http://www.cnr.it/ontology/cnr/individuo/prodotto/ID175703
In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus. (Articolo in rivista)
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- Label
- In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus. (Articolo in rivista) (literal)
- Anno
- 2012-01-01T00:00:00+01:00 (literal)
- Alternative label
Catalano, D.; Pignone, D.; Sonnante, G.; Finetti-Sialer, M.M. (2012)
In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus.
in BMC bioinformatics
(literal)
- Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
- Catalano, D.; Pignone, D.; Sonnante, G.; Finetti-Sialer, M.M. (literal)
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- http://www.biomedcentral.com/bmcbioinformatics/supplements/13/S4 (literal)
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- Istituto di Genetica Vegetale, CNR (literal)
- Titolo
- In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus. (literal)
- Abstract
- Background: MicroRNAs (miRNAs) are small RNAs (21-24 bp) providing an RNA-based system of gene regulation
highly conserved in plants and animals. In plants, miRNAs control mRNA degradation or restrain translation,
affecting development and responses to stresses. Plant miRNAs show imperfect but extensive complementarity to
mRNA targets, making their computational prediction possible, useful when data mining is applied on different
species. In this study we used a comparative approach to identify both miRNAs and their targets, in artichoke and
safflower.
Results: Two complete expressed sequence tags (ESTs) datasets from artichoke (3.6·104 entries) and safflower
(4.2·104), were analysed with a bioinformatic pipeline and in vitro experiments, identifying 17 potential miRNAs. For
each EST, using RNAhybrid program and 953 non redundant miRNA mature sequences, available in mirBase as
reference, we searched matching putative targets. 8730 out of 42011 ESTs from safflower and 7145 of 36323 ESTs
from artichoke showed at least one predicted miRNA target. BLAST analysis showed that 75% of all ESTs shared at
least a common homologous region (E-value < 10-4) and about 50% of these displayed 400 bp or longer aligned
sequences as conserved homologous/orthologous (COS) regions. 960 and 890 ESTs of safflower and artichoke
organized in COS shared 79 different miRNA targets, considered functionally conserved, and statistically significant
when compared with random sequences (signal to noise ratio > 2 and specificity >= 0.85). Four highly significant
miRNAs selected from in silico data were experimentally validated in globe artichoke leaves.
Conclusions: Mature miRNAs and targets were predicted within EST sequences of safflower and artichoke. Most of
the miRNA targets appeared highly/moderately conserved, highlighting an important and conserved function. In
this study we introduce a stringent parameter for the comparative sequence analysis, represented by the
identification of the same target in the COS region. After statistical analysis 79 targets, found on the COS regions
and belonging to 60 miRNA families, have a signal to noise ratio > 2, with >= 0.85 specificity. The putative miRNAs
identified belong to 55 dicotyledon plants and to 24 families only in monocotyledon. (literal)
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