table of contents 
This work represents the first genome-wide analysis of histone acetylation and its …
|
- Li B, Carey M, Workman JL: The role of chromatin during transcription. Cell 2007, 128:707-719.
- Jenuwein T, Allis CD: Translating the histone code. Science 2001, 293:1074-1080.
- Rea S, Eisenhaber F, O'Carroll D, Strahl BD, Sun ZW, Schmid M, Opravil S, Mechtler K, Ponting CP, Allis CD, Jenuwein T: Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 2000, 406:593-599.
- Martin C, Zhang Y: The diverse functions of histone lysine methylation. Nat Rev Mol Cell Biol 2005, 6:838-849.
- Luo RX, Dean DC: Chromatin remodeling and transcriptional regulation. J Natl Cancer Inst 1999, 91:1288-1294.
- Imai S, Armstrong CM, Kaeberlein M, Guarente L: Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 2000, 403:795-800.
- Garcia BA, Hake SB, Diaz RL, Kauer M, Morris SA, Recht J, Shabanowitz J, Mishra N, Strahl BD, Allis CD, Hunt DF: Organismal differences in post-translational modifications in histones H3 and H4. J Biol Chem 2007, 282:7641-7655.
- Earley K, Lawrence RJ, Pontes O, Reuther R, Enciso AJ, Silva M, Neves N, Gross M, Viegas W, Pikaard CS: Erasure of histone acetylation by Arabidopsis HDA6 mediates large-scale gene silencing in nucleolar dominance. Genes Dev 2006, 20:1283-1293.
- Daujat S, Bauer UM, Shah V, Turner B, Berger S, Kouzarides T: Crosstalk between CARM1 methylation and CBP acetylation on histone H3. Curr Biol 2002, 12:2090-2097.
- Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA: Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2004, 119:941-953.
- WHO: Entamoeba taxonomy. Bulletin of the World Health Organization 1997, 75:291-294.
- Weber C, Guigon G, Bouchier C, Frangeul L, Moreira S, Sismeiro O, Gouyette C, Mirelman D, Coppee JY, Guillen N: Stress by heat shock induces massive down regulation of genes and allows differential allelic expression of the Gal/GalNAc lectin in Entamoeba histolytica. Eukaryot Cell 2006, 5:871-875.
- Akbar MA, Chatterjee NS, Sen P, Debnath A, Pal A, Bera T, Das P: Genes induced by a high-oxygen environment in Entamoeba histolytica. Mol Biochem Parasitol 2004, 133:187-196.
- Ehrenkaufer GM, Haque R, Hackney JA, Eichinger DJ, Singh U: Identification of developmentally regulated genes in Entamoeba histolytica: insights into mechanisms of stage conversion in a protozoan parasite. Cell Microbiol 2007.
- Singh U, Rogers JB, Mann BJ, Petri WA Jr.: Transcription initiation is controlled by three core promoter elements in the hgl5 gene of the protozoan parasite Entamoeba histolytica. Proc Natl Acad Sci U S A 1997, 94:8812-8817.
- Ali IK, Ehrenkaufer GM, Hackney JA, Singh U: Growth of the protozoan parasite Entamoeba histolytica in 5-azacytidine has limited effects on parasite gene expression. BMC Genomics 2007, 8:7.
- Banerjee S, Fisher O, Lohia A, Ankri S: Entamoeba histolytica DNA methyltransferase (Ehmeth) is a nuclear matrix protein that binds EhMRS2, a DNA that includes a scaffold/matrix attachment region (S/MAR). Mol Biochem Parasitol 2005, 139:91-97.
- Ramakrishnan G, Gilchrist CA, Musa H, Torok MS, Grant PA, Mann BJ, Petri WA Jr.: Histone acetyltransferases and deacetylase in Entamoeba histolytica. Mol Biochem Parasitol 2004, 138:205-216.
- Byers J, Eichinger D: Acetylation of the Entamoeba histone H4 N-terminal domain is influenced by short chain fatty acids that enter trophozoites in a pH-dependent manner. Submitted to IJP 2007.
- Kiefer J, Beyer-Sehlmeyer G, Pool-Zobel BL: Mixtures of SCFA, composed according to physiologically available concentrations in the gut lumen, modulate histone acetylation in human HT29 colon cancer cells. Br J Nutr 2006, 96:803-810.
- Blottiere HM, Buecher B, Galmiche JP, Cherbut C: Molecular analysis of the effect of short-chain fatty acids on intestinal cell proliferation. Proc Nutr Soc 2003, 62:101-106.
- Hinnebusch BF, Meng S, Wu JT, Archer SY, Hodin RA: The effects of short-chain fatty acids on human colon cancer cell phenotype are associated with histone hyperacetylation. J Nutr 2002, 132:1012-1017.
