Key Points
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Small molecules can target protein and nucleic acid components of chromatin at specific genomic sites and perturb cellular processes.
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Click chemistry relies on bio-orthogonal chemical reactivity that enables the introduction of a fluorophore to visualize small molecules in cells or the introduction of an affinity reagent that can be used for the purpose of target isolation.
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High-throughput sequencing can be used to identify where small molecules influence the genome, which in some cases has provided new insights into drug responses.
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Small molecules can be functionalized with affinity reagents to allow the isolation of DNA and characterization of genomic target sites by means of deep sequencing in a protocol known as Chem–seq.
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A combination of experimental approaches — including ChIP–seq, Chem–seq and genome-wide gene expression analysis — can be used to delineate genome targeting with small molecules and might be useful for predicting cellular responses in the context of personalized medicine.
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Chromatin influences genomic targeting with small molecules, thereby providing the opportunity for epigenome-targeting drugs to regulate and potentially reprogramme the response of certain drugs that operate at the genomic level.
Abstract
Small molecules — including various approved and novel cancer therapeutics — can operate at the genomic level by targeting the DNA and protein components of chromatin. Emerging evidence suggests that functional interactions between small molecules and the genome are non-stochastic and are influenced by a dynamic interplay between DNA sequences and chromatin states. The establishment of genome-wide maps of small-molecule targets using unbiased methodologies can help to characterize and exploit drug responses. In this Review, we discuss how high-throughput sequencing strategies, such as ChIP–seq (chromatin immunoprecipitation followed by sequencing) and Chem–seq (chemical affinity capture and massively parallel DNA sequencing), are enabling the comprehensive identification of small-molecule target sites throughout the genome, thereby providing insights into unanticipated drug effects.
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References
Campos, E. I. & Reinberg, D. Histones: annotating chromatin. Annu. Rev. Genet. 43, 559–599 (2009).
Kornberg, R. D. Chromatin structure: a repeating unit of histones and DNA. Science 184, 868–871 (1974).
Bell, O., Tiwari, V. K., Thoma, N. H. & Schubeler, D. Determinants and dynamics of genome accessibility. Nature Rev. Genet. 12, 554–564 (2011).
Jones, P. A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nature Rev. Genet. 13, 484–492 (2012).
Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007).
Shogren-Knaak, M. et al. Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311, 844–847 (2006).
Arrowsmith, C. H., Bountra, C., Fish, P. V., Lee, K. & Schapira, M. Epigenetic protein families: a new frontier for drug discovery. Nature Rev. Drug Discov. 11, 384–400 (2012).
Musselman, C. A., Lalonde, M. E., Cote, J. & Kutateladze, T. G. Perceiving the epigenetic landscape through histone readers. Nature Struct. Mol. Biol. 19, 1218–1227 (2012).
Margueron, R. & Reinberg, D. Chromatin structure and the inheritance of epigenetic information. Nature Rev. Genet. 11, 285–296 (2010).
Dervan, P. B. Molecular recognition of DNA by small molecules. Bioorg. Med. Chem. 9, 2215–2235 (2001).
Miller, K. M. & Rodriguez, R. G-quadruplexes: selective DNA targeting for cancer therapeutics? Expert Rev. Clin. Pharmacol. 4, 139–142 (2011).
Dawson, M. A. & Kouzarides, T. Cancer epigenetics: from mechanism to therapy. Cell 150, 12–27 (2012).
Dawson, M. A., Kouzarides, T. & Huntly, B. J. Targeting epigenetic readers in cancer. N. Engl. J. Med. 367, 647–657 (2012).
Helin, K. & Dhanak, D. Chromatin proteins and modifications as drug targets. Nature 502, 480–488 (2013).
Zhou, V. W., Goren, A. & Bernstein, B. E. Charting histone modifications and the functional organization of mammalian genomes. Nature Rev. Genet. 12, 7–18 (2011).
Koboldt, D. C., Steinberg, K. M., Larson, D. E., Wilson, R. K. & Mardis, E. R. The next-generation sequencing revolution and its impact on genomics. Cell 155, 27–38 (2013).
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein–DNA interactions. Science 316, 1497–1502 (2007).
Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).
Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome — biological and translational implications. Nature Rev. Cancer 11, 726–734 (2011).
Bernstein, B. E. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Plass, C. et al. Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer. Nature Rev. Genet. 14, 765–780 (2013).
Xhemalce, B. From histones to RNA: role of methylation in cancer. Brief Funct. Genomics 12, 244–253 (2013).
