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Cloning and characterization of microRNAs from wheat (Triticum aestivum L.).

Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q - Genome Biol. (2007)

Bottom Line: These results indicate that both conserved and wheat-specific miRNAs play important roles in wheat growth and development, stress responses and other physiological processes.This study led to the discovery of 58 wheat miRNAs comprising 43 miRNA families; 20 of these families are conserved and 23 are novel in wheat.It provides a first large scale cloning and characterization of wheat miRNAs and their predicted targets.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100094, China.

ABSTRACT

Background: MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenced. Wheat is one of the most important cereal crops worldwide. To date, only a few conserved miRNAs have been predicted in wheat and the computational identification of wheat miRNAs requires the genome sequence, which is unknown.

Results: To identify novel as well as conserved miRNAs in wheat (Triticum aestivum L.), we constructed a small RNA library. High throughput sequencing of the library and subsequent analysis revealed the identification of 58 miRNAs, comprising 43 miRNA families. Of these, 35 miRNAs belong to 20 conserved miRNA families. The remaining 23 miRNAs are novel and form 23 miRNA families in wheat; more importantly, 4 of these new miRNAs (miR506, miR510, miR514 and miR516) appear to be monocot-specific. Northern blot analysis indicated that some of the new miRNAs are preferentially expressed in certain tissues. Based on sequence homology, we predicted 46 potential targets. Thus, we have identified a large number of monocot-specific and wheat-specific miRNAs. These results indicate that both conserved and wheat-specific miRNAs play important roles in wheat growth and development, stress responses and other physiological processes.

Conclusion: This study led to the discovery of 58 wheat miRNAs comprising 43 miRNA families; 20 of these families are conserved and 23 are novel in wheat. It provides a first large scale cloning and characterization of wheat miRNAs and their predicted targets.

Show MeSH
Semi-quantitative RT-PCR analyses of novel miRNAs in wheat. Relative expression of miRNAs in stems, internodes below spikes, leaves, flag leaves, roots and spikes was analyzed by semi-quantitative RT-PCR. A wheat actin gene was selected to normalize the amount of templates added in the PCR reactions. ST, stems; I, internodes below spikes; R, roots; L, leaves; FL, flag leaves; SP, spikes.
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Figure 4: Semi-quantitative RT-PCR analyses of novel miRNAs in wheat. Relative expression of miRNAs in stems, internodes below spikes, leaves, flag leaves, roots and spikes was analyzed by semi-quantitative RT-PCR. A wheat actin gene was selected to normalize the amount of templates added in the PCR reactions. ST, stems; I, internodes below spikes; R, roots; L, leaves; FL, flag leaves; SP, spikes.

Mentions: The expression of four wheat miRNAs (miR504, miR505, miR506 and miR508) was validated by semi-quantitative RT-PCR, as these could not be detected using Northern blot analysis (Figure 4). MiR505 and miR506 had low expression levels in spikes, and miR508 was found to be uniformly expressed in stems, internodes and spikes but could not be detected in leaves and roots. MiR504 showed ubiquitous expression in all the tissues examined (Figure 4).


Cloning and characterization of microRNAs from wheat (Triticum aestivum L.).

Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, Sun Q - Genome Biol. (2007)

Semi-quantitative RT-PCR analyses of novel miRNAs in wheat. Relative expression of miRNAs in stems, internodes below spikes, leaves, flag leaves, roots and spikes was analyzed by semi-quantitative RT-PCR. A wheat actin gene was selected to normalize the amount of templates added in the PCR reactions. ST, stems; I, internodes below spikes; R, roots; L, leaves; FL, flag leaves; SP, spikes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2394755&req=5

Figure 4: Semi-quantitative RT-PCR analyses of novel miRNAs in wheat. Relative expression of miRNAs in stems, internodes below spikes, leaves, flag leaves, roots and spikes was analyzed by semi-quantitative RT-PCR. A wheat actin gene was selected to normalize the amount of templates added in the PCR reactions. ST, stems; I, internodes below spikes; R, roots; L, leaves; FL, flag leaves; SP, spikes.
Mentions: The expression of four wheat miRNAs (miR504, miR505, miR506 and miR508) was validated by semi-quantitative RT-PCR, as these could not be detected using Northern blot analysis (Figure 4). MiR505 and miR506 had low expression levels in spikes, and miR508 was found to be uniformly expressed in stems, internodes and spikes but could not be detected in leaves and roots. MiR504 showed ubiquitous expression in all the tissues examined (Figure 4).

Bottom Line: These results indicate that both conserved and wheat-specific miRNAs play important roles in wheat growth and development, stress responses and other physiological processes.This study led to the discovery of 58 wheat miRNAs comprising 43 miRNA families; 20 of these families are conserved and 23 are novel in wheat.It provides a first large scale cloning and characterization of wheat miRNAs and their predicted targets.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100094, China.

ABSTRACT

Background: MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenced. Wheat is one of the most important cereal crops worldwide. To date, only a few conserved miRNAs have been predicted in wheat and the computational identification of wheat miRNAs requires the genome sequence, which is unknown.

Results: To identify novel as well as conserved miRNAs in wheat (Triticum aestivum L.), we constructed a small RNA library. High throughput sequencing of the library and subsequent analysis revealed the identification of 58 miRNAs, comprising 43 miRNA families. Of these, 35 miRNAs belong to 20 conserved miRNA families. The remaining 23 miRNAs are novel and form 23 miRNA families in wheat; more importantly, 4 of these new miRNAs (miR506, miR510, miR514 and miR516) appear to be monocot-specific. Northern blot analysis indicated that some of the new miRNAs are preferentially expressed in certain tissues. Based on sequence homology, we predicted 46 potential targets. Thus, we have identified a large number of monocot-specific and wheat-specific miRNAs. These results indicate that both conserved and wheat-specific miRNAs play important roles in wheat growth and development, stress responses and other physiological processes.

Conclusion: This study led to the discovery of 58 wheat miRNAs comprising 43 miRNA families; 20 of these families are conserved and 23 are novel in wheat. It provides a first large scale cloning and characterization of wheat miRNAs and their predicted targets.

Show MeSH