo studies indicate that mutation of each of these genes results in hypermethylation in all sequence contexts but at distinct genomic loc”