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Transcriptomics: applications in epigenetic toxicology.

Toxicology and epigenetics, first edition. Sahu SC, ed., Chichester, West Sussex, United Kingdom: John Wiley & Sons, Ltd., 2012 Oct; :445-458
Epigenetics has been defined as the study of mitotically (and potentially meiotically) heritable alterations in gene expression that are not caused by changes in DNA sequence (Waterland, 2006). Some of the other definitions of epigenetics are broader than this and do not necessarily involve inheritance of the gene expression changes. For example, the (US National Institutes of Health NIH, 2009) state that 'epigenetics refers to both heritable changes in gene activity and expression and also stable, long-term, and alterations in the transcriptional potential of a cell that are not necessarily heritable.' Regardless of the definition, the major epigenetic processes responsible for alterations in gene expression are DNA methylation, histone modification, and various RNA-mediated processes. The net result of epigenetics, irrespective of the process involved, is alteration in the expression of one or several genes. Virtually every biological process in a cell is controlled by gene expression. Therefore gene expression changes, including those resulting from epigenetic events, need to be determined in order to understand the biological consequences of gene expression changes. Several techniques are available to determine gene expression profiles of biological samples. These include northern hybridization, quantitative real time PCR (QRT-PCR), subtractive hybridization, serial analysis of gene expression (SAGE), differential display, and microarray analysis. Depending on the objective of the analysis one or more of the previously-mentioned techniques may be employed to determine the gene expression profile of biological samples. However, the most popular techniques employed currently are QRT -PCR and microarray analysis. If the intent is to determine the expression of a single or a limited number of genes expressed in a biological sample, the method of choice clearly is QRT-PCR analysis. QRT-PCR analysis is a relatively simple procedure that involves reverse transcription of mRNA followed by PCR amplification of the resulting eDNA using oligonucleotide primers specific for the gene of interest as well as one or more house-keeping genes and quantification of the PCR amplified gene products. However, if the objective is to determine the expression of several hundreds or thousands or all of the genes expressed in a biological sample, QRT-PCR would not be the practical choice. Microarray analysis has the unique advantage of determining the expression of almost all the genes expressed in a biological sample and, therefore, is the method of choice to determine large scale global gene expression profiles in biological samples. This chapter is, therefore, focused on the microarray analysis of global gene expression profiles. The technical aspects of rnicroarray analysis, advantages of microarray analysis, and the challenges microarray analysis faces currently are presented in this chapter.
Genes; Genetic-factors; Genetics; Toxicology; Environmental-factors; Cell-alteration; Cell-transformation; Cellular-structures; Deoxyribonucleic-acids; Recombinant-DNA; Ribonucleic-acids; Biological-effects; Biological-function; Analytical-instruments; Analytical-processes; Biological-material; Nucleotides; Microscopic-analysis
Pius Joseph, Molecular Carcinogenesis Laboratory, Toxicology and Molecular Biology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health (NIOSH), Morgantown, WV, USA
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Toxicology and epigenetics, first edition.