Conservation analysis of long non-coding RNAs in plants
- 138 Downloads
Long non-coding RNAs (lncRNAs) are gene regulators that have vital roles in development and adaptation to the environment in eukaryotes. However, the structural and evolutionary analyses of plant lncRNAs are limited. In this study, we performed an analysis of lncRNAs in five monocot and five dicot species. Our results showed that plant lncRNA genes were generally shorter and had fewer exons than protein-coding genes. The numbers of lncRNAs were positively correlated with the numbers of protein-coding genes in different plant species, despite a high range of variation. Sequence conservation analysis showed that the majority of lncRNAs had high sequence conservation at the intra-species and sub-species levels, reminiscent of protein-coding genes. At the inter-species level, a subset of lncRNAs were highly diverged at the nucleotide level, but conserved by position. Interestingly, we found that plant lncRNAs have identical splicing signals, and those which can form precursors or targets of miRNAs have a conservative identity in different species. We also revealed that most of the lowly expressed lncRNAs were tissue-specific, while those highly conserved were constitutively transcribed. Meanwhile, we characterized a subset of rice lncRNAs that were co-expressed with their adjacent protein-coding genes, suggesting they may play cis-regulatory roles. These results will contribute to understanding the biological significance and evolution of lncRNAs in plants.
KeywordslncRNA conservation monocots dicots rice
Unable to display preview. Download preview PDF.
This work was supported by Zhejiang Provincial Natural Science Foundation of China (LR16C060001), the National Key Program on Transgenic Research and the Fundamental Research Funds for the Central Universities (2016QNA6014).
- Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D.G., Lagarde, J., Veeravalli, L., Ruan, X., Ruan, Y., Lassmann, T., Carninci, P., Brown, J.B., Lipovich, L., Gonzalez, J.M., Thomas, M., Davis, C.A., Shiekhattar, R., Gingeras, T.R., Hubbard, T.J., Notredame, C., Harrow, J., and Guigó, R. (2012). The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22, 1775–1789.CrossRefPubMedPubMedCentralGoogle Scholar
- Li, L., Eichten, S.R., Shimizu, R., Petsch, K., Yeh, C.T., Wu, W., Chettoor, A.M., Givan, S.A., Cole, R.A., Fowler, J.E., Evans, M.M.S., Scanlon, M.J., Yu, J., Schnable, P.S., Timmermans, M.C.P., Springer, N.M., and Muehlbauer, G.J. (2014). Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol 15, R40.CrossRefPubMedPubMedCentralGoogle Scholar
- St Laurent, G., Shtokalo, D., Tackett, M.R., Yang, Z., Eremina, T., Wahlestedt, C., Urcuqui-Inchima, S., Seilheimer, B., McCaffrey, T.A., and Kapranov, P. (2012). Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells. BMC Genomics 13, 504.CrossRefPubMedPubMedCentralGoogle Scholar
- Yanai, I., Benjamin, H., Shmoish, M., Chalifa-Caspi, V., Shklar, M., Ophir, R., Bar-Even, A., Horn-Saban, S., Safran, M., Domany, E., Lancet, D., and Shmueli, O. (2005). Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21, 650–659.CrossRefPubMedGoogle Scholar