Syngenta CTL, Cheshire SK10 4TJ, United Kingdom
Received March 17, 2004; accepted April 29, 2004
![]() |
ABSTRACT |
---|
Key Words: chromatin; histone; toxicology; genome; epigenetic.
![]() |
PACKAGING OF DNA INTO CHROMATIN |
---|
![]() |
CHANGES IN CHROMATIN DURING THE RESPONSE TO ENVIRONMENTAL STIMULI |
---|
![]() |
CHANGES IN GENE EXPRESSION IN RESPONSE TO XENOBIOTICS |
---|
These observations have, in recent years, precipitated a renewed interest in chromatin structure. This resulted in the seminal hypothesis that the modification of histone tails by lysine acetylation, lysine and arginine methylation, serine and threonine phosphorylation, and lysine ubiquitination constitutes a histone code that, when translated, dictates the activity of a gene (Strahl and Allis, 2000; Turner, 2000
). The central role of these complex chromatin alterations in the response to toxicants is illustrated by the way in which xenobiotics that target nuclear receptors elicit their effects. The nuclear receptors, of which there are more than 48 in mammals, are a family of ligand-activated transcription factors (Enmark and Gustafsson, 2001
). A growing number of xenobiotics have been shown to function by directly altering the activity of nuclear receptors. For example, peroxisome proliferators, dioxins, and estrogenic chemicals act via the peroxisome proliferatoractivated receptor
(Johnson et al., 2002
), aryl hydrocarbon receptor (Denison and Nagy, 2003
), and estrogen receptors (ER; Singleton and Khan, 2003
), respectively.
Once activated by ligand (e.g., a toxicant), it appears that the major mechanistic role of nuclear receptors is to induce alterations in chromatin structure to allow RNA polymerase II and its accessory transcription factors access to the gene to be transcribed (Fig. 1). The molecular mechanism through which ligand activation of a nuclear receptor leads to alterations in chromatin structure and gene activation has been studied in detail for ER (Moggs and Orphanides, 2001
). Ligand binding by ER
induces conformational changes in the receptor that facilitate the successive recruitment and exchange of 46 coregulator proteins during the recognition of specific estrogen response element sequences near to or within ER
target genes (Metivier et al., 2003
). These coregulators include ATP-dependent, nucleosome-remodeling enzymes (the BRG1, BRM1, INI1, and BAF170 subunits of the SWI/SNF complex) and histone-modifying enzymes (the HATs CBP, p300, p/CAF, GCN5, and TIP60; HDAC1 and HDAC7; and the histone methyltransferases [HMTs] CARM1 and PRMT1) that together lead to the decompaction of chromatin structure locally.
|
![]() |
THE ROLE OF CHROMATIN IN THE ACTIVATION OF STRESS RESPONSE GENES |
---|
![]() |
THE ROLE OF CHROMATIN IN THE RESPONSE TO GENOTOXINS |
---|
Double-strand breaks (DSBs) are a more severe form of DNA damage and can lead to genomic rearrangements if left unrepaired. Specific changes in chromatin modification state and structure appear to be at the center of the cellular response to DSBs (Fig. 2). The detection of DNA DSBs by the damage surveillance machinery results in the activation of protein kinases (ATM, ATR, and DNA-PK) that phosphorylate serine 139 within a specialized histone variant, histone H2A.X (reviewed by Downs and Jackson, 2003). The H2A.X variant makes up between 10 and 15% of total cellular H2A in higher eukaryotes, possesses an extended carboxy terminal tail that extends outwards from the nucleosome, and is incorporated into nucleosomes randomly throughout the genome. The role of histone H2A.X phosphorylation in DSB repair has not been defined in detail. However, recent evidence suggests that H2A.X functions as a tumor suppressor gene that protects cells from the deleterious effects of DNA damage. Transgenic mice lacking a functional H2A.X gene have unstable genomes and are susceptible to tumors, indicating that H2A.X functions to maintain genome integrity (Bassing et al., 2003
; Celeste et al., 2003
). Phosphorylation of serine 139 of histone H2A.X also occurs during apoptosis, a process that involves chromatin condensation and DNA fragmentation, the latter of which also generates DSBs.
