miR169 Family Members Research Articles

Identification and characterization of miRNA169 family members in banana (Musa acuminata L.) that respond to fusarium oxysporum f. sp. cubense infection in banana cultivars.

MicroRNAs (miRNAs) play an important role in plant resistance to pathogen infections. However, little is known about the role of miRNAs in banana Fusarium wilt, which is the most economically devastating disease in banana production. In the present study, we identified and characterized a total of 18 miR169 family members in banana (Musa acuminata L.) based on small RNA sequencing. The banana miR169 family clustered into two groups based on miRNA evolutionary analysis. Multiple sequence alignment indicated a high degree of sequence conservation in miRNA169 family members across 28 plant species. Computational target prediction algorithms were used to identify 25 targets of miR169 family members in banana. These targets were enriched in various metabolic pathways that include the following molecules: glycine, serine, threonine, pentose, glycerolipids, nucleotide sugars, starch, and sucrose. Through miRNA transcriptomic analysis, we found that ma-miR169a and ma-miR169b displayed high expression levels, whereas the other 16 ma-miR169 members exhibited low expression in the HG and Baxi banana cultivars. Further experiments indicate that there were negative relationships between ma-miR169a, ma-miR169b and their targets basing on their expression levels to Foc4 (Fusarium oxysporum f. sp. cubense tropical race 4) infection in resistant cultivars. But they were low expressed in susceptive cultivars. These results suggested that the expression levels of ma-miR169a and ma-miR169b were consistent with the resistance degree of the banana cultivars to Foc4. The analysis presented here constitutes a starting point to understand ma-miR169-mediated Fusarium wilt resistance at the transcriptional level in banana and predicts possible candidate targets for the genetic improvement of banana resistance to Foc4.

Transcriptomic analyses of rice (Oryza sativa) genes and non-coding RNAs under nitrogen starvation using multiple omics technologies

BackgroundNitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially in recent decades; however, the applied N is not fully utilized due to the low N use efficiency of crops. To overcome this limitation, it is important to understand the genome-wide responses and functions of key genes and potential regulatory factors in N metabolism.ResultsHere, we characterized changes in the rice (Oryza sativa) transcriptome, including genes, newly identified putative long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) and their target mRNAs in response to N starvation using four different transcriptome approaches. Analysis of rice genes involved in N metabolism and/or transport using strand-specific RNA-Seq identified 2588 novel putative lncRNA encoding loci. Analysis of previously published RNA-Seq datasets revealed a group of N starvation-responsive lncRNAs showing differential expression under other abiotic stress conditions. Poly A-primed sequencing (2P-Seq) revealed alternatively polyadenylated isoforms of N starvation-responsive lncRNAs and provided precise 3′ end information on the transcript models of these lncRNAs. Analysis of small RNA-Seq data identified N starvation-responsive miRNAs and down-regulation of miR169 family members, causing de-repression of NF-YA, as confirmed by strand-specific RNA-Seq and qRT-PCR. Moreover, we profiled the N starvation-responsive down-regulation of root-specific miRNA, osa-miR444a.4-3p, and Degradome sequencing confirmed MADS25 as a novel target gene.ConclusionsIn this study, we used a combination of multiple RNA-Seq analyses to extensively profile the expression of genes, newly identified lncRNAs, and microRNAs in N-starved rice roots and shoots. Data generated in this study provide an in-depth understanding of the regulatory pathways modulated by N starvation-responsive miRNAs. The results of comprehensive, large-scale data analysis provide valuable information on multiple aspects of the rice transcriptome, which may be useful in understanding the responses of rice plants to changes in the N supply status of soil.

Identification of four novel stu-miR169s and their target genes in Solanum tuberosum and expression profiles response to drought stress

Plant microRNAs are important endogenous gene regulators which regulate gene expression at post-transcriptional level. Previous studies have identified that miR169 family members regulated the NF-YA transcription factors which have been implicated in plant development and stress responses. At present, reported potato genome sequence data offered an opportunity for global insights into the molecular mechanisms of the miR169/NF-YA modules in potato. In this work, 4 novel stu-miR169 family members were predicted in potato based on potato genome sequence data. miRNA target prediction showed that mature stu-miR169 sequences have a bite sit on the 5 of StNF-YA genes in potato, and three of them were validated by RNA ligase-mediated 5′RACE (5′ RLM-RACE) assay. The result from investigation of the expression patterns of mature stu-miR169 and their predicted target genes also showed that mature stu-miR169 was down-regulated in response to the drought stress. There were some targeted StNF-YA genes that exhibited a negative expression pattern with mature stu-miR169 during the different periods of drought-treated samples. Taken together, the decreased expression of stu-miR169 might drive over-expression of NF-YA family members, they are related to resistances against drought stress.

Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana

Plants interact with their environment and they often flower earlier under stress conditions, but how such stress-induced flowering is regulated remains poorly understood. Here evidence is presented that the miR169 family plays a key role in stress-induced flowering in plants. The microRNA (miRNA) miR169 family members are up-regulated in Arabidopsis, maize, and soybean under abiotic stresses. Overexpression of miR169d in Arabidopsis results in early flowering, and overexpression of the miR169d target gene, AtNF-YA2, especially a miR169d-resistant version of AtNF-YA2, results in late flowering. The results suggest that the miR169 family regulates stress-induced flowering by repressing the AtNF-YA transcription factor, which in turn reduces the expression of FLOWERING LOCUS C (FLC), allowing for the expression of FLC target genes such as FLOWERING LOCUS T (FT) and LEAFY (LFY) to promote flowering. It was shown that the expression of genes or miRNAs involved in the other flowering pathways, namely the photoperiod (CO), ambient temperature (SVP), ageing (miR156), and gibberelin (SOC1) pathways, was not affected in miR169d-overexpressing plants, suggesting that stress-induced early flowering is a novel signalling pathway mediated by miR169.

