3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA521044 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10044700_1.fastq.gz | Fastqsanger.gz | |||
| SRR10044700_2.fastq.gz | Fastqsanger.gz | |||
| SRR10044701_1.fastq.gz | Fastqsanger.gz | |||
| SRR10044701_2.fastq.gz | Fastqsanger.gz | |||
| SRR10044702_1.fastq.gz | Fastqsanger.gz |
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Project description:To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA-fluorescence in situ hybridization (FISH), RNA-FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.
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Project description:we combined Assay for Transposase-Accessible Chromatin and lattice light-sheet PALM microscopy (3D ATAC-PALM) to selectively image key features of the 3D accessible genome in single cells. We found that accessible chromatin domains (ACDs) form spatially segregated clusters in the nucleus. Rapid depletion of CTCF or Cohesin (RAD21 subunit) induced extensive 3D spatial mixing of ACD clusters and reduced physical separation between ACDs within chromosomes. Experimental perturbations and modeling suggest that both weak, multivalent, dynamic protein-protein interactions together with loop extrusion influence ACD organization. Live-cell studies suggest that ACD clustering regulates transcription factor binding site distribution, target search kinetics and binding dynamics. Here we report the ATAC-seq results from Tn5 PA549 and nextera Tn5 upon various chemical and genetic perturbations.
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