Title:Position Based Nucleotide Analysis of miR168 Family in Higher Plants and its Targets in Mammalian Transcripts
Volume: 6
Issue: 2
Author(s): Mohammed Javed, Manish Solanki, Anshika Sinha and Lata I. Shukla*
Affiliation:
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Puducherry - 605014,India
Keywords:
Cleavage site, mammalian transcripts, miR168, position weight matrix, seed region, target prediction.
Abstract: Background: miRNA are the post transcriptional regulator of the genes. The conserved
miR168 family is evaluated for position based nucleotide preference in higher plants. Low density
lipoprotein receptor adaptor protein 1 (LDLRAP1) target validated for miR168a obtained from rice
origin is reported.
Methods: The mature miRNA sequences include miR168-5p and miR168-3p, were obtained from
miRBase (v21, June 2014) for 15 families (28 plants). The preferred position based nucleotide sequences
were obtained using Data Analysis in Molecular Biology and Evolution software. The
miR168-5p was subjected to cross kingdom analysis using psRNATarget. Target expression and functional
annotation was analyzed by using Human Protein Atlas database WEB-based Gene SeTAnaLysis
Toolkit.
Results: miR168-5p shows same nucleotides at positions 1-6, 8-9, 11-12, 15-17 and 19. Also,
miR168-3p is present in 3 families (10 plants) shows the same nucleotide at position 1-11, 13-15 and
17-21. The 123 targets in human transcriptome were identified showing 58% cleavage and 41% translation
repression. Low density lipoprotein receptor adaptor protein 1 (LDLRAP1) target validated for
miR168a obtained from rice origin, could also be targeted from miR168 from any other plant sources.
The randomly selected 10 targets include some important genes likeRPL34, ATXN1, AKAPI3 and
ALS2 and is involved in transcription, cell trafficking, cell metabolism and neurodegenerative disorder.
Conclusion: Our work suggests that miR168 family has conserved sequence in higher plants. The
seed region position 2-8 shows 70-95% pairing with human targets. Cleavage site at position 10-14
and these were analysed for the base preference with the targets showed 80-96% Watson Crick
pairing.
