Bromodomain-containing proteins of the BET family recognize histone lysine acetylation and mediate transcriptional activation of target genes such as the MYC oncogene. Pharmacological inhibitors of BET domains promise therapeutic benefits in a variety of cancers. We performed a high-diversity chemical compound screen for agents capable of modulating BRD4-dependent heterochromatization of a generic reporter in human cells. In addition to known and new compounds targeting BRD4, we identified small molecules that mimic BRD4 inhibition without direct engagement. One such compound was a potent inhibitor of the second bromodomain of TAF1. Using this inhibitor, we discovered that TAF1 synergizes with BRD4 to control proliferation of cancer cells, making TAF1 an attractive epigenetic target in cancers driven by MYC.
Subscribe to Journal
Get full journal access for 1 year
only $14.08 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Wang, R., Li, Q., Helfer, C.M., Jiao, J. & You, J. Bromodomain protein Brd4 associated with acetylated chromatin is important for maintenance of higher-order chromatin structure. J. Biol. Chem. 287, 10738–10752 (2012).
Dey, A., Chitsaz, F., Abbasi, A., Misteli, T. & Ozato, K. The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis. Proc. Natl. Acad. Sci. USA 100, 8758–8763 (2003).
Filippakopoulos, P. et al. Histone recognition and large-scale structural analysis of the human bromodomain family. Cell 149, 214–231 (2012).
Floyd, S.R. et al. The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. Nature 498, 246–250 (2013).
Wu, S.Y. & Chiang, C.M. The double bromodomain-containing chromatin adaptor Brd4 and transcriptional regulation. J. Biol. Chem. 282, 13141–13145 (2007).
Zuber, J. et al. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478, 524–528 (2011).
Wyce, A. et al. BET inhibition silences expression of MYCN and BCL2 and induces cytotoxicity in neuroblastoma tumor models. PLoS One 8, e72967 (2013).
Yang, Z., He, N. & Zhou, Q. Brd4 recruits P-TEFb to chromosomes at late mitosis to promote G1 gene expression and cell cycle progression. Mol. Cell. Biol. 28, 967–976 (2008).
Nagarajan, S. et al. Bromodomain protein BRD4 is required for estrogen receptor-dependent enhancer activation and gene transcription. Cell Rep. 8, 460–469 (2014).
Wu, T., Pinto, H.B., Kamikawa, Y.F. & Donohoe, M.E. The BET family member BRD4 interacts with OCT4 and regulates pluripotency gene expression. Stem Cell Rep. 4, 390–403 (2015).
Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067–1073 (2010).
Seal, J. et al. Identification of a novel series of BET family bromodomain inhibitors: binding mode and profile of I-BET151 (GSK1210151A). Bioorg. Med. Chem. Lett. 22, 2968–2972 (2012).
Filippakopoulos, P. & Knapp, S. Targeting bromodomains: epigenetic readers of lysine acetylation. Nat. Rev. Drug Discov. 13, 337–356 (2014).
Andersson, B.S. et al. KBM-7, a human myeloid leukemia cell line with double Philadelphia chromosomes lacking normal c-ABL and BCR transcripts. Leukemia 9, 2100–2108 (1995).
Zhu, J. et al. Reactivation of latent HIV-1 by inhibition of BRD4. Cell Rep. 2, 807–816 (2012).
Banerjee, C. et al. BET bromodomain inhibition as a novel strategy for reactivation of HIV-1. J. Leukoc. Biol. 92, 1147–1154 (2012).
Schermelleh, L. et al. Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320, 1332–1336 (2008).
Towbin, B.D. et al. Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery. Cell 150, 934–947 (2012).
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Whyte, W.A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).
Filippakopoulos, P. et al. Benzodiazepines and benzotriazepines as protein interaction inhibitors targeting bromodomains of the BET family. Bioorg. Med. Chem. 20, 1878–1886 (2012).
Zhang, J.H., Chung, T.D. & Oldenburg, K.R. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J. Biomol. Screen. 4, 67–73 (1999).
Fish, P.V. et al. Identification of a chemical probe for bromo and extra C-terminal bromodomain inhibition through optimization of a fragment-derived hit. J. Med. Chem. 55, 9831–9837 (2012).
Mirguet, O. et al. Discovery of epigenetic regulator I-BET762: lead optimization to afford a clinical candidate inhibitor of the BET bromodomains. J. Med. Chem. 56, 7501–7515 (2013).
McLure, K.G. et al. RVX-208, an inducer of ApoA-I in humans, is a BET bromodomain antagonist. PLoS One 8, e83190 (2013).
Ciceri, P. et al. Dual kinase-bromodomain inhibitors for rationally designed polypharmacology. Nat. Chem. Biol. 10, 305–312 (2014).
Roe, J.-S., Mercan, F., Rivera, K., Pappin, D.J. & Vakoc, C.R. BET bromodomain inhibition suppresses the function of hematopoietic transcription factors in acute myeloid leukemia. Mol. Cell 58, 1028–1039 (2015).
Hay, D.A. et al. Discovery and optimization of small-molecule ligands for the CBP/p300 bromodomains. J. Am. Chem. Soc. 136, 9308–9319 (2014).
Hammitzsch, A. et al. CBP30, a selective CBP/p300 bromodomain inhibitor, suppresses human Th17 responses. Proc. Natl. Acad. Sci. USA 112, 10768–10773 (2015).
Picaud, S. et al. Generation of a selective small molecule inhibitor of the CBP/p300 bromodomain for leukemia therapy. Cancer Res. 75, 5106–5119 (2015).
