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Shen J, Yang C, Zhang MS, Chin DWC, Chan FF, Law CT, Wang G, Cheng CLH, Chen M, Wan RTC, Wu M, Kuang Z, Sharma R, Lee TKW, Ng IOL, Wong CCL, Wong CM. Histone chaperone FACT complex coordinates with HIF to mediate an expeditious transcription program to adapt to poorly oxygenated cancers. Cell Rep 2022; 38:110304. [PMID: 35108543 DOI: 10.1016/j.celrep.2022.110304] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 11/16/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Cancer cells adapt to hypoxia through HIFs (hypoxia-inducible factors), which initiate the transcription of numerous genes for cancer cell survival in the hypoxia microenvironment. In this study, we find that the FACT (facilitates chromatin transcription) complex works cooperatively with HIFs to facilitate the expeditious expression of HIF targets for hypoxia adaptation. Knockout (KO) of the FACT complex abolishes HIF-mediated transcription by impeding transcription elongation in hypoxic cancer cells. Interestingly, the FACT complex is post-translationally regulated by PHD/VHL-mediated hydroxylation and proteasomal degradation, in similar fashion to HIF-1/2α. Metabolic tracing confirms that FACT KO suppresses glycolytic flux and impairs lactate extrusion, leading to intracellular acidification and apoptosis in cancer cells. Therapeutically, hepatic artery ligation and anti-angiogenic inhibitors adversely induce intratumoral hypoxia, while co-treatment with FACT inhibitor curaxin remarkably hinders the growth of hypoxic tumors. In summary, our findings suggest that the FACT complex is a critical component of hypoxia adaptation and a therapeutic target for hypoxic tumors.
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Affiliation(s)
- Jialing Shen
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Chunxue Yang
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Misty Shuo Zhang
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Don Wai-Ching Chin
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - For-Fan Chan
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Cheuk-Ting Law
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Gengchao Wang
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Carol Lai-Hung Cheng
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Mengnuo Chen
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Rebecca Ting-Chi Wan
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Mengjie Wu
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Zhijian Kuang
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Rakesh Sharma
- Proteomic and Metabolic Core Facility, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Terence Kin Wah Lee
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Irene Oi-Lin Ng
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Carmen Chak-Lui Wong
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
| | - Chun-Ming Wong
- State Key Laboratory of Liver Research and Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
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Conconi A. The yeast rDNA locus: a model system to study DNA repair in chromatin. DNA Repair (Amst) 2007; 4:897-908. [PMID: 15996904 DOI: 10.1016/j.dnarep.2005.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2005] [Indexed: 11/23/2022]
Abstract
Most of the studies on the effect of chromatin structure and chromatin remodeling on DNA repair are based on in vitro reconstituted assays. In such experiments individual nucleosomes are either released by nuclease digestion of native chromatin fibers or are assembled from purified histones. Though reconstituted assays are valid approaches to follow NER in chromatin they are of somehow limited physiological relevance since single core particles do not exist in vivo [K. van Holde, J. Zlatanova, The nucleosome core particle: does it have structural and physiological relevance? Bioessays 21 (1999) 776-778]. This is particularly true for studies involving core histones tails, as in their natural chromatin context histones tails participate in interactions that are not necessarily present in vitro [J.C. Hansen, C. Tse, A.P. Wolffe, Structure and function of the core histone N-termini: more than meets the eye, Biochemistry 37 (1998) 17637-17641; J.J. Hayes, J.C. Hansen, Nucleosomes and chromatin fiber, Curr. Opin. Genet. Dev. 11 (2001) 124-129]. Indeed it was found that human DNA ligase I has the capability to ligate a nick on the surface of a 215bp nucleosome but not a nick in a nucleosome lacking linker DNA, possibly because of forced interactions between histone tails and core DNA present in the latter complex [D.R. Chafin, J.M. Vitolo, L.A. Henricksen, B.A. Bambara, J.J. Hayes, Human DNA ligase I efficiently seals nicks in nucleosomes, EMBO J. 19 (2000) 5492-5501]. In addition, chromatin remodeling could also occur in the higher ordered folding of chromatin and involve multiple arrays of nucleosomes [P.J. Horn, C.L. Peterson, Chromatin higher order folding: wrapping up transcription, Science 297 (2002) 1824-1827]. By studying the chromatin structure of ribosomal genes in yeast, our knowledge of the fate of nucleosomes during transcription and DNA replication has improved considerably [R. Lucchini, J.M. Sogo, The dynamic structure of ribosomal RNA gene chromatin, in: M.R. Paule (Ed.), Transcription of Ribosomal RNA Genes by Eukaryotic RNA Polymerase I, Springer-Verlag/R.G. Landes Company, 1998, pp. 254-276]. How nuclear processes such as DNA repair take place in chromatin is still largely unknown, and in this review I discuss how the yeast rDNA locus may be exploited to investigate DNA repair and chromatin modification in vivo.
