Genome-wide profiling of rice Double-stranded RNA-Binding Protein 1-associated RNAs by targeted RNA editing.
Journal
Plant physiology
ISSN: 1532-2548
Titre abrégé: Plant Physiol
Pays: United States
ID NLM: 0401224
Informations de publication
Date de publication:
31 05 2023
31 05 2023
Historique:
received:
12
10
2022
accepted:
06
02
2023
pmc-release:
13
03
2024
medline:
2
6
2023
pubmed:
14
3
2023
entrez:
13
3
2023
Statut:
ppublish
Résumé
RNA-binding proteins (RBPs) play essential roles in regulating gene expression. However, the RNA ligands of RBPs are poorly understood in plants, not least due to the lack of efficient tools for genome-wide identification of RBP-bound RNAs. An RBP-fused adenosine deaminase acting on RNA (ADAR) can edit RBP-bound RNAs, which allows efficient identification of RNA ligands of RBPs in vivo. Here, we report the RNA editing activities of the ADAR deaminase domain (ADARdd) in plants. Protoplast experiments indicated that RBP-ADARdd fusions efficiently edited adenosines within 41 nucleotides (nt) of their binding sites. We then engineered ADARdd to profile the RNA ligands of rice (Oryza sativa) Double-stranded RNA-Binding Protein 1 (OsDRB1). Overexpressing the OsDRB1-ADARdd fusion protein in rice introduced thousands of A-to-G and T-to-C RNA‒DNA variants (RDVs). We developed a stringent bioinformatic approach to identify A-to-I RNA edits from RDVs, which removed 99.7% to 100% of background single-nucleotide variants in RNA-seq data. This pipeline identified a total of 1,798 high-confidence RNA editing (HiCE) sites, which marked 799 transcripts as OsDRB1-binding RNAs, from the leaf and root samples of OsDRB1-ADARdd-overexpressing plants. These HiCE sites were predominantly located in repetitive elements, 3'-UTRs, and introns. Small RNA sequencing also identified 191 A-to-I RNA edits in miRNAs and other sRNAs, confirming that OsDRB1 is involved in sRNA biogenesis or function. Our study presents a valuable tool for genome-wide profiling of RNA ligands of RBPs in plants and provides a global view of OsDRB1-binding RNAs.
Identifiants
pubmed: 36913253
pii: 7076677
doi: 10.1093/plphys/kiad158
pmc: PMC10231461
doi:
Substances chimiques
MicroRNAs
0
Adenosine
K72T3FS567
Adenosine Deaminase
EC 3.5.4.4
RNA-Binding Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
805-820Informations de copyright
© American Society of Plant Biologists 2023. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Déclaration de conflit d'intérêts
Conflict of interest statement. None declared.
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