Cited by 674Genomics and Chromatin DynamicsNuclear Structure and FunctionChromosomal and Genetic Variations

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Heterochromatin drives compartmentalization of inverted and conventional nuclei

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Falk, Martin, Feodorova, Yana, Naumova, Natalia, Imakaev, Maxim, Lajoie, Bryan R., Leonhardt, Heinrich, Joffe, Boris, Dekker, Job, Fudenberg, Geoffrey, Solovei, Irina, Mirny, Leonid A.·2019·Nature

DOI 10.1038/s41586-019-1275-3PMC PMC7206897

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Abstract

The nucleus of mammalian cells displays a distinct spatial segregation of active euchromatic and inactive heterochromatic regions of the genome 1,2. In conventional nuclei, microscopy shows that euchromatin is localized in the nuclear interior and heterochromatin at the nuclear periphery 1,2. Genome-wide chromosome conformation capture (Hi-C) analyses show this segregation as a plaid pattern of contact enrichment within euchromatin and heterochromatin compartments 3, and depletion between them. Many mechanisms for the formation of compartments have been proposed, such as attraction of heterochromatin to the nuclear lamina 2,4, preferential attraction of similar chromatin to each other 1,4-12, higher levels of chromatin mobility in active chromatin 13-15 and transcription-related clustering of euchromatin 16,17. However, these hypotheses have remained inconclusive, owing to the difficulty of disentangling intra-chromatin and chromatin-lamina interactions in conventional nuclei 18. The marked reorganization of interphase chromosomes in the inverted nuclei of rods in nocturnal mammals 19,20 provides an opportunity to elucidate the mechanisms that underlie spatial compartmentalization. Here we combine Hi-C analysis of inverted rod nuclei with microscopy and polymer simulations. We find that attractions between heterochromatic regions are crucial for establishing both compartmentalization and the concentric shells of pericentromeric heterochromatin, facultative heterochromatin and euchromatin in the inverted nucleus. When interactions between heterochromatin and the lamina are added, the same model recreates the conventional nuclear organization. In addition, our models allow us to rule out mechanisms of compartmentalization that involve strong euchromatin interactions. Together, our experiments and modelling suggest that attractions between heterochromatic regions are essential for the phase separation of the active and inactive genome in inverted and conventional nuclei, whereas interactions of the chromatin with the lamina are necessary to build the conventional architecture from these segregated phases.

