Unexpected binding motifs for subnucleosomal particles revealed by atomic force microscopy.

Area of Science:

• Molecular Biology
• Biophysics
• Chromatin Structure

Background:

• Nucleosomes are the fundamental units of chromatin, organizing DNA within the nucleus.
• The precise structure and compaction of nucleosome arrays influence gene regulation.
• Understanding nucleosome organization is crucial for deciphering cellular processes.

Purpose of the Study:

• To investigate the structural organization of nucleosomes in reconstituted DNA arrays.
• To analyze nucleosome compaction levels and their relationship with DNA binding.
• To characterize subnucleosomal particles and dynamic DNA loop movements.

Main Methods:

• Tapping mode atomic force microscopy (AFM) was employed to visualize nucleosome arrays.
• Experiments were conducted in both air and liquid environments.
• Reconstitution ratios of histone octamers to DNA were varied to control compaction.

Main Results:

• Extended 'beads-on-a-string' structures were observed at lower histone-to-DNA ratios, with some particles showing ~50 nm DNA binding and others ~25 nm.
• Particles with ~25 nm DNA binding were identified as likely subnucleosomal particles lacking histone dimers.
• Higher reconstitution ratios resulted in compact arrays with 12 nucleosome core particles, exhibiting dynamic DNA loop protrusions in liquid.

Conclusions:

• Nucleosome arrays exhibit distinct structural states dependent on histone-to-DNA ratios.
• Subnucleosomal particles represent a structural variant within nucleosome arrays.
• Dynamic DNA loop movements in compact arrays suggest potential roles in chromatin function.