About Enhancer

Enhancer ID: E_01_198
Enhancer symbol: --
Species: Human
Position : chr14:97410723-97443618
Biosample name: HeLa,293T
Experiment class : Low+High throughput
Enhancer type: Enhancer
Disease: Ewing Sarcoma
DO: DOID:3369
Mesh: D012512
Distance from TSS: >2KB
Pubmed ID:  25453903
Enhancer experiment: shRNA,RNA-seq,qRT-PCR,3C,Immunohistochemistry
Enhancer experiment description: Finally, we sought to address the impact of altered cis-regulatory element activity on the transcriptional landscape of Ewing sarcoma. We performed RNA sequencing (RNA-seq) in the Ewing sarcoma lines before and after EWS-FLI1 knock-down. By mapping EWS-FLI1 distal elements to the nearest expressed genes, we observed a strong relationship between changes in enhancer activity and changes in proximal gene expression (p < 10−10). We confirmed a subset of regulated gene targets by qRT-PCR. We hypothesized that direct regulatory targets of EWS-FLI1 might represent attractive therapeutic targets in Ewing sarcoma and thus ranked target genes by combined changes in chromatin and expression (Fig. 5B). Another top candidate is VRK1, a cell cycle dependent tyrosine kinase involved in G2-M transition (Valbuena et al., 2011). VRK1 is proximal to an EWS-FLI1 dependent enhancer that is active in Ewing sarcoma cell lines and primary tumors and induced de novo by the fusion protein in MSCs (Fig. 5C). Chromatin conformation studies (3C) confirmed the long distance interaction between the EWS-FLI1-bound enhancer and the VRK1 promoter in both SKNMC and A673 cells (Fig. 5D and E, respectively).

About Target gene

Target gene : VRK1(PCH1,PCH1A)
Strong evidence: 3C
Less strong evidence: Immunohistochemistry,shRNA
Target gene experiment description: VRK1 is proximal to an EWS-FLI1 dependent Enhancer that is active in Ewing sarcoma cell lines and primary tumors and induced de novo by the fusion protein in MSCs Chromatin conformation studies (3C) confirmed the long distance interaction between the EWS-FLI1-bound enhancer and the VRK1 promoter in both SKNMC and A673 cells (Fig. 5D and E, respectively). VRK1 protein expression was confirmed in 15/15 primary Ewing sarcoma samples analyzed by immunohistochemistry, which revealed strong VRK1 signals in virtually all cells (Fig.6A and Fig. S5B). EWS-FLI1 knock-down markedly reduced VRK1 expression in the cell lines, while EWS-FLI1 induction was sufficient to up-regulate this kinase in MSCs (Fig. 6B and S5C).

About TF

TF name : EWSR1(EWS,EWS-FLI1,bK984G1.4)
TF experiment: qRT-PCR,3C,shRNA
TF experiment description: We performed RNA sequencing (RNA-seq) in the Ewing sarcoma lines before and after EWS-FLI1 knock-down.We confirmed a subset of regulated gene targets by qRT-PCR (Fig. S5A). VRK1 is proximal to an EWS-FLI1 dependent enhancer that is active in Ewing sarcoma cell lines and primary tumors and induced de novo by the fusion protein in MSCs (Fig. 5C).Chromatin conformation studies (3C) confirmed the long distance interaction between the EWS-FLI1-bound enhancer and the VRK1 promoter in both SKNMC and A673 cells (Fig. 5D and E, respectively). VRK1 protein expression was confirmed in 15/15 primary Ewing sarcoma samples analyzed by immunohistochemistry, which revealed strong VRK1 signals in virtually all cells (Fig.6A and Fig. S5B). EWS-FLI1 knock-down markedly reduced VRK1 expression in the cell lines, while EWS-FLI1 induction was sufficient to up-regulate this kinase in MSCs (Fig. 6B and S5C).

About Function

Enhancer function : --
Enhancer function experiment: --
Enhancer function
experiment description:
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About SNP

SNP ID: --
SNP position: --
SNP experiment: --

Enhancer associated network

The number on yellow line represents the distance between enhancer and target gene

Expression of target genes for the enhancer


Enhancer associated SNPs