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Small RNA and Degradome Sequencing Reveal Complex Roles of miRNAs and Their Targets in Developing Wheat Grains.

Li T, Ma L, Geng Y, Hao C, Chen X, Zhang X - PLoS ONE (2015)

Bottom Line: A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development.Predicted and validated targets of these development-related miRNAs are involved in different cellular responses and metabolic processes including cell proliferation, auxin signaling, nutrient metabolism and gene expression.This study provides insight into the complex roles of miRNAs and their targets in regulating wheat grain development.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.

ABSTRACT
Plant microRNAs (miRNAs) have been shown to play critical roles in plant development. In this study, we employed small RNA combined with degradome sequencing to survey development-related miRNAs and their validated targets during wheat grain development. A total of 186 known miRNAs and 37 novel miRNAs were identified in four small RNA libraries. Moreover, a miRNA-like long hairpin locus was first identified to produce 21~22-nt phased siRNAs that act in trans to cleave target mRNAs. A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development. Predicted and validated targets of these development-related miRNAs are involved in different cellular responses and metabolic processes including cell proliferation, auxin signaling, nutrient metabolism and gene expression. This study provides insight into the complex roles of miRNAs and their targets in regulating wheat grain development.

No MeSH data available.


A miRNA-like long hairpin producing phased 21~22-nt ta-siRNAs.(A) Abundant small RNAs were generated from ten phases of the long hairpin, with red and blue bars representing sequences from the 5′ and 3′ arms, respectively. Their corresponding abundances are shown above as columns in the same color. (B) Degradome analysis confirmed the cleavage of target mRNAs guided by 3′_D2 and 5′_D8. The t-plots showed absolute sequence abundances over the target mRNAs, with red arrows indicating sequence reads consistent with siRNA-directed cleavage. Representative data origins from degradome libraries I or II are also indicated in the t-plots.
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pone.0139658.g002: A miRNA-like long hairpin producing phased 21~22-nt ta-siRNAs.(A) Abundant small RNAs were generated from ten phases of the long hairpin, with red and blue bars representing sequences from the 5′ and 3′ arms, respectively. Their corresponding abundances are shown above as columns in the same color. (B) Degradome analysis confirmed the cleavage of target mRNAs guided by 3′_D2 and 5′_D8. The t-plots showed absolute sequence abundances over the target mRNAs, with red arrows indicating sequence reads consistent with siRNA-directed cleavage. Representative data origins from degradome libraries I or II are also indicated in the t-plots.

Mentions: Trans-acting siRNAs (ta-siRNAs) are an important clade of regulatory small RNAs that are also capable of altering gene expression [4]. The TAS3 locus, a well characterized conserved miR390 target, generates phased ta-siRNAs that mediated cleavage of ARF3 and ARF4 mRNAs [29]. After searching wheat ta-siRNAs generated from TAS3 locus as described [39], we found that they were of very low abundance in our libraries (TPM less than 1), and their targets were not well supported by our degradome sequencing data, suggesting that these ta-siRNAs might be inactive in wheat grains. However, we also identified a long miRNA-like locus (NCBI EST No. JV867359) generating 21–22 nt phased small RNAs (Figs 2A and S3). This locus was originally identified by us as a new miRNA precursor, but then considered as a phased small RNA-related locus after investigating the distributions and numbers of unique sequences along the precursor.


Small RNA and Degradome Sequencing Reveal Complex Roles of miRNAs and Their Targets in Developing Wheat Grains.

Li T, Ma L, Geng Y, Hao C, Chen X, Zhang X - PLoS ONE (2015)

A miRNA-like long hairpin producing phased 21~22-nt ta-siRNAs.(A) Abundant small RNAs were generated from ten phases of the long hairpin, with red and blue bars representing sequences from the 5′ and 3′ arms, respectively. Their corresponding abundances are shown above as columns in the same color. (B) Degradome analysis confirmed the cleavage of target mRNAs guided by 3′_D2 and 5′_D8. The t-plots showed absolute sequence abundances over the target mRNAs, with red arrows indicating sequence reads consistent with siRNA-directed cleavage. Representative data origins from degradome libraries I or II are also indicated in the t-plots.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591353&req=5

pone.0139658.g002: A miRNA-like long hairpin producing phased 21~22-nt ta-siRNAs.(A) Abundant small RNAs were generated from ten phases of the long hairpin, with red and blue bars representing sequences from the 5′ and 3′ arms, respectively. Their corresponding abundances are shown above as columns in the same color. (B) Degradome analysis confirmed the cleavage of target mRNAs guided by 3′_D2 and 5′_D8. The t-plots showed absolute sequence abundances over the target mRNAs, with red arrows indicating sequence reads consistent with siRNA-directed cleavage. Representative data origins from degradome libraries I or II are also indicated in the t-plots.
Mentions: Trans-acting siRNAs (ta-siRNAs) are an important clade of regulatory small RNAs that are also capable of altering gene expression [4]. The TAS3 locus, a well characterized conserved miR390 target, generates phased ta-siRNAs that mediated cleavage of ARF3 and ARF4 mRNAs [29]. After searching wheat ta-siRNAs generated from TAS3 locus as described [39], we found that they were of very low abundance in our libraries (TPM less than 1), and their targets were not well supported by our degradome sequencing data, suggesting that these ta-siRNAs might be inactive in wheat grains. However, we also identified a long miRNA-like locus (NCBI EST No. JV867359) generating 21–22 nt phased small RNAs (Figs 2A and S3). This locus was originally identified by us as a new miRNA precursor, but then considered as a phased small RNA-related locus after investigating the distributions and numbers of unique sequences along the precursor.

Bottom Line: A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development.Predicted and validated targets of these development-related miRNAs are involved in different cellular responses and metabolic processes including cell proliferation, auxin signaling, nutrient metabolism and gene expression.This study provides insight into the complex roles of miRNAs and their targets in regulating wheat grain development.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture / Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.

ABSTRACT
Plant microRNAs (miRNAs) have been shown to play critical roles in plant development. In this study, we employed small RNA combined with degradome sequencing to survey development-related miRNAs and their validated targets during wheat grain development. A total of 186 known miRNAs and 37 novel miRNAs were identified in four small RNA libraries. Moreover, a miRNA-like long hairpin locus was first identified to produce 21~22-nt phased siRNAs that act in trans to cleave target mRNAs. A comparison of the miRNAomes revealed that 55 miRNA families were differentially expressed during the grain development. Predicted and validated targets of these development-related miRNAs are involved in different cellular responses and metabolic processes including cell proliferation, auxin signaling, nutrient metabolism and gene expression. This study provides insight into the complex roles of miRNAs and their targets in regulating wheat grain development.

No MeSH data available.