The exploitation of FRET probes to track bromodomain/histone interactions in cells for bromodomain inhibitors

Miyawaki, 2003, Visualization of the spatial and temporal dynamics of intracellular signaling, Dev Cell, 4, 295, 10.1016/S1534-5807(03)00060-1 Nagai, 2004, Expanded dynamic range of fluorescent indicators for Ca2+ by circularly permuted yellow fluorescent proteins, Proc Natl Acad Sci U S A, 101, 10554, 10.1073/pnas.0400417101 Tsutsui, 2008, Improving membrane voltage measurements using FRET with new fluorescent proteins, Nat Methods, 5, 683, 10.1038/nmeth.1235 Sasaki, 2012, Development of live-cell imaging probes for monitoring histone modifications, Bioorg Med Chem, 20, 1887, 10.1016/j.bmc.2012.01.018 Shimozono, 2013, Visualization of an endogenous retinoic acid gradient across embryonic development, Nature, 496, 363, 10.1038/nature12037 Tsuyama, 2013, In vivo fluorescent adenosine 5′-triphosphate (ATP) imaging of Drosophila melanogaster and Caenorhabditis elegans by using a genetically encoded fluorescent ATP biosensor optimized for low temperatures, Anal Chem, 85, 7889, 10.1021/ac4015325 Ueda, 2015, Asymmetrical diacylglycerol dynamics on the cytosolic and lumenal sides of a single endomembrane in living cells, Sci Rep, 5, 12960, 10.1038/srep12960 Sato, 2016, Genetically encoded fluorescent indicators to visualize protein phosphorylation in living cells, Methods Mol Biol, 1360, 149, 10.1007/978-1-4939-3073-9_11 Sasaki, 2009, Real-time imaging of histone H4 hyperacetylation in living cells, Proc Natl Acad Sci U S A, 106, 16257, 10.1073/pnas.0902150106 Ito, 2011, Real-time imaging of histone H4K12-specific acetylation determines the modes of action of histone deacetylase and bromodomain inhibitors, Chem Biol, 18, 495, 10.1016/j.chembiol.2011.02.009 Nakaoka, 2015, A genetically encoded FRET probe to detect intranucleosomal histone H3K9 or H3K14 acetylation using BRD4, a BET family member, ACS Chem Biol Day, 2009, The fluorescent protein palette: tools for cellular imaging, Chem Soc Rev, 38, 2887, 10.1039/b901966a Nienhaus, 2014, Fluorescent proteins for live-cell imaging with super-resolution, Chem Soc Rev, 43, 1088, 10.1039/C3CS60171D Nguyen, 2005, Evolutionary optimization of fluorescent proteins for intracellular FRET, Nat Biotechnol, 23, 355, 10.1038/nbt1066 Lam, 2012, Improving FRET dynamic range with bright green and red fluorescent proteins, Nat Methods, 9, 1005, 10.1038/nmeth.2171 Bannister, 2011, Regulation of chromatin by histone modifications, Cell Res, 21, 381, 10.1038/cr.2011.22 Portela, 2010, Epigenetic modifications and human disease, Nat Biotechnol, 28, 1057, 10.1038/nbt.1685 Rodríguez-Paredes, 2011, Cancer epigenetics reaches mainstream oncology, Nat Med, 17, 330, 10.1038/nm.2305 Hatziapostolou, 2011, Epigenetic aberrations during oncogenesis, Cell Mol Life Sci, 68, 1681, 10.1007/s00018-010-0624-z Pivot-Pajot, 2003, Acetylation-dependent chromatin reorganization by BRDT, a testis-specific bromodomain-containing protein, Mol Cell Biol, 23, 5354, 10.1128/MCB.23.15.5354-5365.2003 Kanno, 2004, Selective recognition of acetylated histones by bromodomain proteins visualized in living cells, Mol Cell, 13, 33, 10.1016/S1097-2765(03)00482-9 Huang, 2007, Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails, BMC Struct Biol, 7, 57, 