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Series GSE99905 Query DataSets for GSE99905
Status Public on Nov 07, 2017
Title Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Multiple regulatory regions have the potential to regulate a single gene, yet how these elements combine to impact gene expression remains unclear. To uncover the combinatorial relationships between enhancers, we developed Enhancer-interference (Enhancer-i), a CRISPR interference-based approach that can prevent enhancer activation simultaneously at multiple regulatory regions. We applied Enhancer-i to promoter-distal estrogen receptor a binding sites (ERBS), which cluster around estradiol-responsive genes and therefore may collaborate to regulate gene expression. Targeting individual sites revealed predominant ERBS that are completely required for the transcriptional response, indicating a lack of redundancy. Simultaneous interference of different ERBS combinations identified supportive ERBS that contribute only when predominant sites are active. Using mathematical modeling, we find strong evidence for collaboration between predominant and supportive ERBS. Overall, our findings expose a complex functional hierarchy of enhancers, where multiple loci bound by the same transcription factor combine to fine tune the expression of target genes.
 
Overall design ChIP-seq was performed on Enhancer-I and control gRNA treated cells as well as parental Ishikawa lines
 
Contributor(s) Carleton JB, Gertz J
Citation(s) 28964699, 31649055
Submission date Jun 12, 2017
Last update date Nov 25, 2019
Contact name Jay Gertz
E-mail(s) jay.gertz@hci.utah.edu
Organization name University of Utah
Street address 2000 Circle of Hope Dr.
City Salt Lake City
ZIP/Postal code 84103
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (15)
GSM2664030 H3K27ac_Enhi
GSM2664031 H3K27ac_IL1RN
GSM2664032 H3K27ac_EnhiE2
This SubSeries is part of SuperSeries:
GSE99906 Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor Alpha Bound Enhancers
Relations
BioProject PRJNA390058
SRA SRP108978

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Supplementary file Size Download File type/resource
GSE99905_RAW.tar 2.3 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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