Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network

Xu, Xiwen; Zhou, Xionghui; Wang, Ruiru; Peng, Wenlei; An, Yue; Chen, Lingling

doi:10.1038/srep20715

Cited by 66 publications

(57 citation statements)

References 48 publications

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“…Heat stress (high temperature) impedes intracellular homeostasis and can lead to leaf lesions, severe delays in growth and development, risk of disease and even death (Bita andGerats 2013, Liu et al 2013). Studies have shown that under high-temperature stress, the bioaccumulation of cucumber seedling leaves is significantly inhibited, and the chlorophyll concentration is reduced (Zhou et al 2016). As a result, plants have developed specific adaptation mechanisms to address high-temperature stress.…”

Section: Introductionmentioning

confidence: 99%

Systematic identification and analysis of heat‐stress‐responsive lncRNAs, circRNAs and miRNAs with associated co‐expression and ceRNA networks in cucumber (Cucumis sativus L.)

Guo

Wang

et al. 2019

Physiologia Plantarum

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Researchers have shown that long non‐coding RNAs (lncRNAs) and circular RNAs (circRNAs) act as competitive endogenous RNAs (ceRNAs) and are mutually regulated by competition for binding to common microRNA response elements (MREs). However, a comprehensive identification and analysis of lncRNAs and circRNAs as ceRNAs have not yet been completed in cucumber (Cucumis sativus L.) exposed to high‐temperature stress. In our study, 32 663 coding transcripts, 2085 lncRNAs, 2477 circRNAs and 348 differentially expressed miRNAs were identified using RNA sequencing. In addition, six heat‐stress‐responsive miRNAs (five known and one novel miRNAs) and eight lncRNAs were selected for qPCR to confirm their expression profiles. By analyzing the cis effects of lncRNAs, we constructed a lncRNA‐mRNA co‐expression network. Based on the results, the corresponding lncRNAs play a regulatory role in the stress response in cucumber plants. In our study, the PatMatch software was used to predict the potential function of lncRNAs and circRNAs as ceRNAs. A total of 18 lncRNAs and seven circRNAs were predicted to bind to 114 differentially expressed miRNAs and compete with 359 mRNAs for miRNA binding sites. These mRNAs are predicted to be involved in various pathways, such as plant hormone signal transduction, plant–pathogen interaction and glutathione metabolism. Among them, TCONS_00031790, TCONS_00014332, TCONS_00014717, TCONS_00005674, novel_circ_001543 and novel_circ_000876 may interact with miR9748 by plant hormone signal transduction pathways in response to high‐temperature stress. Moreover, indole‐3‐acetic acid (IAA) and 1‐aminocyclopropane‐l‐carboxylic acid (ACC) levels decreased in the high‐temperature treatment group, indicating that IAA and ethylene signaling might be involved in response to high‐temperature stress. In this study, we conducted a full transcriptomic analysis in response to high‐temperature stress in cucumber and, for the first time, integrated the potential ceRNA functions of lncRNAs/circRNAs. The results provide a basis for studying the potential functions of lncRNAs/circRNAs in response to high‐temperature stress.

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Section: Introductionmentioning

confidence: 99%

Systematic identification and analysis of heat‐stress‐responsive lncRNAs, circRNAs and miRNAs with associated co‐expression and ceRNA networks in cucumber (Cucumis sativus L.)

Guo

Wang

et al. 2019

Physiologia Plantarum

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“…A total of 22 334 lincRNAs were obtained from rice and maize by performing both non-directional and strand-specific RNA-sequencing experiments (Wang et al, 2015a). Recently, 3170 lincRNA loci were identified using RNA-sequencing data from wild and phosphate-starved rice (Xu et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Evolutionary dynamics of lincRNA transcription in nine citrus species

