Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+ Channel Blocker.

Feixiong Zhang,Mengyue Xu,Jiaxi Liu,Keshi Ma,Wenshuo Shi

doi:10.3389/fpls.2018.00244

Feixiong Zhang, Mengyue Xu + Show 3 more

Open Access

https://doi.org/10.3389/fpls.2018.00244

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Abstract

It remains unclear whether plant lncRNAs are responsive to Ca2+-channel blocking. When using the Ca2+-channel blocker, LaCl3, to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl3-treated groups. The effect of the Ca2+-channel blocker was verified in three ways: a [Ca2+]cyt decrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca2+ influx detected using Non-invasive Micro-test Technology. Genome-wide high throughput RNA-seq and bioinformatical methods were used to identify lncRNAs, and found 177 differentially expressed lncRNAs that might be in responsive to Ca2+-channel blocking. Among these, 108 were up-regulated and 69 were down-regulated. The validity of identified lncRNAs data from RNA-seq was verified using qPCR. GO and KEGG analysis indicated that a number of lncRNAs might be involved in diverse biological processes upon Ca2+-channel blocking. Further GO analysis showed that 23 lncRNAs might play roles as transcription factor (TF); Moreover, eight lncRNAs might participate in cell cycle regulation, and their relative expressions were detected using qPCR. This study also provides diverse data on wheat lncRNAs that can deepen our understanding of the function and regulatory mechanism of Ca2+-channel blocking in plants.

Highlights

Long non-coding RNAs are non-protein coding transcripts longer than 200 nucleotides and can be divided into at least five categories based on their structural characteristics, including intergenic lncRNAs, intronic lncRNAs, natural antisense transcripts, pseudogenes, and retrotransposons (Kitagawa et al, 2013)
Emerging studies have shown that lncRNAs could play a role in diverse biological processes via a number of complex mechanisms (Chekanova, 2015): they can serve as decoys, scaffolds, and guides (Rinn and Chang, 2012) to regulate gene expression in either cis or trans acting (Kang and Liu, 2015; Li et al, 2015), or they can serve as competing endogenous RNA (Salmena et al, 2011) to compete with microRNA or interfere with the miRNA-mediated regulation of their mRNA targets (Rubio-Somoza et al, 2011; Fan et al, 2015)
Some researchers have described the functions of lncRNAs in cell cycle regulation in animals (Kitagawa et al, 2013; Li et al, 2016)

Summary

Introduction

Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides and can be divided into at least five categories based on their structural characteristics, including intergenic lncRNAs, intronic lncRNAs, natural antisense transcripts, pseudogenes, and retrotransposons (Kitagawa et al, 2013) They have even been known as “transcriptional noise” under low expression (Ponjavic et al, 2007; Ponting et al, 2009). The function of plant lncRNAs has mainly been reported in Arabidopsis and rice (Liu et al, 2015). They can function in cis and/or in trans by sequence complementarity or homology with. Previous studies indicated that plant lncRNAs can play key roles in flowering time (Berry and Dean, 2015), gene silencing (Swiezewski et al, 2009; Bardou et al, 2014), root organogenesis (Matzke and Mosher, 2014), seedling photomorphogenesis (Wang Y. et al, 2014), and reproduction (Zhang et al, 2014)

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