Tsinghua University School of Medicine, Beijing 100084, China.
STAR Protoc. 2022 Jun 7;3(2):101442. doi: 10.1016/j.xpro.2022.101442. eCollection 2022 Jun 17.
Pervasive transcripts (PTs) are difficult to detect by steady-state RNA-seq, because they are degraded immediately by the nuclear exosome complex. Here, we describe a protocol illustrating a bioinformatic pipeline for genome-wide PTs annotation via chromatin-associated RNA-seq data upon DIS3 depletion. Compared to defining PTs by nascent RNA-seq such as TT-seq and PRO-seq, this protocol is more convenient and cost efficient. In addition, this protocol defines 3'-end of PTs more precisely, while reads from PRO-seq have a skew at the 5'-end. For complete details on the use and execution of this protocol, please refer to Liu et al. (2022).
全转录本（PTs）很难通过稳态 RNA-seq 检测，因为它们会被核外切体复合物立即降解。在这里，我们描述了一个通过 DIS3 耗竭的染色质相关 RNA-seq 数据进行全基因组 PTs 注释的生物信息学分析流程。与通过新生 RNA-seq（如 TT-seq 和 PRO-seq）定义 PTs 相比，该方案更方便、更经济。此外，该方案更精确地定义了 PTs 的 3'端，而 PRO-seq 的reads 在 5'端存在偏斜。有关该方案使用和执行的完整详细信息，请参考 Liu 等人（2022 年）。