Anders, L. et al. Genome-wide localization of small molecules. Nature Biotech. 32, 92–96 (2014). This paper reports the first genome-wide localization of a small molecule through the development of a novel technique called Chem–seq.
Greer, E. L. & Shi, Y. Histone methylation: a dynamic mark in health, disease and inheritance. Nature Rev. Genet. 13, 343–357 (2012).
Probst, A. V., Dunleavy, E. & Almouzni, G. Epigenetic inheritance during the cell cycle. Nature Rev. Mol. Cell Biol. 10, 192–206 (2009).
Maze, I., Noh, K. M., Soshnev, A. A. & Allis, C. D. Every amino acid matters: essential contributions of histone variants to mammalian development and disease. Nature Rev. Genet. 15, 259–271 (2014).
Mercer, T. R., Dinger, M. E. & Mattick, J. S. Long non-coding RNAs: insights into functions. Nature Rev. Genet. 10, 155–159 (2009).
Patel, D. J., Phan, A. T. & Kuryavyi, V. Human telomere, oncogenic promoter and 5′-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res. 35, 7429–7455 (2007).
Belotserkovskii, B. P., Mirkin, S. M. & Hanawalt, P. C. DNA sequences that interfere with transcription: implications for genome function and stability. Chem. Rev. 113, 8620–8637 (2013).
Yoo, C. B. & Jones, P. A. Epigenetic therapy of cancer: past, present and future. Nature Rev. Drug Discov. 5, 37–50 (2006).
Smith, K. T. & Workman, J. L. Histone deacetylase inhibitors: anticancer compounds. Int. J. Biochem. Cell Biol. 41, 21–25 (2009).
Kelly, T. K., De Carvalho, D. D. & Jones, P. A. Epigenetic modifications as therapeutic targets. Nature Biotech. 28, 1069–1078 (2010).
Furey, T. S. ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions. Nature Rev. Genet. 13, 840–852 (2012).
Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P. & Dickerson, R. E. The molecular origin of DNA–drug specificity in netropsin and distamycin. Proc. Natl Acad. Sci. USA 82, 1376–1380 (1985).
Dervan, P. B. Design of sequence-specific DNA-binding molecules. Science 232, 464–471 (1986).
Gottesfeld, J. M., Neely, L., Trauger, J. W., Baird, E. E. & Dervan, P. B. Regulation of gene expression by small molecules. Nature 387, 202–205 (1997). This paper describes the first example of a rationally designed synthetic small molecule to target the genome at specific sequences.
Meier, J. L., Yu, A. S., Korf, I., Segal, D. J. & Dervan, P. B. Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J. Am. Chem. Soc. 134, 17814–17822 (2012).
Huppert, J. L. & Balasubramanian, S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33, 2908–2916 (2005).
Lipps, H. J. & Rhodes, D. G-quadruplex structures: in vivo evidence and function. Trends Cell Biol. 19, 414–422 (2009).
Bochman, M. L., Paeschke, K. & Zakian, V. A. DNA secondary structures: stability and function of G-quadruplex structures. Nature Rev. Genet. 13, 770–780 (2012).
Maizels, N. & Gray, L. T. The G4 genome. PLoS Genet. 9, e1003468 (2013).
Balasubramanian, S., Hurley, L. H. & Neidle, S. Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nature Rev. Drug Discov. 10, 261–275 (2011).
Siddiqui-Jain, A., Grand, C. L., Bearss, D. J. & Hurley, L. H. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl Acad. Sci. USA 99, 11593–11598 (2002).
Rodriguez, R. et al. A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres. J. Am. Chem. Soc. 130, 15758–15759 (2008).
Rodriguez, R. et al. Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. Nature Chem. Biol. 8, 301–310 (2012). This is the original report using high-throughput sequencing to identify sites of action of a small molecule genome-wide, which provided evidence for G4 structures in gene bodies. It also reports chemical labelling of a small molecule and its subcellular localization by high-resolution microscopy.
Muller, S., Kumari, S., Rodriguez, R. & Balasubramanian, S. Small-molecule-mediated G-quadruplex isolation from human cells. Nature Chem. 2, 1095–1098 (2010).
Kolb, H. C., Finn, M. G. & Sharpless, K. B. Click chemistry: diverse chemical function from a few good reactions. Angew. Chem. Int. Ed Engl. 40, 2004–2021 (2001).
Rostovtsev, V. V., Green, L. G., Fokin, V. V. & Sharpless, K. B. A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angew. Chem. Int. Ed Engl. 41, 2596–2599 (2002).
