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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 putative miRNA regulatory network in wheat grains.The arrows indicate positive regulation and the nail shapes indicate negative regulation. PSK1, phytosulfokine-alpha 1 precursor; GRF, growth-regulating factor; ARF, auxin response factor; TIR1, transport inhibitor response 1; BCP, blue copper protein; SPX, SPX domain-containing protein; MTERF, mitochondrial transcription termination factor.
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pone.0139658.g007: A putative miRNA regulatory network in wheat grains.The arrows indicate positive regulation and the nail shapes indicate negative regulation. PSK1, phytosulfokine-alpha 1 precursor; GRF, growth-regulating factor; ARF, auxin response factor; TIR1, transport inhibitor response 1; BCP, blue copper protein; SPX, SPX domain-containing protein; MTERF, mitochondrial transcription termination factor.

Mentions: The unique biological process of wheat grain development relies on the complex regulation of gene expression. miRNAs, which are important regulators of gene expression at the transcriptional and post-transcriptional levels, have a role in the wheat grain development [18–20]. In the present study, small RNA sequencing combined with cluster analysis revealed 55 development-related miRNA families differentially expressed during wheat grain development (Fig 3). Degradome analysis confirmed that 22 miRNAs could mediate the cleavage of their targets (S6 Table). On the basis of these results, a putative miRNA-mediated regulation network was proposed in wheat grains (Fig 7).


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 putative miRNA regulatory network in wheat grains.The arrows indicate positive regulation and the nail shapes indicate negative regulation. PSK1, phytosulfokine-alpha 1 precursor; GRF, growth-regulating factor; ARF, auxin response factor; TIR1, transport inhibitor response 1; BCP, blue copper protein; SPX, SPX domain-containing protein; MTERF, mitochondrial transcription termination factor.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139658.g007: A putative miRNA regulatory network in wheat grains.The arrows indicate positive regulation and the nail shapes indicate negative regulation. PSK1, phytosulfokine-alpha 1 precursor; GRF, growth-regulating factor; ARF, auxin response factor; TIR1, transport inhibitor response 1; BCP, blue copper protein; SPX, SPX domain-containing protein; MTERF, mitochondrial transcription termination factor.
Mentions: The unique biological process of wheat grain development relies on the complex regulation of gene expression. miRNAs, which are important regulators of gene expression at the transcriptional and post-transcriptional levels, have a role in the wheat grain development [18–20]. In the present study, small RNA sequencing combined with cluster analysis revealed 55 development-related miRNA families differentially expressed during wheat grain development (Fig 3). Degradome analysis confirmed that 22 miRNAs could mediate the cleavage of their targets (S6 Table). On the basis of these results, a putative miRNA-mediated regulation network was proposed in wheat grains (Fig 7).

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.