Hostname: page-component-78c5997874-s2hrs Total loading time: 0 Render date: 2024-11-10T08:34:22.336Z Has data issue: false hasContentIssue false
  • English
  • Français

Epigenetic transcriptional gene silencing in Entamoeba histolytica: insight into histone and chromatin modifications

Published online by Cambridge University Press:  23 October 2009

MAYA HUGUENIN ,
RIVKA BRACHA ,
THANAT CHOOKAJORN  and
DAVID MIRELMAN
MAYA HUGUENIN
Affiliation:
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot76100, Israel
RIVKA BRACHA
Affiliation:
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot76100, Israel
THANAT CHOOKAJORN
Affiliation:
Department of Biochemistry, Faculty of Science, Mahidol University, Rama VI Rd. Bangkok10400, Thailand
DAVID MIRELMAN*
Affiliation:
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot76100, Israel
*
*Corresponding author: Weizmann Institute of Science, Department of Biological Chemistry, PO Box 26, Rehovot, Israel. Tel: +972 8 9344511. Fax: +972 8 9344118. E-mail: david.mirelman@weizmann.ac.il
Get access Rights & Permissions [Opens in a new window]

Summary

We have previously discovered a unique mechanism of epigenetic transcriptional gene silencing in the Entamoeba histolytica trophozoites of strain HM-1:IMSS that resulted in the persistent downregulation of the amoebapore A (ap-a) gene, and that could be successfully applied to silence other virulence genes (cpA5, lgl1). In order to understand how the silencing is maintained throughout generations, we analysed whether modifications occurred at the chromatin level. Chromatin immunoprecipitation assays were done with antibodies specific to the methylated lysine 4 of E. histolytica histone H3. When the genes were in a transcriptionally silent state, the methylation levels of H3K4 in their coding region were significantly reduced. In contrast, the levels of core histone H3 were consistently higher in the silenced genes. Controlled chromatin digestion with micrococcal nuclease was used to assess changes in nucleosome compaction. We found a significant resistance to digestion in the promoter region of the silenced ap-a and cpA5 genes as compared to the parental strain that expresses those genes. Our data lend further support to the idea that histone modifications and heterochromatin formations are at the basis of the transcriptional silencing of genes in E. histolytica.

Keywords

Entamoeba histolyticaepigenetic silencinghistone methylationchromatin modificationsheterochromatin
Type
Research Article
Information
Parasitology , Volume 137 , Issue 4 , April 2010 , pp. 619 - 627
Copyright
Copyright © Cambridge University Press 2009

