The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold

Moison, Michaël; Pacheco, Javier Martínez; Lucero, Leandro; Fonouni‐Farde, Camille; Rodríguez-Melo, Johan; Mansilla, Natanael; Christ, Aurélie; Bazin, Jérémie; Benhamed, Moussa; Ibáñez, Fernando; Crespi, Martín; Estevez, José M.; Ariel, Federico

doi:10.1016/j.molp.2021.03.008

Cited by 78 publications

(80 citation statements)

References 69 publications

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“…S6, Additional file 1 : Table S6). Several genes in ‘green’ module encoded by WRKY DNA-BINDING PROTEIN (WRKY) TFs with high connectivity, such as WRKY DNA-BINDING PROTEIN 42 ( WRKY42 , ThWRKY-93 ), WRKY DNA-BINDING PROTEIN 33 ( WRKY33 , ThWRKY-2 and ThWRKY-70 ) and WRKY DNA-binding protein 4 ( WRKY4 , ThWRKY-56 ), were related to response to abiotic stress; their homologs are also involved in response to abiotic stress in Arabidopsis [ 48 – 50 ] (Fig. 6 c).…”

Section: Resultsmentioning

confidence: 99%

Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida

et al. 2022

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Background Seed germination is a series of ordered physiological and morphogenetic processes and a critical stage in plant life cycle. Tamarix hispida is one of the most salt-tolerant plant species; however, its seed germination has not been analysed using combined transcriptomics and metabolomics. Results Transcriptomic sequencing and widely targeted metabolomics were used to detect the transcriptional metabolic profiles of T. hispida at different stages of seed germination and young seedling growth. Transcriptomics showed that 46,538 genes were significantly altered throughout the studied development period. Enrichment study revealed that plant hormones, such as auxin, ABA, JA and SA played differential roles at varying stages of seed germination and post-germination. Metabolomics detected 1022 metabolites, with flavonoids accounting for the highest proportion of differential metabolites. Combined analysis indicated that flavonoid biosynthesis in young seedling growth, such as rhoifolin and quercetin, may improve the plant’s adaptative ability to extreme desert environments. Conclusions The differential regulation of plant hormones and the accumulation of flavonoids may be important for the seed germination survival of T. hispida in response to salt or arid deserts. This study enhanced the understanding of the overall mechanism in seed germination and post-germination. The results provide guidance for the ecological value and young seedling growth of T. hispida.

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Section: Resultsmentioning

confidence: 99%

Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida

et al. 2022

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“…lncRNAs have also been shown to contribute to antiviral innate immune responses in mammalian systems (Ouyang et al, 2016;Liu et al, 2020). Similarly, lncRNAs in plants have also been shown to modulate gene expression, epigenetic regulation and response to stresses (Di et al, 2014;Wang et al, 2018;Hamid et al, 2020;Moison et al, 2021). However, the presence of lncRNAs in the extracellular space of plant cells and their roles in cell-to-cell communication or immune responses have not been investigated yet.…”

Section: Discussionmentioning

confidence: 99%

Arabidopsis Apoplastic Fluid Contains sRNA- and Circular RNA-Protein Complexes that Are Located Outside Extracellular Vesicles

Karimi

Baldrich

Rutter

et al. 2021

Preprint

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Previously, we have shown that apoplastic wash fluid purified from Arabidopsis leaves contains small RNAs (sRNAs). To investigate whether these sRNAs are encapsulated inside extracellular vesicles (EVs), we treated EVs isolated from Arabidopsis leaves with the protease trypsin and RNase A, which should degrade RNAs located outside EVs but not those located inside. These analyses revealed that apoplastic RNAs are mostly located outside EVs and are associated with proteins. Further analyses of these extracellular RNAs (exRNAs) revealed that they comprise both sRNAs and long non-coding RNAs (lncRNAs), including circular RNAs (circRNAs). We also found that exRNAs are highly enriched in the post-transcriptional modification N6-methyladenine (m(6)A). Consistent with this, we identified a putative m(6)A-binding protein in apoplastic wash fluid, GLYCINE-RICH RNA-BINDING PROTEIN 7 (GRP7), as well as the small RNA-binding protein ARGONAUTE2 (AGO2). These two proteins co-immunoprecipitated with each other, and with lncRNAs, including circRNAs. Mutation of GRP7 or AGO2 caused changes in both the sRNA and lncRNA content of apoplastic wash fluid, suggesting that these proteins contribute to the secretion and/or stabilization of exRNAs. We propose that these extravesicular RNAs mediate host-induced gene silencing, rather than RNA inside EVs.

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“…Because of the construction of strand-specific libraries, we also predicted lncRNAs harbouring m 6 A peaks and identified DMMSs. While lncRNAs are known to play important roles in mediating transcriptional and posttranscriptional regulation ( Cantile et al, 2021 ; Moison et al, 2021 ), their biological functions in regards to m 6 A modification remain unknown. In general, the m 6 A modification of lncRNAs is very common in cancers.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Analysis of N6-Methyladenosine (m6A) Methylation in Neuromyelitis Optica Spectrum Disorders

Hong

Ding

et al. 2021

Front. Genet.

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Background: N6-Methyladenosine (m6A) methylation is the most prevalent internal posttranscriptional modification on mammalian mRNA. But its role in neuromyelitis optica spectrum disorders (NMOSD) is not known.Aims: To explore the mechanism of m6A in NMOSD patients.Methods: This study assessed the m6A methylation levels in blood from two groups: NMOSD patients and healthy controls. Methylated RNA immunoprecipitation Sequencing (MeRIP-seq) and RNA-seq were performed to assess differences in m6A methylation between NMOSD patients and healthy controls. Ultra-high performance liquid chromatography coupled with triple quadruple mass spectrometry (UPLC-QQQ-MS) method was performed to check m6A level. Differential m6A methylation genes were validated by MeRIP-qPCR.Results: Compared with that in the control group, the total m6A level was decreased in the NMOSD group. Genes with upregulated methylation were primarily enriched in processes associated with RNA splicing, mRNA processing, and innate immune response, while genes with downregulated methylation were enriched in processes associated with the regulation of transcription, DNA-templating, and the positive regulation of I-kappa B kinase/NF-kappa B signalling.Conclusion: These findings demonstrate that differential m6A methylation may act on functional genes to regulate immune homeostasis in NMOSD.

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The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold

Cited by 78 publications

References 69 publications

Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida

Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida

Arabidopsis Apoplastic Fluid Contains sRNA- and Circular RNA-Protein Complexes that Are Located Outside Extracellular Vesicles

Comprehensive Analysis of N6-Methyladenosine (m6A) Methylation in Neuromyelitis Optica Spectrum Disorders

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