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Profiling of microRNAs under wound treatment in Aquilaria sinensis to identify possible microRNAs involved in agarwood formation.

Gao ZH, Yang Y, Zhang Z, Zhao WT, Meng H, Jin Y, Huang JQ, Xu YH, Zhao LZ, Liu J, Wei JH - Int. J. Biol. Sci. (2014)

Bottom Line: MicroRNAs (miRNAs) are a group of gene expression regulators with overwhelming effects on a large spectrum of biological processes.The miR171, miR390, miR394, miR2111, and miR3954 families remained at the reduced level two days after the treatment. 131 homologous miRNAs in the 0.5 h library showed over three-fold variation of read number compared with the control library, of which 12 exhibiting strong expression alterations were further confirmed by real-time quantitative PCR.The cleaveage sites of three newly predicted targets were verified by 5'RACE.

View Article: PubMed Central - PubMed

Affiliation: 1. Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medicinal College (National Engineering Laboratory for Breeding of Endangered Medicinal Materials), Beijing 100193, China.

ABSTRACT
Agarwood, a kind of highly valued non-timber product across Asia, is formed only when its resource trees--the endangered genus Aquilaria are wounded or infected by some microbes. To promote the efficiency of agarwood production and protect the wild resource of Aquilaria species, we urgently need to reveal the regulation mechanism of agarwood formation. MicroRNAs (miRNAs) are a group of gene expression regulators with overwhelming effects on a large spectrum of biological processes. However, their roles in agarwood formation remain unknown. This work aimed at identifying possible miRNAs involved in the wound induced agarwood formation. In this study, the high-throughput sequencing was adopted to identify miRNAs and monitor their expression under wound treatment in the stems of A. sinensis. The miR171, miR390, miR394, miR2111, and miR3954 families remained at the reduced level two days after the treatment. 131 homologous miRNAs in the 0.5 h library showed over three-fold variation of read number compared with the control library, of which 12 exhibiting strong expression alterations were further confirmed by real-time quantitative PCR. Target prediction and annotation of the miRNAs demonstrated that the binding, metabolic process, catalytic activity, and cellular process are the most common functions of the predicted targets of these newly identified miRNAs in A.sinensis. The cleaveage sites of three newly predicted targets were verified by 5'RACE.

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Heat map showing differently expressed conserved and homo-miRNAs in wound tissues compared with the 0h sample.
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Figure 4: Heat map showing differently expressed conserved and homo-miRNAs in wound tissues compared with the 0h sample.

Mentions: The expression levels of all identified homologous/conserved miRNAs in the four samples were compared using the Cluster 3.0 algorithm 51. Expression clustering with different samples showed that the expression characteristic of the 0.5 h sample which represented the short-term response to the wound treatment was different from that of other samples (Figure 4). The 4 h response and 48 h response were the closest among all libraries. In general, 131 miRNAs in the 0.5 h library showed an over three-fold variation in read number compared with those in the CK library. 70 and 29 in the 4 h library and 48 h library respectively showed over three-fold variance. 13 miRNAs including the conserved miRNA miR473 remained at a constant level in all the three time points after treatment.


Profiling of microRNAs under wound treatment in Aquilaria sinensis to identify possible microRNAs involved in agarwood formation.

Gao ZH, Yang Y, Zhang Z, Zhao WT, Meng H, Jin Y, Huang JQ, Xu YH, Zhao LZ, Liu J, Wei JH - Int. J. Biol. Sci. (2014)

Heat map showing differently expressed conserved and homo-miRNAs in wound tissues compared with the 0h sample.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4007363&req=5

Figure 4: Heat map showing differently expressed conserved and homo-miRNAs in wound tissues compared with the 0h sample.
Mentions: The expression levels of all identified homologous/conserved miRNAs in the four samples were compared using the Cluster 3.0 algorithm 51. Expression clustering with different samples showed that the expression characteristic of the 0.5 h sample which represented the short-term response to the wound treatment was different from that of other samples (Figure 4). The 4 h response and 48 h response were the closest among all libraries. In general, 131 miRNAs in the 0.5 h library showed an over three-fold variation in read number compared with those in the CK library. 70 and 29 in the 4 h library and 48 h library respectively showed over three-fold variance. 13 miRNAs including the conserved miRNA miR473 remained at a constant level in all the three time points after treatment.

Bottom Line: MicroRNAs (miRNAs) are a group of gene expression regulators with overwhelming effects on a large spectrum of biological processes.The miR171, miR390, miR394, miR2111, and miR3954 families remained at the reduced level two days after the treatment. 131 homologous miRNAs in the 0.5 h library showed over three-fold variation of read number compared with the control library, of which 12 exhibiting strong expression alterations were further confirmed by real-time quantitative PCR.The cleaveage sites of three newly predicted targets were verified by 5'RACE.

View Article: PubMed Central - PubMed

Affiliation: 1. Institute of Medicinal Plant Development, Chinese Academy of Medical Science & Peking Union Medicinal College (National Engineering Laboratory for Breeding of Endangered Medicinal Materials), Beijing 100193, China.

ABSTRACT
Agarwood, a kind of highly valued non-timber product across Asia, is formed only when its resource trees--the endangered genus Aquilaria are wounded or infected by some microbes. To promote the efficiency of agarwood production and protect the wild resource of Aquilaria species, we urgently need to reveal the regulation mechanism of agarwood formation. MicroRNAs (miRNAs) are a group of gene expression regulators with overwhelming effects on a large spectrum of biological processes. However, their roles in agarwood formation remain unknown. This work aimed at identifying possible miRNAs involved in the wound induced agarwood formation. In this study, the high-throughput sequencing was adopted to identify miRNAs and monitor their expression under wound treatment in the stems of A. sinensis. The miR171, miR390, miR394, miR2111, and miR3954 families remained at the reduced level two days after the treatment. 131 homologous miRNAs in the 0.5 h library showed over three-fold variation of read number compared with the control library, of which 12 exhibiting strong expression alterations were further confirmed by real-time quantitative PCR. Target prediction and annotation of the miRNAs demonstrated that the binding, metabolic process, catalytic activity, and cellular process are the most common functions of the predicted targets of these newly identified miRNAs in A.sinensis. The cleaveage sites of three newly predicted targets were verified by 5'RACE.

Show MeSH
Related in: MedlinePlus