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

Feng Yu; Huanhuan Qi; Li Gao; Sen Luo; Rebecca Njeri Damaris; Yinggen Ke; Wenhua Wu; Pingfang Yang

doi:10.1016/j.gpb.2023.02.002

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

Genomics Proteomics Bioinformatics. 2023 Aug;21(4):788-804. doi: 10.1016/j.gpb.2023.02.002. Epub 2023 Feb 11.

Authors

Feng Yu¹, Huanhuan Qi¹, Li Gao¹, Sen Luo¹, Rebecca Njeri Damaris¹, Yinggen Ke¹, Wenhua Wu¹, Pingfang Yang²

Affiliations

¹ State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
² State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China. Electronic address: yangpf@hubu.edu.cn.

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.

Keywords: Direct RNA sequencing; N(5)-methylcytosine; N(6)-methyladenosine; Polyadenylated transcriptome; Rice.

MeSH terms

Gene Expression Profiling
High-Throughput Nucleotide Sequencing / methods
Oryza* / genetics
RNA Processing, Post-Transcriptional
RNA*
RNA, Messenger
Sequence Analysis, RNA
Transcriptome

Substances

RNA
RNA, Messenger