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Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

View Article: PubMed Central - PubMed

ABSTRACT

Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava.

No MeSH data available.


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Comparison of the expression pattern of lincRNAs and adjacent protein-coding genes.(A,B) A heatmap was generated from the fold change values in the RNA-seq data, and was used to visualize the lincRNA and neighbors expression pattern under cold (A) and drought stress (B), respectively. (C) Gene structures of five lincRNAs and nearby protein-coding genes. (D–I) Expression patterns analysis of lincRNA334 (D), lincRNA308 (E), lincRNA356 (G), lincRNA392 (H), lincRNA105 (F,I) and nearby protein-coding genes by qRT-PCR under cold or drought stress, respectively. Data are presented as means ± SD of three independent replicates. MeACTIN was used as the reference gene.
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f7: Comparison of the expression pattern of lincRNAs and adjacent protein-coding genes.(A,B) A heatmap was generated from the fold change values in the RNA-seq data, and was used to visualize the lincRNA and neighbors expression pattern under cold (A) and drought stress (B), respectively. (C) Gene structures of five lincRNAs and nearby protein-coding genes. (D–I) Expression patterns analysis of lincRNA334 (D), lincRNA308 (E), lincRNA356 (G), lincRNA392 (H), lincRNA105 (F,I) and nearby protein-coding genes by qRT-PCR under cold or drought stress, respectively. Data are presented as means ± SD of three independent replicates. MeACTIN was used as the reference gene.

Mentions: There are relatively few functionally characterized lncRNAs in cassava. Some mammalian lncRNAs can function in cis as scaffolds to recruit co-activator complexes that mediate chromosome looping between enhancer and promoter regions, controlling chromatin topology and modulating gene expression at the transcriptional level54. Emerging evidence showed that lncRNAs tend to influence the expression of adjacent genes or overlapping genes5556. To investigate the possible functions of cassava lncRNAs, we predicted the potential targets of lincRNAs in cis-regulatory relationships. We searched for known protein-coding genes located within 10 Kb upstream and downstream of all the identified cassava lincRNAs. Interestingly, we found most of lincRNAs (76.6%) that were transcribed close to 524 protein-coding neighbors (Supplemental Data S6). We classified stress-responsive lincRNAs-neighbors pairs into two groups: concordant regulated group and discordant regulated group. For concordant lincRNAs-neighbors pairs, the transcripts abundance of neighbor genes should change in the same direction with its lincRNAs partner no less than 1.5 fold. For discordant pairs, the expression of adjacent genes should change in the opposite direction no less than 1.5 fold. We identified 98 and 81 concordant lincRNAs-neighbors pairs potentially involved in cold and drought stress response pathways, respectively. Interestingly, we also found 40 and 35 cold- and drought-responsive discordant lincRNAs-neighbors pairs, respectively (Fig. 7A,B, Supplemental Data S6). We carried out qRT-PCR to confirm the transcription of five lincRNAs and their adjacent protein-coding genes under cold and/or drought stress conditions (Fig. 7C). The results showed that the regulation of these discordant lincRNAs pairs displayed a similar pattern as RNA-seq data (Fig. 7D–I). For examples, the expression of Manes.09G081500, coding a protein tyrosine kinase, was specifically down-regulated after 6 to 72 h of drought treatment accompanied by its up-regulated adjacent lincRNA356 (Fig. 7C,G). During cold treatment, this discordant pair did not show more than two fold expression differences. Moreover, Manes.15G059900 and Manes.15G060000 were transcribed oppositely with their adjacent lincRNA105 under cold and drought stress (Fig. 7C,F and I). It will be interesting to check the function of this lincRNAs in abiotic stress responses. Therefore, a number of discordant lincRNA-neighbor pairs that were identified suggested a potentially widespread occurrence of negative regulation by lincRNAs.


Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava
Comparison of the expression pattern of lincRNAs and adjacent protein-coding genes.(A,B) A heatmap was generated from the fold change values in the RNA-seq data, and was used to visualize the lincRNA and neighbors expression pattern under cold (A) and drought stress (B), respectively. (C) Gene structures of five lincRNAs and nearby protein-coding genes. (D–I) Expression patterns analysis of lincRNA334 (D), lincRNA308 (E), lincRNA356 (G), lincRNA392 (H), lincRNA105 (F,I) and nearby protein-coding genes by qRT-PCR under cold or drought stress, respectively. Data are presented as means ± SD of three independent replicates. MeACTIN was used as the reference gene.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5384091&req=5

f7: Comparison of the expression pattern of lincRNAs and adjacent protein-coding genes.(A,B) A heatmap was generated from the fold change values in the RNA-seq data, and was used to visualize the lincRNA and neighbors expression pattern under cold (A) and drought stress (B), respectively. (C) Gene structures of five lincRNAs and nearby protein-coding genes. (D–I) Expression patterns analysis of lincRNA334 (D), lincRNA308 (E), lincRNA356 (G), lincRNA392 (H), lincRNA105 (F,I) and nearby protein-coding genes by qRT-PCR under cold or drought stress, respectively. Data are presented as means ± SD of three independent replicates. MeACTIN was used as the reference gene.
Mentions: There are relatively few functionally characterized lncRNAs in cassava. Some mammalian lncRNAs can function in cis as scaffolds to recruit co-activator complexes that mediate chromosome looping between enhancer and promoter regions, controlling chromatin topology and modulating gene expression at the transcriptional level54. Emerging evidence showed that lncRNAs tend to influence the expression of adjacent genes or overlapping genes5556. To investigate the possible functions of cassava lncRNAs, we predicted the potential targets of lincRNAs in cis-regulatory relationships. We searched for known protein-coding genes located within 10 Kb upstream and downstream of all the identified cassava lincRNAs. Interestingly, we found most of lincRNAs (76.6%) that were transcribed close to 524 protein-coding neighbors (Supplemental Data S6). We classified stress-responsive lincRNAs-neighbors pairs into two groups: concordant regulated group and discordant regulated group. For concordant lincRNAs-neighbors pairs, the transcripts abundance of neighbor genes should change in the same direction with its lincRNAs partner no less than 1.5 fold. For discordant pairs, the expression of adjacent genes should change in the opposite direction no less than 1.5 fold. We identified 98 and 81 concordant lincRNAs-neighbors pairs potentially involved in cold and drought stress response pathways, respectively. Interestingly, we also found 40 and 35 cold- and drought-responsive discordant lincRNAs-neighbors pairs, respectively (Fig. 7A,B, Supplemental Data S6). We carried out qRT-PCR to confirm the transcription of five lincRNAs and their adjacent protein-coding genes under cold and/or drought stress conditions (Fig. 7C). The results showed that the regulation of these discordant lincRNAs pairs displayed a similar pattern as RNA-seq data (Fig. 7D–I). For examples, the expression of Manes.09G081500, coding a protein tyrosine kinase, was specifically down-regulated after 6 to 72 h of drought treatment accompanied by its up-regulated adjacent lincRNA356 (Fig. 7C,G). During cold treatment, this discordant pair did not show more than two fold expression differences. Moreover, Manes.15G059900 and Manes.15G060000 were transcribed oppositely with their adjacent lincRNA105 under cold and drought stress (Fig. 7C,F and I). It will be interesting to check the function of this lincRNAs in abiotic stress responses. Therefore, a number of discordant lincRNA-neighbor pairs that were identified suggested a potentially widespread occurrence of negative regulation by lincRNAs.

View Article: PubMed Central - PubMed

ABSTRACT

Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava.

No MeSH data available.


Related in: MedlinePlus