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miRNA-mediated competing endogenous RNAs (ceRNAs) networks

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miRNA-mediated competing endogenous RNAs (ceRNAs) networks

Postby rnaworld2110 » Sun Dec 15, 2013 9:29 am

Competing endogenous RNAs (ceRNAs) hypothesis: ceRNAs regulate other RNA transcripts (e.g., PTEN) by competing for shared microRNAs.

They are playing important roles in developmental, physiological and pathological processes, such as cancer. (Salmena et al. 2011 Cell).

Multiple classes of ncRNAs (lncRNAs, circRNAs, pseudogenes) and protein-coding mRNAs function as key ceRNAs and to regulate the expression of mRNAs in plants and mammalian cells (see below references).

ceRNA resoures:
1. ceRNABase: identified ~200,000 (P<0.05) and ~10,000 (FDR<0.05) ceRNA pairs from CLIP-supported miRNA target sites. provided ceRNAFunction tool to predict the functions of lncRNAs and protein-coding genes from ceRNA regulatory networks. website: http://starbase.sysu.edu.cn/mrnaCeRNA.php

2. Competing endogenous RNA database: predicted ceRNA candidates from genome. website: http://www.oncomir.umn.edu/cefinder/

ceRNA References:
1. HMGA2 functions as a competing endogenous RNA to promote lung cancer progression. Nature 2013, Dec 5.
2. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res. 2013 Dec 1.
3. A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell. 2011 Oct 14;147(2):358-69
4. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature. 2010 Jun 24;465(7301):1033-8.
5. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell. 2011 Aug 5;146(3):353-8.
6. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013 Mar 21;495(7441):333-8.
7. Natural RNA circles function as efficient microRNA sponges.Nature. 2013 Mar 21;495(7441):384-8.
8. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev Cell. 2013 Apr 15;25(1):69-80.
9. The Imprinted H19 LncRNA Antagonizes Let-7 MicroRNAs. Mol Cell. 2013 Oct 10;52(1):101-12.
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Postby rnaworld2110 » Sat Jan 18, 2014 4:23 am

A Nature paper has described ceRNA interactions between HMGA2 and TGFBR3. They show that Hmga2 promotes lung cancer progression in mouse and human cells by operating as a competing endogenous RNA (ceRNA) for the let-7 microRNA (miRNA) family.

reference: HMGA2 functions as a competing endogenous RNA to promote lung cancer progression (Nature, 2013 Dec 5)

ceRNABase can captured the above-mentioned HMGA2-TGFBR3 ceRNA pairs.
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Postby rnaworld2110 » Mon Mar 03, 2014 11:42 am

ceRNABase have constructed pan-cancer ceRNA networks from tumor miRNA and mRNA expression profiles (TCGA 14 cancer types with >6000 tumor and normal samples).

For example: known PTEN-ZEB2 ceRNA interactions can be supported in 13 cancer types.
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