Abstract
“Interphase epichromatin” describes the surface of chromatin located adjacent to the interphase nuclear envelope. It was discovered in 2011 using a bivalent anti-nucleosome antibody (mAb PL2-6), now known to be directed against the nucleosome acidic patch. The molecular structure of interphase epichromatin is unknown, but is thought to be heterochromatic with a high density of “exposed” acidic patches. In the 1960s, transmission electron microscopy of fixed, dehydrated, sectioned, and stained inactive chromatin revealed “unit threads,” frequently organized into parallel arrays at the nuclear envelope, which were interpreted as regular helices with ~ 30-nm center-to-center distance. Also observed in certain cell types, the nuclear envelope forms a “sandwich” around a layer of closely packed unit threads (ELCS, envelope-limited chromatin sheets). Discovery of the nucleosome in 1974 led to revised helical models of chromatin. But these models became very controversial and the existence of in situ 30-nm chromatin fibers has been challenged. Development of cryo-electron microscopy (Cryo-EM) gave hope that in situ chromatin fibers, devoid of artifacts, could be structurally defined. Combining a contrast-enhancing phase plate and cryo-electron tomography (Cryo-ET), it is now possible to visualize chromatin in a “close-to-native” situation. ELCS are particularly interesting to study by Cryo-ET. The chromatin sheet appears to have two layers of ~ 30-nm chromatin fibers arranged in a criss-crossed pattern. The chromatin in ELCS is continuous with adjacent interphase epichromatin. It appears that hydrated ~ 30-nm chromatin fibers are quite rare in most cells, possibly confined to interphase epichromatin at the nuclear envelope.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
Not applicable.
Code availability
Not applicable.
References
André AAM, Spruijt E (2020) Liquid-liquid phase separation in crowded environments. Int J Mol Sci 21. https://doi.org/10.3390/ijms21165908
Banani SF, Lee HO, Hyman AA, Rosen MK (2017) Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol 18:285–298. https://doi.org/10.1038/nrm.2017.7
Boulé JB, Mozziconacci J, Lavelle C (2015) The polymorphisms of the chromatin fiber. J Phys Condens Matter 27:033101. https://doi.org/10.1088/0953-8984/27/3/033101
Cai S, Böck D, Pilhofer M, Gan L (2018a) The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin. Mol Biol Cell 29:2450–2457. https://doi.org/10.1091/mbc.E18-05-0331
Cai S, Song Y, Chen C, Shi J, Gan L (2018b) Natural chromatin is heterogeneous and self-associates in vitro. Mol Biol Cell 29:1652–1663. https://doi.org/10.1091/mbc.E17-07-0449
Danev R, Buijsse B, Khoshouei M, Plitzko JM, Baumeister W (2014) Volta potential phase plate for in-focus phase contrast transmission electron microscopy. Proc Natl Acad Sci U S A 111:15635–15640. https://doi.org/10.1073/pnas.1418377111
Davies HG, Haynes ME (1975) Light- and electron-microscope observations on certain leukocytes in a teleost fish and a comparison of the envelope-limited monolayers of chromatin structural units in different species. J Cell Sci 17:263–285
Davies HG, Murray AB, Walmsley ME (1974) Electron-microscope observations on the organization of the nucleus in chicken erythrocytes and a superunit thread hypothesis for chromosome structure. J Cell Sci 16:261–299
Davies HG, Small JV (1968) Structural units in chromatin and their orientation on membranes. Nature 217:1122–1125. https://doi.org/10.1038/2171122a0
Dupraw EJ (1965) The organization of nuclei and chromosomes in honeybee embryonic cells. Proc Natl Acad Sci U S A 53:161–168. https://doi.org/10.1073/pnas.53.1.161
Eltsov M, Sosnovski S, Olins AL, Olins DE (2014) ELCS in ice: cryo-electron microscopy of nuclear envelope-limited chromatin sheets. Chromosoma 123:303–312. https://doi.org/10.1007/s00412-014-0454-0
