The involvement of InMIR167 in the regulation of expression of its target gene InARF8, and their participation in the vegetative and generative development of Ipomoea nil plants

Glazińska, Paulina; Wojciechowski, Waldemar; Wilmowicz, Emilia; Zienkiewicz, Agnieszka; Frankowski, Kamil; Kopcewicz, Jan

doi:10.1016/j.jplph.2013.07.011

Cited by 25 publications

(23 citation statements)

References 41 publications

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“…Enriched GO-terms for miR397 from B. distachyon suggested its association with stress response based on the presence of GO-terms such as “response to stress,” “response to external stimulus,”' and “response to biotic stimulus.” Additionally, miR167 from T. aestivum was associated with “pollen-pistil interaction” suggesting its regulatory role in development. This miRNA family was also associated with the young tissues such as shoot-tips and flowers in Arabidopsis (Glazińska et al, 2014), therefore, further elucidation of its function in T. aestivum might be important for understanding the developmental regulations.…”

Section: Resultsmentioning

confidence: 99%

A Comprehensive Prescription for Plant miRNA Identification

2017

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microRNAs (miRNAs) are tiny ribo-regulatory molecules involved in various essential pathways for persistence of cellular life, such as development, environmental adaptation, and stress response. In recent years, miRNAs have become a major focus in molecular biology because of their functional and diagnostic importance. This interest in miRNA research has resulted in the development of many specific software and pipelines for the identification of miRNAs and their specific targets, which is the key for the elucidation of miRNA-modulated gene expression. While the well-recognized importance of miRNAs in clinical research pushed the emergence of many useful computational identification approaches in animals, available software and pipelines are fewer for plants. Additionally, existing approaches suffers from mis-identification and annotation of plant miRNAs since the miRNA mining process for plants is highly prone to false-positives, particularly in cereals which have a highly repetitive genome. Our group developed a homology-based in silico miRNA identification approach for plants, which utilizes two Perl scripts “SUmirFind” and “SUmirFold” and since then, this method helped identify many miRNAs particularly from crop species such as Triticum or Aegliops. Herein, we describe a comprehensive updated guideline by the implementation of two new scripts, “SUmirPredictor” and “SUmirLocator,” and refinements to our previous method in order to identify genuine miRNAs with increased sensitivity in consideration of miRNA identification problems in plants. Recent updates enable our method to provide more reliable and precise results in an automated fashion in addition to solutions for elimination of most false-positive predictions, miRNA naming and miRNA mis-annotation. It also provides a comprehensive view to genome/transcriptome-wide location of miRNA precursors as well as their association with transposable elements. The “SUmirPredictor” and “SUmirLocator” scripts are freely available together with a reference high-confidence plant miRNA list.

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Section: Resultsmentioning

confidence: 99%

A Comprehensive Prescription for Plant miRNA Identification

2017

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“…As we know, CSD1 is the target of miR398, that is why it is impossible for high expression of miR398 under high salt stress. Previous studies suggested that TIR1 and ARF are regulated by miR393 and miR160/167, and the two targets are located in plant auxin signal pathway (Chen et al ., ; Glazińska et al ., ). Our KEGG analysis showed corresponding results (Figure ).…”

Section: Discussionmentioning

confidence: 97%

“…These targets were probably cleaved by the miRNAs at the post‐transcriptional levels. In fact, studies have shown that the expression of ARF16, classIII HD‐ZIP family protein, ARF8, NAM (NO apical meristem), RAP1 (relative to apetala21), HAM (hairy meristem) and TIR1 were cleaved by miR160, miR166, miR167, miR171, miR172 and miR393, not repressing translation (Chen et al ., ; Glazińska et al ., ; Hu et al ., ; Kohli et al ., ; Lakhotia et al ., ).…”

Section: Discussionmentioning

confidence: 99%

Small RNA deep sequencing reveals the important role of microRNAs in the halophyte Halostachys caspica

Yang

Zeng

et al. 2015

Plant Biotechnology Journal

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SummaryMicroRNAs (miRNAs), an extensive class of small regulatory RNAs, play versatile roles in plant growth and development as well as stress responses. However, the regulatory mechanism is unclear on miRNA-mediated response to abiotic stress in plants. Halostachys caspica is a halophytic plant species and a great model for investigating plant response to salinity stress. However, no research has been performed on miRNAs in H. caspica. In this study, we employed deep sequencing to identify both conserved and novel miRNAs from salinity-exposed H. caspica and its untreated control. Among the 13-19 million sequences generated from both treatments, a total of 170 conserved miRNAs, belonging to 151 miRNA families, were identified; among these miRNAs, 31 were significantly up-regulated and 48 were significantly down-regulated by salinity stress. We also identified 102 novel miRNAs from H. caspica; among them, 12 miRNAs were significantly up-regulated and 13 were significantly down-regulated by salinity. qRT-PCR expression analysis validated the deep sequencing results and also demonstrated that miRNAs and their targeted genes were responsive to high salt stress and existed a negative expression correlation between miRNAs and their targets. miRNA-target prediction, GO and KEGG analysis showed that miRNAs were involved in salt stress-related biological pathway, including calcium signalling pathway, MAPK signalling pathway, plant hormone signal transduction and flavonoid biosynthesis, etc. This suggests that miRNAs play an important role in plant salt stress tolerance in H. caspica. This result could be used to improve salt tolerance in crops and woods.

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“…For each gene amplification, real-time quantitative PCR (qPCR) with specific primers (Table S1) and universal probe library (UPL) hydrolysis probes (Roche) was used. The actin gene (InACT4) was selected as a reference endogenous control for normalization purposes (Glazińska et al 2014;Marciniak et al 2017;Wilmowicz et al 2016b). qPCR with mixtures containing 0.1 µg of cDNA, 0.2 µM FP/RP, 0.05 µM UPL and 1 × LightCycler TaqMan Master Mix (LightCycler TaqMan Master Kit, Roche), was performed in 20 µl volumes in glass capillaries using a LightCycler 2.0 system (Roche).…”

Section: Expression Analysismentioning

confidence: 99%