Isoform switching and exon skipping induced by the DNA methylation inhibitor 5-Aza-2'-deoxycytidine.
Isoform switching and exon skipping induced by the DNA methylation inhibitor 5-Aza-2'-deoxycytidine.
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DOI：
10.1038/srep24545
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发表时间：
2016-04-19
影响因子：
4.6
通讯作者：
Wang K
中科院分区：
文献类型：
--
作者：
Ding XL;Yang X;Liang G;Wang K
基因启动子中的 DNA 甲基化会导致基因沉默，是 5-Aza-2'-脱氧胞苷 (5-Aza-CdR) 等甲基化抑制剂的治疗靶点。通过分析从暴露于 0.1μM 浓度的 5-Aza-CdR 的人膀胱细胞获得的时间序列 RNA-seq 数据（第 5、9、13、17 天），我们发现 5-Aza-CdR 除了对基因表达的影响外，还可以影响异构体转换和差异外显子使用（即外显子跳跃）。我们鉴定出 2,000 多个基因在 5-Aza-CdR 处理后出现显着的表达变化。有趣的是，通过实验鉴定并验证了治疗诱导的 29 个外显子跳跃事件。特别是，Enhancer of Zeste 同源物 2 (EZH2) 中的外显子跳跃事件以及表达变化在第 5 天和第 9 天表现出显着下调，但在第 13 天和第 17 天恢复到正常水平。EZH2 是多亚基多梳抑制复合物 PRC2 的组成部分，外显子跳跃事件的下调可能导致功能性 EZH2 的恢复，这与我们之前的发现一致，即去甲基化可能导致功能恢复。 PRC2 位于去甲基化区域。总之，我们的研究确定了膀胱癌细胞在 5-Aza-CdR 治疗后普遍存在的转录组变化，并为当前临床试验中 5-Aza-CdR 的治疗效果提供了有价值的见解。
DNA methylation in gene promoters leads to gene silencing and is the therapeutic target of methylation inhibitors such as 5-Aza-2′-deoxycytidine (5-Aza-CdR). By analyzing the time series RNA-seq data (days 5, 9, 13, 17) obtained from human bladder cells exposed to 5-Aza-CdR with 0.1 uM concentration, we showed that 5-Aza-CdR can affect isoform switching and differential exon usage (i.e., exon-skipping), in addition to its effects on gene expression. We identified more than 2,000 genes with significant expression changes after 5-Aza-CdR treatment. Interestingly, 29 exon-skipping events induced by treatment were identified and validated experimentally. Particularly, exon-skipping event in Enhancer of Zeste Homologue 2 (EZH2) along with expression changes showed significant down regulation on Day 5 and Day 9 but returned to normal level on Day 13 and Day 17. EZH2 is a component of the multi-subunit polycomb repressive complex PRC2, and the down-regulation of exon-skipping event may lead to the regain of functional EZH2 which was consistent with our previous finding that demethylation may cause regain of PRC2 in demethylated regions. In summary, our study identified pervasive transcriptome changes of bladder cancer cells after treatment with 5-Aza-CdR, and provided valuable insights into the therapeutic effects of 5-Aza-CdR in current clinical trials.