|
![]() |
HISTONE MODIFICATIONS SERVE AS MARKERS OF TOXICITY |
---|
![]() |
DO XENOBIOTICS TARGET CHROMATIN STRUCTURE DIRECTLY? |
---|
|
Another class of chromatin-modifying enzymes that can be directly targeted by toxicants is the HDACs. The promising anticancer agent suberoylanilide hydroxamic acid (Kelly et al., 2003) is an HDAC inhibitor that interferes with differentiation, proliferation, and apoptosis in tumor cells. More recently, the short-chain fatty acid and endocrine disruptor methoxyacetic acid has been shown to enhance nuclear receptor activity through a combination of MAP kinase activation and HDAC inhibition (Jansen et al., 2004
). The disruption of chromatin-modifying enzymes by toxicants might, in principle, be expected to result in a nonspecific dysregulation of genome function and, thus, overt cellular toxicity. However, there is increasing evidence that many chromatin-modifying enzymes target specific subsets of genes. This is exemplified by the distinct transcriptional specificities of the human SWI/SNF BRG1 and BRM nucleosome-remodeling complexes (Kadam and Emerson, 2003
). Furthermore, there is a precedent for the specific inhibition of distinct members of the HAT family: the HATs p300 and PCAF are inhibited by the peptide CoA conjugates Lys-CoA and H3-CoA-20, respectively (Lau et al., 2000
).
What would be the consequences of direct chemical perturbation of chromatin structure? In addition to their role in regulating gene expression and DNA repair, chromatin modifications play an important part in the transmission of epigenetic information, epigenetics being the study of heritable alterations in gene expression that occur in the absence of changes in genome sequence (Wolffe and Matzke, 1999). Thus, the perturbation of chromatin structure by toxicants may lead to long-term and possibly transgenerational changes in epigenetic programming. The key mechanism that controls the epigenetic regulation of mammalian genomes is the methylation of cytosine bases in DNA (Beck and Olek, 2003
), which forms the modified base 5-methylcytosine (5-mC). In mammalian DNA, 5-mC is present at a level of 25% of all cytosines and is found predominantly on CpG dinucleotides. Clusters of CpG sequences (known as CpG islands) tend to be found near the 5' ends of genes and are usually unmethylated. However, a proportion of these CpGs can be methylated in a developmental stage and cell typespecific manner, usually resulting in gene silencing. The fact that more than 50 genes have been shown to be abnormally methylated in human tumors suggests that alterations in DNA methylation status may lead to cellular transformation and carcinogenesis (Jones and Baylin, 2002
). Specifically, it is believed that hypomethylation and hypermethylation of CpG islands can lead to the constitutive activation of oncogenes and the silencing of tumor suppressor genes, respectively.
The influence of chromatin structure on DNA methylation status and the transmission of epigenetic information is just beginning to be revealed (reviewed by Jaenisch and Bird, 2003). DNA methylation is controlled by families of DNA methyltransferase (DNMT) enzymes and methyl-cytosinebinding proteins (MBDs). The interrelationship between DNA methylation and chromatin structure was revealed initially by the identification of a protein complex containing both the MBD MeCP2 and the histone deacetylases HDAC1 and HDAC2 (Nan et al, 1998
). Subsequent studies have revealed numerous interactions among DNMTs, MBDs, and chromatin-modifying enzymes (reviewed by Burgers et al., 2002
). Regions of DNA that are hypermethylated are associated with chromatin that has been modified by methylation of lysine 9 on histone H3 (Lachner et al., 2003
). Moreover, this particular histone modification appears to be important for DNA methylationdriven gene silencing. Chromatin-containing histone H3 modified at this position is recognized by the HP1 protein, which binds and promotes compaction of chromatin into the silent heterochromatin state (Bannister et al., 2001
). Given the role of histone H3 lysine 9 methylation in the silencing of hypermethylated DNA, one may expect that disruption of histone-methylating enzymes (the HMTs) will have adverse consequences. Compelling support for this hypothesis is provided by the observation that stable alterations in the expression of the HMT enzyme EZH2, which methylates histone H3 lysine 27, are associated with numerous prostate and breast cancers (Kleer et al., 2003
; Varambally et al., 2002
). Therefore, we speculate that direct inhibition of the machinery that regulates chromatin structure will disrupt epigenetic programming via perturbations in chromatin function and will precipitate adverse effects (Bombail et al., 2004
).
