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

Area of Science:

• Cell Biology
• Genomics

Background:

• Chromatin compaction influences macromolecule accessibility to DNA.
• Conventional microscopy suggests minor differences between active (ANC) and inactive (INC) nuclear compartments.

Purpose of the Study:

• To map nuclear landscapes with true-to-scale DNA densities.
• To investigate macromolecular assembly accessibility in different nuclear compartments.

Main Methods:

• Single-molecule localization microscopy (SMLM) for high-resolution DNA density mapping.
• Electron spectroscopic imaging.
• Microinjection of fluorescent nanobeads into living cell nuclei.

Main Results:

• Revealed true-to-scale DNA densities ranging from <5 to >300 Mbp/μm³.
• Demonstrated localization and movement of transcription assemblies within the ANC.
• Showed exclusion of assemblies from the INC.

Conclusions:

• Significant chromatin compaction differences exist between ANC and INC.
• High-resolution mapping reveals distinct nuclear environments impacting macromolecular accessibility.