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An approach to identify the novel miRNA encoded from H. Annuus EST sequences.

Gupta H, Tiwari T, Patel M, Mehta A, Ghosh A - Genom Data (2015)

Bottom Line: A total of three miRNAs were detected from which one potential novel miRNA was identified following a range of strict filtering criteria.To study the conserved nature of the miRNAs, predicted phylogenetic analysis was carried out.These findings will significantly provide the broader picture for understanding the functions in H. annuus.

View Article: PubMed Central - PubMed

Affiliation: Xcelris Labs Ltd., Ahmedabad, Gujarat, India.

ABSTRACT
MicroRNAs are a newly discovered class of non-protein small RNAs with 22-24 nucleotides. They play multiple roles in biological processes including development, cell proliferation, apoptosis, stress responses and many other cell functions. In this research, several approaches were combined to make a computational prediction of potential miRNAs and their targets in Helianthus annuus (H. annuus). The already available information of the plant miRNAs present in miRBase v21 was used against expressed sequence tags (ESTs). A total of three miRNAs were detected from which one potential novel miRNA was identified following a range of strict filtering criteria. The target prediction was carried out for these three miRNAs having various targets. These targets were functionally annotated and GO terms were assigned. To study the conserved nature of the miRNAs, predicted phylogenetic analysis was carried out. These findings will significantly provide the broader picture for understanding the functions in H. annuus.

No MeSH data available.


Related in: MedlinePlus

Circos plot between the three predicted miRNAs and their targets.
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f0010: Circos plot between the three predicted miRNAs and their targets.

Mentions: The expressions of miRNAs are regulated by a specific gene via hybridization on mRNA transcripts to promote RNA degradation, inhibit translation or both. To search the putative target genes of three putative miRNAs, a psRNATarget program with default parameters was used to predict the targets against the H. annuus ESTs and Unigenes [13], [14]. A total of 59 and 29 targets were predicted from ESTs and Unigenes respectively. The two miRNA families han-miR160a and han-miR156c show the complementarity with H. annuus miRNAs present in miRBase v21 but, han-miR396 is novel to its species and shows significant similarity with Cynara cardunculus species of the database. The targets of the three miRNAs were plotted against its targets using the circos plot as represented in Fig. 2.


An approach to identify the novel miRNA encoded from H. Annuus EST sequences.

Gupta H, Tiwari T, Patel M, Mehta A, Ghosh A - Genom Data (2015)

Circos plot between the three predicted miRNAs and their targets.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664742&req=5

f0010: Circos plot between the three predicted miRNAs and their targets.
Mentions: The expressions of miRNAs are regulated by a specific gene via hybridization on mRNA transcripts to promote RNA degradation, inhibit translation or both. To search the putative target genes of three putative miRNAs, a psRNATarget program with default parameters was used to predict the targets against the H. annuus ESTs and Unigenes [13], [14]. A total of 59 and 29 targets were predicted from ESTs and Unigenes respectively. The two miRNA families han-miR160a and han-miR156c show the complementarity with H. annuus miRNAs present in miRBase v21 but, han-miR396 is novel to its species and shows significant similarity with Cynara cardunculus species of the database. The targets of the three miRNAs were plotted against its targets using the circos plot as represented in Fig. 2.

Bottom Line: A total of three miRNAs were detected from which one potential novel miRNA was identified following a range of strict filtering criteria.To study the conserved nature of the miRNAs, predicted phylogenetic analysis was carried out.These findings will significantly provide the broader picture for understanding the functions in H. annuus.

View Article: PubMed Central - PubMed

Affiliation: Xcelris Labs Ltd., Ahmedabad, Gujarat, India.

ABSTRACT
MicroRNAs are a newly discovered class of non-protein small RNAs with 22-24 nucleotides. They play multiple roles in biological processes including development, cell proliferation, apoptosis, stress responses and many other cell functions. In this research, several approaches were combined to make a computational prediction of potential miRNAs and their targets in Helianthus annuus (H. annuus). The already available information of the plant miRNAs present in miRBase v21 was used against expressed sequence tags (ESTs). A total of three miRNAs were detected from which one potential novel miRNA was identified following a range of strict filtering criteria. The target prediction was carried out for these three miRNAs having various targets. These targets were functionally annotated and GO terms were assigned. To study the conserved nature of the miRNAs, predicted phylogenetic analysis was carried out. These findings will significantly provide the broader picture for understanding the functions in H. annuus.

No MeSH data available.


Related in: MedlinePlus