Abstract
BackgroundMultifunctional transcription factor (TF) gene EWS/EWSR1 is involved in various cellular processes such as transcription regulation, noncoding RNA regulation, splicing regulation, genotoxic stress response, and cancer generation. Role of a TF gene can be effectively studied by measuring genome-wide gene expression, i.e., transcriptome, in an animal model of Ews/Ewsr1 knockout (KO). However, when a TF gene has complex multi-functions, conventional approaches such as differentially expressed genes (DEGs) analysis are not successful to characterize the role of the EWS gene. In this regard, network-based analyses that consider associations among genes are the most promising approach.MethodsNetworks are constructed and used to show associations among biological entities at various levels, thus different networks represent association at different levels. Taken together, in this paper, we report contributions on both computational and biological sides.ResultsContribution on the computational side is to develop a novel computational framework that combines miRNA-gene network and protein-protein interaction network information to characterize the multifunctional role of EWS gene. On the biological side, we report that EWS regulates G-protein, Gnai1, in the spinal cord of Ews/Ewsr1 KO mice using the two biological network integrated analysis method. Neighbor proteins of Gnai1, G-protein complex subunits Gnb1, Gnb2 and Gnb4 were also down-regulated at their gene expression level. Interestingly, up-regulated genes, such as Rgs1 and Rgs19, are linked to the inhibition of Gnai1 activities. We further verified the altered expression of Gnai1 by qRT-PCR in Ews/Ewsr1 KO mice.ConclusionsOur integrated analysis of miRNA-transcriptome network and PPI network combined with qRT-PCR verifies that Gnai1 function is impaired in the spinal cord of Ews/Ewsr1 KO mice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-016-0195-4) contains supplementary material, which is available to authorized users.
Highlights
Multifunctional transcription factor (TF) gene Ewing sarcoma gene (EWS)/EWS ribonucleic acid (RNA)-Binding Protein 1 (EWSR1) is involved in various cellular processes such as transcription regulation, noncoding RNA regulation, splicing regulation, genotoxic stress response, and cancer generation
The Ewing sarcoma gene (EWS)/EWS RNA-Binding Protein 1 (EWSR1), a transcription factor, encodes an RNA binding protein whose specific functional targets are still largely unknown [4]. Fusion genes such as, EWS-FLI-1, EWSR1-WT1, EWSR1-KLF17, EWSR1-ATF1, and EWSR1-CREB3L1, are known to be produced by rearrangement of the EWSR1 gene with different gene fusion partners and these fusion genes have functions related to a variety of soft tissue tumors [5,6,7,8,9]
Translational regulatory network analysis: MicroRNA-mRNA network Selection of differentially expressed miRNAs We selected 18 significantly expressed miRNAs from the total 1193 mouse miRNAs by SAM tool. 15 miRNAs expression level were significantly up-regulated, and 3 miRNAs were down-regulated in the Ews/Ewsr1 KO mice against WT mice (Additional file 2)
Summary
Multifunctional transcription factor (TF) gene EWS/EWSR1 is involved in various cellular processes such as transcription regulation, noncoding RNA regulation, splicing regulation, genotoxic stress response, and cancer generation. When a TF gene has complex multi-functions, conventional approaches such as differentially expressed genes (DEGs) analysis are not successful to characterize the role of the EWS gene. In this regard, network-based analyses that consider associations among genes are the most promising approach. Fusion genes such as, EWS-FLI-1, EWSR1-WT1, EWSR1-KLF17, EWSR1-ATF1, and EWSR1-CREB3L1, are known to be produced by rearrangement of the EWSR1 gene with different gene fusion partners and these fusion genes have functions related to a variety of soft tissue tumors [5,6,7,8,9]. To characterize functions of EWS, we used RNA-seq gene expression data and miRNA expression data measured by using the spinal cord samples of Ews/Ewsr knockout (KO) mouse and wild type
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