Abstract
A chromatin immunoprecipitation (ChIP) assay is a method to identify how much a protein of interest binds to the DNA region. This method is indispensable to study the mechanisms of how the transcription factors or chromatin modifications regulate the gene expression. Candida albicans is a dimorphic pathogenic fungus, which can change its morphology very rapidly from yeast to hypha in response to the environmental signal. The morphological change of C. albicans is one of the critical factors for its virulence. Therefore, it is necessary to understand how to regulate the expression of genes for C. albicans to change its morphology. One of the essential methods for us to understand this regulation is a ChIP assay. There have been many efforts to optimize the protocol to lower the background signal and to analyze the results accurately because a ChIP assay can provide very different results even with slight differences in the experimental procedure. We have optimized the rapid and efficient ChIP protocol so that it could be applied equally for both yeast and hyphal forms of C. albicans. Our method in this protocol is also comparatively rapid to the method widely used. In this protocol, we described our rapid method for the ChIP assay in C. albicans in detail.
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References
Adli, M. and Bernstein, B.E. 2011. Whole-genome chromatin profiling from limited numbers of cells using nano-ChlP-seq. Nat. Protoc.6, 1656–1668.
Biswas, S., Van Dijck, P., and Datta, A. 2007. Environmental sensing and signal transduction pathways regulating morphopathogenic determinants of Candida albicans. Microbiol. Mol. Biol. Rev.71, 348–376.
Collas, P. 2010. The current state of chromatin immunoprecipitation. Mol. Biotechnol.45, 87–100.
Ernst, J.F. 2000. Transcription factors in Candida albicans — environmental control of morphogenesis. Microbiology146, 1763–1774.
Furey, T.S. 2012. ChIP-seq and beyond: New and improved methodologies to detect and characterize protein-DNA interactions. Nat. Rev. Genet.13, 840–852.
Gow, N.A.R., Brown, A.J.P., and Odds, F.C. 2002. Fungal morphogenesis and host invasion. Curr. Opin. Microbiol.5, 366–371.
Grainger, D.C., Overton, T.W., Reppas, N., Wade, J.T., Tamai, E., Hobman, J.L., Constantinidou, C., Strahl, K., Church, G., and Busby, S.J.W. 2004. Genomic studies with Escherichia coli MelR protein: Applications of chromatin immunoprecipitation and microarrays. J. Bacteriol.186, 6938–6943.
Haring, M., Offermann, S., Danker, T., Horst, L., Peterhansel, C., and Stam, M. 2007. Chromatin immunoprecipitation: Optimization, quantitative analysis and data normalization. Plant Methods3, 11.
Hoffman, E.A., Frey, B.L., Smith, L.M., and Auble, D.T. 2015. Formaldehyde crosslinking: A tool for the study of chromatin complexes. J. Biol. Chem.290, 26404–26411.
Jackson, V. 1978. Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent. Cell15, 945–954.
Kahramanoglou, C., Seshasayee, A.S.N., Prieto, A.I., Ibberson, D., Schmidt, S., Zimmermann, J., Benes, V., Fraser, G.M., and Luscombe, N.M. 2011. Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res.39, 2073–2091.
Kim, J. and Sudbery, P. 2011. Candida albicans, a major human fungal pathogen. J. Microbiol.49, 171–177.
Kitamura, K. and Yamamoto, Y. 1972. Purification and properties of an enzyme, zymolyase, which lyses viable yeast cells. Arch. Biochem. Biophys.153, 403–406.
Klis, F.M., Groot, P.D., and Hellingwerf, K. 2001. Molecular organization of the cell wall of Candida albicans Med. Mycol.39, 1–8.
Li, B., Carey, M., and Workman, J.L. 2007. The role of chromatin during transcription. Cell128, 707–719.
Lohse, M.B., Kongsomboonvech, P., Madrigal, M., Hernday, A.D., and Nobile, C.J. 2016. Genome-wide chromatin immunoprecipitation in Candida albicans and other yeasts. Methods Mol. Biol.1361, 161–184.
Lu, K., Ye, W., Zhou, L., Collins, L.B., Chen, X., Gold, A., Ball, L.M., and Swenberg, J.A. 2010. Structural characterization of formaldehyde-induced cross-links between amino acids and deoxynucleosides and their oligomers. J. Am. Chem. Soc.132, 3388–3399.
Marcilla, A., Elorza, M.V., Mormeneo, S., Rico, H., and Sentandreu, R. 1991. Candida albicans mycelial wall structure: Supramolecular complexes released by zymolyase, chitinase and β-mercaptoethanol. Arch. Microbiol.155, 312–319.
Mayer, F.L., Wilson, D., and Hube, B. 2013. Candida albicans pathogenicity mechanisms. Virulence4, 119–128.
Mitra, S., Rai, L.S., Chatterjee, G., and Sanyal, K. 2016. Chromatin immunoprecipitation (ChIP) assay in Candida albicans. Methods Mol. Biol.1356, 43–57.
Park, P.J. 2009. ChIP-seq: Advantages and challenges of a maturing technology. Nat. Rev. Genet.10, 669–680.
Rodríguez-Peña, J.M., Díez-Muñiz, S., Bermejo, C., Nombela, C., and Arroyo, J. 2013. Activation of the yeast cell wall integrity MAPK pathway by zymolyase depends on protease and glucanase activities and requires the mucin-like protein Hkr1 but not Msb2. FEES Lett.87, 3675–3680.
Scott, J.H. and Schekman, R. 1980. Lyticase: Endoglucanase and protease activities that act together in yeast cell lysis. J. Bacteriol.142, 414–423.
Sudbery, P., Gow, N., and Berman, J. 2004. The distinct morphogenic states of Candida albicans. Trends Microbiol.12, 317–324.
Acknowledgements
This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korean Government (MSIP) (No. NRF-2015R1A4A1041105, NRF-2015R1-D1A1A02061743, and NRF-2018R1D1A1A02048280). Jueun Kim was supported by Global Ph.D. Fellowship Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2014H1A2A-1021300).
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Kim, J., Lee, JS. Rapid method for chromatin immunoprecipitation (ChIP) assay in a dimorphic fungus, Candida albicans. J Microbiol. 58, 11–16 (2020). https://doi.org/10.1007/s12275-020-9143-2
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DOI: https://doi.org/10.1007/s12275-020-9143-2