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

REFERENCES

Adkins, M. W. and Tyler, J. K. (2006). Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions. Molecular Cell 21, 405–416.Google Scholar
An, W. (2007). Histone acetylation and methylation: combinatorial players for transcriptional regulation. Subcellar Biochemistry 41, 351–369.Google ScholarPubMed
Anbar, M., Bracha, R., Nuchamowitz, Y., Li, Y., Florentin, A. and Mirelman, D. (2005). Involvement of a short interspersed element in epigenetic transcriptional silencing of the amoebapore gene in Entamoeba histolytica. Eukaryotic Cell 4, 1775–1784.CrossRefGoogle Scholar
Aravind, L. and Iyer, L. M. (2002). The SWIRM domain: a conserved module found in chromosomal proteins points to novel chromatin-modifying activities. Genome Biology 3, RESEARCH0039.1–0039.7.Google Scholar
Becker, P. B. and Horz, W. (2002). ATP-dependent nucleosome remodeling. Annual Review of Biochemistry 71, 247–273.CrossRefGoogle ScholarPubMed
Bernstein, B. E., Humphrey, E. L., Erlich, R. L., Schneider, R., Bouman, P., Liu, J. S., Kouzarides, T. and Schreiber, S. L. (2002). Methylation of histone H3 Lys 4 in coding regions of active genes. Proceedings of the National Academy of Sciences, USA 99, 8695–8700.Google Scholar
Bracha, R., Nuchamowitz, Y., Anbar, M. and Mirelman, D. (2006). Transcriptional silencing of multiple genes in trophozoites of Entamoeba histolytica. PLoS Pathogen 2, e48.CrossRefGoogle ScholarPubMed
Bracha, R., Nuchamowitz, Y. and Mirelman, D. (2003). Transcriptional silencing of an amoebapore gene in Entamoeba histolytica: molecular analysis and effect on pathogenicity. Eukaryotic Cell 2, 295–305.CrossRefGoogle ScholarPubMed
Bruchhaus, I., Leippe, M., Lioutas, C. and Tannich, E. (1993). Unusual gene organization in the protozoan parasite Entamoeba histolytica. DNA and Cell Biology 12, 925–933.CrossRefGoogle ScholarPubMed
Byers, J., Faigle, W. and Eichinger, D. (2005). Colonic short-chain fatty acids inhibit encystation of Entamoeba invadens. Celullar Microbiology 7, 269–279.Google Scholar
Chen, Y., Yang, Y., Wang, F., Wan, K., Yamane, K., Zhang, Y. and Lei, M. (2006). Crystal structure of human histone lysine-specific demethylase 1 (LSD1). Proceedings of the National Academy of Sciences, USA 103, 13956–13961.Google Scholar
Chookajorn, T., Dzikowski, R., Frank, M., Li, F., Jiwani, A. Z., Hartl, D. L. and Deitsch, K. W. (2007). Epigenetic memory at malaria virulence genes. Proceedings of the National Academy of Sciences, USA 104, 899–902.CrossRefGoogle ScholarPubMed
Csink, A. K., Bounoutas, A., Griffith, M. L., Sabl, J. F. and Sage, B. T. (2002). Differential gene silencing by trans-heterochromatin in Drosophila melanogaster. Genetics 160, 257–269.CrossRefGoogle ScholarPubMed
Diamond, L. S., Harlow, D. R. and Cunnick, C. C. (1978). A new medium for the axenic cultivation of Entamoeba histolytica and other Entamoeba. Transactions of the Royal Society of Tropical Medicine and Hygiene 72, 431–432.CrossRefGoogle ScholarPubMed
Fodinger, M., Ortner, S., Plaimauer, B., Wiedermann, G., Scheiner, O. and Duchene, M. (1993). Pathogenic Entamoeba histolytica: cDNA cloning of a histone H3 with a divergent primary structure. Molecular and Biochemical Parasitology 59, 315–322.CrossRefGoogle ScholarPubMed
Forneris, F., Binda, C., Dall'aglio, A., Fraaije, M. W., Battaglioli, E. and Mattevi, A. (2006). A highly specific mechanism of histone H3-K4 recognition by histone demethylase LSD1. Journal of Biological Chemistry 281, 35289–35295.Google Scholar
Gal-Yam, E. N., Jeong, S., Tanay, A., Egger, G., Lee, A. S. and Jones, P. A. (2006). Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting. PLoS Genetics 2, e160.Google Scholar
Gangaraju, V. K. and Bartholomew, B. (2007). Mechanisms of ATP dependent chromatin remodeling. Mutation Research 618, 3–17.CrossRefGoogle ScholarPubMed
Grewal, S. I. and Elgin, S. C. (2002). Heterochromatin: new possibilities for the inheritance of structure. Current Opinion in Genetics and Development 12, 178–187.CrossRefGoogle ScholarPubMed
Gross, D. S. and Garrard, W. T. (1988). Nuclease hypersensitive sites in chromatin. Annual Review of Biochemistry 57, 159–197.Google Scholar
Hakimi, M. A. and Deitsch, K. W. (2007). Epigenetics in Apicomplexa: control of gene expression during cell cycle progression, differentiation and antigenic variation. Current Opinion in Microbiology 10, 357–362.Google Scholar
Henikoff, S. (2008). Nucleosome destabilization in the epigenetic regulation of gene expression. Nature Reviews Genetics 9, 15–26.CrossRefGoogle ScholarPubMed
