Müller Jason M, Altendorfer Elisabeth, Freier Susanne, Moos Katharina, Mayer Andreas, Tresch Achim
Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany.
Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, 50924 Cologne, Germany.
NAR Genom Bioinform. 2025 Feb 18;7(1):lqaf006. doi: 10.1093/nargab/lqaf006. eCollection 2025 Mar.
We introduce Halfpipe, a tool for analyzing RNA-seq data from metabolic RNA labeling experiments. Its main features are the absolute quantification of 4-thiouridine-labeling-induced T>C conversions in the data as generated by SLAM-seq, calculating the proportion of newly synthesized transcripts, and estimating subcellular RNA half-lives. Halfpipe excels at correcting critical biases caused by typically low labeling efficiency. We measure and compare the RNA metabolism in the G1 phase and during the mitosis of synchronized human cells. We find that RNA half-lives of constantly expressed RNAs are similar in mitosis and G1 phase, suggesting that RNA stability of those genes is constant throughout the cell cycle. Our estimates correlate well with literature values and with known RNA sequence features. Halfpipe is freely available at https://github.com/IMSBCompBio/Halfpipe.
我们介绍了Halfpipe，这是一种用于分析来自代谢RNA标记实验的RNA测序数据的工具。其主要功能包括对SLAM-seq生成的数据中4-硫尿苷标记诱导的T>C转换进行绝对定量、计算新合成转录本的比例以及估计亚细胞RNA半衰期。Halfpipe擅长纠正因通常较低的标记效率而导致的关键偏差。我们测量并比较了同步化人类细胞在G1期和有丝分裂期间的RNA代谢情况。我们发现，持续表达的RNA的半衰期在有丝分裂和G1期相似，这表明这些基因的RNA稳定性在整个细胞周期中是恒定的。我们的估计值与文献值以及已知的RNA序列特征相关性良好。Halfpipe可在https://github.com/IMSBCompBio/Halfpipe上免费获取。
