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新方法可从纳米孔直接RNA测序中识别差异化的RNA修饰
2021-07-25 12:16

新加坡A*STAR研究所Jonathan Göke等研究人员合作开发出一项新技术,可从纳米孔直接RNA测序中识别差异化的RNA修饰。2021年7月19日,国际知名学术期刊《自然—生物技术》在线发表了这一成果。

研究人员开发了一种计算方法,xPore,可从纳米孔直接RNA测序(RNA-seq)数据中识别不同的RNA修饰。研究人员在全转录组的N6-甲基腺苷(m6A)分析数据上评估了这个方法,从而证明xPore能以单碱基分辨率识别m6A位点的位置,估计细胞中被修饰的RNA物种的比例,并量化不同条件下的不同修饰率。

研究人员将xPore应用于六个细胞系和多发性骨髓瘤患者样本的直接RNA-seq数据,但没有匹配的对照样本,发现许多m6A位点在不同的细胞类型中都被保留下来,而有一个亚群在其修饰率上表现出显著的差异。这些结果表明,RNA修饰可以从直接RNA-seq数据中以较高的精度识别出来,从而能够从一个高通量实验中分析不同的修饰和表达。

据了解,RNA修饰(如m6A)调节了细胞RNA物种的功能。然而,量化RNA修饰的差异一直是个挑战。

附:英文原文

Title: Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

Author: Ploy N. Pratanwanich, Fei Yao, Ying Chen, Casslynn W. Q. Koh, Yuk Kei Wan, Christopher Hendra, Polly Poon, Yeek Teck Goh, Phoebe M. L. Yap, Jing Yuan Chooi, Wee Joo Chng, Sarah B. Ng, Alexandre Thiery, W. S. Sho Goh, Jonathan Gke

Issue&Volume: 2021-07-19

Abstract: RNA modifications, such as N6-methyladenosine (m6A), modulate functions of cellular RNA species. However, quantifying differences in RNA modifications has been challenging. Here we develop a computational method, xPore, to identify differential RNA modifications from nanopore direct RNA sequencing (RNA-seq) data. We evaluate our method on transcriptome-wide m6A profiling data, demonstrating that xPore identifies positions of m6A sites at single-base resolution, estimates the fraction of modified RNA species in the cell and quantifies the differential modification rate across conditions. We apply xPore to direct RNA-seq data from six cell lines and multiple myeloma patient samples without a matched control sample and find that many m6A sites are preserved across cell types, whereas a subset exhibit significant differences in their modification rates. Our results show that RNA modifications can be identified from direct RNA-seq data with high accuracy, enabling analysis of differential modifications and expression from a single high-throughput experiment. m6A RNA modifications are quantified in cancer patient samples and cell lines using nanopore sequencing.

DOI: 10.1038/s41587-021-00949-w

Source: https://www.nature.com/articles/s41587-021-00949-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


本期文章:《自然—生物技术》:Online/在线发表

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