Suksamran R, Saithong T, Thammarongtham C, Kalapanulak S.

Genes (Basel). 2020 Mar 28;11(4). pii: E366. doi: 10.3390/genes11040366.

Abstract

Long non-coding RNAs (lncRNAs) play important roles in the regulation of complex cellular processes, including transcriptional and post-transcriptional regulation of gene expression relevant for development and stress response, among others. Compared to other important crops, there is limited knowledge of cassava lncRNAs and their roles in abiotic stress adaptation. In this study, we performed a genome-wide study of ncRNAs in cassava, integrating genomics- and transcriptomics-based approaches. In total, 56,840 putative ncRNAs were identified, and approximately half the number were verified using expression data or previously known ncRNAs. Among these were 2229 potential novel lncRNA transcripts with unmatched sequences, 250 of which were differentially expressed in cold or drought conditions, relative to controls. We showed that lncRNAs might be involved in post-transcriptional regulation of stress-induced transcription factors (TFs) such as zinc-finger, WRKY, and nuclear factor Y gene families. These findings deepened our knowledge of cassava lncRNAs and shed light on their stress-responsive roles.

See https://www.mdpi.com/2073-4425/11/4/366

Figure 7. Potential novel lncRNAs that responded to cold and drought stress by a trans-regulatory relationship through direct binding to mRNAs of target genes. (A) Binding region of lncRNA ncP456 at position 1–179 and mRNA of target gene encoding WRKY DNA-binding protein 33 (Manes.09G112700) at position 1562–1740, including their fold change (FC) under control and cold conditions. (B) Binding region of lncRNA ncP12192 at position 159–240 and mRNA of target gene encoding SLAC1 (Manes.06G154600) at position 1–82, including their fold change (FC) under control and drought conditions. (C) Binding region of lncRNA ncM15664 at position 1–280 and mRNA of target gene encoding ABA responsive elements-binding factor2 (Manes.18G037900) at position 81–360, including their fold change (FC) under control and drought conditions. FC_control = Expression_control/Expression_control; FC_cold = Expression_cold/Expression_control; FC_drought = Expression_drought/Expression_control.