Even-Faitelson L, Hassan-Zadeh V, Baghestani Z, Bazett-Jones DP (2016) Coming to terms with chromatin structure chromosoma 125:95–110. https://doi.org/10.1007/s00412-015-0534-9
Everid AC, Small JV, Davies HG (1970) Electron-microscope observations on the structure of condensed chromatin: evidence for orderly arrays of unit threads on the surface of chicken erythrocyte nuclei. J Cell Sci 7:35–48
Feric M, Misteli T (2021). Phase Separation in Genome Organization across Evolution Trends Cell Biol. https://doi.org/10.1016/j.tcb.2021.03.001
Finch JT, Klug A (1976) Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci U S A 73:1897–1901. https://doi.org/10.1073/pnas.73.6.1897
Fussner E et al. (2012) Open and closed domains in the mouse genome are configured as 10-nm chromatin fibres. EMBO Rep 13:992–996. https://doi.org/10.1038/embor.2012.139
Gall JG (1966) Chromosome fibers studied by a spreading technique. Chromosoma 20:221–233. https://doi.org/10.1007/bf00335209
Gibson BA et al (2019) Organization of chromatin by intrinsic and regulated phase separation. Cell 179:470-484.e421. https://doi.org/10.1016/j.cell.2019.08.037
Gould TJ, Tóth K, Mücke N, Langowski J, Hakusui AS, Olins AL, Olins DE (2017) Defining the epichromatin epitope nucleus 8:625–640. https://doi.org/10.1080/19491034.2017.1380141
Hansen JC (2012) Human mitotic chromosome structure: what happened to the 30-nm fibre? Embo J 31:1621–1623. https://doi.org/10.1038/emboj.2012.66
Haynes ME, Davies HG (1973) Observations on the origin and significance of the nuclear envelope-limited monolayers of chromatin unit threads associated with the cell nucleus. J Cell Sci 13:139–171
Hirano Y, Hizume K, Kimura H, Takeyasu K, Haraguchi T, Hiraoka Y (2012) Lamin B receptor recognizes specific modifications of histone H4 in heterochromatin formation. J Biol Chem 287:42654–42663. https://doi.org/10.1074/jbc.M112.397950
Joti Y et al. (2012) Chromosomes without a 30-nm chromatin fiber Nucleus 3:404–410. https://doi.org/10.4161/nucl.21222
Larson AG, Narlikar GJ (2018) The role of phase separation in heterochromatin formation, function, and regulation. Biochemistry 57:2540–2548. https://doi.org/10.1021/acs.biochem.8b00401
Luger K, Dechassa ML, Tremethick DJ (2012) New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? Nat Rev Mol Cell Biol 13:436–447. https://doi.org/10.1038/nrm3382
Maeshima K, Hihara S, Eltsov M (2010) Chromatin structure: does the 30-nm fibre exist in vivo? Curr Opin Cell Biol 22:291–297. https://doi.org/10.1016/j.ceb.2010.03.001
Maeshima K, Ide S, Hibino K, Sasai M (2016) Liquid-like behavior of chromatin. Curr Opin Genet Dev 37:36–45. https://doi.org/10.1016/j.gde.2015.11.006
Maeshima K, Tamura S, Hansen JC, Itoh Y (2020) Fluid-like chromatin: toward understanding the real chromatin organization present in the cell. Curr Opin Cell Biol 64:77–89. https://doi.org/10.1016/j.ceb.2020.02.016
Mahamid J et al (2016) Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science 351:969–972. https://doi.org/10.1126/science.aad8857
Mollenhauer HH (1993) Artifacts caused by dehydration and epoxy embedding in transmission electron microscopy. Microsc Res Tech 26:496–512. https://doi.org/10.1002/jemt.1070260604
Narlikar GJ (2020) Phase-separation in chromatin organization. J Biosci 45:5
Nishino Y et al. (2012) Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure. Embo J 31:1644–1653. https://doi.org/10.1038/emboj.2012.35
Olins AL, Buendia B, Herrmann H, Lichter P, Olins DE (1998) Retinoic acid induction of nuclear envelope-limited chromatin sheets in HL-60. Exp Cell Res 245:91–104. https://doi.org/10.1006/excr.1998.4210
Olins AL, Ernst A, Zwerger M, Herrmann H, Olins DE (2010a) An in vitro model for Pelger-Huët anomaly: stable knockdown of lamin B receptor in HL-60 cells. Nucleus 1:506–512. https://doi.org/10.4161/nucl.1.6.13271
