The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments - PubMed

Affiliations

• PMID: 26028501
• DOI: 10.1016/j.febslet.2015.05.037

Free article

Review

The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments

Thomas Cremer et al. FEBS Lett. 2015.

Free article

Abstract

Recent methodological advancements in microscopy and DNA sequencing-based methods provide unprecedented new insights into the spatio-temporal relationships between chromatin and nuclear machineries. We discuss a model of the underlying functional nuclear organization derived mostly from electron and super-resolved fluorescence microscopy studies. It is based on two spatially co-aligned, active and inactive nuclear compartments (ANC and INC). The INC comprises the compact, transcriptionally inactive core of chromatin domain clusters (CDCs). The ANC is formed by the transcriptionally active periphery of CDCs, called the perichromatin region (PR), and the interchromatin compartment (IC). The IC is connected to nuclear pores and serves nuclear import and export functions. The ANC is the major site of RNA synthesis. It is highly enriched in epigenetic marks for transcriptionally competent chromatin and RNA Polymerase II. Marks for silent chromatin are enriched in the INC. Multi-scale cross-correlation spectroscopy suggests that nuclear architecture resembles a random obstacle network for diffusing proteins. An increased dwell time of proteins and protein complexes within the ANC may help to limit genome scanning by factors or factor complexes to DNA exposed within the ANC.

Keywords: 4D nucleome; Active nuclear compartment; Electron microscopy; Hi-C; Inactive nuclear compartment; Interchromatin compartment; Nuclear architecture; Perichromatin region; Super-resolution fluorescence microscopy; Topologically associating domains.

Similar articles

• Nuclear compartmentalization, dynamics, and function of regulatory DNA sequences.

  Cremer M, Cremer T. Cremer M, et al. Genes Chromosomes Cancer. 2019 Jul;58(7):427-436. doi: 10.1002/gcc.22714. Epub 2019 Jan 29. Genes Chromosomes Cancer. 2019. PMID: 30520215 Review.

• Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters.

  Cremer M, Schmid VJ, Kraus F, Markaki Y, Hellmann I, Maiser A, Leonhardt H, John S, Stamatoyannopoulos J, Cremer T. Cremer M, et al. Epigenetics Chromatin. 2017 Aug 7;10(1):39. doi: 10.1186/s13072-017-0146-0. Epigenetics Chromatin. 2017. PMID: 28784182 Free PMC article.

• Remodeling of nuclear landscapes during human myelopoietic cell differentiation maintains co-aligned active and inactive nuclear compartments.

  Hübner B, Lomiento M, Mammoli F, Illner D, Markaki Y, Ferrari S, Cremer M, Cremer T. Hübner B, et al. Epigenetics Chromatin. 2015 Nov 17;8:47. doi: 10.1186/s13072-015-0038-0. eCollection 2015. Epigenetics Chromatin. 2015. PMID: 26579212 Free PMC article.

• Three-dimensional super-resolution microscopy of the inactive X chromosome territory reveals a collapse of its active nuclear compartment harboring distinct Xist RNA foci.

  Smeets D, Markaki Y, Schmid VJ, Kraus F, Tattermusch A, Cerase A, Sterr M, Fiedler S, Demmerle J, Popken J, Leonhardt H, Brockdorff N, Cremer T, Schermelleh L, Cremer M. Smeets D, et al. Epigenetics Chromatin. 2014 Apr 28;7:8. doi: 10.1186/1756-8935-7-8. eCollection 2014. Epigenetics Chromatin. 2014. PMID: 25057298 Free PMC article.

• Chromosome territories, interchromatin domain compartment, and nuclear matrix: an integrated view of the functional nuclear architecture.

  Cremer T, Kreth G, Koester H, Fink RH, Heintzmann R, Cremer M, Solovei I, Zink D, Cremer C. Cremer T, et al. Crit Rev Eukaryot Gene Expr. 2000;10(2):179-212. Crit Rev Eukaryot Gene Expr. 2000. PMID: 11186332 Review.

Cited by

• Live imaging of chromatin distribution reveals novel principles of nuclear architecture and chromatin compartmentalization.

  Amiad-Pavlov D, Lorber D, Bajpai G, Reuveny A, Roncato F, Alon R, Safran S, Volk T. Amiad-Pavlov D, et al. Sci Adv. 2021 Jun 2;7(23):eabf6251. doi: 10.1126/sciadv.abf6251. Print 2021 Jun. Sci Adv. 2021. PMID: 34078602 Free PMC article.

• Long Noncoding RNAs-Crucial Players Organizing the Landscape of the Neuronal Nucleus.

  Sas-Nowosielska H, Magalska A. Sas-Nowosielska H, et al. Int J Mol Sci. 2021 Mar 27;22(7):3478. doi: 10.3390/ijms22073478. Int J Mol Sci. 2021. PMID: 33801737 Free PMC article. Review.

• Non-coding RNAs in chromatin folding and nuclear organization.

  Razin SV, Gavrilov AA. Razin SV, et al. Cell Mol Life Sci. 2021 Jul;78(14):5489-5504. doi: 10.1007/s00018-021-03876-w. Epub 2021 Jun 11. Cell Mol Life Sci. 2021. PMID: 34117518 Free PMC article. Review.

• Chromatin arranges in chains of mesoscale domains with nanoscale functional topography independent of cohesin.

  Miron E, Oldenkamp R, Brown JM, Pinto DMS, Xu CS, Faria AR, Shaban HA, Rhodes JDP, Innocent C, de Ornellas S, Hess HF, Buckle V, Schermelleh L. Miron E, et al. Sci Adv. 2020 Sep 23;6(39):eaba8811. doi: 10.1126/sciadv.aba8811. Print 2020 Sep. Sci Adv. 2020. PMID: 32967822 Free PMC article.

• Nuclear Envelope Regulation of Oncogenic Processes: Roles in Pancreatic Cancer.

  Preston CC, Faustino RS. Preston CC, et al. Epigenomes. 2018 Sep;2(3):15. doi: 10.3390/epigenomes2030015. Epub 2018 Sep 2. Epigenomes. 2018. PMID: 31867128 Free PMC article.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Elsevier Science
  • Ovid Technologies, Inc.
  • Wiley

• Research Materials

  • NCI CPTC Antibody Characterization Program