![]() |
SUMMARY |
---|
![]() |
NOTES |
---|
1 To whom correspondence should be addressed at Syngenta CTL, Alderley Park, Cheshire SK10 4TJ, United Kingdom. Fax: +44 1625 585715. E-mail: jonathan.moggs{at}syngenta.com.
![]() |
REFERENCES |
---|
Banath, J. P., and Olive, P. L. (2003). Expression of phosphorylated histone H2AX as a surrogate of cell killing by drugs that create DNA double-strand breaks. Cancer Res. 63, 43474350.
Bannister, A. J., Zegerman, P., Partridge, J. F., Miska, E. A., Thomas, J. O., Allshire, R. C., and Kouzarides, T. (2001). Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120124.[CrossRef][ISI][Medline]
Bassing, C. H., Suh, H., Ferguson, D. O., Chua, K. F., Manis, J., Eckersdorff, M., Gleason, M., Bronson, R., Lee, C., and Alt, F. W. (2003). Histone H2AX: A dosage-dependent suppressor of oncogenic translocations and tumors. Cell 114, 359370.[ISI][Medline]
Beck, S., and Olek, A. (2003). The Epigenome: Molecular Hide and Seek. Wiley-VCH GmbH & Co. KgaA.
Becker, P. B., and Horz, W. (2002). ATP-dependent nucleosome remodeling. Annu. Rev. Biochem. 71, 247273.[CrossRef][ISI][Medline]
Bombail, V., Moggs, J. G., and Orphanides, G. (2004). Perturbation of epigenetic status by toxicants. Toxicol. Lett. 149, 5158.[CrossRef][ISI][Medline]
Broday, L., Peng, W., Kuo, M. H., Salnikow, K., Zoroddu, M., and Costa, M. (2000). Nickel compounds are novel inhibitors of histone H4 acetylation. Cancer Res. 60, 238241.
Burgers, W. A., Fuks, F., and Kouzarides, T. (2002). DNA methyltransferases get connected to chromatin. Trends Genet. 18, 275277.[CrossRef][ISI][Medline]
Carrozza, M. J., Utley, R. T., Workman, J. L., and Cote, J. (2003). The diverse functions of histone acetyltransferase complexes. Trends Genet. 19, 321329.[CrossRef][ISI][Medline]
Celeste, A., Difilippantonio, S., Difilippantonio, M. J., Fernandez-Capetillo, O., Pilch, D. R., Sedelnikova, O. A., Eckhaus, M., Ried, T., Bonner, W. M., and Nussenzweig, A. (2003). H2AX haploinsufficiency modifies genomic stability and tumor susceptibility. Cell 114, 371383.[ISI][Medline]
Cheung, W. L., Ajiro, K., Samejima, K., Kloc, M., Cheung, P., Mizzen, C. A., Beeser, A., Etkin, L. D., Chernoff, J., Earnshaw, W. C., et al. (2003). Apoptotic phosphorylation of histone H2B is mediated by mammalian sterile twenty kinase. Cell 16, 507517.
Clayton, A. L., and Mahadevan, L. C. (2003). MAP kinasemediated phosphoacetylation of histone H3 and inducible gene regulation. FEBS Lett. 546, 5158.[CrossRef][ISI][Medline]
Clayton, A. L., Rose, S., Barratt, M. J., and Mahadevan, L. C. (2000). Phosphoacetylation of histone H3 on c-fos and c-junassociated nucleosomes upon gene activation. EMBO J. 19, 37143726.
