Transcriptomic Profiling of Fe-Responsive lncRNAs and Their Regulatory Mechanism in Rice.

Shoudong Wang,Shuo Sun,Runze Guo,Huixia Shou,Wenying Liao

doi:10.3390/genes12040567

Abstract

Iron (Fe) deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. Recently, long non-coding RNAs (lncRNAs) have been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. However, systematic screening of lncRNAs responding to Fe deficiency and their regulatory mechanism in plants has not been reported. In this work, 171 differently expressed lncRNAs (DE-lncRNAs) were identified based on analysis of strand-specific RNA-seq data from rice shoots and roots under Fe-deficient conditions. We also found several lncRNAs, which could generate miRNAs or act as endogenous target mimics to regulate expression of Fe-related genes. Analysis of interaction networks and gene ontology enrichment revealed that a number of DE-lncRNAs were associated with iron transport and photosynthesis, indicating a possible role of lncRNAs in regulation of Fe homeostasis. Moreover, we identified 76 potential lncRNA targets of OsbHLH156, a key regulator for transcriptional response to Fe deficiency. This study provides insight into the potential functions and regulatory mechanism of Fe-responsive lncRNAs and would be an initial and reference for any further studies regarding lncRNAs involved in Fe deficiency in plants.

Highlights

Iron (Fe) is an essential micronutrient for plants, but is often limited due to low availability in the soil [1]
LncRNAs are classified as sense, antisense, intronic, and intergenic according to their position in relation to neighboring coding genes [16,17]
The results demonstrated that a number of DE-LncRNAs could be regulated by bHLH156 and IRO2 at the transcriptional level

Summary

Introduction

Iron (Fe) is an essential micronutrient for plants, but is often limited due to low availability in the soil [1]. A large number of genes are known for their involvement in Fe uptake and homeostasis, including those that encode transcription factors for regulating expression of downstream Fe-responsive genes, enzymes for synthesis of phytosiderophores (MAs), and transporters of MA-Fe (III). Most of the regulators in the maintenance of plant iron homeostasis are coding genes, whether long non-coding RNAs (lncRNAs) play roles in. Conventional sequencing for mRNA is non-strand-specific, which is limited to identified cis-natural antisense lncRNAs as the antisense strand overlapping with a transcript on the opposite sense strand are unable to be distinguished. Strandspecific RNA-seq (ssRNA) is a powerful tool to definite the transcripts coming from which

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Conclusion