NERD-seq：纳米孔直接 RNA 测序的新方法，可扩展非编码 RNA 的代表性

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-08-28 DOI:10.1186/s13059-024-03375-8

Luke Saville, Li Wu, Jemaneh Habtewold, Yubo Cheng, Babita Gollen, Liam Mitchell, Matthew Stuart-Edwards, Travis Haight, Majid Mohajerani, Athanasios Zovoilis

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引用次数: 0

摘要

非编码 RNA（ncRNA）是经常被记录的 RNA 修饰底物。纳米孔技术可对 RNA 进行直接测序，并检测修饰的核碱基。通常，直接 RNA 测序使用多聚腺苷酸选择，主要研究 mRNA 基因表达。在这里，我们介绍 NERD-seq，它能检测标准方法排除的多种非编码 RNA，以及原生多聚腺苷酸转录本。以神经组织为原理验证，我们发现 NERD-seq 扩展了经常修饰的非编码 RNAs 的代表性，如 snoRNAs、snRNAs、scRNAs、srpRNAs、tRNAs 和 rRFs。NERD-seq代表了一种RNA-seq方法，可同时研究脑组织及其他组织中的mRNA和ncRNA表转录组。

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NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs

Non-coding RNAs (ncRNAs) are frequently documented RNA modification substrates. Nanopore Technologies enables the direct sequencing of RNAs and the detection of modified nucleobases. Ordinarily, direct RNA sequencing uses polyadenylation selection, studying primarily mRNA gene expression. Here, we present NERD-seq, which enables detection of multiple non-coding RNAs, excluded by the standard approach, alongside natively polyadenylated transcripts. Using neural tissues as a proof of principle, we show that NERD-seq expands representation of frequently modified non-coding RNAs, such as snoRNAs, snRNAs, scRNAs, srpRNAs, tRNAs, and rRFs. NERD-seq represents an RNA-seq approach to simultaneously study mRNA and ncRNA epitranscriptomes in brain tissues and beyond.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.