Denison, M. S., and Nagy, S. R. (2003). Activation of the aryl hydrocarbon receptor by structurally diverse exogenous and endogenous chemicals. Annu. Rev. Pharmacol. Toxicol. 43, 309334.[CrossRef][ISI][Medline]
de Ruijter, A. J., van Gennip, A. H., Caron, H. N., Kemp, S., and van Kuilenburg, A. B. (2003). Histone deacetylases (HDACs): Characterization of the classical HDAC family. Biochem. J. 370, 737749.[CrossRef][ISI][Medline]
Downs, J. A., and Jackson, S. P. (2003). Protective packaging for DNA. Nature 424, 732734.[CrossRef][ISI][Medline]
Enmark, E., and Gustafsson, J.-Å. (2001). Comparing nuclear receptors in worms, flies and humans. Trends Pharmacol. Sci. 22, 611615.[CrossRef][ISI][Medline]
Fischle, W., Wang, Y., and Allis, D. (2003a). Binary switches and modification cassettes in histone biology and beyond. Nature 425, 475479.[CrossRef][ISI][Medline]
Fischle, W., Wang, Y., Jacobs, S. A., Kim, Y., Allis, C. D., and Khorasanizadeh, S. (2003b). Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by polycomb and HP1 chromodomains. Genes Dev. 17, 18701881.
Green, C. M., and Almouzni, G. (2002). When repair meets chromatin. First in series on chromatin dynamics. EMBO Rep. 3, 2833.
He, Z., Ma, W. Y., Liu, G., Zhang, Y., Bode, A. M., and Dong, Z. (2003). Arsenite-induced phosphorylation of histone H3 at serine 10 is mediated by Akt1, extracellular signalregulated kinase 2, and p90 ribosomal S6 kinase 2 but not mitogen- and stress-activated protein kinase 1. J. Biol. Chem. 278, 1058810593.
Hebbes, T. R., Thorne, A. W., and Crane-Robinson, C. A. (1988). Direct link between core histone acetylation and transcriptionally active chromatin. EMBO J. 7, 13951402.[Abstract]
Huang, C., Sloan, E. A., and Boerkoel, C. F. (2003) Chromatin remodeling and human disease. Curr. Opin. Genet. Dev. 13, 246252.[CrossRef][ISI][Medline]
Jaenisch, R., and Bird, A. (2003). Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals. Nat. Genet. 33, 245254.[CrossRef][ISI][Medline]
Jansen, M. S., Nagel, S. C., Miranda, P. J., Lobenhofer, E. K., Afshari, C. A., and McDonnell, D. P. (2004). Short-chain fatty acids enhance nuclear receptor activity through mitogen-activated protein kinase activation and histone deacetylase inhibition. Proc. Natl. Acad. Sci. USA 101, 71997204.
Jenuwein, T., and Allis, C. D. (2001). Translating the histone code. Science 293, 10741080.
Johnson, E. F., Hsu, M. H., Savas, U., and Griffin, K. J. (2002). Regulation of P450 4A expression by peroxisome proliferator activated receptors. Toxicology 181182, 203206.[CrossRef][ISI]
Jones, P. A., and Baylin, S. B. (2002). The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415428.[ISI][Medline]
Kadam, S., and Emerson, B. M. (2003). Transcriptional specificity of human SWI/SNF BRG1 and BRM chromatin remodelling complexes. Mol. Cell 11, 377389.[ISI][Medline]
Kanno, T., Kanno, Y., Siegel, R. M., Jang, M. K., Lenardo, M. J., and Ozato, K. (2004). Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. Mol. Cell 13, 3343.[CrossRef][ISI][Medline]
Karaczyn, A. A., Bal, W., North, S. L., Bare, R. M., Hoang, V. M., Fisher, R. J., and Kasprzak, K. S. (2003). The octapeptidic end of the C-terminal tail of histone H2A is cleaved off in cells exposed to carcinogenic nickel(II). Chem. Res. Toxicol. 16, 15551559.[CrossRef][ISI][Medline]
Kelly, W. K., Richon, V. M., O'Connor, O., Curley, T., MacGregor-Curtelli, B., Tong, W., Klang, M., Schwartz, L., Richardson, S., Rosa, E., et al. (2003). Phase I clinical trial of histone deacetylase inhibitor: Suberoylanilide hydroxamic acid administered intravenously. Clin. Cancer Res. 9, 35783588.