Zhou

et al. 2019

The Plant Journal

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Summary Long intergenic non‐coding RNAs (lincRNAs) play important roles in various biological processes in plants. However, little information is known about the evolutionary characteristics of lincRNAs among closely related plant species. Here, we present a large‐scale comparative study of lincRNA transcription patterns in nine citrus species. By strand‐specific RNA‐sequencing, we identified 18 075 lincRNAs (14 575 lincRNA loci) from 34 tissue samples. The results indicated that the evolution of lincRNA transcription is more rapid than that of mRNAs. In total, 82.8–97.6% of sweet orange (Citrus sinensis) lincRNA genes were shown to have homologous sequences in other citrus genomes. However, only 15.5–28.8% of these genes had transcribed homologous lincRNAs in these citrus species, presenting a strong contrast to the high conservation of mRNA transcription (81.6–84.7%). Moreover, primitive and modern citrus lincRNAs were preferentially expressed in reproductive and vegetative organs, respectively. Evolutionarily conserved lincRNAs showed higher expression levels and lower tissue specificity than species‐specific lincRNAs. Notably, we observed a similar tissue expression pattern of homologous lincRNAs in sweet orange and pummelo (Citrus grandis), suggesting that these lincRNAs may be functionally conserved and selectively maintained. We also identified and validated a lincRNA with the highest expression in fruit that acts as an endogenous target mimic (eTM) of csi‐miR166c, and two lincRNAs that act as a precursor and target of csi‐miR166c, respectively. These lincRNAs together with csi‐miR166c could form an eTM166‐miR166c‐targeted lincRNA regulatory network that possibly affects citrus fruit development.

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“…Pi deficiency‐responsive lncRNAs have been identified in genome‐wide studies of Arabidopsis , Medicago and rice (Xu et al ; Yuan et al ; Wang et al ). These lncRNAs were shown to respond to Pi deficiency differently in roots and shoots, with more being detected in the shoot than in the root.…”

Section: Discussionmentioning

confidence: 99%

“…In plants, various biological processes, including flowering time, immunity, fertility, root development and photomorphogenesis, have been shown to be regulated by lncRNAs (Swiezewski et al ; Heo and Sung ; Ding et al ; Zhou et al ; Bardou et al ; Wang et al ; Kim and Sung ; Seo et al )_ENREF_18_ENREF_23. Increasing evidence also implicates lncRNAs in the regulation of Pi homeostasis (Franco‐Zorrilla et al ; Jabnoune et al ; Shah et al ; Cruz de Carvalho et al ; Xu et al ; Yuan et al ; Wang et al ).…”

Section: Introductionmentioning

confidence: 99%

Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency

Zhang

Zheng

Ham

et al. 2018

JIPB

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In response to phosphate (Pi) deficiency, it has been shown that micro-RNAs (miRNAs) and mRNAs are transported through the phloem for delivery to sink tissues. Growing evidence also indicates that long non-coding RNAs (lncRNAs) are critical regulators of Pi homeostasis in plants. However, whether lncRNAs are present in and move through the phloem, in response to Pi deficiency, remains to be established. Here, using cucumber as a model plant, we show that lncRNAs are enriched in the phloem translocation stream and respond, systemically, to an imposed Pi-stress. A well-known lncRNA, IPS1, the target mimic (TM) of miRNA399, accumulates to a high level in the phloem, but is not responsive to early Pi deficiency. An additional 24 miRNA TMs were also detected in the phloem translocation stream; among them miRNA171 TMs and miR166 TMs were induced in response to an imposed Pi stress. Grafting studies identified 22 lncRNAs which move systemically into developing leaves and root tips. A CU-rich PTB motif was further identified in these mobile lncRNAs. Our findings revealed that lncRNAs respond to Pi deficiency, non-cell-autonomously, and may act as systemic signaling agents to coordinate early Pi deficiency signaling, at the whole-plant level.

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Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network

Cited by 66 publications

References 48 publications

Systematic identification and analysis of heat‐stress‐responsive lncRNAs, circRNAs and miRNAs with associated co‐expression and ceRNA networks in cucumber (Cucumis sativus L.)

Systematic identification and analysis of heat‐stress‐responsive lncRNAs, circRNAs and miRNAs with associated co‐expression and ceRNA networks in cucumber (Cucumis sativus L.)

Evolutionary dynamics of lincRNA transcription in nine citrus species

Plant lncRNAs are enriched in and move systemically through the phloem in response to phosphate deficiency

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