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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

(A) Stem loop structure of predicted han-miR160a. (B) Stem loop structure of predicted han-miR156c. (C) Stem loop structure of predicted han-miR396.
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f0005: (A) Stem loop structure of predicted han-miR160a. (B) Stem loop structure of predicted han-miR156c. (C) Stem loop structure of predicted han-miR396.

Mentions: A total of three potential miRNAs were identified with the predicted stem loop precursor structure from the publicly available EST database. There are large numbers of evidences stating the conserved nature of plant miRNAs [12]. This feature of theirs provides the powerful methods to identity the new miRNAs in plant species. After the removal of the repetitive miRNA sequences from the Viridiplantae group the remaining 4617 miRNAs were locally aligned against 134,475 EST sequences of H. annuus by using BLAST program with e-value 1000, percentage identity greater than 85, word size 7 and mismatch less than 4. The BLAST alignment detected the homology of Viridiplantae mature miRNA with the 20 sequences of H. annuus ESTs. The validation process for these miRNAs was initiated by secondary structure prediction using mfold web server. This is a very critical step in deciding the fate of the miRNAs, so the following important parameters were studied: 1) Minimum free energy (negative MFE), 2) adjusted minimal fold energy (AMFE) and 3) the minimal fold energy index (MFEI) were used. The secondary structure prediction filtered out 17 potential miRNA candidates and only three of them passed the criteria which are listed in Table 1 and their predicted secondary structures are shown in Fig. 1A–C. These potential candidates encode as han-miR160a, han-miR156c and han-miR396 families. The potential miRNAs had higher minimal folding free energy (MFE) and minimum free energy index (MFEI); the MEFI ranging between 0.65 to 0.85 and AU content of pre-miRNA within 30% to 70%.


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)

(A) Stem loop structure of predicted han-miR160a. (B) Stem loop structure of predicted han-miR156c. (C) Stem loop structure of predicted han-miR396.
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

f0005: (A) Stem loop structure of predicted han-miR160a. (B) Stem loop structure of predicted han-miR156c. (C) Stem loop structure of predicted han-miR396.
Mentions: A total of three potential miRNAs were identified with the predicted stem loop precursor structure from the publicly available EST database. There are large numbers of evidences stating the conserved nature of plant miRNAs [12]. This feature of theirs provides the powerful methods to identity the new miRNAs in plant species. After the removal of the repetitive miRNA sequences from the Viridiplantae group the remaining 4617 miRNAs were locally aligned against 134,475 EST sequences of H. annuus by using BLAST program with e-value 1000, percentage identity greater than 85, word size 7 and mismatch less than 4. The BLAST alignment detected the homology of Viridiplantae mature miRNA with the 20 sequences of H. annuus ESTs. The validation process for these miRNAs was initiated by secondary structure prediction using mfold web server. This is a very critical step in deciding the fate of the miRNAs, so the following important parameters were studied: 1) Minimum free energy (negative MFE), 2) adjusted minimal fold energy (AMFE) and 3) the minimal fold energy index (MFEI) were used. The secondary structure prediction filtered out 17 potential miRNA candidates and only three of them passed the criteria which are listed in Table 1 and their predicted secondary structures are shown in Fig. 1A–C. These potential candidates encode as han-miR160a, han-miR156c and han-miR396 families. The potential miRNAs had higher minimal folding free energy (MFE) and minimum free energy index (MFEI); the MEFI ranging between 0.65 to 0.85 and AU content of pre-miRNA within 30% to 70%.

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