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3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome
To image the accessible genome at nanometer scale in situ, we developed 3D ATAC-PALM which integrates Assay for Transposase-Accessible Chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with Oligopaint DNA-FISH, RNA-FISH and protein fluorescen...
Autores principales: | , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7207063/ https://www.ncbi.nlm.nih.gov/pubmed/32203384 http://dx.doi.org/10.1038/s41592-020-0775-2 |
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author | Xie, Liangqi Dong, Peng Chen, Xingqi Hsieh, Tsung-Han S. Banala, Sambashiva De Marzio, Margherita English, Brian P. Qi, Yifeng Jung, Seol Kyoung Kieffer-Kwon, Kyong-Rim Legant, Wesley R. Hansen, Anders S. Schulmann, Anton Casellas, Rafael Zhang, Bin Betzig, Eric Lavis, Luke D. Chang, Howard Y. Tjian, Robert Liu, Zhe |
author_facet | Xie, Liangqi Dong, Peng Chen, Xingqi Hsieh, Tsung-Han S. Banala, Sambashiva De Marzio, Margherita English, Brian P. Qi, Yifeng Jung, Seol Kyoung Kieffer-Kwon, Kyong-Rim Legant, Wesley R. Hansen, Anders S. Schulmann, Anton Casellas, Rafael Zhang, Bin Betzig, Eric Lavis, Luke D. Chang, Howard Y. Tjian, Robert Liu, Zhe |
author_sort | Xie, Liangqi |
collection | PubMed |
description | To image the accessible genome at nanometer scale in situ, we developed 3D ATAC-PALM which integrates Assay for Transposase-Accessible Chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with Oligopaint DNA-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. |
format | Online Article Text |
id | pubmed-7207063 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
record_format | MEDLINE/PubMed |
spelling | pubmed-72070632020-09-16 3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome Xie, Liangqi Dong, Peng Chen, Xingqi Hsieh, Tsung-Han S. Banala, Sambashiva De Marzio, Margherita English, Brian P. Qi, Yifeng Jung, Seol Kyoung Kieffer-Kwon, Kyong-Rim Legant, Wesley R. Hansen, Anders S. Schulmann, Anton Casellas, Rafael Zhang, Bin Betzig, Eric Lavis, Luke D. Chang, Howard Y. Tjian, Robert Liu, Zhe Nat Methods Article To image the accessible genome at nanometer scale in situ, we developed 3D ATAC-PALM which integrates Assay for Transposase-Accessible Chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with Oligopaint DNA-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. 2020-03-16 2020-04 /pmc/articles/PMC7207063/ /pubmed/32203384 http://dx.doi.org/10.1038/s41592-020-0775-2 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms |
spellingShingle | Article Xie, Liangqi Dong, Peng Chen, Xingqi Hsieh, Tsung-Han S. Banala, Sambashiva De Marzio, Margherita English, Brian P. Qi, Yifeng Jung, Seol Kyoung Kieffer-Kwon, Kyong-Rim Legant, Wesley R. Hansen, Anders S. Schulmann, Anton Casellas, Rafael Zhang, Bin Betzig, Eric Lavis, Luke D. Chang, Howard Y. Tjian, Robert Liu, Zhe 3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome |
title | 3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome |
title_full | 3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome |
title_fullStr | 3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome |
title_full_unstemmed | 3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome |
title_short | 3D ATAC-PALM: Super-resolution Imaging of the Accessible Genome |
title_sort | 3d atac-palm: super-resolution imaging of the accessible genome |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7207063/ https://www.ncbi.nlm.nih.gov/pubmed/32203384 http://dx.doi.org/10.1038/s41592-020-0775-2 |
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