Chaperoning histones during DNA replication and repair

Abstract

Nuclear DNA is tightly packaged into chromatin, which profoundly influences DNA replication, transcription, repair, and recombination. The extensive interactions between the basic histone proteins and acidic DNA make the nucleosomal unit of chromatin a highly stable entity. For the cellular machinery to access the DNA, the chromatin must be unwound and the DNA cleared of histone proteins. Conversely, the DNA has to be repackaged into chromatin afterward. This review focuses on the roles of the histone chaperones in assembling and disassembling chromatin during the processes of DNA replication and repair.

Figure 1. Anatomy of the nucleosome and histone chaperones

A. Unraveling of the nucleosomal DNA to indicate which regions of the 147 bp of DNA are organized by which histone proteins. The surface of the histones closest to the DNA is the one that binds to the DNA. The interactions within the stable dimer units have been maintained, but all other histone-histone interactions have been dissolved. The orange dotted line indicates the H3/H4 tetramerization interface. The N-terminal alpha helix of H3 interacts with a different DNA gyre from that which the remainder of the H3/H4 dimer interacts. PDB 1KX5. B. The nucleosome core particle (Luger et al., 1997), Protein Data Bank(PDB): 1KX5. C. The H3/H4 dimer binds to the Asf1 histone chaperone via the H3/H4 tetramerization interface (English et al., 2006), PDB: ID2Hue. D. CAF-1 p55 bound to the N-terminal alpha helix of histone H4 (Song et al., 2008), PDB 3C99. E. Chz1 bound to H2AZ-H2B (Zhou et al., 2008), PDB: 2JSS. F. Nucleoplasmin pentamer that binds H2A/H2B (Dutta et al., 2001), PDB: 1K5J. G. NAP1 that binds H2A/H2B (Park and Luger, 2006), PDB: 2AYU. H. N-terminus of FACT Spt16 that binds to H3/H4 (Stuwe et al., 2008), PDB: 3CB5.

Figure 2. Replication coupled chromatin assembly and disassembly

The histone chaperones, but not the ATP-dependent chromatin remodelers involved in these processes are shown. Once the new histones have been post-translationally modified to adopt the pattern carried by the parental histones, they are considered parental histones and are colored accordingly. Question marks indicate steps that are somewhat speculative.

Figure 3. Incorporation of the centromere specific histone variant CENP-A

Parental CENP-A is passed to the newly-replicated DNA through DNA replication, but de novo incorporation of CENP-A, mediated by the histone chaperones HJURP and RbAp48 does not occur until after chromosome segregation to the daughter cells.

Figure 4. H2A histone variants play roles unique to DNA repair

The loss of human histone H2A variant H2AX from chromatin is prevented by ADP-ribosylation of the FACT histone chaperone by PARP1. Rapidly after DNA damage, yeast Chz1 and SWR1 incorporate dimers of H2A.Z/H2B to promote DNA resection of the DNA ends. Phosphorylated H2AX is removed from DNA by the human FACT histone chaperone, and H2A is inserted in its place.