Epigenetic and Three-dimensional Genomic Analysis of Long Non-coding and Circular RNAs in Xian/Indica Rice

Abstract Background: Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) can play important roles in many biological processes. However, no study of the influence of epigenetics factors or the 3D structure of the genome in their regulation is available in plants. Results: In the current analysis, we identified a total of 15,122 lncRNAs and 7,902 circRNAs in three tissues (root, leaf and panicle) of the rice varieties Minghui 63, Zhenshan 97 and their hybrid Shanyou 63. Above 73% of the lncRNAs and parental genes of circRNAs (P-circRNA) are shared among Oryza sativa with high expression specificity. Compared with protein-coding genes, lncRNAs have higher methylation levels. CircRNAs tend to locate in the middle of genes with high CG and CHG methylation. The activated lncRNAs and P-circRNA are mainly transcribed from demethylated regions containing CHH methylation. In addition, ~53% lncRNAs and ~15% P-circRNA are associated with transposable elements, especially miniature inverted-repeat transposable elements and RC/helitron. We didn’t find correlation between the expression of lncRNAs and histone modifications; however, the binding strength and interaction of RNAPII significantly affects lncRNA expression. In contrast, parental genes of circRNAs tend to combine active histone modifications. Finally, lncRNAs and circRNAs acting as competing-endogenous RNAs have the potential to regulate the expression of genes with important roles in the growth and development of rice. Conclusions: Together, our results provide insights into the epigenetic and regulatory mechanisms of lncRNAs and circRNAs in rice and open the door to increase our understanding of ncRNAs in plants.