Smart Computing Lab., Hallym University, Chuncheon 24252, Korea.
Center for Innovation in Engineering Education, Hanyang University, Seoul 04763, Korea.
Int J Mol Sci. 2020 Sep 4;21(18):6452. doi: 10.3390/ijms21186452.
RNA decay is an important regulatory mechanism for gene expression at the posttranscriptional level. Although the main pathways and major enzymes that facilitate this process are well defined, global analysis of RNA turnover remains under-investigated. Recent advances in the application of next-generation sequencing technology enable its use in order to examine various RNA decay patterns at the genome-wide scale. In this study, we investigated human RNA decay patterns using parallel analysis of RNA end-sequencing (PARE-seq) data from -knockdown HeLa cell lines, followed by a comparison of steady state and degraded mRNA levels from RNA-seq and PARE-seq data, respectively. The results revealed 1103 and 1347 transcripts classified as stable and unstable candidates, respectively. Of the unstable candidates, we found that a subset of the transcripts was polyadenylated and rapidly degraded. Additionally, we identified 380 endonucleolytically cleaved candidates by analyzing the most abundant PARE sequence on a transcript. Of these, 41.4% of genes were classified as unstable genes, which implied that their endonucleolytic cleavage might affect their mRNA stability. Furthermore, we identified 1877 decapped candidates, including and having the most abundant PARE sequences at the 5'-end positions of the transcripts. These results provide a useful resource for further analysis of RNA decay patterns in human cells.
RNA 衰变是转录后水平基因表达的重要调控机制。尽管促进这一过程的主要途径和主要酶已得到很好的定义，但 RNA 周转的全面分析仍未得到充分研究。新一代测序技术应用的最新进展使其可用于在全基因组范围内检查各种 RNA 衰变模式。在这项研究中，我们使用来自 -knockdown HeLa 细胞系的 RNA 末端测序（PARE-seq）数据的平行分析（PARE-seq）来研究人类 RNA 衰变模式，然后分别比较 RNA-seq 和 PARE-seq 数据中的稳态和降解 mRNA 水平。结果显示，分别有 1103 和 1347 个转录本被归类为稳定和不稳定的候选物。在不稳定的候选物中，我们发现一部分 polyadenylated 并迅速降解。此外，通过分析转录本上最丰富的 PARE 序列，我们鉴定了 380 个内切核酸酶切割的候选物。其中，41.4%的基因被归类为不稳定基因，这意味着它们的内切核酸酶切割可能会影响其 mRNA 稳定性。此外，我们还鉴定了 1877 个脱帽候选物，包括在转录本 5' 端位置具有最丰富 PARE 序列的 和 。这些结果为进一步分析人类细胞中的 RNA 衰变模式提供了有用的资源。