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Additional file 3 of Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
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Additional file 1 of Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
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Additional file 7 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
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Additional file 4 of Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
Feng, Y., Wang, Y., Wang, X., He, X., Chen, Y., Naseri, A., Pederson, T., Zheng, J., Zhang, S., Xiao, X., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13352153
Additional file 3 of SPIN reveals genome-wide landscape of nuclear compartmentalization
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Additional file 8 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
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Additional file 5 of Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index
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Additional file 3 of Quantifying the phase separation property of chromatin-associated proteins under physiological conditions using an anti-1,6-hexanediol index
Shi, M., You, K., Chen, T., Hou, C., Liang, Z., Liu, M., Wang, J., Wei, T., Qin, J., Chen, Y., et al. (2021) · Figshare · doi:10.6084/m9.figshare.15184565
Additional file 3 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
Xue, L., Gao, Y., Wu, M., Tian, T., Fan, H., Huang, Y., Huang, Z. J., Li, D., & Xu, L. (2021) · Figshare · doi:10.6084/m9.figshare.14966165
Additional file 5 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
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Additional file 2 of Time-dependent effect of 1,6-hexanediol on biomolecular condensates and 3D chromatin organization
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Additional file 4 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
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Additional file 5 of SPIN reveals genome-wide landscape of nuclear compartmentalization
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Additional file 4 of SPIN reveals genome-wide landscape of nuclear compartmentalization
Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Peric‐Hupkes, D., Chen, Y., Gilbert, D. M., van Steensel, B., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13579164
Additional file 9 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
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Additional file 2 of Simultaneous epigenetic perturbation and genome imaging reveal distinct roles of H3K9me3 in chromatin architecture and transcription
Feng, Y., Wang, Y., Wang, X., He, X., Chen, Y., Naseri, A., Pederson, T., Zheng, J., Zhang, S., Xiao, X., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13352147
Additional file 6 of Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair
Xue, L., Gao, Y., Wu, M., Tian, T., Fan, H., Huang, Y., Huang, Z. J., Li, D., & Xu, L. (2021) · Figshare · doi:10.6084/m9.figshare.14966174
Local Volume Concentration, Packing Domains and Scaling Properties of ChromatinPreprint
Carignano, M. A., Kröger, M., Almassalha, L. M., Agrawal, V., Li, W. S., Pujadas-Liwag, E. M., Nap, R. J., Backman, V., & Szleifer, I. G. (2024) · eLife · doi:10.7554/elife.97604.1
Epigenetic Control of Cell Fate Decisions by Enhancer-Derived Long Noncoding RNAs
Mattick, J. S. (2024) · Springer eBooks · doi:10.1007/978-3-031-59286-7_2
Local Volume Concentration, Packing Domains and Scaling Properties of ChromatinPreprint
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Understanding and Simulating the Dynamics of a Polymer-Like Chromatin
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Telomere interactions and structural variants in ALT cells revealed with TelSPRITEPreprint
Wilson, D. G., Soper, S. F. C., Pineda, M. A., Walker, R. L., & Meltzer, P. S. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.22.624895
“Regions with similar chromatin states tend to spatially associate, 14,15,24 so this relationship may reflect spatial clustering of telomeric and centromeric constitutive heterochromatin.”
Cluster size determines internal structure of transcription factories in human cellsPreprint
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“It is also important to specify that, even if an investigation of a transition between small and larger transcription factories have been carried out in mouse embryonic stem cells [53], in serum-stimulated cells [54] and in zebrafish embryos [55], our study aims to provide a broader mechanistic…”
A microfluidic platform for extraction and analysis of bacterial genomic DNA
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Roles and Future Opportunities for Genomic Architecture in Understanding Repeated Evolution
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Disorder in coiled-coils orchestrate chromatin organization and define a new permeability barrier at the nuclear pore basketPreprint
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“Polymer simulations (Jost et al. 2014 ; Nuebler et al. 2018; Falk et al. 2019 ; Mirny et al. 2019) and in vitro demonstrations of condensate formation by transcription factors and other chromatin-bound proteins, as reviewed in (Hildebrand and Dekker 2020), have shed light on this phenomenon.”
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Influential
Analysis of heterochromatin mesoscale architecture by cryo-electron tomography
Kazakov, E. P., Chesnokov, Y. M., Kireev, I. I., & Golyshev, S. A. (2025) · Vestnik Moskovskogo universiteta Seria 16 Biologia · doi:10.55959/msu0137-0952-16-80-3s-18
Heterochromatome wide analyses reveal MBD2 as a phase separation scaffold for heterochromatin compartmentalization and composition
Zhang, H., Ugur, E., Hake, C., Romero, H., Arroyo, M., Mahmoud, M., Lermyte, F., Leonhardt, H., & Cardoso, M. C. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1380
“The constitutive pericentric heterochromatin is particularly important for proper chromatin segregation during mitosis as well as spatial chromosome organization in interphase [ 3 ] yet the precise mechanisms governing its organization and compartmentalization remain incompletely understood.”
Additional file 3 of Time-dependent effect of 1,6-hexanediol on biomolecular condensates and 3D chromatin organization
Liu, X., Jiang, S., Ma, L., Qu, J., Zhao, L., Zhu, X., & Ding, J. (2021) · Figshare · doi:10.6084/m9.figshare.15184682
Additional file 6 of An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype
Shah, P. P., Keough, K. C., Gjoni, K., Santini, G. T., Abdill, R. J., Wickramasinghe, N. M., Dundes, C. E., Karnay, A. M., Chen, A. C., Salomon, R. E. A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26563459
Additional file 2 of Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism
Pujadas-Liwag, E. M., Wei, X., Acosta, N., Carter, L. M., Yang, J., Almassalha, L. M., Jain, S., Daneshkhah, A., Rao, S. S. P., Seker-Polat, F., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26696598
Additional file 7 of An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype
Shah, P. P., Keough, K. C., Gjoni, K., Santini, G. T., Abdill, R. J., Wickramasinghe, N. M., Dundes, C. E., Karnay, A. M., Chen, A. C., Salomon, R. E. A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26563462
Additional file 1 of TAD cliques predict key features of chromatin organization
Ali, T. M. L., Brunet, A., Collas, P., & Paulsen, J. (2021) · Figshare · doi:10.6084/m9.figshare.14906136
Additional file 1 of Time-dependent effect of 1,6-hexanediol on biomolecular condensates and 3D chromatin organization
Liu, X., Jiang, S., Ma, L., Qu, J., Zhao, L., Zhu, X., & Ding, J. (2021) · Figshare · doi:10.6084/m9.figshare.15184673
Additional file 1 of Characterization of H3K9me3 and DNA methylation co-marked CpG-rich regions during mouse development
Yang, H., Wang, Y., & Zhang, Y. (2023) · Figshare · doi:10.6084/m9.figshare.24499374
Additional file 2 of CTCF and cohesin promote focal detachment of DNA from the nuclear lamina
van Schaik, T., Liu, N. Q., Manzo, S. G., Peric‐Hupkes, D., de Wit, E., & van Steensel, B. (2022) · Figshare · doi:10.6084/m9.figshare.20787022
Additional file 6 of SPIN reveals genome-wide landscape of nuclear compartmentalization
Wang, Y., Zhang, Y., Zhang, R., van Schaik, T., Zhang, L., Sasaki, T., Peric‐Hupkes, D., Chen, Y., Gilbert, D. M., van Steensel, B., et al. (2021) · Figshare · doi:10.6084/m9.figshare.13579170
Additional file 5 of An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype
Shah, P. P., Keough, K. C., Gjoni, K., Santini, G. T., Abdill, R. J., Wickramasinghe, N. M., Dundes, C. E., Karnay, A. M., Chen, A. C., Salomon, R. E. A., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26563456

