Structural basis of histone H2A–H2B recognition by the essential chaperone FACT


Facilitates chromatin transcription (FACT) is a conserved histone chaperone that reorganizes nucleosomes and ensures chromatin integrity during DNA transcription, replication and repair1,2,3,4,5,6. Key to the broad functions of FACT is its recognition of histones H2A–H2B (ref. 2). However, the structural basis for how histones H2A–H2B are recognized and how this integrates with the other functions of FACT, including the recognition of histones H3–H4 and other nuclear factors, is unknown. Here we reveal the crystal structure of the evolutionarily conserved FACT chaperone domain Spt16M from Chaetomium thermophilum, in complex with the H2A–H2B heterodimer. A novel ‘U-turn’ motif scaffolded onto a Rtt106-like module7,8,9,10 embraces the α1 helix of H2B. Biochemical and in vivo assays validate the structure and dissect the contribution of histone tails and H3–H4 towards Spt16M binding. Furthermore, we report the structure of the FACT heterodimerization domain that connects FACT to replicative polymerases. Our results show that Spt16M makes several interactions with histones, which we suggest allow the module to invade the nucleosome gradually and block the strongest interaction of H2B with DNA. FACT would thus enhance ‘nucleosome breathing’ by re-organizing the first 30 base pairs of nucleosomal histone–DNA contacts. Our snapshot of the engagement of the chaperone with H2A–H2B and the structures of all globular FACT domains enable the high-resolution analysis of the vital chaperoning functions of FACT, shedding light on how the complex promotes the activity of enzymes that require nucleosome reorganization.

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Figure 1: The histone chaperone complex FACT recognizes the histone H2A-H2B heterodimer through the Spt16M domain of Spt16.
Figure 2: A conserved, hydrophobic groove in the U-turn motif of Spt16M interacts with a hydrophobic patch of H2B.
Figure 3: Multiple interactions support histone binding by FACT, but Spt16M-mediated contacts are key to chaperoning function.
Figure 4: The heterodimerization domain of FACT mediates interaction with the DNA replication machinery.

Accession codes


Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited with the Protein Data Bank under accession codes 4KHA (Spt16M–H2A–H2B), 4KHO (Spt16M) and 4KHB (Spt16D–Pob3N).


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We thank J. Basquin, E. Conti, the MPI for Biochemistry and staff at beamlines Swiss Light Source PXII and European Synchrotron Radiation Facility ID23 for crystallographic support, P. Becker, S. Hake, J. Müller and G. Schotta for H3 peptides, and F. Bonneau, P. Cramer, T. Gibson, D. Gilmour, J. Griesenbeck, C. Häring, M. Hothorn, G. Jankevicius, D. Mokranjac, R. Russell, I. Schäfer, K. Scheffzek, C. Schultz, F. Wieland, M. Winter and E. Wolf for discussion. EMBL, LMU Munich, EC FP6 Marie Curie RTN Chromatin Plasticity (to A.G.L.) and Boehringer Ingelheim Fonds (to M.Ho. and F.H.) funded this research.

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Crystallography on Spt16M–H2A–H2B was conducted by M.Ho., M.Ha. and F.H.; T.S. determined the structure of free Spt16M and Spt16D–Pob3N, with assistance from M.Ho. and E.T.Z.; M.Ho. and T.S. conducted biochemical assays; A.B. conducted the chaperoning assay; M.Ho., T.S. and B.N. purified proteins; M.Ho., C.K. and T.S. conducted yeast work; M.Ho. and V.R. carried out ITC; S.A. and E.H. provided C. thermophilum cDNA sequences; M.Ho., T.S., M.Ha., A.B. and A.G.L. designed the study; M.Ha. and A.G.L. supervised the work; M.H.o, M.Ha., A.B. and A.G.L. wrote the manuscript.

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Correspondence to Andreas G. Ladurner.

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Hondele, M., Stuwe, T., Hassler, M. et al. Structural basis of histone H2A–H2B recognition by the essential chaperone FACT. Nature 499, 111–114 (2013).

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