About Enhancer
| Enhancer ID: | E_02_0821 |
| Species: | human |
| Position : | chr7:129554284-129564284   |
| Biosample name: | |
| Experiment class : | Low+High throughput |
| Enhancer type: | Enhancer |
| Disease: | Skeletal diseases |
| Pubmed ID: | 27881681 |
| Enhancer experiment: | Luciferase Reporter Assay,ChIP-seq |
| Enhancer experiment description: | However, ChIP sequencing revealed that SOX9 does not strongly bind to intron 1, but rather it binds to intron 6 and a site 30 kb upstream of the transcription start site. Here, we aimed to determine the role of the novel SOX9-binding site in intron 6. We prepared reporter constructs that contain a Col2a1 promoter, intron 1 with or without intron 6, and the luciferase gene. |
About Target gene
| Target gene : | Col2a1(ANFH,AOM,COL11A3,SEDC,STL1),Col2a1(ANFH,AOM,COL11A3,SEDC,STL1),Col2a1(ANFH,AOM,COL11A3,SEDC,STL1),Col2a1(ANFH,AOM,COL11A3,SEDC,STL1) |
| Strong evidence: | CRISPR/Cas9 |
| Less strong evidence: | Luciferase Reporter Assay,ChIP-seq |
| Target gene experiment description: | the ChIP-Seq data of SOX9 in the Col2a1 gene using rat chondrosarcoma cells (RCS cells)show that there is a strong SOX9-binding site in intron 6 and a weaker binding site in intron 1.Although the reporter constructs were not activated by SOX9 alone, the construct that contained both introns 1 and 6 was activated 510-fold by the SOX9/SOX5 or the SOX9/SOX6 combination in transient-transfection assays in 293T cells. This enhancement was also observed in rat chondrosarcoma cells that stably expressed the construct. CRISPR/Cas9-induced deletion of intron 6 in RCS cells revealed that a 10-bp region of intron 6 is necessary both for Col2a1 expression and SOX9 binding. ;the ChIP-Seq data of SOX9 in the Col2a1 gene using rat chondrosarcoma cells (RCS cells)show that there is a strong SOX9-binding site in intron 6 and a weaker binding site in intron 1.Although the reporter constructs were not activated by SOX9 alone, the construct that contained both introns 1 and 6 was activated 510-fold by the SOX9/SOX5 or the SOX9/SOX6 combination in transient-transfection assays in 293T cells. This enhancement was also observed in rat chondrosarcoma cells that stably expressed the construct. CRISPR/Cas9-induced deletion of intron 6 in RCS cells revealed that a 10-bp region of intron 6 is necessary both for Col2a1 expression and SOX9 binding. ;the ChIP-Seq data of SOX9 in the Col2a1 gene using rat chondrosarcoma cells (RCS cells)show that there is a strong SOX9-binding site in intron 6 and a weaker binding site in intron 1.Although the reporter constructs were not activated by SOX9 alone, the construct that contained both introns 1 and 6 was activated 510-fold by the SOX9/SOX5 or the SOX9/SOX6 combination in transient-transfection assays in 293T cells. This enhancement was also observed in rat chondrosarcoma cells that stably expressed the construct. CRISPR/Cas9-induced deletion of intron 6 in RCS cells revealed that a 10-bp region of intron 6 is necessary both for Col2a1 expression and SOX9 binding. ;the ChIP-Seq data of SOX9 in the Col2a1 gene using rat chondrosarcoma cells (RCS cells)show that there is a strong SOX9-binding site in intron 6 and a weaker binding site in intron 1.Although the reporter constructs were not activated by SOX9 alone, the construct that contained both introns 1 and 6 was activated 510-fold by the SOX9/SOX5 or the SOX9/SOX6 combination in transient-transfection assays in 293T cells. This enhancement was also observed in rat chondrosarcoma cells that stably expressed the construct. CRISPR/Cas9-induced deletion of intron 6 in RCS cells revealed that a 10-bp region of intron 6 is necessary both for Col2a1 expression and SOX9 binding. |
About TF
| TF name : | Sox9(CMD1,CMPD1,SRA1,SRXX2,SRXY10)Sox9(CMD1,CMPD1,SRA1,SRXX2,SRXY10)Sox9(CMD1,CMPD1,SRA1,SRXX2,SRXY10)Sox9(CMD1,CMPD1,SRA1,SRXX2,SRXY10) |
| TF experiment: | ChIP-seq,ChIP-qPCR,EMSA |
| TF experiment description: | SOX9 bind to intron 6 and the binding of SOX5/SOX6 to intron 6 may facilitate the binding of SOX9 to the intron 1.To explore this possibility, we tested whether SOX9 and SOX5 bound to the SB2 fragment(600bp)shownabove or an even shorter fragment by means of an EMSA.;SOX9 bind to intron 6 and the binding of SOX5/SOX6 to intron 6 may facilitate the binding of SOX9 to the intron 1.To explore this possibility, we tested whether SOX9 and SOX5 bound to the SB2 fragment(600bp)shownabove or an even shorter fragment by means of an EMSA.;SOX9 bind to intron 6 and the binding of SOX5/SOX6 to intron 6 may facilitate the binding of SOX9 to the intron 1.To explore this possibility, we tested whether SOX9 and SOX5 bound to the SB2 fragment(600bp)shownabove or an even shorter fragment by means of an EMSA.;SOX9 bind to intron 6 and the binding of SOX5/SOX6 to intron 6 may facilitate the binding of SOX9 to the intron 1.To explore this possibility, we tested whether SOX9 and SOX5 bound to the SB2 fragment(600bp)shownabove or an even shorter fragment by means of an EMSA. |
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 |
|---|---|---|---|
| Sox9 | Deactivation of the beta-catenin transactivating complex | reactome | 42 |
| Sox9 | TGF_beta_Receptor | netpath | 220 |
| Sox9 | Hs_Neural_Crest_Differentiation_WP2064_79263 | wikipathways | 40 |
| Sox9 | Hs_Spinal_Cord_Injury_WP2431_87678 | wikipathways | 21 |
| Sox9 | Deactivation of the beta-catenin transactivating complex | reactome | 42 |
| Sox9 | TGF_beta_Receptor | netpath | 220 |
| Sox9 | Hs_Neural_Crest_Differentiation_WP2064_79263 | wikipathways | 40 |
| Sox9 | Hs_Spinal_Cord_Injury_WP2431_87678 | wikipathways | 21 |
| Sox9 | Deactivation of the beta-catenin transactivating complex | reactome | 42 |
| Sox9 | TGF_beta_Receptor | netpath | 220 |
| Sox9 | Hs_Neural_Crest_Differentiation_WP2064_79263 | wikipathways | 40 |
| Sox9 | Hs_Spinal_Cord_Injury_WP2431_87678 | wikipathways | 21 |
| Sox9 | Deactivation of the beta-catenin transactivating complex | reactome | 42 |
| Sox9 | TGF_beta_Receptor | netpath | 220 |
| Sox9 | Hs_Neural_Crest_Differentiation_WP2064_79263 | wikipathways | 40 |
| Sox9 | Hs_Spinal_Cord_Injury_WP2431_87678 | wikipathways | 21 |
Enhancer associated network
The number on yellow line represents the distance between enhancer and
target gene