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Interphase epichromatin: last refuge for the 30-nm chromatin fiber?

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.

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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).

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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.

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Correspondence to Donald E. Olins.

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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)

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)

Online Resource 7. Video of the tomographic volume and isosurface representation of ELCS after cryofixation and Cryo-ET, as shown in Fig. 6a, b and Insert. A criss-crossed chromatin fiber pattern can be observed (MP4 33930 KB)

Online Resource 8. Video of the tomographic volume and isosurface representation of the NE associated chromatin layer (epichromatin) after cryofixation and Cryo-ET, as shown in Fig. 6e, f and Insert. A criss-crossed chromatin fiber pattern is not apparent (MP4 69508 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)

CHEM- FIX

Online Resource 4. Schematic 3D representations of criss-crossed chromatin fibers. , 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 5. Methods employed for the cryo-electron tomography (Cryo-ET) (DOCX 19 KB)

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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

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Keywords

  • Nucleosomes
  • Epichromatin
  • Cryo-electron tomography
  • Envelope-limited chromatin sheets