Enhancer ID: | E_01_243 | |
Enhancer symbol: | -- | |
Species: | Human | |
Position : | chr6:31126537-31126685 |
|
Biosample name: | Embryonic Stem Cell | |
Experiment class : | Low throughput |
Enhancer type: | Enhancer | |
Disease: | -- | |
DO: | -- | |
Mesh: | -- | |
Distance from TSS: | >2KB | |
Pubmed ID: | 26813977 |
Enhancer experiment: | CRISPR/Cas9,Luciferase Reporter Assay,4C-seq | |
Enhancer experiment description: | We designed 1964 sgRNA sequences (Supplemental Table S2) targeting these putative cis-regulatory elements with an average of 11 sgRNA per element (Supplemental Fig. S1A). To eliminate these false positives,we required that a positive cis-regulatory element should have at least two distinct sgRNAs enriched by twofold or more in the eGFP− population in at least three out of the four independent experiments (Supplemental Table S3; Supplemental Fig. S2A). By use of this criterion, no negative control sgRNA passed the filter, while six cis-regulatory elements were identified as positives (Fig. 2A). Next, we tested whether the identified elements could function as enhancers in the classical reporter assays (DHS_37,CTCF_38, DHS_65, DHS_108, and DHS_115).We cloned genomic fragments corresponding to each element into a reporter plasmid containing the 360-bp POU5F1 core promoter region and a luciferase reporter gene. All elements, with the exception of DHS_65, exhibited significant enhancer activities in the H1 cells compared with the control plasmid containing only the POU5F1 core promoter sequence (Fig. 2C). We found that all Temp Enhancers, namely, DHS_37, DHS_65, and DHS_108, are located near regions that show high levels of chromatin interactions with the POU5F1 promoter. To confirm this observation, we also performed 4C-seq experiments in H1 POU5F1-eGFP cells. Again, we found these elements near regions displaying high and consistent interaction frequencies with the POU5F1 promoter (Fig. 4D). |
Target gene : | POU5F1(OCT3,OCT4,OTF-3,OTF3,OTF4,Oct-3,Oct-4) | |
Strong evidence: | 4C-seq | |
Less strong evidence: | Luciferase Reporter Assay | |
Target gene experiment description: | Next, we tested whether the identified elements could function as enhancers in the classical reporter assays (DHS_37,CTCF_38, DHS_65, DHS_108, and DHS_115).We cloned genomic fragments corresponding to each element into a reporter plasmid containing the 360-bp POU5F1 core promoter region and a luciferase reporter gene. All elements, with the exception of DHS_65, exhibited significant enhancer activities in the H1 cells compared with the control plasmid containing only the POU5F1 core promoter sequence (Fig. 2C). We found that all Temp Enhancers, namely, DHS_37, DHS_65, and DHS_108, are located near regions that show high levels of chromatin interactions with the POU5F1 promoter. To confirm this observation, we also performed 4C-seq experiments in H1 POU5F1-eGFP cells. Again, we found these elements near regions displaying high and consistent interaction frequencies with the POU5F1 promoter (Fig. 4D). |
TF name : | -- | |
TF experiment: | -- | |
TF experiment description: | -- |
Enhancer function : | DHS_65 and DHS_108 act in cis to regulate POU5F1 expression |
Enhancer function experiment: | CRISPR/Cas9 |
Enhancer function experiment description: |
Those results support our model that DHS_65 and DHS_108 act in cis to regulate POU5F1 transcription. |
SNP ID: | -- | |
SNP position: | -- |
SNP experiment: | -- |
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