Nitiss, J. L. Targeting DNA topoisomerase II in cancer chemotherapy. Nature Rev. Cancer 9, 338–350 (2009).
Jackson, S. P. & Bartek, J. The DNA-damage response in human biology and disease. Nature 461, 1071–1078 (2009).
Deal, R. B., Henikoff, J. G. & Henikoff, S. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones. Science 328, 1161–1164 (2010).
Gaulton, K. J. et al. A map of open chromatin in human pancreatic islets. Nature Genet. 42, 255–259 (2010).
Pang, B. et al. Drug-induced histone eviction from open chromatin contributes to the chemotherapeutic effects of doxorubicin. Nature Commun. 4, 1908 (2013).
Yang, F., Kemp, C. J. & Henikoff, S. Doxorubicin enhances nucleosome turnover around promoters. Curr. Biol. 23, 782–787 (2013).
Azarova, A. M. et al. Roles of DNA topoisomerase II isozymes in chemotherapy and secondary malignancies. Proc. Natl Acad. Sci. USA 104, 11014–11019 (2007).
Haffner, M. C. et al. Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements. Nature Genet. 42, 668–675 (2010).
Cowell, I. G. et al. Model for MLL translocations in therapy-related leukemia involving topoisomerase IIβ-mediated DNA strand breaks and gene proximity. Proc. Natl Acad. Sci. USA 109, 8989–8994 (2012).
Dykhuizen, E. C. et al. BAF complexes facilitate decatenation of DNA by topoisomerase IIα. Nature 497, 624–627 (2013).
Mabb, A. M., Judson, M. C., Zylka, M. J. & Philpot, B. D. Angelman syndrome: insights into genomic imprinting and neurodevelopmental phenotypes. Trends Neurosci. 34, 293–303 (2011).
Huang, H. S. et al. Topoisomerase inhibitors unsilence the dormant allele of Ube3a in neurons. Nature 481, 185–189 (2012). This study identifies the unsilencing of an imprinted gene linked to Angelman syndrome as a result of site-specific targeting of a gene by topoisomerase poisons.
King, I. F. et al. Topoisomerases facilitate transcription of long genes linked to autism. Nature 501, 58–62 (2013).
Bester, A. C. et al. Nucleotide deficiency promotes genomic instability in early stages of cancer development. Cell 145, 435–446 (2011).
Burrell, R. A. et al. Replication stress links structural and numerical cancer chromosomal instability. Nature 494, 492–496 (2013).
Barlow, J. H. et al. Identification of early replicating fragile sites that contribute to genome instability. Cell 152, 620–632 (2013). This study uses ChIP–seq on DNA damage markers to identify genome-wide sites that are susceptible to fragility in the presence of the chemotherapeutic agent hydroxyurea. It identifies a new class of fragile sites in the human genome called ERFs.
Crosetto, N. et al. Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing. Nature Methods 10, 361–365 (2013).
Myatt, S. S. & Lam, E. W. The emerging roles of forkhead box (Fox) proteins in cancer. Nature Rev. Cancer 7, 847–859 (2007).
Hegde, N. S., Sanders, D. A., Rodriguez, R. & Balasubramanian, S. The transcription factor FOXM1 is a cellular target of the natural product thiostrepton. Nature Chem. 3, 725–731 (2011).
Sanders, D. A., Ross-Innes, C. S., Beraldi, D., Carroll, J. S. & Balasubramanian, S. Genome-wide mapping of FOXM1 binding reveals co-binding with estrogen receptor α in breast cancer cells. Genome Biol. 14, R6 (2013).
Chen, X. et al. The forkhead transcription factor FOXM1 controls cell cycle-dependent gene expression through an atypical chromatin binding mechanism. Mol. Cell. Biol. 33, 227–236 (2013).
Verdine, G. L. & Walensky, L. D. The challenge of drugging undruggable targets in cancer: lessons learned from targeting BCL-2 family members. Clin. Cancer Res. 13, 7264–7270 (2007).
List, A. F., Vardiman, J., Issa, J. P. & DeWitte, T. M. Myelodysplastic syndromes. Hematology Am. Soc. Hematol. Educ. Program, 297–317 (2004).
Griffiths, E. A. & Gore, S. D. Epigenetic therapies in MDS and AML. Adv. Exp. Med. Biol. 754, 253–283 (2013).
Hagemann, S., Heil, O., Lyko, F. & Brueckner, B. Azacytidine and decitabine induce gene-specific and non-random DNA demethylation in human cancer cell lines. PLoS ONE 6, e17388 (2011).
