3D ATAC-PALM: super-resolution imaging of the accessible genome.
Journal
Nature methods
ISSN: 1548-7105
Titre abrégé: Nat Methods
Pays: United States
ID NLM: 101215604
Informations de publication
Date de publication:
04 2020
04 2020
Historique:
received:
09
12
2019
accepted:
11
02
2020
revised:
04
02
2020
pubmed:
24
3
2020
medline:
8
7
2020
entrez:
24
3
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32203384
doi: 10.1038/s41592-020-0775-2
pii: 10.1038/s41592-020-0775-2
pmc: PMC7207063
mid: NIHMS1560186
doi:
Substances chimiques
DNA
9007-49-2
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
430-436Subventions
Organisme : NIGMS NIH HHS
ID : DP2 GM136653
Pays : United States
Organisme : NHGRI NIH HHS
ID : P50 HG007735
Pays : United States
Organisme : NHGRI NIH HHS
ID : RM1 HG007735
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Références
Dekker, J. et al. The 4D nucleome project. Nature 549, 219–226 (2017).
pubmed: 28905911
pmcid: 5617335
Dekker, J. et al. Capturing chromosome conformation. Science 295, 1306–1311 (2002).
pubmed: 11847345
Wit, E. De & Laat, W. De A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26, 11–24 (2012).
pubmed: 22215806
pmcid: 3258961
Dekker, J. & Mirny, L. The 3D genome as moderator of chromosomal communication. Cell 164, 1110–1121 (2016).
pubmed: 26967279
pmcid: 4788811
Dekker, J., Marti-Renom, M. A. & Mirny, L. A. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 14, 390–403 (2013).
pubmed: 23657480
pmcid: 3874835
Finn, E. H. et al. Extensive heterogeneity and intrinsic variation in spatial genome organization. Cell 176, 1502–1515 (2019).
pubmed: 30799036
pmcid: 6408223
Levine, M., Cattoglio, C. & Tjian, R. Looping back to leap forward: transcription enters a new era. Cell 157, 13–25 (2014).
pubmed: 24679523
pmcid: 4059561
Wu, C. The 5’ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286, 854–860 (1980).
pubmed: 6774262
Boyle, A. P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008).
pubmed: 18243105
pmcid: 2669738
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).
pubmed: 24097267
pmcid: 3959825
Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–490 (2015).
pubmed: 26083756
pmcid: 4685948
Chen, X. et al. ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing. Nat. Methods 13, 1013–1020 (2016).
pubmed: 27749837
pmcid: 5509561
Grimm, J. B. et al. Bright photoactivatable fluorophores for single-molecule imaging. Nat. Methods 13, 985–988 (2016).
pubmed: 27776112
Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642–1645 (2006).
pubmed: 16902090
Chen, B. C. et al. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346, 1257998 (2014).
pubmed: 25342811
pmcid: 4336192
Legant, W. R. et al. High-density three-dimensional localization microscopy across large volumes. Nat. Methods 13, 359–365 (2016).
pubmed: 26950745
pmcid: 4889433
Huang, B., Wang, W., Bates, M. & Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 319, 810–813 (2008).
pubmed: 18174397
pmcid: 2633023
Peebles, P. J. E. Statistical analysis of catalogs of extragalactic objects. I. theory. Astrophys. J. 185, 413 (1973).
Sengupta, P. et al. Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis. Nat. Methods 8, 969–975 (2011).
pubmed: 21926998
pmcid: 3400087
Ester, M., Kriegel, H. P., Sander, J. & Xu, X. A density-based algorithm for discovering clusters in large spatial databases with noise. In Proc. 2nd International Conference on Knowledge Discovery and Data Mining (KDD ‘96) 226–231 (AAAI Press, 1996).