Olins AL, Gould TJ, Boyd L, Sarg B, Olins DE (2020) Hyperosmotic stress: in situ chromatin phase separation. Nucleus 11:1–18. https://doi.org/10.1080/19491034.2019.1710321
Olins AL, Herrmann H, Lichter P, Olins DE (2000) Retinoic acid differentiation of HL-60 cells promotes cytoskeletal polarization. Exp Cell Res 254:130–142. https://doi.org/10.1006/excr.1999.4727
Olins AL, Ishaque N, Chotewutmontri S, Langowski J, Olins DE (2014) Retrotransposon Alu is enriched in the epichromatin of HL-60 cells. Nucleus 5:237–246. https://doi.org/10.4161/nucl.29141
Olins AL et al (2011) An epichromatin epitope: persistence in the cell cycle and conservation in evolution. Nucleus 2:47–60. https://doi.org/10.4161/nucl.2.1.13271
Olins AL, Olins DE (1979) Stereo electron microscopy of the 25-nm chromatin fibers in isolated nuclei. J Cell Biol 81:260–265. https://doi.org/10.1083/jcb.81.1.260
Olins AL, Rhodes G, Welch DB, Zwerger M, Olins DE (2010b) Lamin B receptor: multi-tasking at the nuclear envelope. Nucleus 1:53–70. https://doi.org/10.4161/nucl.1.1.10515
Olins DE, Olins AL (2003) Chromatin history: our view from the bridge. Nat Rev Mol Cell Biol 4:809–814. https://doi.org/10.1038/nrm1225
Olins DE, Olins AL (2009) Nuclear envelope-limited chromatin sheets (ELCS) and heterochromatin higher order structure. Chromosoma 118:537–548. https://doi.org/10.1007/s00412-009-0219-3
Olins DE, Olins AL (2018) Epichromatin and chromomeres: a ‘fuzzy’ perspective. Open Biol 8. https://doi.org/10.1098/rsob.180058
Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O’Shea CC (2017) ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science 357. https://doi.org/10.1126/science.aag0025
Quénet D, McNally JG, Dalal Y (2012) Through thick and thin: the conundrum of chromatin fibre folding in vivo. EMBO Rep 13:943–944. https://doi.org/10.1038/embor.2012.143
Razin SV, Gavrilov AA (2014) Chromatin without the 30-nm fiber: constrained disorder instead of hierarchical folding. Epigenetics 9:653–657 https://doi.org/10.4161/epi.28297
Robinson PJ, Fairall L, Huynh VA, Rhodes D (2006) EM measurements define the dimensions of the “30-nm” chromatin fiber: evidence for a compact, interdigitated structure. Proc Natl Acad Sci U S A 103:6506–6511. https://doi.org/10.1073/pnas.0601212103
Sanulli S et al. (2019) HP1 reshapes nucleosome core to promote phase separation of heterochromatin. Nature 575:390–394. https://doi.org/10.1038/s41586-019-1669-2
Shin Y, Brangwynne CP (2017) Liquid phase condensation in cell physiology and disease. Science 357. https://doi.org/10.1126/science.aaf4382
Shin Y et al (2018) Liquid nuclear condensates mechanically sense and restructure the genome. Cell 175:1481-1491.e1413. https://doi.org/10.1016/j.cell.2018.10.057
Wolfe SL (1965) The fine structure of isolated chromosomes. J Ultrastruct Res 12:104–112. https://doi.org/10.1016/s0022-5320(65)80010-7
Woodcock CL (1994) Chromatin fibers observed in situ in frozen hydrated sections native fiber diameter is not correlated with nucleosome repeat length. J Cell Biol 125:11–19. https://doi.org/10.1083/jcb.125.1.11
Woodcock CL, Frado LL, Rattner JB (1984) The higher-order structure of chromatin: evidence for a helical ribbon arrangement. J Cell Biol 99:42–52. https://doi.org/10.1083/jcb.99.1.42
Zhou BR et al (2019) Atomic resolution Cryo-eM structure of a native-like CENP-A nucleosome aided by an antibody fragment. Nat Commun 10:2301. https://doi.org/10.1038/s41467-019-10247-4
Funding
The University of New England, School of Pharmacy, provided space and partial support for the research of DEO and ALO. The Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany, directed by WB, provided space, support, and encouragement for the collaboration between PX, ALO, and DEO and the earlier studies of JM and MD. PX is the recipient of postdoctoral fellowships from EMBO (EMBO ALTF 401–2018).
