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Online Journal of Bioinformatics©

Established 1995

ISSN  1443-2250


Volume 23 (2):112-131, 2022.

Micro-RNA’s expressed in brain and genes associated with amyotrophic lateral sclerosis.


Santosh P. Shinde, Neelima Arora and Utpal Bhadra


Functional Genomics and Gene Silencing Group, Centre for Cellular and Molecular Biology, Hyderabad-500007, India




Shinde SP, Arora N, Bhadra U., Micro-RNA’s expressed in brain and genes associated with amyotrophic lateral sclerosis, Onl J Bioinform., 23 (2):112-131, 2022. Amyotrophic Lateral Sclerosis (ALS) is a rare neurological disease affecting mainly motor neurons and often leads to paralysis and death in extreme cases. Though the number of patients of ALS is relatively small compared to other known neurodegenerative diseases, it holds distinct importance owing to high fatality among victims. Various mechanisms are proposed for the disease but exact mechanism still remains a mystery.  For exploring the role of microRNAs in ALS disease genes regulation, miRanda (version1.0 b) was employed for prediction of target sites of miRNAs expressed in various parts of brain and CNS on 35 genes associated with ALS. MicroRNA target sites were classified according to the position and the location of these sites were used to infer their mode of action in target gene silencing. For verification, similar search was conducted using TargetScan (version (5.1) and PicTar for prediction of target sites in 3´ UTR only. Target site hotspots were identified and were recognized as hotspots for multiple miRNAs action, thus, acting as favored sites of action for repression of gene expression. The complex interplay of genes and miRNAs brought about by multiplicity and cooperativity was explored. 1456 target sites were predicted using miRanda. Interestingly, target sites found in 5´ UTR and CDS region were more than those found in 3´ UTR. 11 target sites were predicted to be common by all three algorithms and thus, these represent most significant sites. This investigation will aid in elucidating the mechanism of action of miRNAs for the considered genes.