As a replication fork passes through chromatin, the histones are transiently displaced leaving about 600 nucleotide pairs of non-nucleosomal DNA in its wake. The reestablishment of nucleosomes behind a moving fork occurs in an intriguing way. When a nucleosome is traversed by a replication fork, the histone octamer appears to be broken into an H3-H4 tetramer and two H2A-H2B dimers (discussed in Chapter 4). The H3-H4 tetramer remains loosely associated with DNA and is distributed at random to one or the other daughter duplex, but the H2A-H2B dimers are released completely from DNA. Freshly made H3-H4 tetramers are added to the newly synthesized DNA to fill in the “spaces,” and H2A-H2B dimers—half of which are old and half new—are then added at random to complete the nucleosomes (Figure 5–32). The formation of new nucleosomes behind a replication fork has an important consequence for the process of DNA replication itself. As DNA polymerase δ discontinuously synthesizes the lagging strand (see pp. 253–254), the length of each Okazaki fragment is determined by the point at which DNA polymerase δ is blocked by a newly formed nucleosome. This tight coupling between nucleosome duplication and DNA replication explains why the length of Okazaki fragments in eukaryotes (~200 nucleotides) is approximately the same as the nucleosome repeat length.
262 Chapter 5:  DNA Replication, Repair, and Recombination
H2A-H2B dimer displaced in front of replication fork
The orderly and rapid addition of new H3-H4 tetramers and H2A-H2B dimers behind a replication fork requires histone chaperones (also called chromatin assembly factors). These multisubunit complexes bind the highly basic histones and release them for assembly only in the appropriate context. The histone chaperones, along with their cargoes, are directed to newly replicated DNA through a specific interaction with the eukaryotic sliding clamp called PCNA (see Figure 5–32B). These clamps are left behind moving replication forks and remain on the DNA long enough for the histone chaperones to complete their tasks.
Telomerase Replicates the Ends of Chromosomes
We saw earlier that synthesis of the lagging strand at a replication fork must occur discontinuously through a backstitching mechanism that produces short DNA fragments. This mechanism encounters a special problem when the replication fork reaches an end of a linear chromosome. The final RNA primer synthesized on the lagging-strand template cannot be replaced by DNA because there is no 3ʹ-OH end available for the repair polymerase. Without a mechanism to deal with this problem, DNA would be lost from the ends of all chromosomes each time a cell divides.
Bacteria solve this “end-replication” problem by having circular DNA molecules as chromosomes (see Figure 5–24). Eukaryotes solve it in a different way: they have specialized nucleotide sequences at the ends of their chromosomes that are incorporated into structures called telomeres (discussed in Chapter 4). Telomeres contain many tandem repeats of a short sequence that is similar in organisms as diverse as protozoa, fungi, plants, and mammals. In humans, the sequence of the repeat unit is GGGTTA, and it is repeated roughly a thousand times at each telomere.