Bonen Hamutal, Kol Nitzan, Shomron Noam, Leibowitz-Amit Raya, Quagliata Luca, Lorber Thomas, Sidi Yechezkel, Avni Dror
Laboratory of Molecular Cell Biology, Centre for Cancer Research and Department of Medicine C, Chaim Sheba Medical Centre, Tel-Hashomer 52621, Israel.
Functional Genomics Laboratory, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
Noncoding RNA. 2016 Jun 30;2(3):7. doi: 10.3390/ncrna2030007.
The threshold of 200 nucleotides (nt) conventionally divides non-coding RNAs (ncRNA) into long ncRNA (lincRNA, that have more than 200 nt in length) and the remaining ones which are grouped as "small" RNAs (microRNAs, small nucleolar RNAs and piwiRNAs). Promoter-associated RNAs (paRNAs) are generally 200-500 nt long and are transcribed from sequences positioned in the promoter regions of genes. Growing evidence suggests that paRNAs play a crucial role in controlling gene transcription. Here, we used deep sequencing to identify paRNA sequences that show altered expression in a melanoma cell line compared to normal melanocytes. Thousands of reads were mapped to transcription start site (TSS) regions. We limited our search to paRNAs adjacent to genes with an expression that differed between melanoma and normal melanocytes and a length of 200-500 nt that did not overlap the gene mRNA by more than 300 nt, ultimately leaving us with 11 such transcripts. Using quantitative real-time PCR (qRT-PCR), we found a significant correlation between the expression of the mRNA and its corresponding paRNA for two studied genes: and . Ectopic overexpression of the paRNA of (designated paHSPC) enhanced the expression of the mRNA, and an siRNA targeting the paHSPC152 decreased the expression of the mRNA. Overexpression of paHSPC also affected the epigenetic structure of its putative promoter region along with effects on several biologic features of melanoma cells. The ectopic expression of the paRNA to did not have any effect. Overall, our work indicates that paRNAs may serve as an additional layer in the regulation of gene expression in melanoma, thus meriting further investigation.
传统上，200个核苷酸（nt）的阈值将非编码RNA（ncRNA）分为长链非编码RNA（lincRNA，长度超过200 nt）和其余被归类为“小”RNA的RNA（微小RNA、小核仁RNA和piwiRNA）。启动子相关RNA（paRNA）一般长200 - 500 nt，从基因启动子区域的序列转录而来。越来越多的证据表明，paRNA在控制基因转录中起关键作用。在此，我们使用深度测序来鉴定与正常黑素细胞相比在黑素瘤细胞系中表达发生改变的paRNA序列。数千条读数被定位到转录起始位点（TSS）区域。我们将搜索范围限制在与黑素瘤和正常黑素细胞之间表达不同的基因相邻的paRNA，其长度为200 - 500 nt且与基因mRNA的重叠不超过300 nt，最终得到11个这样的转录本。使用定量实时PCR（qRT-PCR），我们发现两个研究基因的mRNA表达与其相应paRNA之间存在显著相关性： 和 。 （命名为paHSPC）的paRNA异位过表达增强了 mRNA的表达，而靶向paHSPC152的siRNA降低了 mRNA的表达。paHSPC的过表达还影响其假定启动子区域的表观遗传结构，并对黑素瘤细胞的几种生物学特性产生影响。 的paRNA异位表达没有任何作用。总体而言，我们的数据表明paRNA可能是黑素瘤基因表达调控中的一个额外层面，因此值得进一步研究。
