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

Abstract

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. Herein, salt responsive lncRNAs (DE-lncRNAs) were identified in FL478 (salt tolerant) compared to its susceptible parent (IR29) using RNA-seq in root tissues at seedling stage. 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). 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.

Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo

“…There was a clear preference for T across the entire region, except for the −25 to −10 and 0 to 10 regions, which were predominant for A, suggesting a nucleotide bias upstream and downstream of the cleavage site in 3′ UTRs ( Figure 3 C). The nucleotide bias in these sites was similar to that previously reported [ 20 ], which supports the authenticity of the identified poly(A) sites.…”

“…Long non-coding RNAs (lncRNAs) are defined as transcripts longer than 200 bp that cannot encode a full-length protein, and the main difference between lncRNA and mRNA is the lack of coding protein sequence potential in lncRNA [ 19 , 20 , 21 ]. Recently, more and more evidence has suggested that lncRNAs have regulatory roles in various biological processes, such as development, vernalization, and environmental stress adaptation.…”

Genome-wide identification of long non-coding RNAs and their potential functions in radish response to salt stress

“…The interactions between stress-specific TFs and lncRNAs were hypothesized to play a significant role in response to various abiotic stresses, including salt stress (Mirdar Mansuri et al, 2022). For example, in wheat, Shumayla et al (2017) demonstrated that lncRNAs were co-expressed with the TFs related to WRKY, NAC, MYB, ERF, C3H, C2H2, bZIP, and bHLH families under salt stress conditions; several lncRNAs associated with TFs belonging to ARF, C2C2(Zn), and HSF families were found in duckweed (Fu et al, 2020); in maize, 11 target transcripts of the salt-responsive lncRNAs belonging to seven TF families, including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY, were predicted (Liu et al, 2022a).…”

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

“…Limited evidence is available on ncRNAs associated with the regulation of salt stress in plants [177][178][179][180][181][182][183][184][185][186][187][188][189][190], as listed in Table 1. Nearly 75 conserved miRNAs were identified from the control and NaCl-treated salt-tolerant rice varieties [180].…”

“…The study further identified two differentially expressed (DE)-lncRNAs, such as TCONS_00008914 and TCONS_00008749, as potential target mimics of known rice miRNAs. In another study, using another salt-tolerant rice (FL478), Mansuri et al [177,187] identified DE-lncRNA.2-FL, that showed multiple interaction with osa-miR2926 miRNA. This interaction regulates the expression of various salt-stress-responsive genes, such as chloride channel protein, potassium transporter, and some genes involved in sensing and signaling, such as cysteine-rich receptor-like protein kinase 8 precursors and serine/threonine protein kinase.…”