Solution structure of the isolated histone H2A-H2B heterodimer

In eukaryotes, DNA is stably stored in the highly ordered structure chromatin. The fundamental repeating structural unit within chromatin is the nucleosome, which comprises approximately 146 bp of DNA wrapped around a histone octamer, containing two dimers of H2A-H2B and one tetramer of (H3-H4)21. The nucleosome is assembled in a stepwise manner: a tetramer of (H3-H4)2 is first deposited on the central part of DNA; two heterodimers of H2A-H2B are then added to the peripheral parts of DNA, and the nucleosome is completed2. During gene transcription, H2A-H2B seems to dynamically detach from and assemble on the nucleosome with the aid of histone chaperones3, and the isolated H2A-H2B heterodimer is structurally stable. A structural comparison of the isolated H2A-H2B and its counterpart in the nucleosome would help to elucidate both the function of various histone chaperones and nucleosome dynamics4. To date, the structure of H2A-H2B dimer alone has not been solved, whereas two structures of the H2A-H2B dimer within the nucleosome have been available for some time5,6,7,8,9. In addition, structures of H2A-H2B or H2A.Z-H2B with a histone chaperone are available; however, the tail of histone H2A or H2A.Z and that of H2B are not present in these complexes, for example, FACT Spt16M linked to H2B(amino acids 24–122)–H2A(13–106)10, Chz1 bound to H2B(37–131) linked to H2A.Z(29–125)11, Swr1 bound to H2B(36–130) linked to H2A.Z(22–118)12 and ANP32E bound to H2B(30–125)–H2A.Z(18–127)13. Histone tails play important roles in the dynamic functions of chromatin through posttranslational modifications such as acetylation, phosphorylation and methylation14,15,16,17,18,19. Here, we have determined the tertiary structure of the full-length H2A-H2B in isolation by NMR coupled with the CS-Rosetta procedure20,21. The isolated H2A-H2B heterodimer comprises 256 amino acids with long disordered tails, which is big enough for the CS-Rosetta calculation22; as a result, the Rosetta protocols, AbinitioRelax23 and FloppyTail24, were used to obtain structures of H2A-H2B in isolation. The calculated structures show that both histones contain a four-helix core, arranged as α1–β1–α2–β2–α3–αC, similar to their corresponding structures in the nucleosome. Outside the core region of H2A, however, the N-terminal αN helix, C-terminal β3 strand and 310 helix that are present in the nucleosome are entirely disordered in the isolated H2A-H2B, instead becoming long disordered tails of about 30 amino acids at both the N- and C-termini. The αN helix, β3 strand and 310 helix of H2A are stabilized in the nucleosome by interactions with DNA or histones H3-H4. Without these interactions, the αN helix, β3 strand and 310 helix regions become disordered in the isolated H2A-H2B dimer. Furthermore, the calculated structures of H2A-H2B indicate that the positions of the H2A α1 and H2B αC helices are not well fixed as compared with other helices, suggesting that these two helices dynamically fluctuate in solution. To reveal the dynamics of H2A-H2B, we performed hydrogen-deuterium (H/D) exchange25, fast hydrogen exchange26 and {1H}-15N hetero-nuclear NOE27 experiments on H2A-H2B. Comparison of these data with the calculated structures suggests that the long disordered tails of H2A-H2B form some dynamic conformations.