Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota, United States of America.
PLoS Genet. 2012;8(12):e1003127. doi: 10.1371/journal.pgen.1003127. Epub 2012 Dec 13.
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.
转座元件 (TEs) 具有作为调控元件影响基因表达的潜力，并且经常受到异染色质沉默的影响。目前的模式表明，异染色质沉默可以超出 TEs 的边界传播，并影响邻近低拷贝序列的染色质状态。这将允许 TEs 调节强制性或辅助性表观等位基因，并作为调控元件发挥作用。玉米基因组包含大量的 I 类 TE 家族（反转录转座子），它们以中等至高拷贝数存在，许多位于基因附近的区域，这为测试反转录转座子的异染色质扩散是否普遍提供了机会。我们通过分析玉米基因组低拷贝区域的 DNA 甲基化和组蛋白 H3 赖氨酸 9 的二甲基化 (H3K9me2)，研究了异染色质向每个反转录转座子家族侧翼 DNA 扩散的程度。不同反转录转座子家族对局部染色质的影响具有高度的可变性。一些反转录转座子家族在插入位点 800-1200 个碱基对内表现出异染色质标记的富集，而其他家族则几乎没有异染色质标记扩散的证据。在缺乏特定插入的基因型中对染色质状态的分析表明，反转录转座子侧翼低拷贝 DNA 中的异染色质通常是沉默标记扩散的结果，而不是插入位点偏好的结果。位于表现出异染色质扩散的 TEs 附近的基因往往比其他基因表达水平更低。我们的研究结果表明，一部分反转录转座子家族可能作为调控元件影响邻近序列，而大多数反转录转座子对侧翼序列几乎没有影响。
