Global identification of full‐length cassava lncRNAs unveils the role of cold‐responsive intergenic lncRNA 1 in cold stress response

Abstract

Long noncoding RNAs (lncRNAs) have been considered to be important regulators of gene expression in a range of biological processes in plants. A large number of lncRNAs have been identified in plants. However, most of their biological functions still remain to be determined. Here, we identified a total of 3004 lncRNAs in cassava under normal or cold‐treated conditions from Iso‐seq data. We further characterized a cold‐responsive intergenic lncRNA 1 (CRIR1) as a novel positive regulator of the plant response to cold stress. CRIR1 can be significantly induced by cold treatment. Ectopic expression of CRIR1 in cassava enhanced the cold tolerance of transgenic plants. Transcriptome analysis demonstrated that CRIR1 regulated a range of cold stress‐related genes in a CBF‐independent pathway. We further found that CRIR1 RNA can interact with cassava cold shock protein 5 (MeCSP5), which acts as an RNA chaperone, indicating that CRIR1 may recruit MeCSP5 to improve the translation efficiency of messenger RNA. In summary, our study extends the repertoire of lncRNAs in plants as well as their role in cold stress responses. Moreover, it reveals a mechanism by which CRIR1 affected cold stress response by modulating the expression of stress‐responsive genes and increasing their translational yield.

Optimized Phosphorus Application Alleviated Adverse Effects of Short-Term Low-Temperature Stress in Winter Wheat by Enhancing Photosynthesis and Improved Accumulation and Partitioning of Dry Matter

“…Researchers have extensively documented low-temperature stress-induced morphological changes in plants, and morphological changes are the most visible symptom of stress [28,29]. The plant height, tillers number and area of green leaves decreases significantly or even withers after low-temperature stress [9,30].…”

Long Non-Coding RNAs: New Players in Plants

“…Also in Arabidopsis , lncRNA SVALKA can regulate cold tolerance in Arabidopsis [ 101 ] ( Figure 5 e). In cassava (Manihot esculenta Crantz) , CRIR1 (a cold-responsive intergenic lncRNA 1) is a positive regulator of the plant response to cold stress [ 136 ]. CRIR1 is significantly induced by cold treatment to interact with MeCSP5 (cassava cold shock protein 5) [ 136 ].…”

“…In cassava (Manihot esculenta Crantz) , CRIR1 (a cold-responsive intergenic lncRNA 1) is a positive regulator of the plant response to cold stress [ 136 ]. CRIR1 is significantly induced by cold treatment to interact with MeCSP5 (cassava cold shock protein 5) [ 136 ]. Further studies have found that CRIR1 may recruit MeCSP5 to improve the translation efficiency of mRNA.…”

“…Further studies have found that CRIR1 may recruit MeCSP5 to improve the translation efficiency of mRNA. CRIR1 affects the mechanism of the cold stress response by regulating the expression of stress response genes and increasing their translation efficiency [ 136 ]. In apple, 13 variable spliceosomes for lncRNAs MSTRG.85814 were identified, of which five were involved in the iron deficiency response.…”

“…It was further confirmed that the spliceosome MSTRG.85814.11 could positively regulate its target gene SAUR32 to promote the plant rhizosphere response to iron deficiency and stepwise regulation by MSTRG 85814.11-SAUR32-H + -ATPase (AHA10) in iron deficiency response in an apple graft complex [ 107 ] ( Figure 5 f). StCDF1 (CYCLING DOF FACTOR 1) is a transcription factor that regulates potato ( Solanum tuberosum ) tuberization [ 136 ]. StCDF1 and NAT StFLORE together regulate water loss by affecting stomatal growth and diurnal opening [ 137 ].…”