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Genome-Wide Identification of SNPs in MicroRNA Genes and the SNP Effects on MicroRNA Target Binding and Biogenesis
被引:309
作者:
Gong, Jing
[1
,2
]
Tong, Yin
[1
]
Zhang, Hong-Mei
[1
]
Wang, Kai
[3
]
Hu, Tao
[1
]
Shan, Ge
[4
]
Sun, Jun
[2
]
Guo, An-Yuan
[1
]
机构:
[1] Huazhong Univ Sci & Technol, Coll Life Sci & Technol, Dept Syst Biol, Hubei Bioinformat & Mol Imaging Key Lab, Wuhan 430074, Peoples R China
[2] Huazhong Univ Sci & Technol, Dept Biochem & Mol Biol, Tongji Med Coll, Wuhan 430074, Peoples R China
[3] Shanghai Bioladder Co Ltd, Shanghai, Peoples R China
[4] Univ Sci & Technol China, Sch Life Sci, Hefei 230026, Peoples R China
基金:
中国国家自然科学基金;
关键词:
miRNASNP;
database;
target loss and gain;
frequency;
SINGLE NUCLEOTIDE POLYMORPHISM;
COMPREHENSIVE DATABASE;
UNTRANSLATED REGION;
PREDICTION;
SITE;
ASSOCIATION;
RESOURCE;
COMPLEMENTARY;
EXPRESSION;
MECHANISM;
D O I:
10.1002/humu.21641
中图分类号:
Q3 [遗传学];
学科分类号:
071007 ;
090102 ;
摘要:
MicroRNAs (miRNAs) are studied as key regulators of gene expression involved in different diseases. Several single nucleotide polymorphisms (SNPs) in miRNA genes or target sites (miRNA-related SNPs) have been proved to be associated with human diseases by affecting the miRNA-mediated regulatory function. To systematically analyze miRNA-related SNPs and their effects, we performed a genome-wide scan for SNPs in human pre-miRNAs, miRNA flanking regions, target sites, and designed a pipeline to predict the effects of them on miRNA-target interaction. As a result, we identified 48 SNPs in human miRNA seed regions and thousands of SNPs in 3' untranslated regions with the potential to either disturb or create miRNA-target interactions. Furthermore, we experimentally confirmed seven loss-of-function SNPs and one gain-of-function SNP by luciferase assay. This is the first case of experimental validation of an SNP in an miRNA creating a novel miRNA target binding. All useful data were complied into miRNASNP, a user-friendly free online database (http://www.bioguo.org/miRNASNP/). These data will be a useful resource for studying miRNA function, identifying disease-associated miRNAs, and further personalized medicine. Hum Mutat 33: 254-263, 2012. (C) 2011 Wiley Periodicals, Inc.
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页码:254 / 263
页数:10
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