About Enhancer
| Enhancer ID: | E_02_0847 |
| Species: | human |
| Position : | chr11:8271697-8279492   |
| Biosample name: | |
| Experiment class : | Low+High throughput |
| Enhancer type: | Super-Enhancer |
| Disease: | Neuroblastoma |
| Pubmed ID: | 26560027 |
| Enhancer experiment: | ChIP-seq,Luciferase Reporter Assay |
| Enhancer experiment description: | Acetylation of histone H3 at lysine 27 (H3K27ac) is a hallmark of active enhancers, and ChIP-seq analysis of SHSY5Y (G/G; not MYCN amplified), KELLY (G/?; MYCN amplified), BE2 (G/T; MYCN amplified) and NGP (G/T; MYCN amplified) neuroblastoma cells showed extensive H3K27 acetylation in the first intron of LMO1 across rs2168101, which was not observed in BE2C (T/? ; MYCN amplified; Fig. 3c). This region is classified as a super-enhancer in G-allele-containing lines SHSY5Y, KELLY and BE2 based on enhancer clustering and especially high H3K27ac signal (NGP was just below the threshold; see Methods), a pattern also observed for other known oncogenes and tumour suppressor genes in this disease12 (Fig. 3d and Extended Data Fig. 6a). We next performed luciferase reporter assays to measure the effect of rs2168101 alleles on enhancer activity. HEK293T cells transfected with constructs containing the risk G allele demonstrated 30300-fold higher normalized luminescence compared to the T allele (t-test P = 0.002, Fig. 3e), whereas luciferase activity of the T allele was not significantly different from empty vector, indicating that the intact GATA motif is required for robust enhancer activity. |
About Target gene
| Target gene : | LMO1(RBTN1,RHOM1,TTG1) |
| Strong evidence: | -- |
| Less strong evidence: | ChIP-seq,Luciferase Reporter Assay |
| Target gene experiment description: | Acetylation of histone H3 at lysine 27 (H3K27ac) is a hallmark of active enhancers, and ChIP-seq analysis of SHSY5Y (G/G; not MYCN amplified), KELLY (G/?; MYCN amplified), BE2 (G/T; MYCN amplified) and NGP (G/T; MYCN amplified) neuroblastoma cells showed extensive H3K27 acetylation in the first intron of LMO1 across rs2168101, which was not observed in BE2C (T/? ; MYCN amplified; Fig. 3c). This region is classified as a super-enhancer in G-allele-containing lines SHSY5Y, KELLY and BE2 based on enhancer clustering and especially high H3K27ac signal (NGP was just below the threshold; see Methods), a pattern also observed for other known oncogenes and tumour suppressor genes in this disease12 (Fig. 3d and Extended Data Fig. 6a). We next performed luciferase reporter assays to measure the effect of rs2168101 alleles on enhancer activity. HEK293T cells transfected with constructs containing the risk G allele demonstrated 30300-fold higher normalized luminescence compared to the T allele (t-test P = 0.002, Fig. 3e), whereas luciferase activity of the T allele was not significantly different from empty vector, indicating that the intact GATA motif is required for robust enhancer activity. |
About TF
| TF name : | GATA3(HDR,HDRS) |
| TF experiment: | Luciferase Reporter Assay,RNAi |
| TF experiment description: | HEK293T cells transfected with constructs containing the risk G allele demonstrated 30300-fold higher normalized luminescence compared to the T allele (t-test P = 0.002, Fig. 3e), whereas luciferase activity of the T allele was not significantly different from empty vector, indicating that the intact GATA motif is required for robust enhancer activity. Finally, knockdown of GATA3 in SHSY5Y and KELLY cells resulted in both decreased LMO1 protein levels and suppression of cell growth that was rescued by LMO1 overexpression (Fig. 3f and Extended Data Fig. 7), indicating the central role of GATA3 in regulating LMO1 expression levels in neuroblastoma.Finally, knockdown of GATA3 in SHSY5Y and KELLY cells resulted in both decreased LMO1 protein levels and suppression of cell growth that was rescued by LMO1 overexpression (Fig. 3f and Extended Data Fig. 7), indicating the central role of GATA3 in regulating LMO1 expression levels in neuroblastoma. |
About Function
| Enhancer function : | -- |
| Enhancer function experiment: | -- |
| Enhancer function experiment description: |
-- |
About SNP
| SNP ID: | -- |
Upstream Pathway Annotation of TF
| GeneName | Pathway Name | Source | Gene Number |
|---|---|---|---|
| GATA3 | C-MYB transcription factor network | pid | 87 |
| GATA3 | Calcineurin-regulated NFAT-dependent transcription in lymphocytes | pid | 50 |
| GATA3 | Factors involved in megakaryocyte development and platelet production | reactome | 111 |
| GATA3 | Glucocorticoid receptor regulatory network | pid | 85 |
| GATA3 | IL27-mediated signaling events | pid | 26 |
| GATA3 | Notch signaling pathway | pid | 58 |
| GATA3 | Regulation of nuclear SMAD2/3 signaling | pid | 82 |
| GATA3 | Hs_Endochondral_Ossification_WP474_87977 | wikipathways | 43 |
| GATA3 | Hs_White_fat_cell_differentiation_WP3946_90940 | wikipathways | 30 |
Enhancer associated network
The number on yellow line represents the distance between enhancer and
target gene