Long non-coding RNAs as the regulatory hubs in rice response to salt stress

Abstract

Background: Salinity seriously constrains growth and fertility of rice worldwide. Long non-coding RNAs (lncRNAs) play crucial roles in plant abiotic stress response. However, salt responsive lncRNAs are poorly understood in rice. Results: Herein, differentially expressed lncRNAs (DE-lncRNAs) were identified in FL478 (salt tolerant) compared to its susceptible parent (IR29) using RNA-seq. In FL478 and IR29, 8724 and 9235 transcripts with length of >200 bp were nominated as potential lncRNAs, respectively. Rigorous filtering left four (in FL478) and nine (in IR29) DE-lncRNAs with only 2 DE-lncRNAs in common. ATAC-seq data showed that the genomic regions of all four lncRNAs in FL478 and 6/9 in IR29 are significantly accessible for transcription. Weighted correlation network analysis (WGCNA) revealed that lncRNA.2-FL was highly correlated with 173 mRNAs as trans-targets and a gene encoding pentatricopeptide repeat (PPR) protein was predicted as cis-target of lncRNA.2-FL. In silico mutagenesis analysis proposed the same transcription factor binding sites (TFBSs) in vicinity of the trans- and cis-regulatory target genes of lncRNA.2-FL, which significantly affect their transcription start site (TSS). Conclusions: This study provides new insights into involvement of the DE-lncRNAs in rice response to salt stress. Among them, lncRNA.2-FL may play a significant regulatory role in the salt stress tolerance of FL478.

Genome-Wide Identification and Characterization of Long Non-Coding RNAs Associated with Floral Scent Formation in Jasmine (Jasminum sambac)

“…Consequently, the transcription of the NAC3 gene activates salicylic acid biosynthesis, proving the involvement of the lncRNA SABC1 in the plant immune response [8]. The LncRNA.2-FL plays a crucial role in the resistance of rice plants to salt stress and the formation of lateral roots by redistributing auxin concentration under salinity [9]. The two lncRNAs, termed COOLAIR (cool-assisted intronic non-coding RNA) and COLDAIR (cold-assisted intronic non-coding RNA), have been identified as key regulators of flowering time during vernalization in Arabidopsis, by negatively regulating a MADS-box transcription factor FLC (FLOWERING LOCUS C) [10].…”