Abstract
Histone deacetylase enzymes (HDACs) are emerging cancer drug targets. They regulate gene expression by removing acetyl groups from lysine residues in histone tails, resulting in chromatin condensation. The enzymatic activity of most class I HDACs requires recruitment into multi-subunit co-repressor complexes, which are in turn recruited to chromatin by repressive transcription factors. Here we report the structure of a complex between an HDAC and a co-repressor, namely, human HDAC3 with the deacetylase activation domain (DAD) from the human SMRT co-repressor (also known as NCOR2). The structure reveals two remarkable features. First, the SMRT-DAD undergoes a large structural rearrangement on forming the complex. Second, there is an essential inositol tetraphosphate molecule—d-myo-inositol-(1,4,5,6)-tetrakisphosphate (Ins(1,4,5,6)P4)—acting as an ‘intermolecular glue’ between the two proteins. Assembly of the complex is clearly dependent on the Ins(1,4,5,6)P4, which may act as a regulator—potentially explaining why inositol phosphates and their kinases have been found to act as transcriptional regulators. This mechanism for the activation of HDAC3 appears to be conserved in class I HDACs from yeast to humans, and opens the way to novel therapeutic opportunities.
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Accession codes
Data deposits
Atomic coordinates and structure factors are deposited in the Protein Data Bank under accession number 4A69.
References
Pogo, B. G., Allfrey, V. G. & Mirsky, A. E. RNA synthesis and histone acetylation during the course of gene activation in lymphocytes. Proc. Natl Acad. Sci. USA 55, 805–812 (1966)
Struhl, K. Histone acetylation and transcriptional regulatory mechanisms. Genes Dev. 12, 599–606 (1998)
Choudhary, C. et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834–840 (2009)
Hildmann, C., Riester, D. & Schwienhorst, A. Histone deacetylases — an important class of cellular regulators with a variety of functions. Appl. Microbiol. Biotechnol. 75, 487–497 (2007)
Hu, E. et al. Cloning and characterization of a novel human class I histone deacetylase that functions as a transcription repressor. J. Biol. Chem. 275, 15254–15264 (2000)
Lee, H., Rezai-Zadeh, N. & Seto, E. Negative regulation of histone deacetylase 8 activity by cyclic AMP-dependent protein kinase A. Mol. Cell. Biol. 24, 765–773 (2004)
Zhang, Y. et al. Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev. 13, 1924–1935 (1999)
Li, J. et al. Both corepressor proteins SMRT and N-CoR exist in large protein complexes containing HDAC3. EMBO J. 19, 4342–4350 (2000)
Lechner, T. et al. Sds3 (suppressor of defective silencing 3) is an integral component of the yeast Sin3·Rpd3 histone deacetylase complex and is required for histone deacetylase activity. J. Biol. Chem. 275, 40961–40966 (2000)
Zhang, J., Kalkum, M., Chait, B. T. & Roeder, R. G. The N-CoR-HDAC3 nuclear receptor corepressor complex inhibits the JNK pathway through the integral subunit GPS2. Mol. Cell 9, 611–623 (2002)
Guenther, M. G., Barak, O. & Lazar, M. A. The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3. Mol. Cell. Biol. 21, 6091–6101 (2001)
Wen, Y. D. et al. The histone deacetylase-3 complex contains nuclear receptor corepressors. Proc. Natl Acad. Sci. USA 97, 7202–7207 (2000)
Métivier, R. et al. Estrogen receptor-α directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115, 751–763 (2003)
Hoberg, J. E., Yeung, F. & Mayo, M. W. SMRT derepression by the IκB kinase α: a prerequisite to NF-κB transcription and survival. Mol. Cell 16, 245–255 (2004)
Billin, A. N., Thirlwell, H. & Ayer, D. E. β-catenin-histone deacetylase interactions regulate the transition of LEF1 from a transcriptional repressor to an activator. Mol. Cell. Biol. 20, 6882–6890 (2000)
Guan, H.-P., Ishizuka, T., Chui, P. C., Lehrke, M. & Lazar, M. A. Corepressors selectively control the transcriptional activity of PPARγ in adipocytes. Genes Dev. 19, 453–461 (2005)
Marks, P. A. & Breslow, R. Dimethyl sulfoxide to vorinostat: development of this histone deacetylase inhibitor as an anticancer drug. Nature Biotechnol. 25, 84–90 (2007)
Wagner, J. M., Hackanson, B., Lübbert, M. & Jung, M. Histone deacetylase (HDAC) inhibitors in recent clinical trials for cancer therapy. Clin. Epigenet. 1, 117–136 (2010)
Zhang, Y., LeRoy, G., Seelig, H. P., Lane, W. S. & Reinberg, D. The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell 95, 279–289 (1998)
Hakimi, M.-A. et al. A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes. Proc. Natl Acad. Sci. USA 99, 7420–7425 (2002)
Humphrey, G. W. et al. Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1. J. Biol. Chem. 276, 6817–6824 (2001)
Laherty, C. D. et al. Histone deacetylases associated with the mSin3 corepressor mediate mad transcriptional repression. Cell 89, 349–356 (1997)
Heinzel, T. et al. A complex containing N-CoR, mSin3 and histone deacetylase mediates transcriptional repression. Nature 387, 43–48 (1997)
Guenther, M. G. et al. A core SMRT corepressor complex containing HDAC3 and TBL1, a WD40-repeat protein linked to deafness. Genes Dev. 14, 1048–1057 (2000)
