Analytical Ultracentrifugation of Chromatin

The ability of analytical ultracentrifugation to elucidate chromatin structure/function relationships originates directly from its capacity to accurately measure key structural properties of complex macromolecular assemblies in solution. Figure 1 schematically illustrates the complex nature of chromatin. Newly replicated
DNA
is wrapped around core histone octamers spaced at approx 200 bp intervals to form nucleosomal arrays, which then interact with linker histones and numerous other nonhistone chromosomal proteins to form “chromatin.” Chromatin is conformationally dynamic, undergoing a number of short-range and long-range folding transitions to produce highly condensed interphase chromosomal fibers (Fig. 1 ). For short chromatin fragments studied in vitro, fiber condensation manifests both in the form of intramolecular conformational changes and reversible oligomerization (
1
–
4
). In addition, the structure of chromatin fibers and functions such as transcription and replication are irrevocably linked; any given region of a chromosomal fiber can be either functionally active or inactive depending on both its specific complement of chromatin-associated proteins and its overall state of condensation (
1
,
2
). Consequently, to biochemically characterize chromatin structure/function relationships in vitro, one must be able to analyze both the intramolecular conformational dynamics and intermolecular interactions of an exceedingly complex macromolecular assembly (e.g., a 12-mer nucleosomal array containing one H1 molecule per nucleosome consists of >100 proteins and 2400 bp of DNA, has a molecular mass of approx 3.5�10
6
D, yet represents only roughly one millionth of an intact eukaryotic chromosome.)
Fig. 1.
Schematic illustration of the hierarchical relationships between DNA, chromatin, and interphase chromosomal fibers.