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Background: MicroRNAs (miRNAs) have emerged as key regulators of post-transcriptional degradation and/or translational repression in both plants and animals. Increasing evidence has pointed to the important role of intergenic miRNAs in response to environmental stresses; however, detailed information about intronic miRNAs in plants is not clear. Results: Here, we performed quantitative real-time PCR (qRT-PCR) analysis using transgenic plants to investigate the relationship between intronic miRNAs and their respective host genes in Arabidopsis. Here, we found that three Arabidopsis thaliana intronic miRNAs (miR400, miR838, and miR848) were co-transcribed with their host genes in different organs. Intriguingly, both miR400 and its host gene (At1g32583) were up-regulated during cold stress. Unlike intronic miRNAs in animals, the change of expression levels of plant intronic miRNAs in transgenic lines did not affect the transcriptional levels of their host genes. This result indicates that there is no feedback regulation loop between the intronic miRNAs and their host genes in Arabidopsis. In miRNAs-cropping mutants, the mature miRNAs were significantly reduced, while the expression levels of host genes did not change, suggestting the microprocessor also play roles in intronic miRNA processing. Conclusions: Together, these results provide the evidence that there is an independent relationship between the processing of intronic miRNAs and their host genes in Arabidopsis. [ABSTRACT FROM AUTHOR]

Aims/hypothesis: miR-153 is an intronic miRNA embedded in the genes that encode IA-2 (also known as PTPRN) and IA-2β (also known as PTPRN2). Islet antigen (IA)-2 and IA-2β are major autoantigens in type 1 diabetes and are important transmembrane proteins in dense core and synaptic vesicles. miR-153 and its host genes are co-regulated in pancreas and brain. The present experiments were initiated to decipher the regulatory network between miR-153 and its host gene Ia-2β (also known as Ptprn2) . Methods: Insulin secretion was determined by ELISA. Identification of miRNA targets was assessed using luciferase assays and by quantitative real-time PCR and western blots in vitro and in vivo. Target protector was also employed to evaluate miRNA target function. Results: Functional studies revealed that miR-153 mimic suppresses both glucose- and potassium-induced insulin secretion (GSIS and PSIS, respectively), whereas miR-153 inhibitor enhances both GSIS and PSIS. A similar effect on dopamine secretion also was observed. Using miRNA target prediction software, we found that miR-153 is predicted to target the 3′UTR region of the calcium channel gene, Cacna1c. Further studies confirmed that Cacna1c mRNA and protein are downregulated by miR-153 mimics and upregulated by miR-153 inhibitors in insulin-secreting freshly isolated mouse islets, in the insulin-secreting mouse cell line MIN6 and in the dopamine-secreting cell line PC12. Conclusions/interpretation: miR-153 is a negative regulator of both insulin and dopamine secretion through its effect on Cacna1c expression, which suggests that IA-2β and miR-153 have opposite functional effects on the secretory pathway. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are potent regulators of gene transcription and posttranscriptional processes. The majority of miRNAs are localized within intronic regions of protein-coding genes (host genes) and have diverse functions in regulating important cellular processes in animals. To date, few plant intronic miRNAs have been studied functionally. Here we report a comprehensive computational analysis to characterize intronic miRNAs in rice and Arabidopsis. RT-PCR analysis confirmed that the identified intronic miRNAs were derived from the real introns of host genes. Interestingly, 13 intronic miRNAs in rice and two in Arabidopsis were located within seven clusters, of which four polycistronic clusters contain miRNAs derived from different families, suggesting that these clustered intronic miRNAs might be involved in extremely complex regulation in rice. Length analysis of miRNA-carrying introns, promoter prediction and qRT-PCR analysis results indicated that intronic miRNAs are coexpressed with their host genes. Expression pattern analysis demonstrated that host genes had a very broad expression spectrum in different stages of development, suggesting the intronic miRNAs might play an important role in plant development. This comparative genomics analysis of intronic miRNAs in rice and Arabidopsis provides new insight into the functions and regulatory mechanisms of intronic miRNAs in monocots and dicots. [ABSTRACT FROM AUTHOR]

5′ UTR of the coding gene affected gene expression at the transcription and translation levels. For miRNA, 5′ UTR (termed 5′ UTR-like) is similar to UTR of encoding protein gene. However, the function of 5′ UTR-like has not been reported in the regulation of pre-miRNA formation and the process of miRNA’s formation. In this study, the regulated elements of 5′ UTR-like of intron miR3029 were analyzed by bioinformatics. The function analysis of primary structure of 5′ UTR-like was studied by the transient expression system of Arabidopsis thaliana protoplast. The function of second-structure stem loops of 5′ UTR-like was conducted by detecting the expression of miRNA3029 and pri-miRNA3029 in transgenic tobacco. In this study, we found that 5′ UTR-like region of miR3029 existences low temperature (LTR), oxygen stress element (ARE) and stem loop structure. These elements and structure may control miRNA’s stability and thereby affect the formation of mature miR3029. There also existed a translation enhancer similar to that of the UTRs of coding genes. The function analysis of second structure found that the predicted stem loop 5 can promote the expression of mature miR3029; stem loops 1, 2, 3 and 4 can inhibit the formation of mature miR3029. To sum up, this study lays a foundation for exploring the mechanism of how the primary transcript is cleaved into pre-miRNA, and provides reference for the study of the regulation of miRNA. [ABSTRACT FROM AUTHOR]