Pandiyan, K. et al. Functional DNA demethylation is accompanied by chromatin accessibility. Nucleic Acids Res. 41, 3973–3985 (2013).
Glozak, M. A. & Seto, E. Histone deacetylases and cancer. Oncogene 26, 5420–5432 (2007).
Gong, F. & Miller, K. M. Mammalian DNA repair: HATs and HDACs make their mark through histone acetylation. Mutat. Res. 750, 23–30 (2013).
Camphausen, K. & Tofilon, P. J. Inhibition of histone deacetylation: a strategy for tumor radiosensitization. J. Clin. Oncol. 25, 4051–4056 (2007).
Miller, K. M. et al. Human HDAC1 and HDAC2 function in the DNA-damage response to promote DNA nonhomologous end-joining. Nature Struct. Mol. Biol. 17, 1144–1151 (2010).
Cameron, E. E., Bachman, K. E., Myohanen, S., Herman, J. G. & Baylin, S. B. Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nature Genet. 21, 103–107 (1999). This paper provides the first evidence that drugs affecting the epigenome can act synergistically on chromatin to target novel genes that are not affected by single agents alone.
Belinsky, S. A. et al. Combination therapy with vidaza and entinostat suppresses tumor growth and reprograms the epigenome in an orthotopic lung cancer model. Cancer Res. 71, 454–462 (2011).
Okada, Y. et al. hDOT1L links histone methylation to leukemogenesis. Cell 121, 167–178 (2005).
Daigle, S. R. et al. Selective killing of mixed lineage leukemia cells by a potent small-molecule DOT1L inhibitor. Cancer Cell 20, 53–65 (2011).
Bernt, K. M. et al. MLL-rearranged leukemia is dependent on aberrant H3K79 methylation by DOT1L. Cancer Cell 20, 66–78 (2011).
Grembecka, J. et al. Menin–MLL inhibitors reverse oncogenic activity of MLL fusion proteins in leukemia. Nature Chem. Biol. 8, 277–284 (2012).
Cao, F. et al. Targeting MLL1 H3K4 methyltransferase activity in mixed-lineage leukemia. Mol. Cell 53, 247–261 (2014).
Varambally, S. et al. The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature 419, 624–629 (2002).
Takawa, M. et al. Validation of the histone methyltransferase EZH2 as a therapeutic target for various types of human cancer and as a prognostic marker. Cancer Sci. 102, 1298–1305 (2011).
Morin, R. D. et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nature Genet. 42, 181–185 (2010).
Morin, R. D. et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 476, 298–303 (2011).
Pasqualucci, L. et al. Analysis of the coding genome of diffuse large B-cell lymphoma. Nature Genet. 43, 830–837 (2011).
McCabe, M. T. et al. EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations. Nature 492, 108–112 (2012).
Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067–1073 (2010).
Nicodeme, E. et al. Suppression of inflammation by a synthetic histone mimic. Nature 468, 1119–1123 (2010). References 93 and 94 describe unprecedented examples of targeting the BET bromodomain family of epigenetic readers with small molecules.
Chung, C. W. et al. Discovery and characterization of small molecule inhibitors of the BET family bromodomains. J. Med. Chem. 54, 3827–3838 (2011).
Dawson, M. A. et al. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature 478, 529–533 (2011).
Delmore, J. E. et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146, 904–917 (2011).
Mertz, J. A. et al. Targeting MYC dependence in cancer by inhibiting BET bromodomains. Proc. Natl Acad. Sci. USA 108, 16669–16674 (2011).
Zuber, J. et al. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478, 524–528 (2011).
Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013).
Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).
Chapuy, B. et al. Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma. Cancer Cell 24, 777–790 (2013).
Loven, J. et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320–334 (2013).
Matzuk, M. M. et al. Small-molecule inhibition of BRDT for male contraception. Cell 150, 673–684 (2012).
Jin, C. et al. Chem–seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens. Proc. Natl Acad. Sci. USA 111, 9235–9240 (2014).
Larrieu, D., Britton, S., Demir, M., Rodriguez, R. & Jackson, S. P. Chemical inhibition of NAT10 corrects defects of laminopathic cells. Science 344, 527–532 (2014).
Charrier, J. D. et al. Discovery of potent and selective inhibitors of ataxia telangiectasia mutated and Rad3 related (ATR) protein kinase as potential anticancer agents. J. Med. Chem. 54, 2320–2330 (2011).
