Genome-wide identification of Arabidopsis long noncoding RNAs in response to the blue light

Zujing Han,Kai Huang,Pan Wang,Yuda Fang,Zhenfei Sun

doi:10.1038/s41598-020-63187-1

Abstract

Long non-coding RNAs (lncRNAs) have been shown in animals to play roles in a wide range of biological processes. In plant, light modulates the growth and development as a key external signal. However, little is known about the role of plant lncRNA in response to light. In this study, we sequenced the messenger RNAs (mRNAs), lncRNAs and microRNAs (miRNAs) in Arabidopsis seedlings under blue light for 2 h and 8 h. Compared to dark, we identified 4197 mRNAs, 375 miRNAs and 481 lncRNAs, or 5207 mRNAs, 286 miRNAs and 545 lncRNAs of differential expressions under blue light treatments for 2 h or 8 h respectively. Subsequently, a total of 407 competing endogenous RNA (ceRNA) pairs (lncRNA-mRNA-miRNA) were constructed. We identified a blue light-induced lncRNA which plays roles in blue light-directed plant photomorphogenesis and response to mannitol stress by serving as a ceRNA to sequester miR167 in a type of target mimicry. These results revealed previously unknown roles of the lncRNA in blue light signaling and mannitol stress, and provided useful resources of lncRNAs associated with miRNAs in response to blue light.

Highlights

Long non-coding RNAs have been shown in animals to play roles in a wide range of biological processes
To annotate the relationships between Long non-coding RNAs (lncRNAs) and miRNAs in Arabidopsis under blue light, we performed lncRNA sequencing of three biological replicates, each with three samples using 4 day dark-grown WT seedlings exposed to continuous blue light for 0 h, 2 h and 8 h (Fig. 1A). 1,095,370–1,100,180 M paired-end reads with 100 bp in length for the messenger RNAs (mRNAs) and lncRNAs, and 11,600,936–12,413,799 single-end reads with 50 bp in length for the miRNAs were acquired from nine samples (Table S1 in Supporting Information)
The recent discovery of lncRNAs has shown that lncRNAs play roles in many regulatory pathways, such as the regulation of chromatin structure and determination of cell fate[1,2,6,7,8,9,10,11,12,13,14]

Summary

Introduction

Long non-coding RNAs (lncRNAs) have been shown in animals to play roles in a wide range of biological processes. We identified a blue light-induced lncRNA which plays roles in blue light-directed plant photomorphogenesis and response to mannitol stress by serving as a ceRNA to sequester miR167 in a type of target mimicry. The non-coding IPS1 (INDUCED BY PHOSPHATE STARVATION 1) RNA can serve as a molecular bait, which binds directly to ceRNA to block the role of the targets (Franco-Zorrilla et al, 2007), or to transcription factor/regulator to inhibit the related signal transduction. We revealed that CDF2 is involved in miRNA transcription and processing[24], and PIF4, which was known to interact with phyB and CRY125,26, plays a role in miRNA biogenesis to affect red light-directed plant photomorphogenesis[27]

Methods

Results

Conclusion