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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.

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The frequency of conserved miRNAs present in the sequenced small RNA library.
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Figure 2: The frequency of conserved miRNAs present in the sequenced small RNA library.

Mentions: Interestingly, we found that one miRNA, TamiR507, mapped to the wheat genome by searching the NCBI database. This locus resides in the promoter region of the gene VRN-A1 (AY747601). The genomic sequence has high (73%) nucleotide similarity in the stem-loop region with EST CK217185, the precursor of TamiR507. Both the EST and genomic sequence can form a hairpin structure, and the miRNA was detected on small RNA gel blots as a discrete band (Figure 2), suggesting that it is not a degradation product. The existence of miRNA loci in promoter regions was hitherto unknown, and most miRNAs map to intergenic regions and only a few to introns or exons [11].


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)

The frequency of conserved miRNAs present in the sequenced small RNA library.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: The frequency of conserved miRNAs present in the sequenced small RNA library.
Mentions: Interestingly, we found that one miRNA, TamiR507, mapped to the wheat genome by searching the NCBI database. This locus resides in the promoter region of the gene VRN-A1 (AY747601). The genomic sequence has high (73%) nucleotide similarity in the stem-loop region with EST CK217185, the precursor of TamiR507. Both the EST and genomic sequence can form a hairpin structure, and the miRNA was detected on small RNA gel blots as a discrete band (Figure 2), suggesting that it is not a degradation product. The existence of miRNA loci in promoter regions was hitherto unknown, and most miRNAs map to intergenic regions and only a few to introns or exons [11].

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