Jenuwein, T. and Allis, C. D. (2001). Translating the histone code. Science 293, 1074–1080.CrossRefGoogle ScholarPubMed
Kawasaki, H., Taira, K. and Morris, K. V. (2005). siRNA induced transcriptional gene silencing in mammalian cells. Cell Cycle 4, 442–448.CrossRefGoogle ScholarPubMed
Kornberg, R. D. and Lorch, Y. (1999). Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome. Cell 98, 285–294.Google Scholar
Kouzarides, T. (2002). Histone methylation in transcriptional control. Current Opinion in Genetics & Development 12, 198–209.Google Scholar
Lachner, M. and Jenuwein, T. (2002). The many faces of histone lysine methylation. Current Opinion in Cell Biology 14, 286–298.CrossRefGoogle ScholarPubMed
Lachner, M., O'carroll, D., Rea, S., Mechtler, K. and Jenuwein, T. (2001). Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature, London 410, 116–120.Google Scholar
Lin, J. C., Jeong, S., Liang, G., Takai, D., Fatemi, M., Tsai, Y. C., Egger, G., Gal-Yam, E. N. and Jones, P. A. (2007). Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. Cancer Cell 12, 432–444.CrossRefGoogle ScholarPubMed
Loo, S. and Rine, J. (1995). Silencing and heritable domains of gene expression. Annual Review Cell and Developmental Biology 11, 519–548.CrossRefGoogle ScholarPubMed
Lopez-Rubio, J. J., Riviere, L. and Scherf, A. (2007). Shared epigenetic mechanisms control virulence factors in protozoan parasites. Current Opinion in Microbiology 10, 560–568.CrossRefGoogle ScholarPubMed
Mirelman, D., Anbar, M. and Bracha, R. (2008). Epigenetic transcriptional gene silencing in Entamoeba histolytica. International Union of Biochemistry and Molecular Biology Life 60, 598–604.CrossRefGoogle ScholarPubMed
Moazed, D. (2001). Common themes in mechanisms of gene silencing. Molecular Cell 8, 489–498.Google Scholar
Nakayama, J., Rice, J. C., Strahl, B. D., Allis, C. D. and Grewal, S. I. (2001). Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292, 110–113.Google Scholar
Parnell, T. J., Huff, J. T. and Cairns, B. R. (2008). RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes. EMBO Journal 27, 100–110.Google Scholar
Pokholok, D. K., Harbison, C. T., Levine, S., Cole, M., Hannett, N. M., Lee, T. I., Bell, G. W., Walker, K., Rolfe, P. A., Herbolsheimer, E., Zeitlinger, J., Lewitter, F., Gifford, D. K. and Young, R. A. (2005). Genome-wide map of nucleosome acetylation and methylation in yeast. Cell 122, 517–527.CrossRefGoogle ScholarPubMed
Richard-Foy, H. and Hager, G. L. (1987). Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter. EMBO Journal 6, 2321–2328.Google Scholar
Santos-Rosa, H., Schneider, R., Bannister, A. J., Sherriff, J., Bernstein, B. E., Emre, N. C., Schreiber, S. L., Mellor, J. and Kouzarides, T. (2002). Active genes are tri-methylated at K4 of histone H3. Nature, London 419, 407–411.Google Scholar
Schotta, G., Lachner, M., Sarma, K., Ebert, A., Sengupta, R., Reuter, G., Reinberg, D. and Jenuwein, T. (2004). A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes & Development 18, 1251–1262.CrossRefGoogle ScholarPubMed
Schubeler, D., Macalpine, D. M., Scalzo, D., Wirbelauer, C., Kooperberg, C., Van Leeuwen, F., Gottschling, D. E., O'neill, L. P., Turner, B. M., Delrow, J., Bell, S. P. and Groudine, M. (2004). The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes & Development 18, 1263–1271.Google Scholar
Strahl, B. D. and Allis, C. D. (2000). The language of covalent histone modifications. Nature, London 403, 41–45.CrossRefGoogle ScholarPubMed
Sun, Z. W. and Allis, C. D. (2002). Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature, London 418, 104–108.CrossRefGoogle ScholarPubMed
Taverna, S. D., Li, H., Ruthenburg, A. J., Allis, C. D. and Patel, D. J. (2007). How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nature Structural and Molecular Biology 14, 1025–1040.Google Scholar
Van Rietschoten, J. G., Gal-Yam, E. N., Jeong, S., Cortez, C. C., Verweij, C. L. and Jones, P. A. (2008). Epigenetic regulation and nucleosome positioning in the human TATA-less IL-1 alpha promoter. Genes and Immunity 9, 582–590.Google Scholar
Vaucheret, H. and Fagard, M. (2001). Transcriptional gene silencing in plants: targets, inducers and regulators. Trends in Genetics 17, 29–35.Google Scholar
Wang, H., Cao, R., Xia, L., Erdjument-Bromage, H., Borchers, C., Tempst, P. and Zhang, Y. (2001). Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase. Molecular Cell 8, 1207–1217.Google Scholar