Circular RNAs (circRNAs) are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon treatment with gibberellins (GAs) and auxins (1-naphthaleneacetic acid, NAA) remain unknown. Here, we systematically identified and characterized the expression patterns, evolutionary conservation, genomic features, and internal structures of circRNAs using RNase R-treated libraries from moso bamboo (Phyllostachys edulis) seedlings. Moreover, we investigated the biogenesis of circRNAs dependent on both cis- and trans-regulation. We explored the function of circRNAs, including their roles in regulating microRNA (miRNA)-related genes and modulating the alternative splicing of their linear counterparts. Importantly, we developed a customized degradome sequencing approach to detect miRNA-mediated cleavage of circRNAs. Finally, we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and NAA. Collectively, our study provides insights into the biogenesis, function, and miRNA-mediated degradation of circRNAs in moso bamboo.
RNA, Circular/metabolism* ; Multiomics ; Poaceae/metabolism* ; Seedlings/genetics* ; Hormones/metabolism* ; MicroRNAs/metabolism* ; Gene Expression Regulation, Plant

Objective To analyze the expression of Kruppel-like factor 4 (KLF4 ) and CD44 in esophageal squamous cell carcinoma (ESCC) tissues and adjacent non-cancerous tissues ,and to investigate their effects on the prognosis .Methods From June 2012 to September 2016 ,in The Second People′s Hospital of Nanyang ,a total of 100 patients with ESCC who receiving operation were selected .The ESCC tissues and the adjacent non-cancerous tissues (control) of the patients were collected .The expression levels of KLF4 and CD44 protein were detected by immunohistochemistry .The expressions of KLF4 and CD44 at mRNA and protein level of 50 paired fresh tissues were examined by quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting ,respectively . T-test ,chi-square ,Kaplan-Meier method and Pearson correlation analysis were performed for statistical analysis .Results The positive expression rate of KLF4 protein in ESCC tissues was 55％ (55/100) ,which was lower than that in adjacent non-cancerous tissues (77％ ,77/100) ,and the difference was statistically significant (χ2 =10 .778 ,P=0 .001) .The positive expression rate of CD44 protein in ESCC tissues was 81％ (81/100) ,which was higher than that in adjacent non-cancerous tissues (11％ ,11/100) ,and the difference was statistically significant (χ2=112 .600 ,P<0 .01) .The expression level of KLF4 mRNA in 43 cases was lower than that in adjacent non-cancerous tissues ,the expression level of CD44 mRNA in 46 cases was much higher than that of adjacent non-cancerous tissues ,and the differences were statistically significant (χ2 =51 .837 and 70 .563 ,both P< 0 .01) .There were statistically significant differences in positive expression rates of KLF4 in cancer tissues between different gender , differentiation degree , invasion depth ,TNM stage and lymph node metastasis (all P<0 .05) .Similarly there were statistically significant differences in positive expression rates of CD 44 in cancer tissues between different differentiation degree ,invasion depth ,TNM stage and lymph node metastasis (all P< 0 .05) .The expression of KLF4 was negatively correlated with CD44 expression ,either at protein level or mRNA level (r= -0 .284、-0 .518 ,both P< 0 .01) .The median survival time of patients with positive KLF4 expression in cancer tissues was 33 months ,which was longer than that of patients with negative KLF4 expression (20 months) ,and the difference was statistically significant (χ2 =4 .021 , P= 0 .019) .The median survival time of patients with positive CD44 expression in cancer tissues was 24 months ,which was shorter than that of patients with negative CD44 expression (37 months) , and the difference was statistically significant (χ2 = 4 .379 , P= 0 .016) .The results of univariate analysis showed that TNM stage ,KLF4 expression and CD44 expression were correlated with overall survival time (all P<0 .05) . The results of multivariate analysis indicated that TNM stage ,lower KLF4 expression and higher CD44 expression were the independent risk factors for survival (all P<0 .05) .Conclusion Lower expression of KLF4 and higher expression of CD44 in ESCC may be closely correlated with its occurrence ,development and prognosis .