About Enhancer
| Enhancer ID: | E_01_189 | |
| Enhancer symbol: | -- | |
| Species: | Human | |
| Position : | chr22:42411333-42413643   |
|
| Biosample name: | Human Primary Hepatocytes | |
| Experiment class : | Low throughput |
| Enhancer type: | Enhancer | |
| Disease: | -- | |
| DO: | -- | |
| Mesh: | -- | |
| Distance from TSS: | >2KB | |
| Pubmed ID: | 25381333 |
| Enhancer experiment: | 4C,ChIP | |
| Enhancer experiment description: | To search for regions that interact with the CYP2D6 promoter, we performed 4C assays with the CYP2D6 promoter as an anchor.With the exception of R1 and R6, peak signals were all associated with an annotated gene locus (gene body, promoter or upstream region, R2, R3, R4, R5 and R7), suggesting cross-regulation between genes. R1 corresponds to the previously identified downstream enhancer region (7), while R6 appears to be novel. To test whether any of these regions could serve as an enhancer, we performed ChIP assays with an antibody against P300, a universal transcription co-factor that binds to enhancer elements. R1 and R2 displayed the highest signals in both HepG2 and hepatocytes (Fig. 1B and C), consistent with R1 serving as an enhancer for CYP2D6, while R2 corresponds to the 3′ end of CYP2D6, indicative of active transcription of CYP2D6 in both cells. R6 showed low ChIP signals in both cells, arguing against an enhancer role. |
About Target gene
| Target gene : | CYP2D6(CPD6,CYP2D,CYP2D7AP,CYP2D7BP,CYP2D7P2,CYP2D8P2,CYP2DL1,CYPIID6,P450-DB1,P450C2D,P450DB1) | |
| Strong evidence: | 4C | |
| Less strong evidence: | ChIP | |
| Target gene experiment description: | To search for regions that interact with the CYP2D6 promoter, we performed 4C assays with the CYP2D6 promoter as an anchor.With the exception of R1 and R6, peak signals were all associated with an annotated gene locus (gene body, promoter or upstream region, R2, R3, R4, R5 and R7), suggesting cross-regulation between genes. R1 corresponds to the previously identified downstream enhancer region (7), while R6 appears to be novel. To test whether any of these regions could serve as an enhancer, we performed ChIP assays with an antibody against P300, a universal transcription co-factor that binds to enhancer elements. R1 and R2 displayed the highest signals in both HepG2 and hepatocytes (Fig. 1B and C), consistent with R1 serving as an enhancer for CYP2D6, while R2 corresponds to the 3′ end of CYP2D6, indicative of active transcription of CYP2D6 in both cells. R6 showed low ChIP signals in both cells, arguing against an enhancer role. |
About TF
| TF name : | -- | |
| TF experiment: | -- | |
| TF experiment description: | -- |
About Function
| Enhancer function : | A region 115 kb downstream of CYP2D6 as Enhancer for CYP2D6, containing two completely linked SNPs, rs133333 and rs5758550, associated with enhanced transcription. |
| Enhancer function experiment: | DNaseI Accessibility Assay,qPCR,CRISPR/Cas9 |
| Enhancer function experiment description: |
To determine the relative chromatin accessibility along the R1 region, we performed DNaseI accessibility assays in both HepG2 and primary human hepatocytes, followed by real-time PCR (12). As expected, the region surrounding rs5758550 (A5) showed the highest accessibility in both cell types (Fig. 4), consistent with its role as enhancer.Among three highly linked SNPs in this region, we identify rs5758550 as the causative variant that regulates enhancer activity, with the minor allele rs5758550G displaying higher activity than the major allele rs5758550A. Moreover, using CRISPR-mediated genomic deletion in HepG2 cells, we demonstrate that deletion of the enhancer region surrounding rs5758550 by 70% decreased CYP2D6 mRNA level >2-fold. |
About SNP
| SNP ID: | rs133333 | |
| SNP position: | 42412365 |
| SNP experiment: | 4C,ChIP,Luciferase Reporter Assay,PCR |
Enhancer associated network
The number on yellow line represents the distance between enhancer and target gene
