Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

Nature

Volumn 529, Issue 7586, 2016, Pages 418-422

  Boettiger, Alistair N ^a   Bintu, Bogdan ^a   Moffitt, Jeffrey R ^a   Wang, Siyuan ^a   Beliveau, Brian J ^b   Fudenberg, Geoffrey ^c   Imakaev, Maxim ^c   Mirny, Leonid A ^c   Wu, Chao Ting ^b   Zhuang, Xiaowei ^a  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; POLYCOMB GROUP PROTEIN; CHROMATIN;

CHROMOSOME; DNA; FLY; GENE EXPRESSION; GENOME; IMAGING METHOD; METAZOAN; PROTEIN; THREE-DIMENSIONAL MODELING;

ARTICLE; CHROMATIN; CHROMATIN FOLDING; DROSOPHILA; EPIGENETICS; GENE CONTROL; IMAGE DISPLAY; IMAGING; INSECT CELL; NONHUMAN; PRIORITY JOURNAL; SUPER RESOLUTION IMAGING; THREE DIMENSIONAL IMAGING; ANIMAL; CELL LINE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOME POSITIONING; CYTOLOGY; DROSOPHILA MELANOGASTER; EPIGENETIC REPRESSION; FRACTAL ANALYSIS; GENETIC EPIGENESIS; GENETIC TRANSCRIPTION; GENETICS; GENOME; METABOLISM;

METAZOA;

ANIMALS; CELL LINE; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMOSOME POSITIONING; DROSOPHILA MELANOGASTER; EPIGENESIS, GENETIC; EPIGENETIC REPRESSION; FRACTALS; GENOME; POLYCOMB-GROUP PROTEINS; TRANSCRIPTION, GENETIC;

EID: 84955290042     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature16496     Document Type: Article

References (30)

1. Kornberg, R. D., Lorch, Y. Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285-294 (1999).
2. Bickmore, W. A. The spatial organization of the human genome. Annu. Rev. Genomics Hum. Genet. 14, 67-84 (2013).
3. Gibcus, J. H., Dekker, J. The hierarchy of the 3D genome. Mol. Cell 49, 773-782 (2013).
4. Levine, M., Cattoglio, C., Tjian, R. Looping back to leap forward: transcription enters a new era. Cell 157, 13-25 (2014).
5. Cremer, T., Cremer, M. Chromosome territories. Cold Spring Harb. Perspect. Biol. 2, a003889 (2010).
6. Gorkin, D. U., Leung, D., Ren, B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 14, 762-775 (2014).
7. Sexton, T., Cavalli, G. The role of chromosome domains in shaping the functional genome. Cell 160, 1049-1059 (2015).
8. Galupa, R., Heard, E. X-chromosome inactivation: new insights into cis and trans regulation. Curr. Opin. Genet. Dev. 31, 57-66 (2015).
9. Bernstein, B. E., Meissner, A., Lander, E. S. The mammalian epigenome. Cell 128, 669-681 (2007).
10. Bickmore, W. A., van Steensel, B. Genome architecture: domain organization of interphase chromosomes. Cell 152, 1270-1284 (2013).
11. Rivera, C. M., Ren, B. Mapping human epigenomes. Cell 155, 39-55 (2013).
12. Gómez-Diáz, E., Corces, V. G. Architectural proteins: regulators of 3D genome organization in cell fate. Trends Cell Biol. 24, 703-711 (2014).
13. 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).
14. Beliveau, B. J. et al. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat. Commun. 6, 7147 (2015).
15. Boyle, S., Rodesch, M. J., Halvensleben, H. A., Jeddeloh, J. A., Bickmore, W. A. Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis. Chromosome Res. 19, 901-909 (2011).
16. Yamada, N. A. et al. Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH. Cytogenet. Genome Res. 132, 248-254 (2011).
17. Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., Zhuang, X. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348, 412 (2015).
18. Rust, M. J., Bates, M., Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nature Methods 3, 793-796 (2006).
19. Huang, B., Wang, W., Bates, M., Zhuang, X. Three-dimensional superresolution imaging by stochastic optical reconstruction microscopy. Science 319, 810-813 (2008).
20. Filion, G. J. et al. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143, 212-224 (2010).
21. Simon, J. A., Kingston, R. E. Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol. Cell 49, 808-824 (2013).
22. Grossniklaus, U., Paro, R. Transcriptional silencing by polycomb-group proteins. Cold Spring Harb. Perspect. Biol. 6, a019331 (2014).
23. Cheutin, T., Cavalli, G. Polycomb silencing: from linear chromatin domains to 3D chromosome folding. Curr. Opin. Genet. Dev. 25, 30-37 (2014).
24. Sexton, T. et al., Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 148, 458-472 (2012).
25. Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-293 (2009).
26. Mirny, L. A. The fractal globule as a model of chromatin architecture in the cell. Chromosome Res. 19, 37-51 (2011).
27. Halverson, J. D., Smrek, J., Kremer, K., Grosberg, A. Y. From a melt of rings to chromosome territories: the role of topological constraints in genome folding. Rep. Prog. Phys. 77, 022601 (2014).
28. Nicodemi, M., Pombo, A. Models of chromosome structure. Curr. Opin. Cell Biol. 28, 90-95 (2014).
29. Isono, K. et al. SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing. Dev. Cell 26, 565-577 (2013).
30. Spitz, F., Furlong, E. E. M. Transcription factors: from enhancer binding to developmental control. Nature Rev. Genet. 13, 613-626 (2012).