Table 1.

List of genes upregulated during dormancy in various in-vitro and in-vivo models.

Model	Method of study	Selected genes upregulated during dormancy	Ref
Hypoxia	qPCR	Dormancy regulon gene- devR, acr, tgs1 fad26 gene required for cell wall lipid phthioceroldimycocerosate’s (PDIM) synthesis Sigma factors- sigB, SigE, rpoB, (trxB1)- for antioxidant defense Hexose monophosphate shunt (HMP) for maintaining carbon homeostasis during dormancy narX is a nitrate reductase involved in anaerobic respiration.	(Iona et al., 2016)
Hypoxia	RNA-seq	DosRST, MprAB- two-component systemalternative sigma factors SigE, SigH icl-1- with role in glyoxylate shunt pathway, methylcitrate lyase, KstR regulated genes involved in lipid degradation and cholesterol catabolism Mce transport systems: encodes ABC transporters involved in lipid transportation and utilization.	(Du et al., 2016)
Lung from Mice model- Balb/c and SCID were compared with invitro grown bacterium under hypoxic conditions	Micro array	Core in-vivo regulated genes with role in dormancy were found to be rubB, dinF, and fdxA. In-vitro regulated genes-cstA (carbon starvation-induced stress response protein), cysW (sulfate transport system permease protein), Rv3383c (transferase involved in lipid biosynthesis), sigJ and Rv1167c or Rv1994c (transcriptional regulators).	(Talaat et al., 2004)
Lung from C57BL/6 mice model	Quantitative real time PCR	Icl, pckA, hspX	(Iona et al., 2016)
Non-human primate model (NHP)	Intra- granulomatous gene expression study using transcriptomics	Genes belonging to dosR regulon, toxin-antitoxin genes, alternate sigma factors- sigF, sigD, sigJ, sigI, sigB, sigK, and sigH	(Hudock et al., 2017)
Human lung granuloma	RNA-RNA in-situ hybridization	Icl, narX Rv2557 and Rv2558- carbon starvation inducible genes iniB and kasA- upregulation due to isoniazid exposure.	(Fenhalls et al., 2002)