True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin

• Published in: Cell reports (Cambridge) Vol. 42; no. 6; p. 112567
• Main Authors: Gelléri, Márton, Chen, Shih-Ya, Hübner, Barbara, Neumann, Jan, Kröger, Ole, Sadlo, Filip, Imhoff, Jorg, Hendzel, Michael J., Cremer, Marion, Cremer, Thomas, Strickfaden, Hilmar, Cremer, Christoph
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 27-06-2023; Elsevier
• Subjects: active and inactive nuclear compartments; ANC; CP: Molecular biology; electron spectroscopic imaging; ESI; INC; microinjected nanobeads; quantitative image analysis; single molecule localization microscopy; SMLM; true-to-scale DNA density maps; Voronoi tessellation; microinjected nanobeads; Voronoi tessellation; ANC; CP: Molecular biology; active and inactive nuclear compartments; ESI; electron spectroscopic imaging; true-to-scale DNA density maps; SMLM; single molecule localization microscopy; INC; quantitative image analysis
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2023.112567

Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based on fluorescence microscopy with conventional resolution, however, suggest only modest compaction differences (∼2–10×) between the active nuclear compartment (ANC) and inactive nuclear compartment (INC). Here, we present maps of nuclear landscapes with true-to-scale DNA densities, ranging from <5 to >300 Mbp/μm3. Maps are generated from individual human and mouse cell nuclei with single-molecule localization microscopy at ∼20 nm lateral and ∼100 nm axial optical resolution and are supplemented by electron spectroscopic imaging. Microinjection of fluorescent nanobeads with sizes corresponding to macromolecular assemblies for transcription into nuclei of living cells demonstrates their localization and movements within the ANC and exclusion from the INC.
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•Maps of nuclear landscapes at ∼20 nm lateral and ∼100 nm axial optical resolution•Absolute DNA densities range from <5 Mbp/μm3 in the ANC to >300 Mbp/μm3 in the INC•Based on modeling, DNA densities >40 Mbp/μm3 are provisionally attributed to the INC•Movements of microinjected nanobeads in nuclei of living cells are restricted to the ANC
Gelléri et al. report major differences of absolute DNA densities between active (ANCs) and inactive nuclear compartments (INCs) in human and mouse cell nuclei and demonstrate that movements of microinjected fluorescent nanobeads with sizes corresponding to functional macromolecular machineries are restricted to the ANC.