Limits...
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.


Validated targets of newly identified miRNAs using degradome sequencing.The target plots (t-plots) show sequence abundances (read counts) throughout the length of the indicated transcripts. The arrows in the t-plot indicate significant sequences consistent with miRNA-directed cleavage. miRNA:mRNA alignments along with the cleavage positions are shown above. Representative data origins from degradome libraries I or II are also indicated in the t-plots.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4591353&req=5

pone.0139658.g001: Validated targets of newly identified miRNAs using degradome sequencing.The target plots (t-plots) show sequence abundances (read counts) throughout the length of the indicated transcripts. The arrows in the t-plot indicate significant sequences consistent with miRNA-directed cleavage. miRNA:mRNA alignments along with the cleavage positions are shown above. Representative data origins from degradome libraries I or II are also indicated in the t-plots.

Mentions: To further investigate the functions of new miRNAs, we predicted their targets in wheat (S5 Table). Unlike the conserved miRNAs whose targets are mainly transcription factors [7], the majority of new miRNAs are predicted to have a diverse set of target genes encoding protein kinases, disease resistance proteins, other enzymes or even unknown proteins, indicating that these miRNAs are widely involved in the regulation of various biological processes including cell metabolism and signaling transduction. Cleavage of target mRNAs mediated by some new miRNAs has been validated by degradome sequencing data (Fig 1). These verified targets had at least one degradome tag with a 5′ end precisely opposite the 10th nucleotide of the miRNAs, which is a characteristic feature of miRNA-guided slicing [22]. Both miR5048.2 and Ta-miRn3 target a class of mRNAs encoding cysteine-rich receptor-like protein kinases (Fig 1). Furthermore, Ta-miRn1, Ta-miRn7, Ta-miRn8 and Ta-miRn10 target mRNAs encoding disease resistance proteins, cell division protein ftsY homologs, a MIT (microtubule interacting and transport) domain protein and an unknown protein, respectively (Fig 1).


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)

Validated targets of newly identified miRNAs using degradome sequencing.The target plots (t-plots) show sequence abundances (read counts) throughout the length of the indicated transcripts. The arrows in the t-plot indicate significant sequences consistent with miRNA-directed cleavage. miRNA:mRNA alignments along with the cleavage positions are shown above. 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.g001: Validated targets of newly identified miRNAs using degradome sequencing.The target plots (t-plots) show sequence abundances (read counts) throughout the length of the indicated transcripts. The arrows in the t-plot indicate significant sequences consistent with miRNA-directed cleavage. miRNA:mRNA alignments along with the cleavage positions are shown above. Representative data origins from degradome libraries I or II are also indicated in the t-plots.
Mentions: To further investigate the functions of new miRNAs, we predicted their targets in wheat (S5 Table). Unlike the conserved miRNAs whose targets are mainly transcription factors [7], the majority of new miRNAs are predicted to have a diverse set of target genes encoding protein kinases, disease resistance proteins, other enzymes or even unknown proteins, indicating that these miRNAs are widely involved in the regulation of various biological processes including cell metabolism and signaling transduction. Cleavage of target mRNAs mediated by some new miRNAs has been validated by degradome sequencing data (Fig 1). These verified targets had at least one degradome tag with a 5′ end precisely opposite the 10th nucleotide of the miRNAs, which is a characteristic feature of miRNA-guided slicing [22]. Both miR5048.2 and Ta-miRn3 target a class of mRNAs encoding cysteine-rich receptor-like protein kinases (Fig 1). Furthermore, Ta-miRn1, Ta-miRn7, Ta-miRn8 and Ta-miRn10 target mRNAs encoding disease resistance proteins, cell division protein ftsY homologs, a MIT (microtubule interacting and transport) domain protein and an unknown protein, respectively (Fig 1).

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.