About Enhancer
| Enhancer ID: | E_02_0773 |
| Species: | human |
| Position : | chr4:55859107-55860311   |
| Biosample name: | |
| Experiment class : | Low throughput |
| Enhancer type: | Enhancer |
| Disease: | -- |
| Pubmed ID: | 29236325 |
| Enhancer experiment: | PCR,Luciferase Reporter Assay,ChIP-qPCR,ChIP-3C |
| Enhancer experiment description: | Intriguingly, we also identified a DHS site located at 30 kb downstream of TSS, which was also enriched by p300 (GSE6284728) and thus defined as the intronic enhancer (Figure 2a).To verify whether these co-factors binding to the promoter and intron regions of cKIT, we performed ChIP-qPCR assays with a series of primers for these regions using t(8;21) positive Kasumi-1 cells (Figure 2c). |
About Target gene
| Target gene : | KIT(C-Kit,CD117,MASTC,PBT,SCFR),KIT(C-Kit,CD117,MASTC,PBT,SCFR) |
| Strong evidence: | ChIP-3C |
| Less strong evidence: | Luciferase Reporter Assay,ChIP-qPCR |
| Target gene experiment description: | We firstly detected the luciferase activity of c-KIT promoter or promoter plus intronic enhancer in Kasumi-1 cells.As shown in Figure 4c, the activity of c-KIT promoter plus intronic enhancer (pGL3-c-KIT-P+I) was significantly higher than that of the c-KIT promoter (pGL3-c-KIT-P).The motif analysis (Figure 2b) as well as the finding that the intronic enhance region increased the activity of c-KIT promoter prompt us to ask whether there exists an interaction between the promoter and intronic enhancer region of c-KIT. To demonstrate our speculation, we firstly performed ChIPqPCR experiments using antibodies of CTCF and a cohesion complex member, RAD21, in Kasumi-1 cell line.Secondly, to provide further evidence that looping occurs in vivo between promoter and enhancer, we performed ChIP combined chromosome conformation capture (ChIP-3C) assays in Kasumi-1 cells. ;We firstly detected the luciferase activity of c-KIT promoter or promoter plus intronic enhancer in Kasumi-1 cells.As shown in Figure 4c, the activity of c-KIT promoter plus intronic enhancer (pGL3-c-KIT-P+I) was significantly higher than that of the c-KIT promoter (pGL3-c-KIT-P).The motif analysis (Figure 2b) as well as the finding that the intronic enhance region increased the activity of c-KIT promoter prompt us to ask whether there exists an interaction between the promoter and intronic enhancer region of c-KIT. To demonstrate our speculation, we firstly performed ChIPqPCR experiments using antibodies of CTCF and a cohesion complex member, RAD21, in Kasumi-1 cell line.Secondly, to provide further evidence that looping occurs in vivo between promoter and enhancer, we performed ChIP combined chromosome conformation capture (ChIP-3C) assays in Kasumi-1 cells. |
About TF
| TF name : | RUNX1(AML1,AML1-EVI-1,AMLCR1,CBF2alpha,CBFA2,EVI-1,PEBP2aB,PEBP2alpha)RUNX1(AML1,AML1-EVI-1,AMLCR1,CBF2alpha,CBFA2,EVI-1,PEBP2aB,PEBP2alpha) |
| TF experiment: | ChIP-3C |
| TF experiment description: | Knockdown of AML1/ETO led to a dramatic decrease of the activity of both reporter plasmids.Secondly, to provide further evidence that looping occurs in vivo between promoter and Enhancer, we performed ChIP combined chromosome conformation capture (ChIP-3C) assays in Kasumi-1 cells. Collectively, these findings suggest that AML1/ETO prompts the formation of DNA looping between the c-KIT promoter and intronic Enhancer. ;Knockdown of AML1/ETO led to a dramatic decrease of the activity of both reporter plasmids.Secondly, to provide further evidence that looping occurs in vivo between promoter and Enhancer, we performed ChIP combined chromosome conformation capture (ChIP-3C) assays in Kasumi-1 cells. Collectively, these findings suggest that AML1/ETO prompts the formation of DNA looping between the c-KIT promoter and intronic Enhancer. |
About Function
| Enhancer function : | The intronic Enhancer region of c-KIT prompts the transactivation of AML1/ETO to c-KIT. |
| Enhancer function experiment: | Luciferase Reporter Assay,siRNA |
| Enhancer function experiment description: |
We firstly detected the luciferase activity of c-KIT promoter or promoter plus intronic Enhancer in Kasumi-1 cells. As shown in Figure 4c, the activity of c-KIT promoter plus intronic Enhancer (pGL3-c-KIT-P+I) was significantly higher than that of the c-KIT promoter (pGL3-c-KIT-P). Further knockdown of AML1/ETO (Figure 4c) led to a dramatic decrease of the activity of both reporter plasmids (Figure 4b). Secondly, we induced AML1/ETO expression using PA in U937-AE cell line (Figure 4d) and measured the luciferase activity of the aforementioned plasmids before and after AML1/ETO induction. As shown in Figure 4e, the luciferase activity of all the reporter plasmids was increased after 48 hours of AML1/ETO induction. The activity of reporter plasmid that contained both c-KIT promoter and intronic Enhancer regions was significantly higher than that contain only c-KIT promoter region. |
About SNP
| SNP ID: | -- |
Upstream Pathway Annotation of TF
| GeneName | Pathway Name | Source | Gene Number |
|---|---|---|---|
| RUNX1 | AndrogenReceptor | netpath | 167 |
| RUNX1 | Organic cation transport | reactome | 9 |
| RUNX1 | RANKL | netpath | 84 |
| RUNX1 | Regulation of nuclear SMAD2/3 signaling | pid | 82 |
| RUNX1 | TGF_beta_Receptor | netpath | 220 |
| RUNX1 | Validated transcriptional targets of deltaNp63 isoforms | pid | 47 |
| RUNX1 | Pathways in cancer | kegg | 321 |
| RUNX1 | Chronic myeloid leukemia | kegg | 69 |
| RUNX1 | Acute myeloid leukemia | kegg | 53 |
| RUNX1 | AndrogenReceptor | netpath | 167 |
| RUNX1 | Organic cation transport | reactome | 9 |
| RUNX1 | RANKL | netpath | 84 |
| RUNX1 | Regulation of nuclear SMAD2/3 signaling | pid | 82 |
| RUNX1 | TGF_beta_Receptor | netpath | 220 |
| RUNX1 | Validated transcriptional targets of deltaNp63 isoforms | pid | 47 |
| RUNX1 | Pathways in cancer | kegg | 321 |
| RUNX1 | Chronic myeloid leukemia | kegg | 69 |
| RUNX1 | Acute myeloid leukemia | kegg | 53 |
Enhancer associated network
The number on yellow line represents the distance between enhancer and
target gene