Notice: Users may be experiencing issues with displaying some pages on stanfordhealthcare.org. We are working closely with our technical teams to resolve the issue as quickly as possible. Thank you for your patience.
 

Learn about the flu shot, COVID-19 vaccine, and our masking policy »

Stanford Health Care

3D ATAC-PALM: super-resolution imaging of the accessible genome. Nature methods Xie, L., Dong, P., Chen, X., Hsieh, T. S., Banala, S., De Marzio, M., English, B. P., Qi, Y., Jung, S. K., Kieffer-Kwon, K., Legant, W. R., Hansen, A. S., Schulmann, A., Casellas, R., Zhang, B., Betzig, E., Lavis, L. D., Chang, H. Y., Tjian, R., Liu, Z. 2020

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.

View details for DOI 10.1038/s41592-020-0775-2

View details for PubMedID 32203384