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Tang Y, Yan X, Gu C, Yuan X. Biogenesis, Trafficking, and Function of Small RNAs in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:825477. [PMID: 35251095 PMCID: PMC8891129 DOI: 10.3389/fpls.2022.825477] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/19/2022] [Indexed: 05/03/2023]
Abstract
Small RNAs (sRNAs) encoded by plant genomes have received widespread attention because they can affect multiple biological processes. Different sRNAs that are synthesized in plant cells can move throughout the plants, transport to plant pathogens via extracellular vesicles (EVs), and transfer to mammals via food. Small RNAs function at the target sites through DNA methylation, RNA interference, and translational repression. In this article, we reviewed the systematic processes of sRNA biogenesis, trafficking, and the underlying mechanisms of its functions.
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Affiliation(s)
- Yunjia Tang
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaoning Yan
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Chenxian Gu
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaofeng Yuan
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, China
- Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
- *Correspondence: Xiaofeng Yuan,
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Jia L, Li Y, Huang F, Jiang Y, Li H, Wang Z, Chen T, Li J, Zhang Z, Yao W. LIRBase: a comprehensive database of long inverted repeats in eukaryotic genomes. Nucleic Acids Res 2021; 50:D174-D182. [PMID: 34643715 PMCID: PMC8728187 DOI: 10.1093/nar/gkab912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/20/2021] [Accepted: 09/25/2021] [Indexed: 11/14/2022] Open
Abstract
Small RNAs (sRNAs) constitute a large portion of functional elements in eukaryotic genomes. Long inverted repeats (LIRs) can be transcribed into long hairpin RNAs (hpRNAs), which can further be processed into small interfering RNAs (siRNAs) with vital biological roles. In this study, we systematically identified a total of 6 619 473 LIRs in 424 eukaryotic genomes and developed LIRBase (https://venyao.xyz/lirbase/), a specialized database of LIRs across different eukaryotic genomes aiming to facilitate the annotation and identification of LIRs encoding long hpRNAs and siRNAs. LIRBase houses a comprehensive collection of LIRs identified in a wide range of eukaryotic genomes. In addition, LIRBase not only allows users to browse and search the identified LIRs in any eukaryotic genome(s) of interest available in GenBank, but also provides friendly web functionalities to facilitate users to identify LIRs in user-uploaded sequences, align sRNA sequencing data to LIRs, perform differential expression analysis of LIRs, predict mRNA targets for LIR-derived siRNAs, and visualize the secondary structure of candidate long hpRNAs encoded by LIRs. As demonstrated by two case studies, collectively, LIRBase bears the great utility for systematic investigation and characterization of LIRs and functional exploration of potential roles of LIRs and their derived siRNAs in diverse species.
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Affiliation(s)
- Lihua Jia
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.,National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Yang Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Fangfang Huang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Yingru Jiang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Haoran Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhizhan Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Tiantian Chen
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiaming Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhang Zhang
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China
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