小柯机器人

美国芝加哥大学Chuan He，Qing Dai和Li-Sheng Zhang共同合作近期取得重要工作进展，他们研究利用BID-seq定量测序法在碱基分辨率下揭示哺乳动物mRNA中丰富的假尿苷。相关工作2022年10月27日在线发表于《自然—生物技术》学杂志上。

研究人员报道了亚硫酸盐诱导的缺失测序法（BID-seq），该方法利用亚硫酸氢盐介导的反应，在没有胞嘧啶脱氨基的情况下，通过反转录将假尿苷按比例转化为缺失。BID-seq能够在几种人类细胞系和12种不同的小鼠组织中检测到丰富的Ψ位点，只需要10-20 ng的RNA输入量。研究组发现了哺乳动物mRNA中Ψ的一致序列，并将不同的“writer”蛋白分配到单个Ψ沉积位点。研究结果揭示了TRUB1在人类癌细胞中安装的Ψ位点的转录稳定作用。研究人员还检测到哺乳动物mRNA终止密码子内Ψ的存在，并证实了Ψ在体内促进终止密码子读通方面的作用。BID-seq法将使未来对Ψ在各种生物过程中的作用的研究成为可能。

据介绍，哺乳动物mRNA中假尿苷（Ψ）的功能特征由于缺乏一种在整个转录组中绘制Ψ的定量方法而受到阻碍。

附：英文原文

Title: Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution

Author: Dai, Qing, Zhang, Li-Sheng, Sun, Hui-Lung, Pajdzik, Kinga, Yang, Lei, Ye, Chang, Ju, Cheng-Wei, Liu, Shun, Wang, Yuru, Zheng, Zhong, Zhang, Linda, Harada, Bryan T., Dou, Xiaoyang, Irkliyenko, Iryna, Feng, Xinran, Zhang, Wen, Pan, Tao, He, Chuan

Issue&Volume: 2022-10-27

Abstract: Functional characterization of pseudouridine (Ψ) in mammalian mRNA has been hampered by the lack of a quantitative method that maps Ψ in the whole transcriptome. We report bisulfite-induced deletion sequencing (BID-seq), which uses a bisulfite-mediated reaction to convert pseudouridine stoichiometrically into deletion upon reverse transcription without cytosine deamination. BID-seq enables detection of abundant Ψ sites with stoichiometry information in several human cell lines and 12 different mouse tissues using 10–20ng input RNA. We uncover consensus sequences for Ψ in mammalian mRNA and assign different ‘writer’ proteins to individual Ψ deposition. Our results reveal a transcript stabilization role of Ψ sites installed by TRUB1 in human cancer cells. We also detect the presence of Ψ within stop codons of mammalian mRNA and confirm the role of Ψ in promoting stop codon readthrough in vivo. BID-seq will enable future investigations of the roles of Ψ in diverse biological processes.

DOI: 10.1038/s41587-022-01505-w

Source: https://www.nature.com/articles/s41587-022-01505-w

Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
投稿链接：https://mts-nbt.nature.com/cgi-bin/main.plex