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

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

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47 Scopus citations

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.

Original language	English (US)
Pages (from-to)	430-436
Number of pages	7
Journal	Nature Methods
Volume	17
Issue number	4
DOIs	https://doi.org/10.1038/s41592-020-0775-2
State	Published - Apr 1 2020
Externally published	Yes

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/s41592-020-0775-2

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Xie, L., Dong, P., Chen, X., Hsieh, T. H. S., Banala, S., De Marzio, M., English, B. P., Qi, Y., Jung, S. K., Kieffer-Kwon, K. R., 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). 3D ATAC-PALM: super-resolution imaging of the accessible genome. Nature Methods, 17(4), 430-436. https://doi.org/10.1038/s41592-020-0775-2

Xie, L, Dong, P, Chen, X, Hsieh, THS, Banala, S, De Marzio, M, English, BP, Qi, Y, Jung, SK, Kieffer-Kwon, KR, Legant, WR, Hansen, AS, Schulmann, A, Casellas, R, Zhang, B, Betzig, E, Lavis, LD, Chang, HY, Tjian, R & Liu, Z 2020, '3D ATAC-PALM: super-resolution imaging of the accessible genome', Nature Methods, vol. 17, no. 4, pp. 430-436. https://doi.org/10.1038/s41592-020-0775-2

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title = "3D ATAC-PALM: super-resolution imaging of the accessible genome",

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.",

author = "Liangqi Xie and Peng Dong and Xingqi Chen and Hsieh, {Tsung Han S.} and Sambashiva Banala and {De Marzio}, Margherita and English, {Brian P.} and Yifeng Qi and Jung, {Seol Kyoung} and Kieffer-Kwon, {Kyong Rim} and Legant, {Wesley R.} and Hansen, {Anders S.} and Anton Schulmann and Rafael Casellas and Bin Zhang and Eric Betzig and Lavis, {Luke D.} and Chang, {Howard Y.} and Robert Tjian and Zhe Liu",

note = "Funding Information: We thank X. Darzacq, S. Chong, T. Graham, D. McSwiggen and C. Cattoglio for critical reading of the manuscript, the Tjian-Darzacq laboratory members for helpful discussions and P. Sengupta and H. Rouault for advice on data analysis. We thank D. Walpita and K. Schaefer with assistance for fluorescence-activated cell sorting experiments, D. Alcor for Airyscan Imaging and M. Radcliff for assistance. This work is supported by the Howard Hughes Medical Institute (HHMI) and the Janelia Visitor Program. Y.F.Q. and B.Z. acknowledge support by the National Science Foundation Grant MCB-1715859. H.Y.C. acknowledges support by NIH grant P50-HG007735. X.C. is supported by Swedish Research Council International Postdoctoral Fellowship (VR-2016-06794) and starting grant (VR-2017-02074), Jeanssons foundation grant (JS2018-0004) and a Vleugl grant. W.R.L. acknowledges support from the Searle Scholars Program, the Beckman Young Investigator Program, an NIH New Innovator Award (DP2GM136653) and the Packard Fellows Program. Publisher Copyright: {\textcopyright} 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2020",

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doi = "10.1038/s41592-020-0775-2",

language = "English (US)",

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journal = "Nature Methods",

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T1 - 3D ATAC-PALM

T2 - super-resolution imaging of the accessible genome

AU - Xie, Liangqi

AU - Dong, Peng

AU - Chen, Xingqi

AU - Hsieh, Tsung Han S.

AU - Banala, Sambashiva

AU - De Marzio, Margherita

AU - English, Brian P.

AU - Qi, Yifeng

AU - Jung, Seol Kyoung

AU - Kieffer-Kwon, Kyong Rim

AU - Legant, Wesley R.

AU - Hansen, Anders S.

AU - Schulmann, Anton

AU - Casellas, Rafael

AU - Zhang, Bin

AU - Betzig, Eric

AU - Lavis, Luke D.

AU - Chang, Howard Y.

AU - Tjian, Robert

AU - Liu, Zhe

N1 - Funding Information: We thank X. Darzacq, S. Chong, T. Graham, D. McSwiggen and C. Cattoglio for critical reading of the manuscript, the Tjian-Darzacq laboratory members for helpful discussions and P. Sengupta and H. Rouault for advice on data analysis. We thank D. Walpita and K. Schaefer with assistance for fluorescence-activated cell sorting experiments, D. Alcor for Airyscan Imaging and M. Radcliff for assistance. This work is supported by the Howard Hughes Medical Institute (HHMI) and the Janelia Visitor Program. Y.F.Q. and B.Z. acknowledge support by the National Science Foundation Grant MCB-1715859. H.Y.C. acknowledges support by NIH grant P50-HG007735. X.C. is supported by Swedish Research Council International Postdoctoral Fellowship (VR-2016-06794) and starting grant (VR-2017-02074), Jeanssons foundation grant (JS2018-0004) and a Vleugl grant. W.R.L. acknowledges support from the Searle Scholars Program, the Beckman Young Investigator Program, an NIH New Innovator Award (DP2GM136653) and the Packard Fellows Program. Publisher Copyright: © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc.

PY - 2020/4/1

Y1 - 2020/4/1

N2 - 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.

AB - 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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JO - Nature Methods

JF - Nature Methods

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ER -

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

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