Authors: Falk, M., Feodorova, Y., Naumova, N., Imakaev, M., Lajoie, B. R., Leonhardt, H., Joffe, B., Dekker, J., Fudenberg, G., Solovei, I., & Mirny, L. A.
Affiliations: Massachusetts Institute of Technology (US)
Medical University Plovdiv (BG)
Howard Hughes Medical Institute (US)
Ludwig-Maximilians-Universität München (DE)
Gladstone Institutes (US)
Corresponding author: Fudenberg, Geoffrey
Solovei, Irina
Mirny, Leonid A.
ORCID: Falk, Martin
Feodorova, Yana
Imakaev, Maxim
Lajoie, Bryan R.
Leonhardt, Heinrich
Dekker, Job
Fudenberg, Geoffrey
Solovei, Irina
Mirny, Leonid A.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2019-06
Volume: 570
Issue: 7761
Pages: 395-399
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/s41586-019-1275-3
PMC: PMC7206897
OpenAlex: W2948487481
Cited by: 646
References: 55
Citations by year: 2026: 50 · 2025: 84 · 2024: 95 · 2023: 90 · 2022: 90 · 2021: 116 · 2020: 88 · 2019: 33
FWCI: 28.63
Type: journal article
Language: en
Update notices: correction (2019-08-02)
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
eScholarship@UMassChan (submittedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: Howard Hughes Medical Institute
National Human Genome Research Institute (RM1HG007743, R01HG003143)
National Institute of General Medical Sciences (R01GM114190)
National Institute of Diabetes and Digestive and Kidney Diseases (U54DK107980)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Keywords: nuclear compartmentalization, heterochromatin, rod photoreceptors, nuclear lamina, euchromatin, pericentromeric heterochromatin, facultative heterochromatin, phase separation, chromosome conformation, chromatin organization, polymer simulation
MeSH terms: Animals, Cell Compartmentation, Cell Nucleus, Heterochromatin, Models, Biological, Time Factors, Euchromatin, Nuclear Lamina, Mice

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Heterochromatin drives compartmentalization of inverted and conventional nuclei

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