Transcriptomics is the study of the transcriptome, which is defi ned as the complete set of transcripts or a specifi c subset of transcripts (e.g., messenger RNA molecules) produced from the genome in one cell or a population of cells of a given organism at any one time. Recent studies of plant development and environmental stress responses have converged on the roles of RNA and its metabolism as primary regulators of gene action (Hollick 2008). Most translational regulation factors such as proteases and kinases are also products of transcripts. Importantly, the RNA-dependent
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epigenome plays an essential role in both development and evolution of higher organisms. The epigenome forms a complex network, which cannot be studied only at the classical single gene level. For example, there are both positive and negative regulatory interactions among substantial numbers of transcription factors but no single transcription factor is both necessary and suffi cient to drive the human cell differentiation process (Center 2009). Transcriptomics approaches are particularly suitable for analysis of the cell epigenome as a whole at the transcriptional level.