- Byers J, Faigle W, Eichinger D: Colonic short-chain fatty acids inhibit encystation of Entamoeba invadens. Cell Microbiol 2005, 7:269-279.
- Saksouk N, Bhatti MM, Kieffer S, Smith AT, Musset K, Garin J, Sullivan WJ Jr., Cesbron-Delauw MF, Hakimi MA: Histone-modifying complexes regulate gene expression pertinent to the differentiation of the protozoan parasite Toxoplasma gondii. Mol Cell Biol 2005, 25:10301-10314.
- Boyle JP, Saeij JP, Cleary MD, Boothroyd JC: Analysis of gene expression during development: lessons from the Apicomplexa. Microbes Infect 2006, 8:1623-1630.
- Freitas-Junior LH, Hernandez-Rivas R, Ralph SA, Montiel-Condado D, Ruvalcaba-Salazar OK, Rojas-Meza AP, Mancio-Silva L, Leal-Silvestre RJ, Gontijo AM, Shorte S, Scherf A: Telomeric heterochromatin propagation and histone acetylation control mutually exclusive expression of antigenic variation genes in malaria parasites. Cell 2005, 121:25-36.
- Gilchrist CA, Houpt E, Trapaidze N, Fei Z, Crasta O, Asgharpour A, Evans C, Martino-Catt S, Baba DJ, Stroup S, Hamano S, Ehrenkaufer G, Okada M, Singh U, Nozaki T, Mann BJ, Petri WA Jr.: Impact of intestinal colonization and invasion on the Entamoeba histolytica transcriptome. Mol Biochem Parasitol 2006, 147:163-176.
- Field J, Van Dellen K, Ghosh SK, Samuelson J: Responses of Entamoeba invadens to heat shock and encystation are related. J Eukaryot Microbiol 2000, 47:511-514.
- Sakata T, von Engelhardt W: Stimulatory effect of short chain fatty acids on the epithelial cell proliferation in rat large intestine. Comp Biochem Physiol A 1983, 74:459-462.
- Fusunyan RD, Quinn JJ, Fujimoto M, MacDermott RP, Sanderson IR: Butyrate switches the pattern of chemokine secretion by intestinal epithelial cells through histone acetylation. Mol Med 1999, 5:631-640.
- Drozdowski LA, Dixon WT, McBurney MI, Thomson AB: Short-chain fatty acids and total parenteral nutrition affect intestinal gene expression. JPEN J Parenter Enteral Nutr 2002, 26:145-150.
- Sanderson IR: Short chain fatty acid regulation of signaling genes expressed by the intestinal epithelium. J Nutr 2004, 134:2450S-2454S.
- Chang S, Pikaard CS: Transcript profiling in Arabidopsis reveals complex responses to global inhibition of DNA methylation and histone deacetylation. J Biol Chem 2005, 280:796-804.
- Ou JN, Torrisani J, Unterberger A, Provencal N, Shikimi K, Karimi M, Ekstrom TJ, Szyf M: Histone deacetylase inhibitor Trichostatin A induces global and gene-specific DNA demethylation in human cancer cell lines. Biochem Pharmacol 2007.
- Diamond LS, Harlow DR, Cunnick CC: A new medium for the axenic cultivation of Entamoeba histolytica and other Entamoeba. Trans R Soc Trop Med Hyg 1978, 72:431-432.
- Ali IK, Zaki M, Clark CG: Use of PCR amplification of tRNA gene-linked short tandem repeats for genotyping Entamoeba histolytica. J Clin Microbiol 2005, 43:5842-5847.
- Haghighi A, Kobayashi S, Takeuchi T, Thammapalerd N, Nozaki T: Geographic diversity among genotypes of Entamoeba histolytica field isolates. J Clin Microbiol 2003, 41:3748-3756.
- CMGM: Stanford Pan facility. [http://cmgm.stanford.edu/pan/]
- Affymetrix P: Affymetrix protocols. [http://www.affymetrix.com/support/technical/manual/expression_manual.affx]
- GCOS: GCOS manual. [http://www.affymetrix.com/products/software/specific/gcos.affx]
- Bioconductor: Bioconductor. [http://www.bioconductor.org]
- Wu Z, Irizarry R, Gentleman R, Murillo F, F S: A model based background adjustment for oligonucleotide expression arrays. Technical report; John Hopkins University, Dept of Biostatistics Working Papers 2004.
- Jain N, Thatte J, Braciale T, Ley K, O'Connell M, Lee JK: Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. Bioinformatics 2003, 19:1945-1951.
- Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 1995, 57:289-300.
- Genespring: Genespring. [http://www.chem.agilent.com/scripts/pds.asp?lpage=27881]
rating: 0.00 from 0 votes | updated on: 26 Mar 2008 | views: 780 |
|