Dawson, M. A. et al. JAK2 phosphorylates histone H3Y41 and excludes HP1α from chromatin. Nature 461, 819–822 (2009).
Hickson, I. et al. Identification and characterization of a novel and specific inhibitor of the ataxia-telangiectasia mutated kinase ATM. Cancer Res. 64, 9152–9159 (2004).
Leahy, J. J. et al. Identification of a highly potent and selective DNA-dependent protein kinase (DNA-PK) inhibitor (NU7441) by screening of chromenone libraries. Bioorg. Med. Chem. Lett. 14, 6083–6087 (2004).
Konze, K. D. et al. An orally bioavailable chemical probe of the lysine methyltransferases EZH2 and EZH1. ACS Chem. Biol. 8, 1324–1334 (2013).
Kim, M. S. et al. Inhibition of histone deacetylase increases cytotoxicity to anticancer drugs targeting DNA. Cancer Res. 63, 7291–7300 (2003).
Sharma, S. V. et al. A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell 141, 69–80 (2010). This paper reports that drug-tolerant cancer cells can be resensitized towards anticancer drugs by altering chromatin.
Pommier, Y. Topoisomerase I inhibitors: camptothecins and beyond. Nature Rev. Cancer 6, 789–802 (2006).
Aggarwal, M., Sommers, J. A., Shoemaker, R. H. & Brosh, R. M. Jr. Inhibition of helicase activity by a small molecule impairs Werner syndrome helicase (WRN) function in the cellular response to DNA damage or replication stress. Proc. Natl Acad. Sci. USA 108, 1525–1530 (2011).
Nguyen, G. H. et al. A small molecule inhibitor of the BLM helicase modulates chromosome stability in human cells. Chem. Biol. 20, 55–62 (2013).
Drygin, D. et al. Targeting RNA polymerase I with an oral small molecule CX-5461 inhibits ribosomal RNA synthesis and solid tumor growth. Cancer Res. 71, 1418–1430 (2011).
Bowers, E. M. et al. Virtual ligand screening of the p300/CBP histone acetyltransferase: identification of a selective small molecule inhibitor. Chem. Biol. 17, 471–482 (2010).
Knutson, S. K. et al. Durable tumor regression in genetically altered malignant rhabdoid tumors by inhibition of methyltransferase EZH2. Proc. Natl Acad. Sci. USA 110, 7922–7927 (2013).
Bryant, H. E. et al. Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase. Nature 434, 913–917 (2005).
Farmer, H. et al. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature 434, 917–921 (2005).
Kreso, A. et al. Self-renewal as a therapeutic target in human colorectal cancer. Nature Med. 20, 29–36 (2014).
Leung, J. W. et al. Nucleosome acidic patch promotes RNF168- and RING1B/BMI1-dependent H2AX and H2A ubiquitination and DNA damage signaling. PLoS Genet. 10, e1004178 (2014).
Wang, L. et al. A small molecule modulates Jumonji histone demethylase activity and selectively inhibits cancer growth. Nature Commun. 4, 2035 (2013).
Kruidenier, L. et al. A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Nature 488, 404–408 (2012).
Chen, J. et al. Selective and cell-active inhibitors of the USP1/ UAF1 deubiquitinase complex reverse cisplatin resistance in non-small cell lung cancer cells. Chem. Biol. 18, 1390–1400 (2011).
Wagner, E. K., Nath, N., Flemming, R., Feltenberger, J. B. & Denu, J. M. Identification and characterization of small molecule inhibitors of a plant homeodomain finger. Biochemistry 51, 8293–8306 (2012).
Pessetto, Z. Y., Yan, Y., Bessho, T. & Natarajan, A. Inhibition of BRCT(BRCA1)–phosphoprotein interaction enhances the cytotoxic effect of olaparib in breast cancer cells: a proof of concept study for synthetic lethal therapeutic option. Breast Cancer Res. Treat. 134, 511–517 (2012).
Brueckner, B. et al. Epigenetic reactivation of tumor suppressor genes by a novel small-molecule inhibitor of human DNA methyltransferases. Cancer Res. 65, 6305–6311 (2005).
Acknowledgements
R.R. is supported by the French National Centre for Scientific Research (CNRS). K.M.M.'s laboratory is supported by start-up funds from University of Texas at Austin, USA, and by the Cancer Prevention Research Institute of Texas (CPRIT, R116). K.M.M. is a CPRIT Scholar in Cancer Research. The authors thank B. Xhemalce, M. Dawson and members of K.M.M.'s laboratory for critical reading of the manuscript.