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Affiliation(s)
- Antonio Conconi
- Department de Microbiologie et Infectiologie, Faculte de Medecine, Universite de Sherbrooke, 3001, 12(e) Avenue Nord, Sherbrooke, Que., Canada J1H 5N4
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Smith AT, Tucker-Samaras SD, Fairlamb AH, Sullivan WJ. MYST family histone acetyltransferases in the protozoan parasite Toxoplasma gondii. EUKARYOTIC CELL 2006; 4:2057-65. [PMID: 16339723 PMCID: PMC1317489 DOI: 10.1128/ec.4.12.2057-2065.2005] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The restructuring of chromatin precedes tightly regulated events such as DNA transcription, replication, and repair. One type of chromatin remodeling involves the covalent modification of nucleosomes by histone acetyltransferase (HAT) complexes. The observation that apicidin exerts antiprotozoal activity by targeting a histone deacetyltransferase has prompted our search for more components of the histone modifying machinery in parasitic protozoa. We have previously identified GNAT family HATs in the opportunistic pathogen Toxoplasma gondii and now describe the first MYST (named for members MOZ, Ybf2/Sas3, Sas2, and Tip60) family HATs in apicomplexa (TgMYST-A and -B). The TgMYST-A genomic locus is singular and generates a approximately 3.5-kb transcript that can encode two proteins of 411 or 471 amino acids. TgMYST-B mRNA is approximately 7.0 kb and encodes a second MYST homologue. In addition to the canonical MYST HAT catalytic domain, both TgMYST-A and -B possess an atypical C2HC zinc finger and a chromodomain. Recombinant TgMYST-A exhibits a predilection to acetylate histone H4 in vitro at lysines 5, 8, 12, and 16. Antibody generated to TgMYST-A reveals that both the long and short (predominant) versions are present in the nucleus and are also plentiful in the cytoplasm. Moreover, both TgMYST-A forms are far more abundant in rapidly replicating parasites (tachyzoites) than encysted parasites (bradyzoites). A bioinformatics survey of the Toxoplasma genome reveals numerous homologues known to operate in native MYST complexes. The characterization of TgMYST HATs represents another important step toward understanding the regulation of gene expression in pathogenic protozoa and provides evolutionary insight into how these processes operate in eukaryotic cells in general.
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Affiliation(s)
- Aaron T Smith
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 635 Barnhill Drive, Medical Sciences Building Room A-525, Indianapolis, IN 46202-5120, USA
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Pindolia KR, Lutter LC. Purification and Characterization of the Simian Virus 40 Transcription Elongation Complex. J Mol Biol 2005; 349:922-32. [PMID: 15907936 DOI: 10.1016/j.jmb.2005.04.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Revised: 04/21/2005] [Accepted: 04/23/2005] [Indexed: 11/22/2022]
Abstract
The transcriptional regulatory region of the simian virus 40 minichromosome that is being transcribed in the cell is nucleosome-free, while that of the non-transcribed minichromosome is nucleosome covered. Although additional studies have shown that the two structures are otherwise similar, the precision of these indirect studies has not been sufficient to determine if the transition between the two involves nucleosome displacement or nucleosome sliding. In order to address this question directly, we have developed a new function-based affinity isolation method that is capable of purifying the native transcription elongation complex of a single gene from mammalian cells. The simian virus 40 transcription elongation complex was purified by this method and the topological linking number of its DNA was compared directly to that of the bulk, non-transcribed minichromosome. The results show that the two types of minichromosome contain the same number of nucleosomes as well as nucleosomal structure. These findings indicate that interconversion between the non-transcribing and transcribing states is accomplished by a remodeling event involving nucleosome sliding rather than nucleosome displacement.
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Affiliation(s)
- Kirit R Pindolia
- Molecular Biology Research Program, Henry Ford Hospital, Detroit, MI 48202-3450, USA
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