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Series GSE185912 Query DataSets for GSE185912
Status Public on Aug 22, 2022
Title Bioorthogonal Chemical Epigenetic Modifiers Enable Dose-dependent CRISPR Targeted Gene Activation
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary CRISPR-Cas9 systems have been developed to regulate gene expression by using either fusions to epigenetic regulators or, more recently, through the use of chemically mediated strategies. These approaches have armed researchers with new tools to examine the function of proteins by intricately controlling expression levels of specific genes. Here, we present a CRISPR based chemical approach that uses a new Chemical Epigenetic Modifier (CEM) to hone to a gene targeted with a catalytically inactive Cas9 (dCas9) bridged to an FK506-binding protein (FKBP). One arm of the bifunctional CEM recruits BRD4 to the target site and the other arm is composed of a bumped ligand that binds to a mutant FKBP with a compensatory hole at F36V. This bump-and-hole strategy allows for activation of target genes in a dose dependent and reversible fashion with increased specificity and high efficacy.
Overall design ChIP-seq for BRD4 in conditions sgNT, sgCXCR4, 25nM CEM207, and sgCXCR4+25nM CEM207 to analyze the specificity of BRD4 binding in each.
Contributor(s) Lu D, Foley CA, Birla SV, Hepperla AJ, Simon JM, James LI, Hathaway NA
Citation(s) 35302756
Submission date Oct 14, 2021
Last update date Aug 25, 2022
Contact name Austin J Hepperla
Organization name University of North Carolina at Chapel Hill
Department Genetics
Street address 7018B Mary Ellen Jones Building
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (16)
GSM5625649 sgCXCR4_BRD4_ChIP_Rep1
GSM5625650 sgCXCR4_BRD4_ChIP_Rep2
GSM5625651 sgCXCR4_BRD4_ChIP_Rep3
BioProject PRJNA771351
SRA SRP341405

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE185912_HCT116_BRD4_signal_over_union_roe_all_samples.txt.gz 1.0 Mb (ftp)(http) TXT
GSE185912_RAW.tar 2.5 Gb (http)(custom) TAR (of BW, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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