Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice.

IF 11.5 2区 生物学 Q1 GENETICS & HEREDITY Genomics, Proteomics & Bioinformatics Pub Date : 2023-08-01 Epub Date: 2023-02-11 DOI:10.1016/j.gpb.2023.02.002
Feng Yu, Huanhuan Qi, Li Gao, Sen Luo, Rebecca Njeri Damaris, Yinggen Ke, Wenhua Wu, Pingfang Yang
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Abstract

Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies. However, the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA, which is an important element for the post-transcriptional regulation of gene expression. To comprehensively profile the N6-methyladenosine (m6A) and N5-methylcytosine (m5C) modifications on RNA, direct RNA sequencing (DRS) using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice. Approximately 94 million reads were generated, with an average length ranging from 619 nt to 1013 nt, and a total of 45,707 transcripts across 34,763 genes were detected. Expression profiles of transcripts at the isoform level were quantified among tissues. Transcriptome-wide mapping of m6A and m5C demonstrated that both modifications exhibited tissue-specific characteristics. The transcripts with m6A modifications tended to be modified by m5C, and the transcripts with modifications presented higher expression levels along with shorter poly(A) tails than transcripts without modifications, suggesting the complexity of gene expression regulation. Gene Ontology analysis demonstrated that m6A- and m5C-modified transcripts were involved in central metabolic pathways related to the life cycle, with modifications on the target genes selected in a tissue-specific manner. Furthermore, most modified sites were located within quantitative trait loci that control important agronomic traits, highlighting the value of cloning functional loci. The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome, improving our understanding of the rice genome.

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通过直接RNA测序鉴定RNA修饰揭示水稻表观转录组动力学的复杂性。
基于cDNA文库高通量测序的转录组分析已广泛应用于功能基因组研究。然而,大多数RNA测序技术对cDNA的依赖限制了它们检测RNA上的碱基修饰的能力,而RNA修饰是基因转录后调控的重要元素。为了全面分析n6 -甲基腺苷(m6A)和n5 -甲基胞嘧啶(m5C)在RNA上的修饰,采用最新的牛津纳米孔技术(Oxford Nanopore Technology)对水稻6个组织的转录组进行了直接RNA测序(DRS)分析。共生成了约9400万个reads,平均长度为619 ~ 1013 nt,共检测到34,763个基因的45707个转录本。在同工型水平上定量组织间转录本的表达谱。m6A和m5C的转录组图谱显示,这两种修饰都具有组织特异性。m6A修饰的转录本更容易被m5C修饰,修饰后的转录本比未修饰的转录本表达量更高,多A尾更短,表明基因表达调控的复杂性。基因本体分析表明,m6A和m5c修饰的转录本参与了与生命周期相关的中枢代谢途径,并以组织特异性的方式选择了靶基因的修饰。此外,大多数修饰位点位于控制重要农艺性状的数量性状位点内,这突出了克隆功能位点的价值。研究结果对水稻转录组和表转录组的表达调控复杂性和数据来源提供了新的认识,提高了我们对水稻基因组的认识。
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来源期刊
Genomics, Proteomics & Bioinformatics
Genomics, Proteomics & Bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry
CiteScore
14.30
自引率
4.20%
发文量
844
审稿时长
61 days
期刊介绍: Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.
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