Mar 24, 2020

3D ATAC-PALM: super-resolution imaging of the accessible genome

Nature Methods
Liangqi XieZhe Liu

Abstract

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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Mentioned in this Paper

CTCF gene
Diagnostic Imaging
Transposase
Structure
Genome
XCL1 protein, human
In Situ
Fluorescent in Situ Hybridization
Genes
Microscopy

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