DNA modifications can influence a variety of processes in many organisms, including gene expression, gene silencing, host pathogen interactions, and DNA replication, repair, and transcription regulation [65].
Over the last decade, microarray-based expression profiling has provided a reliable high-throughput platform for genome-wide analysis of gene expression in many organisms.
MPSS has been used for whole genome transcription analysis in the last decade and has generated abundant data concerning expression in many organisms (Vega-Sanchez et al. 2007; Simon et al. 2009).
In recent years, many studies have focused on heterochromatin located at chromosome ends, which plays an important role in regulating gene expression in many organisms ranging from yeast to humans.
Subsequent studies have shown that EGS technology can be used to down-regulate gene expression in many organisms, such as bacteria, [ 9- 12] mammalian cells [ 13- 19]and maize cells[ 20].
In addition methylation is known to be involved in control of gene expression in many organisms and these enzymes may be involved in such a process during CPt10 infection, either through modification of its own DNA or by modification and possibly silencing of host gene expression.
Natural antisense transcripts (NATs) have been detected in many organisms and shown to regulate gene expression.
The programmable sequence specificity of Cas9 has been harnessed for genome editing and gene expression control in many organisms.
These genes are under the control of antioxidant response elements (AREs) in many organisms [ 67], and their coordinate expression may be associated with detoxification events in response to variations of the redox status.
MPSS and SBS have been recently used for whole-genome transcription analysis and have generated abundant expression data for many organisms [ 42, 44, 45].
