Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome

MicroRNAs (miRNAs) are small noncoding RNA that play an important role in posttranscriptional regulation of mRNA. Genetic variations in miRNAs or their target sites have been shown to alter miRNA function and have been associated with risk for several diseases. Previous studies have focused on the m...

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Main Authors:	Bhattacharya, Anindya, Ziebarth, Jesse D., Cui, Yan
Format:	Online
Language:	English
Published:	Public Library of Science 2012
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457991/

id	pubmed-3457991
recordtype	oai_dc
spelling	pubmed-34579912012-10-03 Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome Bhattacharya, Anindya Ziebarth, Jesse D. Cui, Yan Research Article MicroRNAs (miRNAs) are small noncoding RNA that play an important role in posttranscriptional regulation of mRNA. Genetic variations in miRNAs or their target sites have been shown to alter miRNA function and have been associated with risk for several diseases. Previous studies have focused on the most abundant type of genetic variations, single nucleotide polymorphisms (SNPs) that affect miRNA-mRNA interactions. Here, we systematically identified small insertions and deletions (indels) in miRNAs and their target sites, and investigated the effects of indels on miRNA targeting. We studied the distribution of indels in miRNAs and their target sites and found that indels in mature miRNAs, experimentally supported miRNA target sites and PAR-CLIP footprints have significantly lower density compared to flanking regions. We identified over 20 indels in the seed regions of miRNAs, which may disrupt the interactions between these miRNAs and their target genes. We also identified hundreds of indels that alter experimentally supported miRNA target sites. We mapped these genes to human disease pathways to identify indels that affect miRNA targeting in these pathways. We also used the results of genome-wide association studies (GWAS) to identify potential links between miRNA-related indels and diseases. Public Library of Science 2012-09-25 /pmc/articles/PMC3457991/ /pubmed/23049969 http://dx.doi.org/10.1371/journal.pone.0046176 Text en © 2012 Bhattacharya et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Bhattacharya, Anindya Ziebarth, Jesse D. Cui, Yan
spellingShingle	Bhattacharya, Anindya Ziebarth, Jesse D. Cui, Yan Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome
author_facet	Bhattacharya, Anindya Ziebarth, Jesse D. Cui, Yan
author_sort	Bhattacharya, Anindya
title	Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome
title_short	Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome
title_full	Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome
title_fullStr	Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome
title_full_unstemmed	Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome
title_sort	systematic analysis of microrna targeting impacted by small insertions and deletions in human genome
description	MicroRNAs (miRNAs) are small noncoding RNA that play an important role in posttranscriptional regulation of mRNA. Genetic variations in miRNAs or their target sites have been shown to alter miRNA function and have been associated with risk for several diseases. Previous studies have focused on the most abundant type of genetic variations, single nucleotide polymorphisms (SNPs) that affect miRNA-mRNA interactions. Here, we systematically identified small insertions and deletions (indels) in miRNAs and their target sites, and investigated the effects of indels on miRNA targeting. We studied the distribution of indels in miRNAs and their target sites and found that indels in mature miRNAs, experimentally supported miRNA target sites and PAR-CLIP footprints have significantly lower density compared to flanking regions. We identified over 20 indels in the seed regions of miRNAs, which may disrupt the interactions between these miRNAs and their target genes. We also identified hundreds of indels that alter experimentally supported miRNA target sites. We mapped these genes to human disease pathways to identify indels that affect miRNA targeting in these pathways. We also used the results of genome-wide association studies (GWAS) to identify potential links between miRNA-related indels and diseases.
publisher	Public Library of Science
publishDate	2012
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457991/
_version_	1611911741252304896

Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome

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