Research ArticleSTRUCTURAL BIOLOGY

Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies

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Science Advances  08 Jan 2021:
Vol. 7, no. 2, eabd4413
DOI: 10.1126/sciadv.abd4413
  • Fig. 1 A triangle-shaped HDAC complex and its size heterogeneity were captured by cryo-EM.

    (A) Domain organization of HDAC protomer complex (HDAC-PC) subunits. (B) Representative 2D class averages of uncross-linked and BS3–cross-linked HDAC complexes. (C) A 3.11-Å-resolution cryo-EM map (left) and cartoon representation (right) of HDAC-PC. The subunit color code is used throughout.

  • Fig. 2 Nucleosome recognition by the class II HDAC complex.

    (A) EMSA (top) and MST analysis (bottom) of HDAC-PC and its variant carrying Hda1 K664A/R666A/K667A/K668A, Hda2 K216A, and Hda3 K98A/R103A/K166A/K168A/Q169A/K170A binding to unmodified nucleosome. A dissociation constant (KD) was measured from three independent replicates (shown as means ± SD). bp, base pairs. (B) Representative 2D classes of HDAC-PC bound to nucleosome. (C) Three views of cryo-EM reconstruction of HDAC-PC in complex with nucleosome at a resolution of 4.43 Å (left) and ribbon diagram of the HDAC-nucleosome complex with cryo-EM map (far-right).

  • Fig. 3 Multiple contacts with DNA and histone H2B orient HDAC-PC on the nucleosome.

    (A) Two views of a cartoon representation of HDAC-PC bound to nucleosome (left) and close-up views of the interfaces between HDAC-PC and nucleosome. Two histone H2Bs are indicated by arrows. (B) Overview of recognition of histone H2B N-terminal tail by HDAC-PC.

  • Fig. 4 The class II HDAC complex is enriched at the nucleosome by dimerization.

    (A) Representative 2D class averages of the uncross-linked HDAC-DC-nucleosome complex. (B) Stereo views of cryo-EM reconstruction of HDAC-DC in complex with nucleosome at a resolution of 10.60 Å (left) and ribbon diagrams of the HDAC-DC-nucleosome complex with cryo-EM map (far right). (C) Overlay of HDAC-DC with HDAC-PC observed in the nucleosome-bound complexes. Two nucleosomes (dashed trapezoid) are superimposed. (D) Relative domain movements within one HDAC-PC upon asymmetric dimerization with the other HDAC-PC in the nucleosome-bound state. A surface representation of the constructed model is shown. (E) Overview of recognition of histone H2B, H3, and/or H4 N-terminal tails by two individual HDAC-PCs in the nucleosome-bound HDAC-DC.

  • Fig. 5 The higher-order assembly is a nucleosome binding–deficient HDAC complex.

    (A) Cryo-EM map of the 1.3-MDa HDAC-TC at a resolution of 3.80 Å. (B) Two orthogonal views of a cartoon representation of HDAC-TC. (C) Magnified views showing tetramerization interfaces between NTD3 and C2 symmetry–related NTD2 (NTD2sym). The HDAC-TC structure was built by rigid-body fitting of four high-resolution structures of the HDAC-PC followed by PHENIX real-space refinement. (D) Quaternary structure (left) and subunit distribution (top right and middle) of HDAC-TC and overlay of HDAC-DC with C2 dimer observed in the halves of HDAC-TC (bottom center). (E) In vitro deacetylase activities of purified HDAC complexes with and without TSA. The assay was performed in triplicate, and the error bars are the SD of the data (n = 3).

  • Fig. 6 Multisubunit class I and II HDAC complexes share a general regulatory mechanism in HDAC activity.

    (A) Ribbon diagrams of the yeast Hda1 HDACD-Hda2 NTD2/CCD2, Hda1 HDACD-Hda3 NTD3, human class I HDAC3 bound to SMRT-DAD (PDB 4A69), and human class I HDAC1 in complex with MTA1 (PDB 4BKX) are illustrated on the basis of superposition. The multiple-sequence alignment of HDAC from the yeast and human is shown. (B) Superposition in stereo of one Hda1 HDACD with the other Hda1 HDACD and class I HDACs (PDB 4A69 and 5THU for HDAC3-SMRT-DAD and HDAC8 G304A-M-344, respectively). The cryo-EM density for Y378 in the active site of Hda1 in complex with Hda3 NTD3 is shown as blue mesh. (C) Schematic representation of the catalytic sites of S. cerevisiae Hda1 HDACD dimer with an acetyl-lysine model.

Supplementary Materials

  • Supplementary Materials

    Structural basis for the regulation of nucleosome recognition and HDAC activity by histone deacetylase assemblies

    Jung-Hoon Lee, Daniel Bollschweiler, Tillman Schäfer, Robert Huber

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