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

Liangqi Xie; Peng Dong; Xingqi Chen; Tsung-Han S 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

doi:10.1038/s41592-020-0775-2

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

Nat Methods. 2020 Apr;17(4):430-436. doi: 10.1038/s41592-020-0775-2. Epub 2020 Mar 16.

Authors

Liangqi Xie^#^{1

2

3}, Peng Dong^#¹, Xingqi Chen^{4

5}, Tsung-Han S Hsieh^{2

3}, Sambashiva Banala¹, Margherita De Marzio⁶, Brian P English¹, Yifeng Qi⁶, Seol Kyoung Jung⁷, Kyong-Rim Kieffer-Kwon⁷, Wesley R Legant¹, Anders S Hansen², Anton Schulmann¹, Rafael Casellas⁷, Bin Zhang⁶, Eric Betzig¹, Luke D Lavis¹, Howard Y Chang⁴, Robert Tjian^{8

9}, Zhe Liu¹⁰

Affiliations

¹ Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
² Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA, USA.
³ Howard Hughes Medical Institute, Berkeley, CA, USA.
⁴ Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
⁵ Department of Immunology, Genomics and Pathology, Uppsala University, Uppsala, Sweden.
⁶ Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁷ Lymphocyte Nuclear Biology, NIAMS and Center of Cancer Research, NCI, NIH, Bethesda, MD, USA.
⁸ Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, CA, USA. [email protected].
⁹ Howard Hughes Medical Institute, Berkeley, CA, USA. [email protected].
¹⁰ Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA. [email protected].

^# Contributed equally.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosome Painting
DNA / metabolism*
Genome, Human
Genomics / methods*
High-Throughput Nucleotide Sequencing
Humans
Image Processing, Computer-Assisted
In Situ Hybridization, Fluorescence / methods*
Microscopy / methods*
Sequence Analysis, DNA / methods

Substances

DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding