Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers

Yang, Weibing; Schuster, Christoph; Prunet, Nathanaël; Dong, Qingkun; Landrein, Benoît; Wightman, Raymond; Meyerowitz, Elliot M.

doi:10.1104/pp.19.00980

Cited by 18 publications

(18 citation statements)

References 68 publications

(69 reference statements)

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“…The samples for ISH were prepared as described previously (W. Yang et al, 2019). Full expanded young leaves from 3‐week‐old cassava seedlings were fixed in 4% paraformaldehyde for 20 min and the leaves were then dehydrated and embedded in paraffin.…”

Section: Methodsmentioning

confidence: 99%

Global identification of full‐length cassava lncRNAs unveils the role of cold‐responsive intergenic lncRNA 1 in cold stress response

Cheng

Dong

et al. 2021

Plant Cell & Environment

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Long noncoding RNAs (lncRNAs) have been considered to be important regulators of gene expression in a range of biological processes in plants. A large number of lncRNAs have been identified in plants. However, most of their biological functions still remain to be determined. Here, we identified a total of 3004 lncRNAs in cassava under normal or cold‐treated conditions from Iso‐seq data. We further characterized a cold‐responsive intergenic lncRNA 1 (CRIR1) as a novel positive regulator of the plant response to cold stress. CRIR1 can be significantly induced by cold treatment. Ectopic expression of CRIR1 in cassava enhanced the cold tolerance of transgenic plants. Transcriptome analysis demonstrated that CRIR1 regulated a range of cold stress‐related genes in a CBF‐independent pathway. We further found that CRIR1 RNA can interact with cassava cold shock protein 5 (MeCSP5), which acts as an RNA chaperone, indicating that CRIR1 may recruit MeCSP5 to improve the translation efficiency of messenger RNA. In summary, our study extends the repertoire of lncRNAs in plants as well as their role in cold stress responses. Moreover, it reveals a mechanism by which CRIR1 affected cold stress response by modulating the expression of stress‐responsive genes and increasing their translational yield.

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Section: Methodsmentioning

confidence: 99%

Global identification of full‐length cassava lncRNAs unveils the role of cold‐responsive intergenic lncRNA 1 in cold stress response

Cheng

Dong

et al. 2021

Plant Cell & Environment

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“…The roots and stems of hydroponically grown Md seedlings were used as RNA FISH experimental materials. The roots and stems of ∼1-cm long were fixed as described previously ( Yang et al, 2020 ). The samples were then dehydrated and buried in paraffin ( Yang et al, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

RBP differentiation contributes to selective transmissibility of OPT3 mRNAs

Sun

Hao

et al. 2021

Plant Physiology

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Long-distance mobile mRNAs play key roles in gene regulatory networks that control plant development and stress tolerance. However, the mechanisms underlying species-specific delivery of mRNA still need to be elucidated. Here, the use of grafts involving highly heterozygous apple (Malus) genotypes allowed us to demonstrate that apple (Malus domestica) oligopeptide transporter3 (MdOPT3) mRNA can be transported over a long distance, from the leaf to the root, to regulate Fe uptake; however, the mRNA of Arabidopsis (Arabidopsis thaliana) oligopeptide transporter 3 (AtOPT3), the MdOPT3 homolog from A. thaliana, does not move from shoot to root. Reciprocal heterologous expression of the two types of mRNAs showed that the immobile AtOPT3 became mobile and moved from the shoot to the root in two woody species, Malus and Populus, while the mobile MdOPT3 became immobile in two herbaceous species, A. thaliana and tomato (Solanum lycopersicum). Furthermore, we demonstrated that the different transmissibility of OPT3 in A. thaliana and Malus might be caused by divergence in RNA-binding proteins (RBPs) between herbaceous and woody plants. This study provides insights into mechanisms underlying differences in mRNA mobility and validates the important physiological functions associated with this process.

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“…The samples for ISH were prepared as described previously (Yang, Schuster, Prunet, Dong, Landrein, Wightman & Meyerowitz, 2019). Full expanded young leaves from three-week-old cassava seedlings were fixed in 4% paraformaldehyde for 20 mins, and the leaves were then dehydrated and embedded in paraffin.…”

Section: Fluorescence In Situ Hybridization (Fish) Analysismentioning

confidence: 99%

Global identification of full-length cassava lncRNAs unveils the role of CRIR1 in cold stress response

Cheng

Dong

et al. 2021

Preprint

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Long non-coding RNAs (lncRNAs) have been considered to be important regulators of gene expression in a range of biological processes in plants. A large number of lncRNAs have been identified in plants. However, most of their biological functions still remain to be determined. Here, we identified total 3 004 lncRNAs in cassava under normal or cold-treated conditions from Iso-seq data. We further characterized a lincRNA, CRIR1, as a novel positive regulator of the plant response to cold stress. CRIR1 can be significantly induced by cold treatment. Overexpression of CRIR1 in cassava enhanced the cold tolerance of transgenic plants. Transcriptome analysis demonstrated that CRIR1 regulates a range of cold stress-related genes in a CBF-independent pathway. We further found that CRIR1 RNA can interact with MeCSP5, a homolog of the cold shock protein that acts as RNA chaperones, indicating that CRIR1 may recruit MeCSP5 to improve the translation efficiency of mRNA. In summary, our study greatly extends the repertoire of lncRNAs in plants as well as its responding to cold stress. Moreover, it reveals a sophisticated mechanism by which CRIR1 regulates plant cold stress response by modulating the expression of stress-responsive genes and increasing the translational yield.

show abstract

Visualization of Protein Coding, Long Noncoding, and Nuclear RNAs by Fluorescence in Situ Hybridization in Sections of Shoot Apical Meristems and Developing Flowers

Cited by 18 publications

References 68 publications

Global identification of full‐length cassava lncRNAs unveils the role of cold‐responsive intergenic lncRNA 1 in cold stress response

Global identification of full‐length cassava lncRNAs unveils the role of cold‐responsive intergenic lncRNA 1 in cold stress response

RBP differentiation contributes to selective transmissibility of OPT3 mRNAs

Global identification of full-length cassava lncRNAs unveils the role of CRIR1 in cold stress response

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