Genome-wide mapping of DNA-binding sites identifies stemness-related genes as directly repressed targets of SNAIL1 in colorectal cancer cells
Genome-wide mapping of DNA-binding sites identifies stemness-related genes as directly repressed targets of SNAIL1 in colorectal cancer cells
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DOI：
10.1038/s41388-019-0905-4
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发表时间：
2019-10-03
期刊：
影响因子：
8
通讯作者：
Hecht, Andreas
中科院分区：
文献类型：
--
作者：
Beyes, Sven;Andrieux, Geoffroy;Hecht, Andreas
在分子水平上，上皮-间质转化 (EMT) 需要广泛的转录重编程，这是由包括锌指 DNA 结合蛋白 SNAIL1 在内的一小群基因调控因子精心策划的。尽管 SNAIL1 是众所周知的 EMT 主要调节因子，但对其直接靶基因的了解并不完整。在这里，我们使用 ChIP-seq 来鉴定结直肠腺癌细胞中受 SNAIL1 直接调控的基因。当将 SNAIL1 的基因组分布与肠干细胞 (ISC) 转录因子 ASCL2 和 TCF7L2 的基因组分布进行比较时，我们观察到显着的重叠。此外，SNAIL1 ChIP-seq 峰与 ISC 特征基因的很大一部分相关。在两种结直肠癌细胞系中，我们验证了 SNAIL1 降低了 ISC 标志物的表达。同样，SNAIL1 直接抑制原癌基因 MYB 和长非编码 RNA (lncRNA) WiNTRLINC1（最近描述的 ASCL2 调节因子）。 SNAIL1 靶向 MYB 和 WiNTRLINC1 位点的多个调控元件，并在 MYB 下游调控元件的结合区域取代 ASCL2 和 TCF7L2。相关性分析和表达谱显示，SNAIL1 和 MYB 在结直肠癌细胞系和乳腺癌细胞系以及肿瘤转录组中呈反向平行表达，表明 SNAIL1 控制不同组织中 MYB 的表达。 MYB 功能丧失会减弱二维和三维细胞培养物中的增殖并损害克隆形成能力。因此，SNAIL1 介导的 MYB 和 ISC 标记物（如 WiNTRLINC1）的下调可能导致已知与 EMT 相关的增殖减少，同时消除结直肠癌细胞的干性特征。显然，EMT 与干性之间的关系在不同的肿瘤实体中有所不同。
At the molecular level, epithelial-to-mesenchymal transition (EMT) necessitates extensive transcriptional reprogramming which is orchestrated by a small group of gene-regulatory factors that include the zinc-finger DNA-binding protein SNAIL1. Although SNAIL1 is a well-known master regulator of EMT, knowledge of its immediate target genes is incomplete. Here, we used ChIP-seq to identify genes directly regulated by SNAIL1 in colorectal adenocarcinoma cells. When comparing the genomic distribution of SNAIL1 to that of the intestinal stem cell (ISC) transcription factors ASCL2 and TCF7L2, we observed a significant overlap. Furthermore, SNAIL1 ChIP-seq peaks are associated with a substantial fraction of ISC signature genes. In two colorectal cancer cell lines, we verified that SNAIL1 decreases ISC marker expression. Likewise, SNAIL1 directly represses the proto-oncogene MYB, and the long noncoding RNA (lncRNA) WiNTRLINC1, a recently described regulator of ASCL2. SNAIL1 targets multiple regulatory elements at the MYB and WiNTRLINC1 loci, and displaces ASCL2 and TCF7L2 from their binding regions at a MYB downstream regulatory element. Correlation analyses and expression profiling showed antiparallel expression of SNAIL1 and MYB in colorectal and breast cancer cell lines and tumor transcriptomes, suggesting that SNAIL1 controls MYB expression in different tissues. MYB loss-of-function attenuated proliferation and impaired clonogenicity in two- and three-dimensional cell cultures. Therefore, SNAIL1-mediated downregulation of MYB and ISC markers like WiNTRLINC1 likely contributes to the decrease in proliferation known to be associated with EMT, while simultaneously abrogating stemness features of colorectal cancer cells. Apparently, the relationship between EMT and stemness varies in different tumor entities.