Abstract
Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs (retrotransposons) that are present in moderate to high copy numbers, and many are found in regions near genes, which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into DNA flanking each family of retrotransposons by profiling DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. The effects of different retrotransposon families on local chromatin are highly variable. Some retrotransposon families exhibit enrichment of heterochromatic marks within 800–1,200 base pairs of insertion sites, while other families exhibit very little evidence for the spreading of heterochromatic marks. The analysis of chromatin state in genotypes that lack specific insertions suggests that the heterochromatin in low-copy DNA flanking retrotransposons often results from the spreading of silencing marks rather than insertion-site preferences. Genes located near TEs that exhibit spreading of heterochromatin tend to be expressed at lower levels than other genes. Our findings suggest that a subset of retrotransposon families may act as controlling elements influencing neighboring sequences, while the majority of retrotransposons have little effect on flanking sequences.
Highlights
A substantial fraction of most eukaryotic genomes is composed of transposable elements (TEs) [1,2,3,4]
Transposable elements comprise a substantial portion of many eukaryotic genomes
There is evidence that the majority of transposable elements are epigenetically silenced, and in some cases this silencing may spread to neighboring sequences
Summary
A substantial fraction of most eukaryotic genomes is composed of transposable elements (TEs) [1,2,3,4]. While these TEs are sometimes referred to as ‘‘junk’’ DNA, there is evidence for potential functional roles in some instances [5]. Mobile genetic elements include class I retrotransposons and class II DNA transposons [2]. The class I TEs transpose via an RNA intermediate while class II TEs utilize a DNA intermediate for transposition. There are a variety of subfamilies of both types of TEs [2] that differ in structure, activity, and integration patterns
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