Sakaue-Sawano, A. et al. Genetically encoded tools for optical dissection of the mammalian cell cycle. Mol. Cell 68, 626–640 (2017).
pubmed: 29107535
Kieffer-Kwon, K. R. et al. Myc regulates chromatin decompaction and nuclear architecture during B cell activation. Mol. Cell 67, 566–578.e10 (2017).
pubmed: 28803781
pmcid: 5854204
Beliveau, B. J. et al. Versatile design and synthesis platform for visualizing genomes with oligopaint FISH probes. Proc. Natl Acad. Sci. USA 109, 21301–21306 (2012).
pubmed: 23236188
Beliveau, B. J. et al. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat. Commun. 6, e7147 (2015).
Boettiger, A. N. et al. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529, 418–422 (2016).
pubmed: 26760202
pmcid: 4905822
Wang, S. et al. Spatial organization of chromatin domains and compartments in single chromosomes. Science 353, 598–602 (2016).
pubmed: 27445307
pmcid: 4991974
Bintu, B. et al. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362, eaau1783 (2018).
pubmed: 30361340
pmcid: 6535145
Sabari, B. R. et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science 361, 387–392 (2018).
Jin, C. H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions. Nat. Genet. 41, 941–945 (2009).
pubmed: 19633671
pmcid: 3125718
Nora, E. P. et al. Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169, 930–944 (2017).
pubmed: 28525758
pmcid: 5538188
Nishimura, K., Fukagawa, T., Takisawa, H., Kakimoto, T. & Kanemaki, M. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat. Methods 6, 917–922 (2009).
pubmed: 19915560
Wutz, G. et al. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J. 36, 3573–3599 (2017).
pubmed: 29217591
pmcid: 5730888
Hsieh, T. H. S. Mapping nucleosome resolution chromosome folding in yeast by Micro-C. Cell 162, 108–119 (2015).
pubmed: 26119342
pmcid: 4509605
Hsieh, T.-H. S. et al. Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Preprint at bioRxiv https://doi.org/10.1101/638775 (2019).
Fudenberg, G. et al. Formation of chromosomal domains by loop extrusion. Cell Rep. 15, 2038–2049 (2016).
pubmed: 27210764
pmcid: 4889513
Sanborn, A. L. et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc. Natl Acad. Sci. USA 112, E6456–E6465 (2015).
pubmed: 26499245
Alipour, E. & Marko, J. F. Self-organization of domain structures by DNA-loop-extruding enzymes. Nucleic Acids Res. 40, 11202–11212 (2012).
pubmed: 23074191
pmcid: 3526278
Fudenberg, G., Abdennur, N., Imakaev, M., Goloborodko, A. & Mirny, L. A. Emerging evidence of chromosome folding by loop extrusion. Cold Spring Harb. Symp. Quant. Biol. 82, 45–55.
Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98 (2012).
pubmed: 22265404
pmcid: 3339270
Xie, L. et al. A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency. Genes Dev. 31, 1795–1808 (2017).
pubmed: 28982762
pmcid: 5666677
Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S. & Zhuang, X. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, 356–372 (2015).
Shah, S. et al. Dynamics and spatial genomics of the nascent transcriptome by intron seqFISH. Cell 174, 363–376.e16 (2018).
pubmed: 29887381
pmcid: 6046268
Corces, M. R. et al. The chromatin accessibility landscape of primary human cancers. Science 362, e1898 (2018).
Picelli, S. et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24, 2033–2040 (2014).
pubmed: 25079858
pmcid: 4248319
Liu, Z. et al. 3D imaging of Sox2 enhancer clusters in embryonic stem cells. eLife 3, 1–29 (2014).
Kiskowski, M. A., Hancock, J. F. & Kenworthy, A. K. On the use of Ripley’s K-function and its derivatives to analyze domain size. Biophys. J. 97, 1095–1103 (2009).
pubmed: 19686657
pmcid: 2726315
Veatch, S. L. et al. Correlation functions quantify super-resolution images and estimate apparent clustering due to over-counting. PLoS ONE 7, e31457 (2012).
pubmed: 22384026
pmcid: 3288038