Abstract
Long intergenic non-coding RNAs (lincRNAs) may play widespread roles in gene regulation and other biological processes, however, a systematic examination of the functions of lincRNAs in the biological responses of rice to phosphate (Pi) starvation has not been performed. Here, we used a computational method to predict the functions of lincRNAs in Pi-starved rice. Overall, 3,170 lincRNA loci were identified using RNA sequencing data from the roots and shoots of control and Pi-starved rice. A competing endogenous RNA (ceRNA) network was constructed for each tissue by considering the competing relationships between lincRNAs and genes, and the correlations between the expression levels of RNAs in ceRNA pairs. Enrichment analyses showed that most of the communities in the networks were related to the biological processes of Pi starvation. The lincRNAs in the two tissues were individually functionally annotated based on the ceRNA networks, and the differentially expressed lincRNAs were biologically meaningful. For example, XLOC_026030 was upregulated from 3 days after Pi starvation, and its functional annotation was ‘cellular response to Pi starvation’. In conclusion, we systematically annotated lincRNAs in rice and identified those involved in the biological response to Pi starvation.
Highlights
To Pi-starved or Pi-sufficient conditions[6]
If a longer-than-200 nt transcript with no coding capability is located in the intergenic regions and is not similar to known protein-coding genes, it is identified as a candidate lincRNA
The remaining large transcripts that were expressed frequently and did not overlap with known genes were identified as lincRNAs in rice
Summary
To Pi-starved or Pi-sufficient conditions[6]. Second, based on predictions of miRNA-gene and miRNA-lincRNA target pairs, we used a hypergeometric cumulative distribution function test to select ceRNA pairs with common miRNA regulators and to identify those that constitute a ceRNA network. Pi is an important element of phosphatide[27], and phosphatide or phosphatide metabolism-related GO terms were identified as another common function of the lincRNAs. The most interesting annotation of the lincRNAs was ‘cellular response to Pi starvation’, which may indicate that some of the lincRNAs play a role in the metabolic adaptations of rice undergoing Pi starvation.
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