[Transcriptome analysis of bacterial pathogens in vivo: problems and solutions].
This review considers modern strategy of whole-transcriptome investigation of intracellular pathogens in vivo. The methods of preliminary enrichment for bacterial RNA are discussed in details, including hybridization-based approaches and the peculiarities of cDNA synthesis in bacteria; methods of synthesizing cDNA from the view of features of prokaryotic RNAs and methods of bacterial cDNA analysis are also described, including high-throughput RNA-seq. The discussed methods are exemplified by analysis of Mycobacterium tuberculosis in different infection models: in cell lines, infected animal tissues and organs, and human surgical samples of lung. The advantages and limitations of different methodological approaches are discussed.
T A
TA
Skvortsov
T L
TL
Azhikina
D000818:Animals; D004269:DNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D018076:DNA, Complementary / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D054884:Host-Pathogen Interactions; D006801:Humans; D008168:Lung / Q000382:microbiology; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000378:metabolism; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism
D004269:DNA, Bacterial; D018076:DNA, Complementary; D012329:RNA, Bacterial