About Enhancer
| Enhancer ID: | E_02_0774 |
| Species: | human |
| Position : | chr13:28545205-28547205   |
| Biosample name: | |
| Experiment class : | Low+High throughput |
| Enhancer type: | Enhancer |
| Disease: | -- |
| Pubmed ID: | 29155818 |
| Enhancer experiment: | ChIP-seq,ChIP,EMSA,Luciferase Reporter Assay |
| Enhancer experiment description: | To identify candidate cis-regulatory elements targeted by FOXA factors, we performed literature search, interrogated the ECR browser for evolutionary conserved regions (ECRs), and integrated this information with the results of the FOXA1 and FOXA2 ChIP-seq analysis.Moreover, the ENCODE data base lists several FOXA1 ChIP-seq peaks at the CDH1 locus in different cell lines, especially in the second intron. Notably, at the +7.8 kb enhancer region a FOXA1 ChIP-seq signal overlapped with an ECR (Fig 5A). To find out if FOXA factors could be involved in the function of the intronic CDH1 enhancer in CRC cells, we performed ChIP analyses. |
About Target gene
| Target gene : | CDX2(CDX-3,CDX2/AS,CDX3),CDX2(CDX-3,CDX2/AS,CDX3) |
| Strong evidence: | -- |
| Less strong evidence: | ChIP,Luciferase Reporter Assay |
| Target gene experiment description: | To test for binding of FOXA proteins at this site of the CDX2 locus in CRC cells we performed ChIP analyses. Indeed, this region was occupied by FOXA1 in LS174T and HT29 cells. Furthermore, FOXA3 was bound at the CDX2 +10.0 kb region in LS174T, SW480 and HT29 cells (Fig 5D). Even though binding did not correlate with CDX2 expression in the CRC cells (S10 Fig, panel B), this result suggests that FOXA proteins act upon a transcriptional enhancer at the CDX2 locus in CRC cells.To test the importance of the FOXA binding sites for CDH1, CDX2 and EPHB3 enhancer activity, we performed luciferase reporter assays in LS174T cells.;To test for binding of FOXA proteins at this site of the CDX2 locus in CRC cells we performed ChIP analyses. Indeed, this region was occupied by FOXA1 in LS174T and HT29 cells. Furthermore, FOXA3 was bound at the CDX2 +10.0 kb region in LS174T, SW480 and HT29 cells (Fig 5D). Even though binding did not correlate with CDX2 expression in the CRC cells (S10 Fig, panel B), this result suggests that FOXA proteins act upon a transcriptional enhancer at the CDX2 locus in CRC cells.To test the importance of the FOXA binding sites for CDH1, CDX2 and EPHB3 enhancer activity, we performed luciferase reporter assays in LS174T cells. |
About TF
| TF name : | FOXA1(HNF3A,TCF3A)FOXA1(HNF3A,TCF3A) |
| TF experiment: | EMSA,Luciferase Reporter Assay |
| TF experiment description: | EMSA to test for in vitro binding of FOXA1 and FOXA3 to the CDX2 +10.0 kb enhancer. (C) (Top) Scheme of the EPHB3 ?2.3 kb enhancer with its known transcription factor binding sites. TBE: TCF/LEF-binding element. (Bottom) EMSA to test for in vitro binding of FOXA1 and FOXA3 to the EPHB3 ?2.3 kb enhancer. (D, E, F) Luciferase reporter assay in LS174T cells with constructs covering the CDH1 (D), the CDX2 (E), and the EPHB3 (F) enhancer. Mutations of the respective FOX binding motifs are indicated by red crosses. Shown is the mean and SEM; n_x0015_3. RLA: relative luciferase activity. Statistical significance was calculated relative to the wild-type luciferase reporter constructs. ;EMSA to test for in vitro binding of FOXA1 and FOXA3 to the CDX2 +10.0 kb enhancer. (C) (Top) Scheme of the EPHB3 ?2.3 kb enhancer with its known transcription factor binding sites. TBE: TCF/LEF-binding element. (Bottom) EMSA to test for in vitro binding of FOXA1 and FOXA3 to the EPHB3 ?2.3 kb enhancer. (D, E, F) Luciferase reporter assay in LS174T cells with constructs covering the CDH1 (D), the CDX2 (E), and the EPHB3 (F) enhancer. Mutations of the respective FOX binding motifs are indicated by red crosses. Shown is the mean and SEM; n_x0015_3. RLA: relative luciferase activity. Statistical significance was calculated relative to the wild-type luciferase reporter constructs. |
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 |
|---|---|---|---|
| FOXA1 | AndrogenReceptor | netpath | 167 |
| FOXA1 | Direct p53 effectors | pid | 141 |
| FOXA1 | FOXA1 transcription factor network | pid | 45 |
| FOXA1 | FOXA2 and FOXA3 transcription factor networks | pid | 45 |
| FOXA1 | Hs_Endoderm_Differentiation_WP2853_88152 | wikipathways | 62 |
| FOXA1 | AndrogenReceptor | netpath | 167 |
| FOXA1 | Direct p53 effectors | pid | 141 |
| FOXA1 | FOXA1 transcription factor network | pid | 45 |
| FOXA1 | FOXA2 and FOXA3 transcription factor networks | pid | 45 |
| FOXA1 | Hs_Endoderm_Differentiation_WP2853_88152 | wikipathways | 62 |
Enhancer associated network
The number on yellow line represents the distance between enhancer and
target gene