10.1186/1472-6807-7-57 LeRoy, 2008, The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription, Mol Cell, 30, 51, 10.1016/j.molcel.2008.01.018 Zeng, 2008, Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300, Structure, 16, 643, 10.1016/j.str.2008.01.010 Morinière, 2009, Cooperative binding of two acetylation marks on a histone tail by a single bromodomain, Nature, 461, 664, 10.1038/nature08397 Vollmuth, 2010, Interaction of propionylated and butyrylated histone H3 lysine marks with Brd4 bromodomains, Angew Chem Int Ed Engl, 49, 6768, 10.1002/anie.201002724 Umehara, 2010, Structural implications for K5/K12-di-acetylated histone H4 recognition by the second bromodomain of BRD2, FEBS Lett, 584, 3901, 10.1016/j.febslet.2010.08.013 Umehara, 2010, Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain, J Biol Chem, 285, 7610, 10.1074/jbc.M109.062422 Li, 2014, AF9 YEATS domain links histone acetylation to DOT1L-mediated H3K79 methylation, Cell, 159, 558, 10.1016/j.cell.2014.09.049 Schulze, 2014, Reading chromatin, Epigenetics, 5, 573, 10.4161/epi.5.7.12856 Mottamal, 2015, Histone deacetylase inhibitors in clinical studies as templates for new anticancer agents, Molecules, 20, 3898, 10.3390/molecules20033898 Furumai, 2002, FK228 (depsipeptide) as a natural prodrug that inhibits class I histone deacetylases, Cancer Res, 62, 4916 Belkina, 2012, BET domain co-regulators in obesity, inflammation and cancer, Nat Rev Cancer, 12, 465, 10.1038/nrc3256 Grunwald, 2006, Expression of multiple epigenetically regulated cancer/germline genes in nonsmall cell lung cancer, Int J Cancer, 118, 2522, 10.1002/ijc.21669 French, 2003, BRD4-NUT fusion oncogene: a novel mechanism in aggressive carcinoma, Cancer Res, 63, 304 French, 2008, BRD-NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and maintain the growth of carcinoma cells, Oncogene, 27, 2237, 10.1038/sj.onc.1210852 Zuber, 2011, RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia, Nature, 478, 524, 10.1038/nature10334 Filippakopoulos, 2010, Selective inhibition of BET bromodomains, Nature, 468, 1067, 10.1038/nature09504 Nicodeme, 2010, Suppression of inflammation by a synthetic histone mimic, Nature, 468, 1119, 10.1038/nature09589 Dawson, 2011, Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia, Nature, 478, 529, 10.1038/nature10509 Shi, 2014, The mechanisms behind the therapeutic activity of BET bromodomain inhibition, Mol Cell, 54, 728, 10.1016/j.molcel.2014.05.016 Fong, 2015, BET inhibitor resistance emerges from leukaemia stem cells, Nature, 525, 538, 10.1038/nature14888 Rathert, 2015, Transcriptional plasticity promotes primary and acquired resistance to BET inhibition, Nature, 525, 543, 10.1038/nature14898 Picaud, 2013, PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains, Cancer Res, 73, 3336, 10.1158/0008-5472.CAN-12-3292 Jung, 2014, Affinity map of bromodomain protein 4 (BRD4) interactions with the histone H4 tail and the small molecule inhibitor JQ1, J Biol Chem, 289, 9304, 10.1074/jbc.M113.523019 Philpott, 2014, Assessing cellular efficacy of bromodomain inhibitors using fluorescence recovery after photobleaching, Epigenet Chromatin, 7, 14, 10.1186/1756-8935-7-14 Komatsu, 2011, Development of an optimized backbone of FRET biosensors for kinases and GTPases, Mol Biol Cell, 22, 4647, 10.1091/mbc.e11-01-0072