IC4R004-lncRNA-2016-26860696

Project Title

Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network

The Background of This Project

• 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.
• Inorganic phosphate (Pi) is essential for the growth and productivity of plants; however, those in agricultural environments can be exposed to Pi starvation 1 . Understanding the biological responses of plants to Pi starvation is vital for improving the efficiency of Pi use and maintaining an acceptable yield 2 . A number of studies have attempted to investigate the complex mechanisms regulating Pi homeostasis in rice, and have reported regulation at the transcript level 3–6 . Long integrate non-coding RNAs (lincRNAs) exist in both mammalian and plants and may play widespread roles in gene regulation and other biological processes 7–9 , however, the function of lincRNAs that response to Pi starvation are poorly understood.
• The competing endogenous RNA (ceRNA) theory has been proved and is now acknowledged widely 10,11 . This theory states that ceRNAs, including mRNA, lincRNAs, pseudogenes, and other microRNAs (miRNA) sponges, share common miRNA binding sites and can act as molecular sponges because the amount of a given miRNAs is limited 11 . LincRNAs compete with other miRNA sponges to play important roles in both plants and animals 9,12–15 . In addition, ceRNA networks are useful for studying cancer biology and other biological problems 16–19 . However, to our knowledge, ceRNA networks have not yet been used to study the functions of lincRNAs in plants such as Arabidopsis and rice.

Figure 1 The basic characteristics of lincRNAs in rice.

Figure 2 The ceRNA network of the rice root and shoot.

Research Findings

• The pipeline shown in Figure. 1a was used to identify lincRNAs from the RNA-seq data of rice undergoing Pi starvation 6 . In brief, 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 details of the pipeline are shown as follow.

• We compared the genomic features of the identified lincRNAs with those of protein-coding genes in rice. The mean exon length of the lincRNA was larger than that of the mRNA (Figure. 1b), while more than 70% of the lincRNAs, but less than 10% of the mRNAs, contained only one exon (Fig. 1c). In the meanwhile, lincRNAs in rice have fewer, but longer, exons than mRNAs 9 . The GC content of the lincRNAs was also lower than that of the mRNAs (Figure. 1d).

Labs working on this Project

• National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, P.R. China
• College of Informatics, Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, P.R. China

Corresponding Author

• LingLing Chen (llchen@mail.hzau.edu.cn)