Kirschmann, D. A., Lininger, R. A., Gardner, L. M., Seftor, E. A., Odero, V. A., Ainsztein, A. M., Earnshaw, W. C., Wallrath, L. L., and Hendrix, M. J. (2000). Down-regulation of HP1Hs expression is associated with the metastatic phenotype in breast cancer. Cancer Res. 60, 33593363.
Kleer, C. G., Cao, Q., Varambally, S., Shen, R., Ota, I., Tomlins, S. A., Ghosh, D., Sewalt, R. G., Otte, A. P., Hayes, D. F., et al. (2003). EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells. Proc. Natl. Acad. Sci. USA 100, 1160611611.
Konishi, A., Shimizu, S., Hirota, J., Takao, T., Fan, Y., Matsuoka, Y., Zhang, L., Yoneda, Y., Fujii, Y., Skoultchi, A. I., et al. (2003). Involvement of histone H1.2 in apoptosis induced by DNA double-strand breaks. Cell 114, 673688.[ISI][Medline]
Lachner, M., O'Sullivan, R. J., and Jenuwein, T. (2003). An epigenetic road map for histone lysine methylation. J. Cell Sci. 116, 21172124.
Lau, O. D., Kundu, T. K., Soccio, R. E., Ait-Si-Ali, S., Khalil, E. M., Vassilev, A., Wolffe, A. P., Nakatani, Y., Roeder, R. G., and Cole, P. A. (2000). HATs off: Selective synthetic inhibitors of the histone acetyltransferases p300 and PCAF. Mol. Cell 5, 589595.[ISI][Medline]
Luger, K., Mäder, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J. (1997). Crystal structure of the nucleosome core particle at 2.8 Angstrom resolution. Nature 389, 251260.[CrossRef][ISI][Medline]
Metivier, R., Penot, G., Hubner, M. R., Reid, G., Brand, H., Kos, M., and Gannon, F. (2003). Estrogen receptor- directs ordered, cyclical, and combinatorial recruitment of cofactors on a natural target promoter. Cell 115, 751763.[CrossRef][ISI][Medline]
Min, J., Zhang, Y., and Xu, R. M. (2003). Structural basis for specific binding of polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev. 17, 18231828.
Moggs, J. G., and Orphanides, G. (2001). Estrogen receptors: Orchestrators of pleiotropic cellular responses. EMBO Rep. 2, 775781.
Nan, X., Ng, H. H., Johnson, C. A., Laherty, C. D., Turner, B. M., Eisenman, R. N., and Bird, A. (1998). Transcriptional repression by the methyl-CpG binding protein MeCP2 involves a histone deacetylase complex. Nature 393, 386389.[CrossRef][ISI][Medline]
Neely, K. E., and Workman, J. L. (2002). The complexity of chromatin remodeling and its links to cancer. Biochim. Biophys. Acta 1603, 1929.[CrossRef][ISI][Medline]
Olive, P. L., and Banath, J. P. (2004). Phosphorylation of histone H2AX as a measure of radiosensitivity. Int. J. Radiat. Oncol. Biol. Phys. 58, 331335.[CrossRef][ISI][Medline]
Orphanides, G., and Reinberg, D. (2002). A unified theory of gene expression. Cell 108, 439451.[ISI][Medline]
Ota, T., Suto, S., Katayama, H., Han, Z. B., Suzuki, F., Maeda, M., Tanino, M., Terada, Y., and Tatsuka, M. (2002). Increased mitotic phosphorylation of histone H3 attributable to AIM-1/Aurora-B overexpression contributes to chromosome number instability. Cancer Res. 62, 51685177.
Rogakou, E. P., Nieves-Neira, W., Boon, C., Pommier, Y., and Bonner, W. M. (2000). Initiation of DNA fragmentation during apoptosis induces phosphorylation of H2AX histone at serine 139. J. Biol. Chem. 275, 93909395.
Sassone-Corsi, P., Mizzen, C. A., Cheung, P., Crosio, C., Monaco, L., Jacquot, S., Hanauer, A., and Allis, C. D. (1999). Requirement of Rsk-2 for epidermal growth factoractivated phosphorylation of histone H3. Science 285, 886891.
