Deep neural network prediction of interplay between lncRNAs and salinity response in rice

Salt stress seriously constrains growth and fertility of rice worldwide. Long noncoding RNAs (lncRNAs)play crucial roles in plant abiotic stress response, however, no systematic screening of lncRNAs under saltstress in rice has been reported. Herein, a transcriptional study using RNA-seq was conducted which resultedin the identification of differentially expressed lncRNAs (DE-lncRNAs) in FL۴۷۸ as salt tolerant ricegenotypes compared to its susceptible parent (IR۲۹). Initially, a total of ۱۵۱۳۱ and ۱۶۲۵۶ potential noncodingRNAs were respectively identified in FL۴۷۸ and IR۲۹, among which ۸۷۲۴ (FL۴۷۸) and ۹۲۳۵ (IR۲۹)transcripts with length of > ۲۰۰ bp were nominated as lncRNAs. Applying a strict pipeline, four and nineDE-lncRNAs were respectively detected in FL۴۷۸ (۲ up- and ۲ down-regulated) and IR۲۹ (۶ up- and ۳ downregulated)under salt conditions, while only ۲ DE-lncRNAs were in common among both genotypes. UsingATAC-seq data, the genomic regions of all four lncRNAs in FL۴۷۸ and ۶/۹ in IR۲۹ were confirmed to besignificantly accessible for transcription. To identify the potential functions of salt-responsive DE-lncRNAsin cis-regulation, protein-coding genes were initially searched ۱۰۰ kb upstream and downstream of theselncRNAs; then DE-lncRNAs and their neighboring mRNA were subjected to co-expression network analysis.We further explored potential functions of salt-responsive DE-lncRNAs to identify trans-regulatory networksof lncRNAs in each genotype. The crosstalk between DE-lncRNAs and miRNAs were subsequentlyinvestigated by exploring the DE-lncRNAs acting as target mimic of known miRNAs in Oryza sativa.WGCNA analyses identified ۴۹ modules in the two genotypes. Interestingly, lncRNA.۲-FL in FL۴۷۸ washighly correlated with ۱۷۳ mRNAs in the transcriptional module M۳۹, whereas this module was notsignificant in IR۲۹. Furthermore, we used a deep neural network trained on the rice genome to predict theeffect of nearby mutations on the expression of mRNAs. We identified many important regulatory elementsand showed the causal effect of lncRNA.۲-FL on the expression level of a differentially expressed gene inthe tolerant genotype. The identified DE-lncRNAs might be involved in rice response to salt stress, andlncRNA.۲-FL may play a role as a regulatory hub in the salt stress tolerance of FL۴۷۸.

Keywords:

Oryza Sativa , Salinity , LncRNA , co-expression , weighted correlation network analysis