Open Access3D ATAC-PALM: super-resolution imaging of the accessible genome
Author(s) -
Liangqi Xie,
Peng Dong,
Xingqi Chen,
Tsung Han Hsieh,
Sambashiva Banala,
Margherita De Marzio,
Brian P. English,
Yifeng Qi,
Seol Kyoung Jung,
Kyong-Rim Kieffer-Kwon,
Wesley R. Legant,
Anders S. Hansen,
Anton Schulmann,
Rafael Casellas,
Bin Zhang,
Eric Betzig,
Luke D. Lavis,
Howard Y. Chang,
Robert Tjian,
Zhe Liu
Publication year - 2020
Publication title -
nature methods
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 19.469
H-Index - 318
eISSN - 1548-7105
pISSN - 1548-7091
DOI - 10.1038/s41592-020-0775-2
Subject(s) - chromatin , transposase , genome , computational biology , biology , fluorescence in situ hybridization , photoactivated localization microscopy , microscopy , fluorescence microscope , dna , microbiology and biotechnology , gene , genetics , super resolution microscopy , transposable element , fluorescence , chromosome , optics , physics
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.