Schneider, R., Bannister, A. J., and Kouzarides, T. (2002). Unsafe SETs: Histone lysine methyltransferases and cancer. Trends Biochem. Sci. 27, 396402.[CrossRef][ISI][Medline]
Singleton, D. W., and Khan, S. A. (2003). Xenoestrogen exposure and mechanisms of endocrine disruption. Front. Biosci. 8, S110S118.[ISI][Medline]
Strahl, B. D., and Allis, C. D. (2000). The language of covalent histone modifications. Nature 403, 4145.[CrossRef][ISI][Medline]
Taneja, N., Davis, M., Choy, J. S., Beckett, M. A., Singh, R., Kron, S. J., and Weichselbaum, R. R. (2004). Histone H2AX phosphorylation as a predictor of radiosensitivity and target for radiotherapy. J. Biol. Chem. 279, 22732280.
Thomson, S., Clayton, A. L., Hazzalin, C. A., Rose, S., Barratt, M. J., and Mahadevan, L. C. (1999). The nucleosomal response associated with immediate-early gene induction is mediated via alternative MAP kinase cascades: MSK1 as a potential histone H3/HMG-14 kinase. Embo. J. 18, 47794793.
Tibbles, L. A., and Woodgett, J. R. (1999). The stress-activated protein kinase pathways. Cell. Mol. Life Sci. 55, 12301254.[CrossRef][ISI][Medline]
Timmermann, S., Lehrmann, H., Polesskaya, A., and Harel-Bellan, A. (2001). Histone acetylation and disease. Cell. Mol. Life Sci. 58, 728736.[ISI][Medline]
Turner, B. M. (2000). Histone acetylation and an epigenetic code. Bioessays 22, 836845.[CrossRef][ISI][Medline]
Turner, B. M. (2002). Cellular memory and the histone code. Cell 111, 285291.[ISI][Medline]
Van Holde, K. E. (1997). Chromatin. Springer-Verlag, New York.
Vaquero, A., Loyola, A., and Reinberg, D. (2003). The constantly changing face of chromatin. Sci. Aging Knowledge Environ. 14, RE4.
Varambally, S., Dhanasekaran, S. M., Zhou, M., Barrette, T. R., Kumar-Sinha, C., Sanda, M. G., Ghosh, D., Pienta, K. J., Sewalt, R. G. A. B., Otte, A. P., et al. (2002). The polycomb protein EZH2 is involved in progression of prostate cancer. Nature 419, 624629.[CrossRef][ISI][Medline]
Wang, D., and Lippard, S. J. (2004). Cisplatin-induced post-translational modification of histones H3 and H4. J. Biol. Chem. (Epub ahead of print).
Wei, Y.-D., Tepperman, K., Huang, M.-Y., Sartor, M. A., and Puga, A. (2004). Chromium inhibits transcription from polycyclic aromatic hydrocarbon inducible promoters by blocking the release of histone deacetylase and preventing the binding of p300 to chromatin. J. Biol. Chem. 279, 41104119.
Wolffe, A. P., and Matzke, M. A. (1999). Epigenetics: Regulation through repression. Science 286, 481486.
Wood, R. D. (1996). DNA repair in eukaryotes. Annu. Rev. Biochem. 65, 135167.[CrossRef][ISI][Medline]
Yan, Y., Kluz, T., Zhang, P., Chen, H. B., and Costa, M. (2003). Analysis of specific lysine histone H3 and H4 acetylation and methylation status in clones of cells with a gene silenced by nickel exposure. Toxicol. Appl. Pharmacol. 190, 272277.[CrossRef][ISI][Medline]
Yang, J., Yu, Y., and Duerksen-Hughes, P. J. (2003). Protein kinases and their involvement in the cellular responses to genotoxic stress. Mutat. Res. 543, 3158.[ISI][Medline]
Zhang, Q., Salnikow, K., Kluz, T., Chen, L. C., Su, W. C., and Costa, M. (2003). Inhibition and reversal of nickel-induced transformation by the histone deacetylase inhibitor trichostatin A. Toxicol. Appl. Pharmacol. 192, 201211.[CrossRef][ISI][Medline]