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Glossary
- Chromatin
-
Nucleoprotein complex that packages and controls accessibility of the genome, thereby regulating transcription, DNA replication and repair.
- Nucleosome
-
The basic unit of chromatin composed of ~147 base pairs of DNA wrapped around an octamer containing two copies of four core histone proteins (H2A, H2B, H3 and H4).
- Post-translational modifications
-
(PTMs). Chemical modifications of, and ligation of small proteins (for example, ubiquitin and SUMO) on, substrate proteins that can serve as platforms for the binding of other proteins containing a 'reader' domain for specific PTMs.
- Epigenome
-
Combination of chemical alterations of DNA, histone post-translational modifications and their interacting proteins that regulate genome accessibility and function.
- Epigenetic
-
Pertaining to heritable phenotypic changes that are independent of alterations in the DNA sequence. A more general definition includes chromatin-mediated processes that are reliant on post-translational modifications of histone proteins, DNA methylation, histone variants or non-coding RNAs.
- G-quadruplex
-
(G4). Alternative, non-Watson–Crick nucleic acid structures that arise from particular G-rich sequences. Guanine residues interact with one another within the same strand by means of hydrogen bonding and stacking interactions to produce four-stranded higher-order architectures. A broader definition also includes intermolecular structures formally composed of more than one strand.
- Epigenetic modifier proteins
-
Proteins that 'write', 'erase' or 'read' epigenetic marks on chromatin.
- Next-generation sequencing
-
(Also known as massively parallel sequencing). Post-Sanger sequencing techniques that can generate a DNA sequence from a single molecule of DNA rather than from multiple DNA templates, allowing millions of DNA fragments to be sequenced at the same time from a single sample.
- ChIP–seq
-
(Chromatin immunoprecipitation followed by sequencing). An unbiased molecular biology-based protocol designed to identify interaction sites of chromatin-binding proteins with the genome. This method uses specific antibodies to precipitate the protein of interest, which isolates bound DNA fragments that are then subjected to sequencing.
- Chem–seq
-
(Chemical affinity capture and massively parallel DNA sequencing). An unbiased molecular biology-based protocol designed to identify sites of interaction of small molecules with the genome. This method involves the use of small molecules of interest to isolate bound DNA targets, which are then analysed by sequencing.
- Click chemistry
-
Selective, high-yielding and biocompatible chemical reactions used to covalently link two or more molecules. The copper-catalysed azide–alkyne cycloaddition (CuAAC) and its copper-free version are the most commonly used.
- Topoisomerase 2
-
(TOP2). An enzyme that regulates DNA topology by cutting a pair of strands from a DNA helix to allow another unbroken helix to pass through, followed by resealing of the broken ends. TOP2 activity is essential for many DNA transactions and represents the target of several chemotherapeutic drugs.
- CATCH-IT
-
(Covalent attachment of tagged histones to capture and identify turnover). A method for measuring genome-wide nucleosome turnover using metabolically labelled, newly synthesized histones for affinity-based chromatin capture.
- FAIRE–seq
-
(Formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing). A method for identifying DNA from nucleosome-free regions.
- Therapy-related secondary malignancies
-
Malignancies triggered by cancer treatment, including therapy-related myelodysplastic syndrome and acute myeloid leukaemia. These diseases have been linked to treatments with topoisomerase inhibitors. Potential causes include mutations such as chromosomal translocations that result from the inappropriate repair of treatment-induced DNA breaks.
- Genomic imprinting
-
An epigenetic phenomenon that results in the monoallelic expression of a gene due to parental-dependent marking of the gene by DNA methylation or other epigenetic mechanisms.
- TOP1
-
An enzyme that regulates DNA topology by breaking and rejoining a single strand from a DNA helix. TOP1 activity is essential for many DNA processes, including transcription and DNA replication, and is the target of several chemotherapeutic drugs.
- Super enhancers
-
Specialized large cis-regulatory regions identified in embryonic stem cells and cancer cells that regulate the principal genes involved in cell identity and disease.
- Personalized medicine
-
Customized health care in which clinical treatments are tailored to the patient. Diagnostic evaluation based on genetic and epigenetic information can be exploited in that context to select appropriate therapies.
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Rodriguez, R., Miller, K. Unravelling the genomic targets of small molecules using high-throughput sequencing. Nat Rev Genet 15, 783–796 (2014). https://doi.org/10.1038/nrg3796
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DOI: https://doi.org/10.1038/nrg3796
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