Use of DNA arrays to study transcriptional responses to antimycobacterial compounds

Analysis of the transcriptional profiles of Mycobacterium tuberculosis after treatment with antimycobacterial compounds has improved our understanding of the ways mycobacteria respond to antibiotic stress, and revealed new insights into the mode of action of different antimycobacterial compound classes. RNA profiling of drug-induced changes has become an important tool in multiple stages of the antibacterial drug development process from target elucidation, to identifying target drift, and ultimately to revealing drug resistance mechanisms. The transcriptional response of M. tuberculosis to antimycobacterial compounds may be determined in isolation, in comparison with other compound classes, or between drug-sensitive and drug-resistant mycobacterial isolates. Additional information confirming the growth state of mycobacteria on addition of the antibacterial compound, and the effect that this compound has on mycobacterial growth, is essential for interpreting the transcriptional signatures acquired. This chapter describes the methods required for the extraction of representative total mycobacterial RNA, the subsequent hybridisation of this RNA to an M. tuberculosis complex microarray, and the analysis strategies employed to interpret the transcriptional data generated.