Yoon, H.-G. et al. Purification and functional characterization of the human N-CoR complex: the roles of HDAC3, TBL1 and TBLR1. EMBO J. 22, 1336–1346 (2003)
Oberoi, J. et al. Structural basis for the assembly of the SMRT/NCoR core transcriptional repression machinery. Nature Struct. Mol. Biol. 18, 177–184 (2011)
You, S.-H., Liao, X., Weiss, R. E. & Lazar, M. A. The interaction between nuclear receptor corepressor and histone deacetylase 3 regulates both positive and negative thyroid hormone action in vivo . Mol. Endocrinol. 24, 1359–1367 (2010)
Ishizuka, T. & Lazar, M. A. The nuclear receptor corepressor deacetylase activating domain is essential for repression by thyroid hormone receptor. Mol. Endocrinol. 19, 1443–1451 (2005)
Yin, L. et al. Rev-erbα, a heme sensor that coordinates metabolic and circadian pathways. Science 318, 1786–1789 (2007)
Guenther, M. G. Assembly of the SMRT-histone deacetylase 3 repression complex requires the TCP-1 ring complex. Genes Dev. 16, 3130–3135 (2002)
Codina, A. et al. Structural insights into the interaction and activation of histone deacetylase 3 by nuclear receptor corepressors. Proc. Natl Acad. Sci. USA 102, 6009–6014 (2005)
Yang, W.-M., Tsai, S.-C., Wen, Y.-D., Fejer, G. & Seto, E. Functional domains of histone deacetylase-3. J. Biol. Chem. 277, 9447–9454 (2002)
Dowling, D. P., Gantt, S. L., Gattis, S. G., Fierke, C. A. & Christianson, D. W. Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry 47, 13554–13563 (2008)
Somoza, J. R. et al. Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure 12, 1325–1334 (2004)
Bressi, J. C. et al. Exploration of the HDAC2 foot pocket: synthesis and SAR of substituted N-(2-aminophenyl)benzamides. Bioorg. Med. Chem. Lett. 20, 3142–3145 (2010)
Odom, A. R. A role for nuclear inositol 1,4,5-trisphosphate kinase in transcriptional control. Science 287, 2026–2029 (2000)
Steger, D. J. Regulation of chromatin remodeling by inositol polyphosphates. Science 299, 114–116 (2003)
El Alami, M., Messenguy, F., Scherens, B. & Dubois, E. Arg82p is a bifunctional protein whose inositol polyphosphate kinase activity is essential for nitrogen and PHO gene expression but not for Mcm1p chaperoning in yeast. Mol. Microbiol. 49, 457–468 (2003)
Shen, X., Xiao, H., Ranallo, R., Wu, W.-H. & Wu, C. Modulation of ATP-dependent chromatin-remodeling complexes by inositol polyphosphates. Science 299, 112–114 (2003)
Saiardi, A. et al. Mammalian inositol polyphosphate multikinase synthesizes inositol 1,4,5-trisphosphate and an inositol pyrophosphate. Proc. Natl Acad. Sci. USA 98, 2306–2311 (2001)
Nalaskowski, M. M., Deschermeier, C., Fanick, W. & Mayr, G. W. The human homologue of yeast ArgRIII protein is an inositol phosphate multikinase with predominantly nuclear localization. Biochem. J. 366, 549–556 (2002)
Craxton, A., Caffrey, J. J., Burkhart, W., Safrany, S. T. & Shears, S. B. Molecular cloning and expression of a rat hepatic multiple inositol polyphosphate phosphatase. Biochem. J. 328, 75–81 (1997)
Caffrey, J. J., Darden, T., Wenk, M. R. & Shears, S. B. Expanding coincident signaling by PTEN through its inositol 1,3,4,5,6-pentakisphosphate 3-phosphatase activity. FEBS Lett. 499, 6–10 (2001)
Di Cristofano, A. & Pandolfi, P. P. The multiple roles of PTEN in tumor suppression. Cell 100, 387–390 (2000)
Mattingly, R. R., Stephens, L. R., Irvine, R. F. & Garrison, J. C. Effects of transformation with the v-src oncogene on inositol phosphate metabolism in rat-1 fibroblasts. D-myo-inositol 1,4,5,6-tetrakisphosphate is increased in v-src-transformed rat-1 fibroblasts and can be synthesized from D-myo-inositol 1,3,4-trisphosphate in cytosolic extracts. J. Biol. Chem. 266, 15144–15153 (1991)
Feng, D. et al. A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science 331, 1315–1319 (2011)
Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)
Collaborative Computational Project, 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010)
Acknowledgements
We thank R. Owen and the other beamline staff at DIAMOND I24 for help with data collection; J. Goodchild for help with biochemical experiments; and S. Cowley, M. Lazar, P. Moody, L. Nagy, P. Tontonoz and S. Shears for literature and discussions. This work was supported by the Wellcome Trust (grant WT085408).
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P.J.W. expressed, purified and crystallized the protein and performed the biochemical studies. P.J.W., L.F. and J.W.R.S. performed the structural determination and wrote the paper. G.M.S. and L.F. performed early expression/purification trials in insect cells. J.W.R.S. conceived the study.
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Watson, P., Fairall, L., Santos, G. et al. Structure of HDAC3 bound to co-repressor and inositol tetraphosphate. Nature 481, 335–340 (2012). https://doi.org/10.1038/nature10728
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DOI: https://doi.org/10.1038/nature10728
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