BMC Genomics 2008, 9:298 http://www.biomedcentral.com/1471-2164/9/298 Table 2: Expression changes accompanying environmental challenge in T. brucei. (Continued) VSG RNAi induced vs uninduced Day3 nothing CLH RNAi induced vs uninduced 24 hr Rab5AWT overexpressing PCF line vs PCF WT (both with 20% FBS) alpha tubulin Gp63 (TbMSP-C) ISG65-like CLH GMP-PDE delta CBL-interacting protein kinase 9 histone H3 Rab5a RabX3 40S ribosomal protein S25 Amphiphysin Hsp70 cysteine peptidase COPI epsilon adenylate kinase 3 CBL-interacting protein kinase 9 Ubiquitin conjugating ARPC5 histone H3 40S ribosomal protein S25 Rab5a adenylate kinase 3 alpha tubulin COPI epsilon RabX3 mitochondrial intermediate peptidase mitochondrial zinc metallopeptidase Rab5b adenylate kinase 3 COPI epsilon RabX3 Tb10.70.5290 Tb927.5.410 Tb10.70.0830 Tb927.2.4580 Tb927.8.870 Tb927.1.2400 Tb927.1.2430 Tb10.389.0550 Tb11.01.6670 Tb927.3.1370 Tb11.01.6740 Tb927.6.3740 Tb927.6.960 Tb11.01.6530 Tb10.70.5150 Tb927.8.870 Tb11.02.0815 Tb10.406.0320 Tb927.1.2430 Tb927.3.1370 Tb10.389.0550 Tb10.70.5150 Tb927.1.2400 Tb11.01.6530 Tb11.01.6670 Tb10.6k15.0490 Tb927.4.3300 Tb11.02.2160 Tb10.70.5150 Tb11.01.6530 Tb11.01.6670 2.7 2.8 (2.5) (2.3) (2.0) 2.9 2.7 2.6 2.5 2.2 2.2 2.0 2.0 2.0 2.0 (2.3) (2.1) (2.0) 2.3 2.1 2.0 1.6 1.6 1.4 1.3 (2.4) (2.0) 2.5 1.6 1.5 1.5 3.6 3.8 1.7 1.5 9.5 3.5 1.2 2.6 3.1 1.6 1.6 1.6 1.1 9.8 3.8 2.1 3.0 3.4 16.7 3.5 3.4 2.8 Rab5AQL overexpressing PCF line vs PCF WT Rab5BQL overexpressing PCF line vs PCF WT The most significantly altered mRNAs detected by microarray for differing serum conditions, dithiothreitol and tunicamycin treatment, RNAi of VSG or CLH, and Rab5 overexpressing PCF lines are shown. The ratios obtained by qRT-PCR for selected transcripts are also shown. Ratios are given on a linear (not log) scale, and those indicating a reduction compared to the control state are in parentheses. Only ORFs that display at least a two-fold change, by either qRT-PCR or array, are included; except the 4 hour DTT treatment, where only the top ten hits are shown. Ratios which correspond to a value >1 for the B-statistic in limma analysis are shown in bold. changes, then depletion of these two ORFs by RNAi would be expected to elicit a response. We analysed the transcriptome of cells 24 hours after induction of the CLH RNAi, as the CLH protein levels are significantly reduced at that stage [see Additional file 5], growth is arrested, and the big eye morphology is clearly visible (data not shown). Despite a clear phenotype, we observed very limited transcriptome changes (Figure 4K, Table 2). Only TbMSP-C and an ISG-like ORF (Tb927.5.410) were significantly upregulated, while only a putative Rab effector, GMP-PDEδ (Tb927.2.4580) and a putative CBL-interacting protein kinase (Tb927.8.870) were significantly downregulated (Table 2). For the VSG RNAi, we analysed cells 24 and 72 hours after induction to examine both early and late effects of VSG depletion. No major transcriptome changes were observed (Figure 4I–J, Table 2) despite growth arrest [see Additional file 5]. Indeed, only one ORF, a putative RabGEF (Tb927.3.2430) was significantly upregulated (Table 2). The absence of a coordinated response within the transcriptome as a result of these severe perturbations of cellular homeostasis sug- gests that trypanosomes lack mechanisms for response at the mRNA level to altered circumstances. The transcriptome is unaltered in cells with augmented endocytic activity As a final test of transcriptome responsiveness we ana- lysed the effects of over-expression of the early endosome small GTPases Rab5A and Rab5B in PCF, which results in Page 15 of 28 (page number not for citation purposes)