Limits...
A Survey of MicroRNA Length Variants Contributing to miRNome Complexity in Peach (Prunus Persica L.).

Colaiacovo M, Bernardo L, Centomani I, Crosatti C, Giusti L, Orrù L, Tacconi G, Lamontanara A, Cattivelli L, Faccioli P - Front Plant Sci (2012)

Bottom Line: Three hundred-ninety-two isomiRs (miRNA and miRNA*-related) corresponding to 26 putative miRNA coding loci, have been highlighted by mirDeep-P and analyzed.The degree of mature sequence heterogeneity is very different for each individual locus.Results obtained in the present work can thus contribute to a deeper view of the miRNome complexity and to better explore the mechanism of action of these tiny regulators.

View Article: PubMed Central - PubMed

Affiliation: CRA Genomics Research Centre, Fiorenzuola d'Arda Italy.

ABSTRACT
MicroRNAs (miRNAs) are short non-coding RNA molecules produced from hairpin structures and involved in gene expression regulation with major roles in plant development and stress response. Although each annotated miRNA in miRBase (www.mirbase.org) is a single defined sequence with no further details on possible variable sequence length, isomiRs - namely the population of variants of miRNAs coming from the same precursors - have been identified in several species and could represent a way of broadening the regulatory network of the cell. Next-gen-based sequencing makes it possible to comprehensively and accurately assess the entire miRNA repertoire including isomiRs. The aim of this work was to survey the complexity of the peach miRNome by carrying out Illumina high-throughput sequencing of miRNAs in three replicates of five biological samples arising from a set of different peach organs and/or phenological stages. Three hundred-ninety-two isomiRs (miRNA and miRNA*-related) corresponding to 26 putative miRNA coding loci, have been highlighted by mirDeep-P and analyzed. The presence of the same isomiRs in different biological replicates of a sample and in different tissues demonstrates that the generation of most of the detected isomiRs is not random. The degree of mature sequence heterogeneity is very different for each individual locus. Results obtained in the present work can thus contribute to a deeper view of the miRNome complexity and to better explore the mechanism of action of these tiny regulators.

No MeSH data available.


Reports the results obtained by cluster analysis of the five tissues on the basis of the frequencies of all the reads (A) or on the basis of the frequency of the most frequent read in each locus (B). For each tissue, the average frequency across the three replicates was considered (miRNA* -related reads are included). In (B), the analysis included only those loci where the most frequent read was the same in all the samples. BF, pink; F, bloom; GF, swollen flower bud; O, half-inch green; GL, swollen leaf bud.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3405489&req=5

Figure 1: Reports the results obtained by cluster analysis of the five tissues on the basis of the frequencies of all the reads (A) or on the basis of the frequency of the most frequent read in each locus (B). For each tissue, the average frequency across the three replicates was considered (miRNA* -related reads are included). In (B), the analysis included only those loci where the most frequent read was the same in all the samples. BF, pink; F, bloom; GF, swollen flower bud; O, half-inch green; GL, swollen leaf bud.

Mentions: The average Pearson correlation between all the possible pairs of replicates belonging to the same biological sample was calculated, in order to evaluate whether it was in agreement with the “Standards, guidelines, and best practices for RNA-seq” adopted by ENCODE Consortium.4 Average correlation coefficients were equal to 0.98 for BF, 0.95 for F, 0.98 for GF, 0.95 for GL, and 0.97 for O. For the sake of completeness and in order to allow a comparison between related and unrelated samples, we also calculated the average Pearson correlation between samples of different tissues, which was equal to 0.66 on the basis of the reads reported in Table 2. All the Pearson coefficients are reported in File S10 in Supplementary Material. Figure 1A reports the results obtained from clustering the five samples on the basis of all the reads frequencies (average frequencies of three replicates, reads included miRNA*-related reads; reads assigned by miRDeep-P to more than one locus were counted once) at the 26 loci analyzed. Additionally, a clustering analysis was performed by considering only the count of the most frequent read in each locus. The analysis included those loci where the most frequent read was the same in all the samples (16 different reads, Figure 1B). Figure A1 in Appendix reports clustering results obtained without averaging the three replicates of each sample. As it can be seen, replicates are always grouped correctly.


