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. 2011 Feb 4;6(2):e16657.
doi: 10.1371/journal.pone.0016657.

dPORE-miRNA: Polymorphic Regulation of microRNA Genes

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Free PMC article

dPORE-miRNA: Polymorphic Regulation of microRNA Genes

Sebastian Schmeier et al. PLoS One. .
Free PMC article

Abstract

Background: MicroRNAs (miRNAs) are short non-coding RNA molecules that act as post-transcriptional regulators and affect the regulation of protein-coding genes. Mostly transcribed by PolII, miRNA genes are regulated at the transcriptional level similarly to protein-coding genes. In this study we focus on human miRNAs. These miRNAs are involved in a variety of pathways and can affect many diseases. Our interest is on possible deregulation of the transcription initiation of the miRNA encoding genes, which is facilitated by variations in the genomic sequence of transcriptional control regions (promoters).

Methodology: Our aim is to provide an online resource to facilitate the investigation of the potential effects of single nucleotide polymorphisms (SNPs) on miRNA gene regulation. We analyzed SNPs overlapped with predicted transcription factor binding sites (TFBSs) in promoters of miRNA genes. We also accounted for the creation of novel TFBSs due to polymorphisms not present in the reference genome. The resulting changes in the original TFBSs and potential creation of new TFBSs were incorporated into the Dragon Database of Polymorphic Regulation of miRNA genes (dPORE-miRNA).

Conclusions: The dPORE-miRNA database enables researchers to explore potential effects of SNPs on the regulation of miRNAs. dPORE-miRNA can be interrogated with regards to: a/miRNAs (their targets, or involvement in diseases, or biological pathways), b/SNPs, or c/transcription factors. dPORE-miRNA can be accessed at http://cbrc.kaust.edu.sa/dpore and http://apps.sanbi.ac.za/dpore/. Its use is free for academic and non-profit users.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Result page example.
The figure shows the result page for miRNA hsa-let-7a-1. It shows the expanded detailed view for SNP rs11788788 found on chromosome 9 in the promoter extracted from Corcoran et al. . In this case the observed state of the SNP leads to a loss of the overlapping TFBS (V$PAX4_01) and the creation of a new binding site (V$SZF11_01).

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References

    1. Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature. 2010;466:835–840. - PMC - PubMed
    1. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116:281–297. - PubMed
    1. Bracht J, Hunter S, Eachus R, Weeks P, Pasquinelli AE. Trans-splicing and polyadenylation of let-7 microRNA primary transcripts. RNA. 2004;10:1586–1594. - PMC - PubMed
    1. Cai X, Hagedorn CH, Cullen BR. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA. 2004;10:1957–1966. - PMC - PubMed
    1. Lee Y, Kim M, Han J, Yeom KH, Lee S, et al. MicroRNA genes are transcribed by RNA polymerase II. The EMBO Journal. 2004;23:4051–4060. - PMC - PubMed
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