Corrigendum

Plant, Cell & EnvironmentVolume 35, Issue 7 p. 1358-1358 Free Access Corrigendum This article corrects the following: Expression and tissue-specific localization of nitrate-responsive miRNAs in roots of maize seedlings SARA TREVISAN, ALBERTO NONIS, MAURA BEGHELDO, ALESSANDRO MANOLI, KLAUS PALME, GIOVANNI CAPORALE, BENEDETTO RUPERTI, SILVIA QUAGGIOTTI, Volume 35Issue 6Plant, Cell & Environment pages: 1137-1155 First Published online: January 28, 2012 First published: 11 June 2012 https://doi.org/10.1111/j.1365-3040.2012.02528.xAboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL The article ‘Expression and tissue-specific localization of nitrate-responsive miRNAs in roots of maize seedlings’ published in volume 35 issue 6 of Plant, Cell & Environment (Trevisan et al. 2012) contains an incorrect reference citation in the Discussion section. In page 14, the first paragraph, right column, should read as follows: Interestingly, we found that miR169i/j/k and miR166j/k/n were present exclusively in the root's vascular tissues, but whereas miR169i/j/k was found only in nitrate-supplied root tips, miR166j/k/n was detected in the vascular tissue of both nitrogen-depleted and -supplied roots. These findings suggest that the presence of a specific miRNA in the vascular system could be actively regulated by N availability and strengthen the already hypothesized role of miR169 family members as novel candidates for long-distance signalling of the N status in the plant system (Pant et al. 2009; Li et al. 2010). miR169 constitute a large miRNA's family that is widespread in the plant kingdom (Li et al. 2010), and plays important roles in plant development and responses to environmental cues (Combier et al. 2006).The localization of members of miR169 family in the vascular tissue has been also demonstrated in Arabidopsis by Li et al. (2010). The correct publication details for Li et al. (2010) are as follows: Li Y., Fu Y., Ji L., Wu C., Zheng C. (2010) Characterization and expression analysis of the Arabidopsis mir169 family. Plant Science178, 271–280. The authors sincerely apologize for this error. REFERENCE Trevisan S., Nonis A., Begheldo M., Manoli A., Palme K., Caporale G., Ruperti B. & Quaggiotti S. (2012) Expression and tissue-specific localization of nitrate-responsive miRNAs in roots of maize seedlings. Plant, Cell & Environment 35, 1137– 1155. Volume35, Issue7July 2012Pages 1358-1358 ReferencesRelatedInformation

Characterization and expression analysis of the Arabidopsis mir169 family

The mir169 family is a large and conserved miRNA family in many plant species. The Arabidopsis genome contains 14 members of the mir169 family, including three tandem clusters that were transcribed as polycistrons. To investigate the regulation of mir169 expression, all the 11 promoter sequences were cloned and fused to GUS and introduced into Arabidopsis to generate pMir169:GUS transgenic plants. Histochemical GUS staining and activity assay in different tissues and developmental stages of the transgenic plants revealed unique and overlapping as well as spatio-temporal expression patterns among the family members. The endogenous transcript level of each member detected by semi-quantitative RT-PCR is largely accordant with the GUS expression profiles. Interestingly, the tandem arrayed gene pairs mir169i/j, mir169k/l and mir169m/n show greatly overlapping expression patterns. Further comparative analysis of their upstream sequences revealed significant sequence similarities, indicating that the three gene pairs may result from a duplication event. Additionally, when the transgenic plants were exposed to various abiotic stresses, a subset of family members were observed to be regulated by certain treatments, especially ABA and heat. Our results provide valuable information for functional analysis of the Arabidopsis mir169 family members as ubiquitous regulators in both developmental processes and stimuli pathways.

Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor

BackgroundMicroRNAs (miRNAs) are endogenously expressed small RNAs with a length of about 21 nt. MiRNAs silence their target genes at the post-transcriptional level. In plants, miRNAs play various developmental and physiological roles by cleavaging mRNAs predominantly. Drought and high salinity are the most severe environmental abiotic stresses and cause crop losses all over the world.ResultsIn this study, we identified miR-169g and miR-169n (o) as high salinity-responsive miRNAs in rice. MiR-169n and miR169o were in a miRNA cluster with a distance of 3707 base pairs (bp). The high degree of conservation and close phylogenic distance of pre-miR-169n and pre-miR-169o indicated that they were derived from a very recent tandem duplication evolutionary event. The existence of a cis-acting abscisic acid responsive element (ABRE) in the upstream region of miR-169n (o) suggested that miR-169n (o) may be regulated by ABA. In our previous study, we found that miR-169g was induced by the osmotic stress caused by drought via a dehydration-responsive element (DRE). Thus, our data showed that there were both overlapping and distinct responses of the miR-169 family to drought and salt stresses. We also showed that these miR-169 members selectively cleaved one of the NF-YA genes, Os03g29760, which is a CCAAT-box binding transcription factor and participates in transcriptional regulation of large number genes. Finally, we found one or more ath-miR-169 member that was also induced by high salinity.ConclusionWe identified members of the miR-169 family as salt-induced miRNAs and analyzed their evolution, gene organization, expression, transcriptional regulation motif and target gene. Our data also indicated that the salt-induction of some miR-169 members was a general property in plants.