A Survey of MicroRNA Length Variants Contributing to miRNome Complexity in Peach (Prunus Persica L.).

Colaiacovo M, Bernardo L, Centomani I, Crosatti C, Giusti L, Orrù L, Tacconi G, Lamontanara A, Cattivelli L, Faccioli P - Front Plant Sci (2012)

Reports the results obtained by cluster analysis of the five tissues on the basis of the frequencies of all the reads (A) or on the basis of the frequency of the most frequent read in each locus (B). For each tissue, the average frequency across the three replicates was considered (miRNA* -related reads are included). In (B), the analysis included only those loci where the most frequent read was the same in all the samples. BF, pink; F, bloom; GF, swollen flower bud; O, half-inch green; GL, swollen leaf bud.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3405489&req=5

Figure 1: Reports the results obtained by cluster analysis of the five tissues on the basis of the frequencies of all the reads (A) or on the basis of the frequency of the most frequent read in each locus (B). For each tissue, the average frequency across the three replicates was considered (miRNA* -related reads are included). In (B), the analysis included only those loci where the most frequent read was the same in all the samples. BF, pink; F, bloom; GF, swollen flower bud; O, half-inch green; GL, swollen leaf bud.
Mentions: The average Pearson correlation between all the possible pairs of replicates belonging to the same biological sample was calculated, in order to evaluate whether it was in agreement with the “Standards, guidelines, and best practices for RNA-seq” adopted by ENCODE Consortium.4 Average correlation coefficients were equal to 0.98 for BF, 0.95 for F, 0.98 for GF, 0.95 for GL, and 0.97 for O. For the sake of completeness and in order to allow a comparison between related and unrelated samples, we also calculated the average Pearson correlation between samples of different tissues, which was equal to 0.66 on the basis of the reads reported in Table 2. All the Pearson coefficients are reported in File S10 in Supplementary Material. Figure 1A reports the results obtained from clustering the five samples on the basis of all the reads frequencies (average frequencies of three replicates, reads included miRNA*-related reads; reads assigned by miRDeep-P to more than one locus were counted once) at the 26 loci analyzed. Additionally, a clustering analysis was performed by considering only the count of the most frequent read in each locus. The analysis included those loci where the most frequent read was the same in all the samples (16 different reads, Figure 1B). Figure A1 in Appendix reports clustering results obtained without averaging the three replicates of each sample. As it can be seen, replicates are always grouped correctly.

Bottom Line: Three hundred-ninety-two isomiRs (miRNA and miRNA*-related) corresponding to 26 putative miRNA coding loci, have been highlighted by mirDeep-P and analyzed.The degree of mature sequence heterogeneity is very different for each individual locus.Results obtained in the present work can thus contribute to a deeper view of the miRNome complexity and to better explore the mechanism of action of these tiny regulators.

View Article: PubMed Central - PubMed

Affiliation: CRA Genomics Research Centre, Fiorenzuola d'Arda Italy.

ABSTRACT
MicroRNAs (miRNAs) are short non-coding RNA molecules produced from hairpin structures and involved in gene expression regulation with major roles in plant development and stress response. Although each annotated miRNA in miRBase (www.mirbase.org) is a single defined sequence with no further details on possible variable sequence length, isomiRs - namely the population of variants of miRNAs coming from the same precursors - have been identified in several species and could represent a way of broadening the regulatory network of the cell. Next-gen-based sequencing makes it possible to comprehensively and accurately assess the entire miRNA repertoire including isomiRs. The aim of this work was to survey the complexity of the peach miRNome by carrying out Illumina high-throughput sequencing of miRNAs in three replicates of five biological samples arising from a set of different peach organs and/or phenological stages. Three hundred-ninety-two isomiRs (miRNA and miRNA*-related) corresponding to 26 putative miRNA coding loci, have been highlighted by mirDeep-P and analyzed. The presence of the same isomiRs in different biological replicates of a sample and in different tissues demonstrates that the generation of most of the detected isomiRs is not random. The degree of mature sequence heterogeneity is very different for each individual locus. Results obtained in the present work can thus contribute to a deeper view of the miRNome complexity and to better explore the mechanism of action of these tiny regulators.

No MeSH data available.