Real-Time Multistep Asymmetrical Disassembly of Nucleosomes and Chromatosomes Visualized by High-Speed Atomic Force Microscopy
[1];
[2];
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California 94720, United States, Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
- Laboratoire Photonique Numérique et Nanosciences, LP2N UMR 5298, Université de Bordeaux, Institut d’Optique, CNRS, F-33400 Talence, France
- Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California 94720, United States, Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States, Kavli Energy Nanoscience Institute, University of California, Berkeley, California 94720, United States
During replication, expression, and repair of the eukaryotic genome, cellular machinery must access the DNA wrapped around histone proteins forming nucleosomes. These octameric protein·DNA complexes are modular, dynamic, and flexible and unwrap or disassemble either spontaneously or by the action of molecular motors. Thus, the mechanism of formation and regulation of subnucleosomal intermediates has gained attention genome-wide because it controls DNA accessibility. Here, we imaged nucleosomes and their more compacted structure with the linker histone H1 (chromatosomes) using high-speed atomic force microscopy to visualize simultaneously the changes in the DNA and the histone core during their disassembly when deposited on mica. Furthermore, we trained a neural network and developed an automatic algorithm to track molecular structural changes in real time. Our results show that nucleosome disassembly is a sequential process involving asymmetrical stepwise dimer ejection events. The presence of H1 restricts DNA unwrapping, significantly increases the nucleosomal lifetime, and affects the pathway in which heterodimer asymmetrical dissociation occurs. We observe that tetrasomes are resilient to disassembly and that the tetramer core (H3·H4)2 can diffuse along the nucleosome positioning sequence. Tetrasome mobility might be critical to the proper assembly of nucleosomes and can be relevant during nucleosomal transcription, as tetrasomes survive RNA polymerase passage. These findings are relevant to understanding nucleosome intrinsic dynamics and their modification by DNA-processing enzymes.
- Research Organization:
- University of California, Berkeley, CA (United States)
- Sponsoring Organization:
- USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH)
- Grant/Contract Number:
- AC02-05CH11231; R01GM032543
- OSTI ID:
- 2251553
- Alternate ID(s):
- OSTI ID: 2282861
- Journal Information:
- ACS Central Science, Journal Name: ACS Central Science Vol. 10 Journal Issue: 1; ISSN 2374-7943
- Publisher:
- American Chemical SocietyCopyright Statement
- Country of Publication:
- United States
- Language:
- English
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