Supporting data for "Landscape of RNA pseudouridylation in human hepatocellular carcinoma"

Hepatocellular carcinoma (HCC) is one of the most prevalent cancers in the world. In recent years, RNA modifications, such as N6-methyladenosine (m6A), has emerged as important players in cancer progression. They have been reported to regulate various RNA processes, such as splicing, nuclear export, mRNA stability and translation. However, the role of many RNA modifications in HCC development has remained largely unknown. Pseudouridine, an isomer of uridine, is an abundant RNA modifcation, which is present in mRNA, rRNA, tRNA and other non-coding RNA. In humans, pseudouridylation is catalyzed by 13 pseudouridine synthases (PUSs). In this study, we employed bisulfite-induced deletion sequencing (BID-seq), a novel sequencing technique allowing transcriptome-wide detection of pseudouridine at single-base resolution, to investigate the landscape of RNA pseudouridylation in HCC. Our integrated analysis has revealed the dysregulations and clinical significance of pseudouridine in HCC. Using a multi-omics approach, we also investigated the role of pseudouridine in mRNA translation. The dataset includes 1) numerical data for plotting figures in the study, 2) omics data in the study and 3) Western blot and cell colony images in the study.

肝细胞癌（Hepatocellular carcinoma）是全球最常见的恶性肿瘤之一。近年来，N6-甲基腺苷（N6-methyladenosine, m6A）等RNA修饰在肿瘤进展中发挥了关键调控作用，其可参与剪接、核输出、mRNA稳定性调控及翻译等多种RNA生物学过程。然而，多数RNA修饰在肝细胞癌发生发展中的作用仍未得到充分阐明。假尿苷（Pseudouridine）作为尿苷（uridine）的同分异构体，是一种丰度较高的RNA修饰形式，广泛存在于mRNA、rRNA、tRNA及其他非编码RNA中。在人类体内，假尿苷化修饰由13种假尿苷合酶（Pseudouridine synthases, PUSs）催化完成。本研究采用亚硫酸氢盐诱导缺失测序（bisulfite-induced deletion sequencing, BID-seq）这一可在单碱基分辨率下实现转录组范围假尿苷检测的新型测序技术，对肝细胞癌中RNA假尿苷化的整体调控图谱展开系统性探究。通过整合多维度数据分析，本研究揭示了假尿苷在肝细胞癌中的表达失调现象及其临床意义。此外，本研究借助多组学（multi-omics）方法，进一步探讨了假尿苷在mRNA翻译过程中的调控功能。本数据集包含以下三类内容：1）本研究中用于绘图的数值数据；2）本研究产生的多组学数据；3）本研究中的蛋白质免疫印迹（Western blot）及细胞集落成像结果。