The histone chaperone FACT: structural insights and mechanisms for nucleosome reorganization

Abstract

Changes in chromatin architecture induced by epigenetic mechanisms are essential for normal cellular processes such as gene expression, DNA repair, and cellular division. Compact chromatin presents a barrier to these processes and is highly regulated by epigenetic markers binding to components of the nucleosome. Histone modifications directly influence chromatin dynamics and facilitate recruitment of additional factors such as chromatin remodelers and histone chaperones. One member of this last class of factors, FACT (facilitates chromatin transcription), is categorized as a histone chaperone critical for nucleosome reorganization during replication, transcription, and DNA repair. Significant discoveries regarding the role of histone chaperones and specifically FACT have come over the past dozen years from a number of independent laboratories. Here, we review the structural and biophysical basis for FACT-mediated nucleosome reorganization and discuss up-to-date models for FACT function.

FIGURE 1.

Domain architecture and structural alignment of the h/yFACT complexes. The hFACT heterodimeric complex is composed of the hSpt16 (cyan) and SSRP1 (dark green) subunits. Dimerization is accomplished through specific interactions between adjacent DDs in Spt16 and SSRP1/Pob3. The yPob3 (light green) protein is analogous to the SSRP1 protein and combines with ySpt16 and the HMG domain-containing protein Nhp6 to form the yFACT complex. Structural alignments of the h/ySpt16 subunits and SSRP1/Pob3-Nhp6 subunits are based upon previous limited proteolysis experiments and functional analysis of truncated FACT constructs (11, 20, 22, 23).

FIGURE 2.

Structural catalog of the individual domains in FACT with respect to their location in the overall architecture of the complex. Upper panel, the Spt16 subunit of FACT is shown in blue with the NTD displayed as a ribbon diagram from the crystal structure of the ySpt16 NTD (22). The structure reveals an aminopeptidase-like peptide-binding fold suitable for interaction with histone tails. The structures of the remaining domains within h/ySpt16 are presently unknown. Lower panel, the known structures of the Pob3 subunit of FACT are displayed as respective domains in the Pob3 molecule. The NTD/DD and MD present similar PH ligand-binding domains (NTD/DD, single; and MD, double) (Protein Data Bank code 3F5R) (19). The structure of Nhp6a in complex with DNA is also shown (green) and is aligned with the HMG domain from SSRP1 (orange) (29, 30). Structures for remaining SSRP1 domains analogous to those shown for Pob3 are unavailable.

FIGURE 3.

Dual models for FACT-mediated nucleosome reorganization. The dimer eviction model proceeds through the schematic in steps 1a, 2a, and 3a. In step 1a, the FACT complex binds to the nucleosome, which is thought to be dependent upon the acidic CTD of Spt16 (13) and the N-terminal tails of the core histones (7). Next (step 2a), the FACT complex binds and evicts a single H2A-H2B dimer, creating a hexasome structure. The last step (step 3a) reinserts the evicted H2A-H2B dimer (after the cellular machinery has performed the necessary function, i.e. transcription, replication, or DNA repair) to restore a complete nucleosome. The global accessibility/non-eviction model progresses through steps 1b, 2b, and 3b. This model is also shown using yFACT, which utilizes numerous copies of Nhp6 to recognize and bind nucleosomes in the first step (step 1b) (18). In step 2b, the ySpt16-Pob3 complex is then recruited to the Nhp6-bound nucleosome, and binding induces gross conformational changes and accessibility within the nucleosome but without H2A-H2B dimer eviction (7). The H2A-H2B dimer remains tethered to the nucleosome via FACT, which facilitates reinsertion after relevant cellular processes have concluded (step 3b). Although the latter model utilizes yFACT, the overall mechanism driving global accessibility without dimer eviction could also be applicable to metazoan forms of FACT.