Methods for mapping 3D chromosome architecture

doi:10.1038/s41576-019-0195-2

Review

. 2020 Apr;21(4):207-226.

doi: 10.1038/s41576-019-0195-2. Epub 2019 Dec 17.

Methods for mapping 3D chromosome architecture

Rieke Kempfer^{1

2}, Ana Pombo^{3

4}

Affiliations

¹ Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. rieke.kempfer@mdc-berlin.de.
² Institute for Biology, Humboldt University of Berlin, Berlin, Germany. rieke.kempfer@mdc-berlin.de.
³ Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. ana.pombo@mdc-berlin.de.
⁴ Institute for Biology, Humboldt University of Berlin, Berlin, Germany. ana.pombo@mdc-berlin.de.

PMID: 31848476
DOI: 10.1038/s41576-019-0195-2

Review

Methods for mapping 3D chromosome architecture

Rieke Kempfer et al. Nat Rev Genet. 2020 Apr.

. 2020 Apr;21(4):207-226.

doi: 10.1038/s41576-019-0195-2. Epub 2019 Dec 17.

Authors

Rieke Kempfer^{1

2}, Ana Pombo^{3

4}

Affiliations

¹ Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. rieke.kempfer@mdc-berlin.de.
² Institute for Biology, Humboldt University of Berlin, Berlin, Germany. rieke.kempfer@mdc-berlin.de.
³ Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany. ana.pombo@mdc-berlin.de.
⁴ Institute for Biology, Humboldt University of Berlin, Berlin, Germany. ana.pombo@mdc-berlin.de.

PMID: 31848476
DOI: 10.1038/s41576-019-0195-2

Abstract

Determining how chromosomes are positioned and folded within the nucleus is critical to understanding the role of chromatin topology in gene regulation. Several methods are available for studying chromosome architecture, each with different strengths and limitations. Established imaging approaches and proximity ligation-based chromosome conformation capture (3C) techniques (such as DNA-FISH and Hi-C, respectively) have revealed the existence of chromosome territories, functional nuclear landmarks (such as splicing speckles and the nuclear lamina) and topologically associating domains. Improvements to these methods and the recent development of ligation-free approaches, including GAM, SPRITE and ChIA-Drop, are now helping to uncover new aspects of 3D genome topology that confirm the nucleus to be a complex, highly organized organelle.

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References

1. Pombo, A. & Dillon, N. Three-dimensional genome architecture: players and mechanisms. Nat. Rev. Mol. Cell Biol. 16, 245–257 (2015). - PubMed - DOI - PMC
1. Dekker, J. et al. The 4D nucleome project. Nature 549, 219–226 (2017). - PubMed - PMC - DOI
1. Spielmann, M., Lupiáñez, D. G. & Mundlos, S. Structural variation in the 3D genome. Nat. Rev. Genet. 19, 453–467 (2018). This review explains the influence of disrupted chromatin folding on gene regulation in disease with examples from developmental disorders. - PubMed - DOI - PMC
1. Krijger, P. H. & de Laat, W. Regulation of disease-associated gene expression in the 3D genome. Nat. Rev. Mol. Cell Biol. 17, 771–782 (2016). - PubMed - DOI - PMC
1. Gall, J. G. & Pardue, M. L. Formation and detection of RNA–DNA hybrid molecules in cytological preparations. Proc. Natl Acad. Sci. USA 63, 378–383 (1969). - PubMed - DOI - PMC

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[1] Pombo, A. & Dillon, N. Three-dimensional genome architecture: players and mechanisms. Nat. Rev. Mol. Cell Biol. 16, 245–257 (2015). - PubMed - DOI - PMC

[2] Pombo, A. & Dillon, N. Three-dimensional genome architecture: players and mechanisms. Nat. Rev. Mol. Cell Biol. 16, 245–257 (2015). - PubMed - DOI - PMC

[3] Dekker, J. et al. The 4D nucleome project. Nature 549, 219–226 (2017). - PubMed - PMC - DOI

[4] Dekker, J. et al. The 4D nucleome project. Nature 549, 219–226 (2017). - PubMed - PMC - DOI

[5] Spielmann, M., Lupiáñez, D. G. & Mundlos, S. Structural variation in the 3D genome. Nat. Rev. Genet. 19, 453–467 (2018). This review explains the influence of disrupted chromatin folding on gene regulation in disease with examples from developmental disorders. - PubMed - DOI - PMC

[6] Spielmann, M., Lupiáñez, D. G. & Mundlos, S. Structural variation in the 3D genome. Nat. Rev. Genet. 19, 453–467 (2018). This review explains the influence of disrupted chromatin folding on gene regulation in disease with examples from developmental disorders. - PubMed - DOI - PMC

[7] Krijger, P. H. & de Laat, W. Regulation of disease-associated gene expression in the 3D genome. Nat. Rev. Mol. Cell Biol. 17, 771–782 (2016). - PubMed - DOI - PMC

[8] Krijger, P. H. & de Laat, W. Regulation of disease-associated gene expression in the 3D genome. Nat. Rev. Mol. Cell Biol. 17, 771–782 (2016). - PubMed - DOI - PMC

[9] Gall, J. G. & Pardue, M. L. Formation and detection of RNA–DNA hybrid molecules in cytological preparations. Proc. Natl Acad. Sci. USA 63, 378–383 (1969). - PubMed - DOI - PMC

[10] Gall, J. G. & Pardue, M. L. Formation and detection of RNA–DNA hybrid molecules in cytological preparations. Proc. Natl Acad. Sci. USA 63, 378–383 (1969). - PubMed - DOI - PMC

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Methods for mapping 3D chromosome architecture

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Methods for mapping 3D chromosome architecture

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