Author information
Authors and Affiliations
Contributions
DEO, ALO conceived the experiments and wrote the paper. PX, JM and MD conducted the Cryo-ET studies and prepared the relevant figures, under the supervision of WB.
Corresponding author
Ethics declarations
Declaration of interests
The authors of this manuscript declare that all experiments comply with the current laws of the country in which they were performed.
Ethics approval
Not applicable.
Consent to participate
Not applicable.
Consent for publication
Not applicable.
Conflict of interest
The authors declare no competing interests.
Additional information
Publisher's note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Online Resource 1. Originally published in (Eltsov et al. 2014) as 412_2014_454_MOESM3_ESM.mpg Video of an isosurface representation from a stack of EM tomographic slices of Chem-fixed ELCS, first oriented to display a cross sectional view electron micrograph (Fig. 4a), then turned to display longitudinal views of the isosurface of the criss-crossed chromatin fibers running tangential to the inner nuclear membranes (Fig. 4b). Scale bar 100 nm (MPG 13000 KB)
Online Resource 2. Originally published in (Eltsov et al. 2014) as 412_2014_454_MOESM4_ESM.mpg Video of an second isosurface representation from a stack of EM tomographic slices of Chem-fixed ELCS, oriented to display the z-axis as the ordinate, with views of the criss-crossed chromatin fibers running tangential to the inner nuclear membranes. Scale bar 100 nm (MPG 10461 KB)
412_2021_759_MOESM3_ESM.docx
Online Resource 3. Schematic of two layers of criss-crossed chromatin fibers in a segment of Chem-fixed ELCS (e.g., Fig 4). Each fiber is represented as a string with clusters of nucleosomes (thick regions) alternating with thin regions. Each layer is drawn with parallel chromatin fibers. The two layers intermingle in a criss-crossed pattern. The top window of the schematic drawing attempts to show a density projection along the fibers from the chromatin fiber cut ends, as in Fig. 4a and Online Resource 1 (DOCX 7367 KB)
412_2021_759_MOESM4_ESM.docx
Online Resource 4. Schematic 3D representations of criss-crossed chromatin fibers. CHEM- FIX, chemically-fixed, dehydrated and plastic embedded chromatin fibers, yielding ELCS with INM-to-INM separation of ~30 nm. CRYO-FIX, frozen hydrated chromatin fibers, yielding ELCS with INM-to-INM separation of ~60 nm. The “cylindrical” representations of the chromatin fibers do not imply regularity, but only represent “boundaries” for the individual fibers (DOCX 291 KB)
Online Resource 6. Video of tomographic volume of a nuclear lobule connected to ELCS in an HL-60/S4 granulocyte after cryofixation and Cryo-ET, region shown in Fig. 5 (MOV 19458 KB)
Rights and permissions
About this article
Cite this article
Xu, P., Mahamid, J., Dombrowski, M. et al. Interphase epichromatin: last refuge for the 30-nm chromatin fiber?. Chromosoma 130, 91–102 (2021). https://doi.org/10.1007/s00412-021-00759-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00412-021-00759-8