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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.


Identification of two unique targets for non-conserved development-related miRNAs.(A) A target (TC453857) was regulated by two different miRNAs. The predicted cleavage sites (C1 and C2) were shown in the blue and red boxes in the transcript, respectively. The blue or red lines in the t-plot indicate sequence abundances consistent with the C1 site or C2 site. miRNA:mRNA alignments along with C1 and C2 sites are shown above. (B) A target (TC389301) with multiple similar miRNA sites was intensively regulated by miR9666. The predicted cleavage sites are shown as red boxes in the transcript. The red lines in the t-plot indicate sequence abundances consistent with the C1–C4 sites. miRNA:mRNA alignments along with C1–C4 sites are shown above. Degradome data origins are indicated in the t-plots.
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pone.0139658.g005: Identification of two unique targets for non-conserved development-related miRNAs.(A) A target (TC453857) was regulated by two different miRNAs. The predicted cleavage sites (C1 and C2) were shown in the blue and red boxes in the transcript, respectively. The blue or red lines in the t-plot indicate sequence abundances consistent with the C1 site or C2 site. miRNA:mRNA alignments along with C1 and C2 sites are shown above. (B) A target (TC389301) with multiple similar miRNA sites was intensively regulated by miR9666. The predicted cleavage sites are shown as red boxes in the transcript. The red lines in the t-plot indicate sequence abundances consistent with the C1–C4 sites. miRNA:mRNA alignments along with C1–C4 sites are shown above. Degradome data origins are indicated in the t-plots.

Mentions: For wheat-specific miRNAs related to grain development, only a small fraction of their targets could be confirmed by degradome data (S6 Table). However, there were complex regulatory patterns present among these non-conserved miRNAs and their targets. For example, two different miRNAs, miR9662 and miR9670, were predicted to target TC453857 transcript at the C1 or C2 sites (Fig 5A). Degradome data confirmed that this target could be cleaved at each site, but the cleavage frequency was most abundant at the C2 site targeted by miR9670 (Fig 5A), indicating that some targets may be preferentially regulated by two or even more different miRNAs in a combinatorial manner. More interestingly, we also found a target with multiple nearly identical miRNA sites at different positions. As shown in Fig 5B, there are at least eight sites of miR9666 distributed in tandem or individually on the TC389301 transcript. Degradome data verified cleavage at four sites (C1–C4), and the C3 site had many more observed cleavages than other sites (Fig 5B). We supposed that multiple miRNA sites at one target might originate from insertion and/or duplication of repeat sequences in the genome. We also identified TC402663 as a major target of miR2009 in wheat grains despite as many as 4.0 mismatches, because this target had much more abundant reads in its predicted cleavage site than other targets of miR2009 (S4 Fig). It is noted that miRNAs and their variants also affect the cleavage sites of target mRNAs, as shown by similar target mRNA cleavage frequencies mediated by miR9655a and miR9655b (S4 Fig).


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)

Identification of two unique targets for non-conserved development-related miRNAs.(A) A target (TC453857) was regulated by two different miRNAs. The predicted cleavage sites (C1 and C2) were shown in the blue and red boxes in the transcript, respectively. The blue or red lines in the t-plot indicate sequence abundances consistent with the C1 site or C2 site. miRNA:mRNA alignments along with C1 and C2 sites are shown above. (B) A target (TC389301) with multiple similar miRNA sites was intensively regulated by miR9666. The predicted cleavage sites are shown as red boxes in the transcript. The red lines in the t-plot indicate sequence abundances consistent with the C1–C4 sites. miRNA:mRNA alignments along with C1–C4 sites are shown above. Degradome data origins are indicated in the t-plots.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0139658.g005: Identification of two unique targets for non-conserved development-related miRNAs.(A) A target (TC453857) was regulated by two different miRNAs. The predicted cleavage sites (C1 and C2) were shown in the blue and red boxes in the transcript, respectively. The blue or red lines in the t-plot indicate sequence abundances consistent with the C1 site or C2 site. miRNA:mRNA alignments along with C1 and C2 sites are shown above. (B) A target (TC389301) with multiple similar miRNA sites was intensively regulated by miR9666. The predicted cleavage sites are shown as red boxes in the transcript. The red lines in the t-plot indicate sequence abundances consistent with the C1–C4 sites. miRNA:mRNA alignments along with C1–C4 sites are shown above. Degradome data origins are indicated in the t-plots.
Mentions: For wheat-specific miRNAs related to grain development, only a small fraction of their targets could be confirmed by degradome data (S6 Table). However, there were complex regulatory patterns present among these non-conserved miRNAs and their targets. For example, two different miRNAs, miR9662 and miR9670, were predicted to target TC453857 transcript at the C1 or C2 sites (Fig 5A). Degradome data confirmed that this target could be cleaved at each site, but the cleavage frequency was most abundant at the C2 site targeted by miR9670 (Fig 5A), indicating that some targets may be preferentially regulated by two or even more different miRNAs in a combinatorial manner. More interestingly, we also found a target with multiple nearly identical miRNA sites at different positions. As shown in Fig 5B, there are at least eight sites of miR9666 distributed in tandem or individually on the TC389301 transcript. Degradome data verified cleavage at four sites (C1–C4), and the C3 site had many more observed cleavages than other sites (Fig 5B). We supposed that multiple miRNA sites at one target might originate from insertion and/or duplication of repeat sequences in the genome. We also identified TC402663 as a major target of miR2009 in wheat grains despite as many as 4.0 mismatches, because this target had much more abundant reads in its predicted cleavage site than other targets of miR2009 (S4 Fig). It is noted that miRNAs and their variants also affect the cleavage sites of target mRNAs, as shown by similar target mRNA cleavage frequencies mediated by miR9655a and miR9655b (S4 Fig).

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.