JBM  Vol.3 No.6 , June 2015
Comparative Epigenetic Analyses of Acute and Chronic Leukemia
Abstract: Comparative analysis of epigenetic alterations between acute vs. chronic leukemia, with an emphasis on histone modifications, was conducted. We focus on the promoter regions of the whole genomes as well as oncogenes. Our results revealed that obvious differential histone modifications pattern exists between the two subtypes. H3K27ac has a high tag density in the promoter region in both Dnd41 cell lines and K562 cell lines. H3K27ac and H3K4me1 have high correlation between the two cell lines of oncogenes. Similar results were also achieved in the promoter region of high expression genes in the Jurkat and K562 cell lines based on RNA-seq data. This suggests that H2K27ac and H3K4me1 are active regulators in leukemia cell lines.
Cite this paper: Zhang, Y. and Guo, D. (2015) Comparative Epigenetic Analyses of Acute and Chronic Leukemia. Journal of Biosciences and Medicines, 3, 29-35. doi: 10.4236/jbm.2015.36005.

[1]   Skinner, M.K., Manikkam, M. and Guerrero-Bosagna, C. (2010) Epigenetic Transgenerational Actions of Environmental Factors in Disease Etiology. Trends in Endocrinology & Metabolism, 21, 214-222.

[2]   Doherty, R., Farrelly, C.O. and Meade, K.G. (2014) Comparative Epigenetics: Relevance to the Regulation of Production and Health Traits in Cattle. Animal Genetics, 45, 3-14.

[3]   Bhat, A.A., Wani, H.A., Beigh, M.A., Bhat, S.A., Jeelani, S., Massood, A., et al. (2013) Epigenetic Promoter Methylation of hmlh1 Gene in Human Gut Malignancies: A Comparative Study. Journal of Investigational Biochemistry, 2, 101-108.

[4]   Feinberg, A.P. and Tycko, B. (2004) The History of Cancer Epigenetics. Nature Reviews Cancer, 4, 143-153.

[5]   Deakin, J.E., Domaschenz, R., Lim, P.S., Ezaz, T. and Rao, S. (2014) Comparative Epigenomics: An Emerging Field with Breakthrough Potential to Understand Evolution of Epigenetic Regulation. AIMS Genetics, 1, 34-54. Wit, E. and McClure, J. (2004) Statistics for Microarrays: Design, Analysis, and Inference. 5th Edition, John Wiley & Sons Ltd., Chichester.

[6]   Henrique, R., Luis, A. and Jerónimo, C. (2012) The Epigenetics of Renal Cell Tumors: From Biology to Biomarkers. Frontiers in Genetics, 3, 94. Giambastiani, B.M.S. (2007) Evoluzione Idrologica ed Idrogeologica Della Pineta di san Vitale (Ravenna). Ph.D. Thesis, Bologna University, Bologna.

[7]   Kouzarides, T. (2007) Chromatin Modifications and Their Function. Cell, 128, 693-705. Honeycutt, L. (1998) Communication and Design Course.

[8]   Shi, Y. (2007) Histone Lysine Demethylases: Emerging Roles in Development, Physiology and Disease. Nature Reviews Genetics, 8, 829-833.

[9]   Fraga, M.F., Ballestar, E., Villar-Garea, A., Boix-Chornet, M., Espada, J., Schotta, G., et al. (2005) Loss of Acetylation at Lys16 and Trimethylation at Lys20 of Histone H4 Is a Common Hallmark of Human Cancer. Nature Genetics, 37, 391-400.

[10]   Nguyen, C.T., Weisenberger, D.J., Velicescu, M., Gonzales, F.A., Lin, J.C., Liang, G., et al. (2002) Histone H3-Lysine 9 Methylation Is Associated with Aberrant Gene Silencing in Cancer Cells and Is Rapidly Reversed by 5-Aza-2′- deoxycytidine. Cancer Research, 62, 6456-6461.

[11]   Li, Y., Li, S., Chen, J., Shao, T., Jiang, C., Wang, Y., et al. (2014) Comparative Epigenetic Analyses Reveal Distinct Patterns of Oncogenic Pathways Activation in Breast Cancer Subtypes. Human Molecular Genetics, 23, 5378-5393.

[12]   Langmead, B. and Salzberg, S.L. (2012) Fast Gapped-Read Alignment with Bowtie 2. Nature Methods, 9, 357-359.

[13]   Wang, L., Feng, Z., Wang, X., Wang, X. and Zhang, X. (2010) DEGseq: An R Package for Identifying Differentially Expressed Genes from RNA-seq Data. Bioinformatics, 26, 136-138.

[14]   Pruitt, K.D., Tatusova, T. and Maglott, D.R. (2007) NCBI Ref-erence Sequences (RefSeq): A Curated Non-Redundant Sequence Database of Genomes, Transcripts and Proteins. Nucleic Acids Research, 35, D61-D65.

[15]   Xu, H., Wei, C.-L., Lin, F. and Sung, W.-K. (2008) An HMM Approach to Genome-Wide Identification of Differential Histone Modification Sites from ChIP-seq Data. Bioinformatics, 24, 2344-2349.

[16]   DeWoskin, V.A. and Million, R.P. (2013) The Epigenetics Pipeline. Nature Reviews Drug Discovery, 12, 661-662.