Department of Leukemia, The University of Texas MD Anderson Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA.
Mol Cancer Res. 2012 Oct;10(10):1332-42. doi: 10.1158/1541-7786.MCR-12-0351. Epub 2012 Sep 4.
Almost half of the human genome and as much as 40% of the mouse genome is composed of repetitive DNA sequences. The majority of these repeats are retrotransposons of the SINE and LINE families, and such repeats are generally repressed by epigenetic mechanisms. It has been proposed that these elements can act as methylation centers from which DNA methylation spreads into gene promoters in cancer. Contradictory to a methylation center function, we have found that retrotransposons are enriched near promoter CpG islands that stay methylation-free in cancer. Clearly, it is important to determine which influence, if any, these repetitive elements have on nearby gene promoters. Using an in vitro system, we confirm here that SINE B1 elements can influence the activity of downstream gene promoters, with acquisition of DNA methylation and loss of activating histone marks, thus resulting in a repressed state. SINE sequences themselves did not immediately acquire DNA methylation but were marked by H3K9me2 and H3K27me3. Moreover, our bisulfite sequencing data did not support that gain of DNA methylation in gene promoters occurred by methylation spreading from SINE B1 repeats. Genome-wide analysis of SINE repeats distribution showed that their enrichment is directly correlated with the presence of USF1, USF2, and CTCF binding, proteins with insulator function. In summary, our work supports the concept that SINE repeats interfere negatively with gene expression and that their presence near gene promoters is counter-selected, except when the promoter is protected by an insulator element.
人类基因组的近一半和老鼠基因组的多达 40%由重复 DNA 序列组成。这些重复序列的大多数是 SINE 和 LINE 家族的逆转录转座子，而这些重复序列通常受到表观遗传机制的抑制。有人提出，这些元件可以作为甲基化中心，从这些中心DNA 甲基化扩散到癌症中的基因启动子。与甲基化中心的功能相反，我们发现逆转录转座子在癌症中保持非甲基化的启动子 CpG 岛附近富集。显然，重要的是要确定这些重复元件对附近基因启动子有何影响，如果有的话。在这里，我们使用体外系统证实了 SINE B1 元件可以影响下游基因启动子的活性，导致 DNA 甲基化和激活组蛋白标记的丧失，从而导致抑制状态。SINE 序列本身并没有立即获得 DNA 甲基化，但被 H3K9me2 和 H3K27me3 标记。此外，我们的亚硫酸氢盐测序数据不支持基因启动子中的 DNA 甲基化通过从 SINE B1 重复获得的甲基化扩散发生。SINE 重复序列分布的全基因组分析表明，它们的富集与 USF1、USF2 和 CTCF 结合蛋白的存在直接相关，这些蛋白具有绝缘子功能。总之，我们的工作支持这样一种概念，即 SINE 重复序列会对基因表达产生负面影响，并且它们在基因启动子附近的存在是反选择的，除非启动子被绝缘子元件保护。
