|
| Status |
Public on Feb 20, 2020 |
| Title |
ATAC-seq analysis in G1E-ER4 cells during erythroid differentiation |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
The spatiotemporal control of 3D chromatin structure is fundamental for gene regulation, yet it remains challenging to obtain high-resolution chromatin interacting profiles at cis-regulatory elements (CREs) by chromatin conformation capture (3C)-based methods. Here, we describe the redesigned dCas9-based CAPTURE method for multiplexed, high-throughput and high-resolution analysis of locus-specific chromatin interactions. Using C-terminally biotinylated dCas9, endogenous biotin ligase and pooled sgRNAs, the new system enables quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling systematic comparisons across CREs within and between gene clusters. We reveal the hierarchical structure of super-enhancers (SEs) and distinct modes of SE-gene interactions. Multiplexed capture of temporal dynamics of promoter-centric interactions establishes the instructive function of enhancer-promoter looping in transcriptional regulation during lineage differentiation. These applications illustrate the ability of multiplexed CAPTURE for decoding the organizational principles of genome structure and function.
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| |
|
| Overall design |
ATAC-seq was performed to determine the chromatin accessibility in G1E-ER4 without (0 hour) or with β-estradiol treatment for 2, 6, 12, and 24 hours
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| |
|
| Contributor(s) |
Liu X, Zhang Y, Xu J |
| Citation(s) |
32138752 |
| |
| Submission date |
Oct 18, 2019 |
| Last update date |
Mar 16, 2020 |
| 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 |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE139117 |
Analysis of CRE-mediated chromatin interactions by CAPTURE2.0 |
|
| Relations |
| BioProject |
PRJNA578391 |
| SRA |
SRP226224 |
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