ArticlePloS one2012
miRNA-mediated relationships between Cis-SNP genotypes and transcript intensities in lymphocyte cell lines.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- Polymorphisms in sex steroid receptors: From gene sequence to behavior.Frontiers in neuroendocrinology · 2017Review
- The modularity and dynamicity of miRNA-mRNA interactions in high-grade serous ovarian carcinomas and the prognostic implication.Computational biology and chemistry · 2016Article
- Article
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- Integrative genomics and transcriptomics analysis of human embryonic and induced pluripotent stem cells.BioData mining · 2014Article
- Research progress in allele-specific expression and its regulatory mechanisms.Journal of applied genetics · 2013Review
- Single Nucleotide Polymorphisms Associated with MicroRNA Regulation.Biomolecules · 2013Article
- Article
- Why does melanoma metastasize into the brain? Genes with pleiotropic effects might be the key.Frontiers in genetics · 2013Article
- MicroRNA-3148 modulates allelic expression of toll-like receptor 7 variant associated with systemic lupus erythematosus.PLoS genetics · 2013Article
- miRNA-mRNA correlation-network modules in human prostate cancer and the differences between primary and metastatic tumor subtypes.PloS one · 2012Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
In metazoans, miRNAs regulate gene expression primarily through binding to target sites in the 3' UTRs (untranslated regions) of messenger RNAs (mRNAs). Cis-acting variants within, or close to, a gene are crucial in explaining the variability of gene expression measures. Single nucleotide polymorphisms (SNPs) in the 3' UTRs of genes can affect the base-pairing between miRNAs and mRNAs, and hence disrupt existing target sites (in the reference sequence) or create novel target sites, suggesting a possible mechanism for cis regulation of gene expression. Moreover, because the alleles of different SNPs within a DNA sequence of limited length tend to be in strong linkage disequilibrium (LD), we hypothesize the variants of miRNA target sites caused by SNPs potentially function as bridges linking the documented cis-SNP markers to the expression of the associated genes. A large-scale analysis was herein performed to test this hypothesis. By systematically integrating multiple latest information sources, we found 21 significant gene-level SNP-involved miRNA-mediated post-transcriptional regulation modules (SNP-MPRMs) in the form of SNP-miRNA-mRNA triplets in lymphocyte cell lines for the CEU and YRI populations. Among the cognate genes, six including ALG8, DGKE, GNA12, KLF11, LRPAP1, and MMAB are related to multiple genetic diseases such as depressive disorder and Type-II diabetes. Furthermore, we found that ~35% of the documented transcript intensity-related cis-SNPs (~950) in a recent publication are identical to, or in significant linkage disequilibrium (LD) (p<0.01) with, one or multiple SNPs located in miRNA target sites. Based on these associations (or identities), 69 significant exon-level SNP-MPRMs and 12 disease genes were further determined for two populations. These results provide concrete in silico evidence for the proposed hypothesis. The discovered modules warrant additional follow-up in independent laboratory studies.
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Registered trials
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