ABSTRACT
Ever since the discovery of the nucleosome in 1974, scientists have stumbled upon discrete particles in which DNA is wrapped around histone complexes of different stoichiometries: octasomes, hexasomes, tetrasomes, "split" half-nucleosomes, and, recently, bona fide hemisomes. Do all these particles exist in vivo? Under what conditions? What is their physiological significance in the complex DNA transactions in the eukaryotic nucleus? What are their dynamics? This review summarizes research spanning more than three decades and provides a new meaning to the term "nucleosome." The nucleosome can no longer be viewed as a single static entity: rather, it is a family of particles differing in their structural and dynamic properties, leading to different functionalities.
Subject(s)
Nucleosomes/metabolism , Nucleosomes/physiology , Protein Multimerization/physiology , Animals , DNA/chemistry , DNA/metabolism , Histones/chemistry , Histones/metabolism , Humans , Models, Biological , Models, Molecular , Multigene Family , Nucleic Acid Conformation , Nucleosomes/chemistry , Nucleosomes/genetics , Protein BindingABSTRACT
Accessibility of nucleosomal DNA to protein factor binding is ensured by at least three mechanisms: post-synthetic modifications to the histones, chromatin remodeling, and spontaneous unwrapping of the DNA from the histone core. We have previously used single-pair fluorescence resonance energy transfer (spFRET) experiments to investigate long-range conformational fluctuations in nucleosomal DNA (Tomschik M, Zheng H, van Holde K, Zlatanova J, Leuba SH in Proc Natl Acad Sci USA 102(9):3278-3283, 2005). Recent work has drawn attention to a major artifact in such studies due to photoblinking of the acceptor fluorophore. We have now used formaldehyde-crosslinked nucleosomes and imaging in the presence of Trolox, an efficient triplet-state quencher that suppresses photoblinking, to reevaluate our previous conclusions. Careful analysis of the data indicates that most of the events previously characterized as nucleosome 'opening' must have corresponded to photoblinking. There is, nevertheless, evidence for the existence of infrequent, rapid opening events.
Subject(s)
Fluorescence Resonance Energy Transfer , Nucleosomes/chemistry , Nucleosomes/metabolism , Chromans/chemistry , DNA/chemistry , Formaldehyde/chemistry , Mercaptoethanol/chemistry , Nucleic Acid Conformation , Time FactorsABSTRACT
The structure of the "30 nm chromatin fiber", as observed in vitro, has been a matter of controversy for 30 years. Recent studies with new and more powerful techniques give some promise for resolution. However, this will not necessarily inform us as to the in vivo structure, which may be both heteromorphic and dynamic. In this chapter, we briefly review the older conjectures and some more recent studies of special interest. We attempt to point out the remaining contradictions and hopeful lines of future research.
Subject(s)
Chromatin/chemistry , Chromatin/ultrastructure , Computer Simulation , Crystallography, X-Ray , Microscopy, Atomic Force , Microscopy, Electron , Models, Molecular , Protein Conformation , Protein Folding , Protein Structure, SecondaryABSTRACT
The nucleosome core particle, the basic repeated structure in chromatin fibers, consists of an octamer of eight core histone molecules, organized as dimers (H2A/H2B) and tetramers [(H3/H4)2] around which DNA wraps tightly in almost two left-handed turns. The nucleosome has to undergo certain conformational changes to allow processes that need access to the DNA template to occur. By single-pair fluorescence resonance energy transfer, we demonstrate fast, long-range, reversible conformational fluctuations in nucleosomes between two states: fully folded (closed), with the DNA wrapped around the histone core, or open, with the DNA significantly unraveled from the histone octamer. The brief excursions into an extended open state may create windows of opportunity for protein factors involved in DNA transactions to bind to or translocate along the DNA.
