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| Status |
Public on Aug 24, 2017 |
| Title |
RNA-seq transcriptonal profiling in human K562 cells with or without dCas9 and sgRNAs |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated endonuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization of enhancer structure. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally controlled super-enhancers reveals spatial features causally regulate gene transcription. Thus, comprehensive analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.
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| Overall design |
RNA-seq was performed to determine the effects on global gene expression in K562 cells stably expressing Flag-bio-tagged dCas9 and sgRNAs targeting several regulatory elements within the β-globin cluster (sgHS2, sgHBG and sgHS1-5) or the non-targeting sgRNA (sgGal4).
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| Contributor(s) |
Liu X, Zhang Y, Xu J |
| Citation(s) |
28841410 |
| Submission date |
May 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@stjude.org
|
| Phone |
9015955208
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place, MS 345
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (14)
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| This SubSeries is part of SuperSeries: |
| GSE88817 |
In situ CAPTURE of chromatin interactions by biotinylated dCas9 |
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| Relations |
| BioProject |
PRJNA387465 |
| SRA |
SRP107789 |
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