Biogenesis, evolution, and functions of plant microRNAs

Pashkovskiy, Pavel P.; Ryazansky, Sergei

doi:10.1134/s0006297913060084

Cited by 35 publications

(20 citation statements)

References 104 publications

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“…Small RNAs are a class of non-coding RNAs that play vital roles in growth and development, signal transduction, biotic and abiotic stresses (Jones-Rhoades et al, 2006; Dalmay, 2010; Mohorianu et al, 2011; Zuo et al, 2012; Pashkovskiy and Ryazansky, 2013). Numerous studies have demonstrated that miRNAs were involved in the regulation of diverse physiological processes by repressing the expression of their target genes.…”

Section: Discussionmentioning

confidence: 99%

Parsing the Regulatory Network between Small RNAs and Target Genes in Ethylene Pathway in Tomato

Wang

Gao

et al. 2017

Front. Plant Sci.

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Small RNAs are a class of short non-coding endogenous RNAs that play essential roles in many biological processes. Recent studies have reported that microRNAs (miRNAs) are also involved in ethylene signaling in plants. LeERF1 is one of the ethylene response factors (ERFs) in tomato that locates in the downstream of ethylene signal transduction pathway. To elucidate the intricate regulatory roles of small RNAs in ethylene signaling pathway in tomato, the deep sequencing and bioinformatics methods were combined to decipher the small RNAs landscape in wild and sense-/antisense-LeERF1 transgenic tomato fruits. Except for the known miRNAs, 36 putative novel miRNAs, 6 trans-acting short interfering RNAs (ta-siRNAs), and 958 natural antisense small interfering RNAs (nat-siRNAs) were also found in our results, which enriched the tomato small RNAs repository. Among these small RNAs, 9 miRNAs, and 12 nat-siRNAs were differentially expressed between the wild and transgenic tomato fruits significantly. A large amount of target genes of the small RNAs were identified and some of them were involved in ethylene pathway, including AP2 TFs, auxin response factors, F-box proteins, ERF TFs, APETALA2-like protein, and MADS-box TFs. Degradome sequencing further confirmed the targets of miRNAs and six novel targets were also discovered. Furthermore, a regulatory model which reveals the regulation relationships between the small RNAs and their targets involved in ethylene signaling was set up. This work provides basic information for further investigation of the function of small RNAs in ethylene pathway and fruit ripening.

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Section: Discussionmentioning

confidence: 99%

Parsing the Regulatory Network between Small RNAs and Target Genes in Ethylene Pathway in Tomato

Wang

Gao

et al. 2017

Front. Plant Sci.

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“…As a novel type of regulatory factor, plant miRNAs play an important role in plant-pathogen interaction37. For instance, our previous work has shown that the miR396 family miRNAs target growth-regulating factor (GRF) genes.…”

Section: Discussionmentioning

confidence: 99%

MiR1918 enhances tomato sensitivity to Phytophthora infestans infection

Luan

Cui

Wang

et al. 2016

Sci Rep

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Late blight of tomato is caused by the oomycete pathogen Phytophthora infestans. In our previous work, we identified and characterized a miR1918 in P. infestans (pi-miR1918), and showed that its sequence is similar to the sequence of tomato miR1918 (sly-miR1918). In this study, we used Arabidopsis thaliana pre-miR159a as a backbone to synthesize pi-miR1918 via PCR and mutagenesis. The artificial pi-miR1918 was used to investigate the role of miR1918 in tomato-P. infestans interaction. Trangenic tomato plants that overexpressed the artificial pi-miR1918 displayed more serious disease symptoms than wild-type tomato plants after infection with P. infestans, as shown by increased number of necrotic cells, lesion sizes and number of sporangia per leaf. The target genes of pi-miR1918 and sly-miR1918 were also predicted for tomato and P. infestans, respectively. qPCR analysis of these targets also performed during tomato-P. infestans interaction. The expression of target gene, RING finger were negatively correlated with miR1918 in the all Lines of transgenic tomato plants. In addition, we used the 5′ RACE to determine the cleavage site of miR1918 to RING finger. These results suggested that miR1918 might be involved in the silencing of target genes, thereby enhancing the susceptibility of tomato to P. infestans infection.

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“…MiRNAs are known to regulate gene expression either through mRNA cleavage, progressive mRNA decay, or translation inhibition (Llave et al 2002;Jin et al 2013;Pashkovskiy and Ryazansky 2013;Budak et al 2015a). In order to gain further insight into miRNA regulatory networks involved in drought stress response, targets of the putative miRNAs were predicted.…”

Section: Stress Induced Mirna Target Regulationmentioning

confidence: 99%

“…In plants, miRNAs are involved in a variety of processes, ranging from their own biogenesis to development and stress responses (Budak and Akpinar 2011;Sunkar et al 2012;Jin et al 2013;Pashkovskiy and Ryazansky 2013;Budak and Akpinar 2015;Budak et al 2015a). Several miRNAs have been identified in plants so far, including wheat, for which 293 mature miRNA sequences are deposited in the current release of miRBase (http://mirbase.org/), while some others are reported in various publications (Budak et al 2015b).…”

Section: Introductionmentioning

confidence: 98%

Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

Akpınar

Kantar

Budak

2015

Funct Integr Genomics

111

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MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees of drought tolerance, to identify miRNA candidates and their targets involved in drought stress response. Root transcriptomes of Triticum turgidum ssp. durum variety Kızıltan and two Triticum turgidum ssp. dicoccoides genotypes TR39477 and TTD-22 under control and drought conditions were assembled from individual RNA-Seq reads and used for in silico identification of miRNAs. A total of 66 miRNAs were identified from all species, across all conditions, of which 46 and 38 of the miRNAs identified from modern durum wheat and wild genotypes, respectively, had not been previously reported. Genotype- and/or stress-specific miRNAs provide insights into our understanding of the complex drought response. Particularly, miR1435, miR5024, and miR7714, identified only from drought-stress roots of drought-tolerant genotype TR39477, can be candidates for future studies to explore and exploit the drought response to develop tolerant varieties.

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Biogenesis, evolution, and functions of plant microRNAs

Cited by 35 publications

References 104 publications

Parsing the Regulatory Network between Small RNAs and Target Genes in Ethylene Pathway in Tomato

Parsing the Regulatory Network between Small RNAs and Target Genes in Ethylene Pathway in Tomato

MiR1918 enhances tomato sensitivity to Phytophthora infestans infection

Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress

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