McKeown, M.R. et al. Biased multicomponent reactions to develop novel bromodomain inhibitors. J. Med. Chem. 57, 9019–9027 (2014).
Fedorov, O. et al. [1,2,4]triazolo[4,3-a]phthalazines: inhibitors of diverse bromodomains. J. Med. Chem. 57, 462–476 (2014).
Chaikuad, A., Petros, A.M., Fedorov, O., Xu, J. & Knapp, S. Structure-based approaches towards identification of fragments for the low-druggability ATAD2 bromodomain. MedChemComm 5, 1843–1848 (2014).
Bliss, C.I. The toxicity of poisons applied jointly. Ann. Appl. Biol. 26, 585–615 (1939).
Johnson, R.L. et al. A quantitative high-throughput screen identifies potential epigenetic modulators of gene expression. Anal. Biochem. 375, 237–248 (2008).
Best, A.M., Chang, J., Dull, A.B., Beutler, J.A. & Martinez, E.D. Identification of four potential epigenetic modulators from the NCI structural diversity library using a cell-based assay. J. Biomed. Biotechnol. 2011, 868095 (2011).
Wang, L. et al. A small molecule modulates Jumonji histone demethylase activity and selectively inhibits cancer growth. Nat. Commun. 4, 2035 (2013).
Tchasovnikarova, I.A. et al. Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells. Science 348, 1481–1485 (2015).
Blank, J. et al. Imidazopyrrolidinone derivatives and their use in the treatment of disease. WPO patent WO/2014/191894 (2014).
Engelhardt, H. et al. Triazolopyridazine. US Patent Office patent US 2014/0135336 (2014).
Blank, J. et al. Pyrazolopyrrolidine derivatives and their use in the treatment of disease. WPO patent WO/2014/191896 (2014).
Albrecht, B.K., Harmange, J., Côté, A. & Taylor, A. Bromodomain inhibitors and uses thereof. WPO patent WO/2012/17448 (2012).
Lee, D.H. et al. Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. Mol. Cell. Biol. 25, 9674–9686 (2005).
Kloet, S.L., Whiting, J.L., Gafken, P., Ranish, J. & Wang, E.H. Phosphorylation-dependent regulation of cyclin D1 and cyclin A gene transcription by TFIID subunits TAF1 and TAF7. Mol. Cell. Biol. 32, 3358–3369 (2012).
Kandiah, E., Trowitzsch, S., Gupta, K., Haffke, M. & Berger, I. More pieces to the puzzle: recent structural insights into class II transcription initiation. Curr. Opin. Struct. Biol. 24, 91–97 (2014).
Wang, T. et al. Identification and characterization of essential genes in the human genome. Science 350, 1096–1101 (2015).
Blomen, V.A. et al. Gene essentiality and synthetic lethality in haploid human cells. Science 350, 1092–1096 (2015).
Arrowsmith, C.H. et al. The promise and peril of chemical probes. Nat. Chem. Biol. 11, 536–541 (2015).
Workman, P. & Collins, I. Probing the probes: fitness factors for small molecule tools. Chem. Biol. 17, 561–577 (2010).
Frye, S.V. The art of the chemical probe. Nat. Chem. Biol. 6, 159–161 (2010).
Bielefeld-Sevigny, M. AlphaLISA immunoassay platform—the “no-wash” high-throughput alternative to ELISA. Assay Drug Dev. Technol. 7, 90–92 (2009).
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
Wang, L., Wang, S. & Li, W. RSeQC: quality control of RNA-seq experiments. Bioinformatics 28, 2184–2185 (2012).
Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).
Mootha, V.K. et al. Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell 115, 629–640 (2003).
Huang, W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
Huang, W., Sherman, B.T. & Lempicki, R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1–13 (2009).
Research in the Kubicek laboratory is supported by the Austrian Federal Ministry of Science, Research and Economy; the National Foundation for Research, Technology, and Development; the Marie Curie Career Integration Grant EPICAL; and the JDRF. This project was supported by SFB grant F4710 of the Austrian Science Fund (FWF). S.S. acknowledges support by JDRF postdoctoral fellowship 3-PDF-2014-206-A-N “Reprogramming by Loss of Function”. J.B., C.T., O.F. and S.M. are funded by the Structural Genomics Consortium, a registered charity (number 1097737) that receives funds from AbbVie, Bayer, Boehringer Ingelheim, the Canada Foundation for Innovation, the Canadian Institutes for Health Research, Genome Canada, GlaxoSmithKline, Janssen, Lilly Canada, the Novartis Research Foundation, the Ontario Ministry of Economic Development and Innovation, Pfizer, Takeda and the Wellcome Trust (092809/Z/10/Z). We thank all the members of the BioOptic Facility of the Research Institute of Molecular Pathology (IMP) and the Institute of Molecular Biotechnology GmbH (IMBA) for their help with cell sorting; S. Gresko and V. Ivanov (Enamine Ltd) for compound synthesis; J.E. Bradner (Dana-Farber Cancer Institute) for an initial batch of JQ1 and for library compounds; and K.M. Pugh (Target Discovery Institute; Oxford) for help with analytical chemistry. Dedicated to S.L. Schreiber on the occasion of his 60th birthday.
S.S. and S. Kubicek have filed a patent application (EP16155781) with claims derived from work described in this manuscript.
About this article
Cite this article
Sdelci, S., Lardeau, CH., Tallant, C. et al. Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk. Nat Chem Biol 12, 504–510 (2016). https://doi.org/10.1038/nchembio.2080
Biochemical Pharmacology (2021)
ACS Medicinal Chemistry Letters (2019)
Nature Reviews Drug Discovery (2019)