ArticleAnnals of botany2019
Genome-wide identification of long non-coding RNA targets of the tomato MADS box transcription factor RIN and function analysis.
Article in Annals of botany, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 60 citations in OpenAlex.
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- Efficient large fragment deletion in plants: double pairs of sgRNAs are better than dual sgRNAs.Horticulture research · 2023Article
- Transcriptional profiling of long noncoding RNAs associated with flower color formation in Ipomoea nil.Planta · 2023Article
- Coordinating Diverse Functions of miRNA and lncRNA in Fleshy Fruit.Plants (Basel, Switzerland) · 2023Review
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- Genome-wide identification and characterization of long noncoding RNAs during peach (Prunus persica) fruit development and ripening.Scientific reports · 2022Article
- Novel Translational and Phosphorylation Modification Regulation Mechanisms of Tomato (International journal of molecular sciences · 2021Article
- Genome editing in fruit, ornamental, and industrial crops.Transgenic research · 2021Review
- Review
- Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation.Computational and structural biotechnology journal · 2021Review
- From "Dark Matter" to "Star": Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs.Frontiers in plant science · 2021Review
- Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated WithFrontiers in plant science · 2021Article
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
BACKGROUND AND
aimsIn recent years, increasing numbers of long non-coding RNAs (lncRNAs) have been identified in humans, animals and plants, and several of them have been shown to play important roles in diverse biological processes. However, little work has been performed on the regulation mechanism of lncRNA biogenesis and expression, especially in plants. Compared with studies of tomato MADS-box transcription factor RIPENING INHIBITOR (RIN) target coding genes, there are few reports on its relationship to non-coding RNAs. The aim of the present study was to identify and explore the specific role of RIN target lncRNAs in tomato fruit development and ripening.
methodslncRNA targets of RIN were identified by chromatin immunoprecipitation sequencing (ChIP-seq) combined with RNA deep sequencing analysis. Six selected lncRNA targets were validated by quantitative real-time PCR, ChIP and electrophoretic mobility shift assays, and we further confirmed differential expression between wild-type and ripening-deficient mutant fruit, and RIN direct binding in the promoter regions. By means of virus-induced gene silencing (VIGS) assays and a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing strategy, the ripening-related function of a specific target lncRNA (lncRNA2155) was studied. KEY
resultsWe identified 187 lncRNAs as direct RIN targets, which exhibited RIN binding sites in their promoters and showed different expression between the wild-type and rin mutant. Six target lncRNAs were shown to bind with RIN directly in their promoters in vivo and in vitro. Moreover, using CRISPR/Cas9 technology to knock out the locus of the target lncRNA2155 indicated that it delayed fruit ripening in tomato.
conclusionsCollectively, these findings provide new insight into RIN in the transcriptional regulation of lncRNAs and suggest that lncRNAs will contribute to a better understanding of the RIN regulatory network that controls fruit ripening.
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