背景:lncRNAELF3-AS1的生物学功能在癌症中仍然未知。肿瘤转移中SNAI2过度表达的原因仍不清楚。反义lncRNAs和相邻蛋白编码基因高表达的分子机制尚不清楚。
方法:RNA-seq,进行CHIP和双荧光素酶报告基因测定以鉴定由SNAI2调节的lncRNA。进行了MicroRNA-seq和RNA-seq研究以揭示ELF3-AS1在GC中的生物学功能。进行RNA下拉和CHIRP测定以鉴定与ELF3-AS1相互作用的蛋白质。
结果:通过RNA测序鉴定了总共123个lncRNA在GC中被SNAI2调节。ELF3基因和反义lncRNAELF3-AS1均被SNAI2或SNAI1转录抑制。ELF3-AS1和ELF3下调预测GC预后不良。核定位lncRNAELF3-AS1通过抑制G1/S转换和组蛋白合成负调控GC细胞周期进程。ELF3-AS1主要通过抑制SNAI2信号抑制GC转移。此外,ELF3-AS1通过RNA-RNA相互作用调节ELF3mRNA稳定性。由ELF3mRNA和lncRNA形成的RNA双链体ELF3-AS1直接与双链RNA(dsRNA)结合蛋白复合物ILF2/ILF3(NF45/NF90)相互作用。反过来,ILF2/ILF3复合物通过影响dsRNA稳定性动态调节ELF3-AS1和ELF3的表达。
结论:SNAI2-ELF3-AS1反馈环在转录和转录后水平调节ELF3的表达,并通过维持SNAI2过表达来驱动胃癌转移。ILF2/ILF3复合物在调节dsRNA稳定性中起关键作用。此外,我们的工作提供了一个直接的证据,即头对头反义lncRNAs可以与相邻的编码基因共享启动子,这使得它们的表达受到类似的转录调控,导致高共表达。
BACKGROUND: The biological function of lncRNA ELF3-AS1 remains largely unknown in cancers. The cause of SNAI2 overexpression in tumor metastasis remains largely unclear. The molecular mechanisms underlying the high co-expression of antisense lncRNAs and adjacent protein-coding genes remains unclear.
METHODS: RNA-seq, CHIP and dual-luciferase reporter assay were performed to identify lncRNAs regulated by SNAI2. MicroRNA-seq and RNA-seq studies were conducted to reveal the biological function of ELF3-AS1 in GC. RNA pulldown and CHIRP assays were conducted to identify the protein that interacts with ELF3-AS1.
RESULTS: A total of 123 lncRNAs were identified to be regulated by SNAI2 in GC by RNA sequencing. The ELF3 gene and antisense lncRNA ELF3-AS1 were both transcriptionally repressed by SNAI2 or SNAI1. Down-regulation of ELF3-AS1 and ELF3 predicted poor prognosis in GC. Nuclear localized lncRNA ELF3-AS1 negatively regulated GC cell cycle progression via suppressing G1/S transition and histone synthesis. ELF3-AS1 mainly inhibited GC metastasis by repressing SNAI2 signaling. Additionally, ELF3-AS1 modulated ELF3 mRNA stability by RNA-RNA interaction. The RNA duplexes formed by ELF3 mRNA and lncRNA ELF3-AS1 directly interacted with the double-stranded RNA (dsRNA) binding protein complex ILF2/ILF3 (NF45/NF90). In turn, the ILF2/ILF3 complex dynamically regulated the expression of ELF3-AS1 and ELF3 by affecting the dsRNA stability.
CONCLUSIONS: The SNAI2-ELF3-AS1 feedback loop regulates ELF3 expression at transcriptional and post-transcriptional levels and drives gastric cancer metastasis by maintaining SNAI2 overexpression. The ILF2/ILF3 complex plays a critical role in regulating dsRNA stability. In addition, our work provides a direct evidence that head-to-head antisense lncRNAs can share promoters with neighboring coding genes, which make their expression subject to similar transcriptional regulation, leading to high co-expression.