Introduction to the Chromatin

Chromatin has a compact organization in which most DNA sequences are structurally inaccessible and functionally inactive.
Within this mass is the minority of active sequences. What is the general structure of chromatin, and what is the difference between active and inactive sequences? The fundamental subunit of chromatin has the same type of design in all eukaryotes. The nucleosome contains about 200 base pairs (bp) of DNA, organized by an octamer of small, basic proteins into a beadlike structure. The protein components are histones. They form an interior core; the DNA lies on the surface of the particle. Additional regions of the histones, known as the histone tails, extend from the surface. Nucleosomes are an invariant component of euchromatin and heterochromatin in the interphase nucleus and of mitotic chromosomes. The nucleosome provides the first level of organization, compacting the DNA about 6-fold over the length of naked DNA, resulting in a “beads-on-a-string” fiber of approximately 10 nm in diameter. Its components and structure are well characterized.
The secondary level of organization involves interactions between nucleosomes of the 10-nm fiber, leading to more condensed chromatin fibers. Biochemical studies have shown that nucleosomes can assemble into helical arrays that form a fiber of approximately 30 nm in diameter. The structure of this fiber requires the histone tails and is stabilized by linker histones.
Whether the 30-nm fiber is a dominant feature of chromatin within cells remains a topic of debate.
The final, tertiary level of chromatin organization requires the further folding and compacting of chromatin fibers into the 3D structures of interphase chromatin or mitotic chromosomes. This results in about 1,000-fold linear compaction in euchromatin, cyclically interchangeable with packing into mitotic chromosomes to achieve an overall compaction of up to 10,000-fold.
Heterochromatin generally maintains this approximately 10,000-fold compaction in both interphase and mitosis.
In this chapter, we describe the structure of and relationships between these levels of organization to characterize the events involved in cyclical packaging, replication, and transcription.
Association with additional proteins, as well as modifications of existing chromosomal proteins, is involved in changing the structure of chromatin. Replication and transcription, and most DNA repair processes, require unwinding of DNA, and thus first involve an unfolding of the structure that allows the relevant enzymes to manipulate the DNA. This is likely to involve changes in all levels of organization.
When chromatin is replicated, the nucleosomes must be reproduced on both daughter duplex molecules. In addition to asking how the nucleosome itself is assembled, we must inquire what happens to other proteins present in chromatin. Replication disrupts the structure of chromatin, which indicates that it poses a problem for maintaining regions with specific structure but also offers an opportunity to change the structure.
The mass of chromatin contains up to twice as much protein as DNA. Approximately half of the protein mass is accounted for by the nucleosomes. The mass of RNA is less than 10% of the mass of DNA. Much of the RNA consists of nascent transcripts still associated with the template DNA.
The nonhistones include all the proteins found in chromatin except the histones. They are more variable between tissues and species, and they comprise a smaller proportion of the mass than the histones. They also comprise a much larger number of proteins, so that any individual protein is present in amounts much smaller than any histone. The functions of nonhistone proteins include control of gene expression and higher-order structure. Thus, RNA polymerase can be considered to be a prominent nonhistone. The high-mobility group (HMG) proteins comprise a discrete and well-defined subclass of nonhistones (at least some of which are transcription factors).