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

Anindya Bhattacharya, Jesse D. Ziebarth, Yan Cui

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Article numbere46176
JournalPloS one
Volume7
Issue number9
DOIs
StatePublished - Sep 25 2012

Fingerprint

Human Genome
MicroRNAs
microRNA
Genes
genome
Small Untranslated RNA
Messenger RNA
genetic variation
Genome-Wide Association Study
Polymorphism
human diseases
single nucleotide polymorphism
Single Nucleotide Polymorphism
Seed
Seeds
genes
Nucleotides

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome. / Bhattacharya, Anindya; Ziebarth, Jesse D.; Cui, Yan.

In: PloS one, Vol. 7, No. 9, e46176, 25.09.2012.

Research output: Contribution to journalArticle

@article{2c3a97f8cb8f4eb4b9e1b657077ff6c1,
title = "Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome",
abstract = "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.",
author = "Anindya Bhattacharya and Ziebarth, {Jesse D.} and Yan Cui",
year = "2012",
month = "9",
day = "25",
doi = "10.1371/journal.pone.0046176",
language = "English (US)",
volume = "7",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "9",

}

TY - JOUR

T1 - Systematic Analysis of microRNA Targeting Impacted by Small Insertions and Deletions in Human Genome

AU - Bhattacharya, Anindya

AU - Ziebarth, Jesse D.

AU - Cui, Yan

PY - 2012/9/25

Y1 - 2012/9/25

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84866648693&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84866648693&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0046176

DO - 10.1371/journal.pone.0046176

M3 - Article

VL - 7

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 9

M1 - e46176

ER -