TABLE 2.
Identities of clones showing the greatest reproducible regulation after overexpression of TbUBP2
| Well | Fold regulationa
|
Gene annotation and datab | |
|---|---|---|---|
| TbUBP2 | TcUBP1 | ||
| 35G1 | 2.00 | 1.13 | Tb927.1.1500 hypothetical conserved, GPI signal; predicted mRNA is 11 kb with a 6-kb 3′-UTR which contains many poly(U) tracts exceeding 17/20 residues |
| 06F13 | 1.84 | 1.71 | Tb927.1.1500 (see 35G1) |
| 10F17 | 2.07 | 1.86 | Tb927.1.1500 (see 35G1) |
| 58D11 | 2.37 | 1.50 | Tb927.1.3450 hypothetical conserved, protein with PS50325; threonine-rich region profile (all three clone sequences are identical); the predicted size of the RNA is around 4.5 kb; a band of about 10 kb appears upon UBP1/2 overexpression; the RNA of the expected size is not regulated |
| 50I8 | 6.47 | 3.41 | Tb927.1.3450 (see 58D11) |
| 50I16 | 2.73 | 1.20 | Tb927.1.3450 (see 58D11) |
| 16L6 | 6.55 | 2.83 | Tb927.1.4560-Tb927.1.4650 cyclin F-box protein array; regulation confirmed, mediated by 3′-UTR (see the text) |
| 30L21 | 6.52 | 2.96 | Tb927.1.4560-Tb927.1.4650 (see 16L6) |
| 20P20 | 6.10 | 1.49 | Tb927.1.4560-Tb927.1.4650 (see 16L6) |
| 19F12 | 5.10 | 1.67 | Tb927.1.4560-Tb927.1.4650 (see 16L6) |
| 39F24 | 6.06 | 2.65 | Tb927.1.4560-Tb927.1.4650 (see 16L6) |
| 08A12 | 3.97 | 3.17 | Tb927.1.4560-Tb927.1.4650 (see 16L6) |
| 12D15 | 2.63 | 1.31 | Tb927.3.1220 conserved hypothetical endo/excinuclease amino-terminal domain … Tb927.3.1210 3′-UTR of protein transport protein Sec24C |
| 10J21 | 1.86 | 2.00 | Tb927.3.1220 (see 12D15) |
| 50I12 | 4.48 | 2.21 | Tb927.4.3920 hypothetical, 122 kDa, 12 transmembrane helices; predicted RNA of 4.5 kb, best poly(U) is 18/22; Northern blots indicated twofold regulation |
| 36G14 | 2.16 | −1.33 | Tb927.4.2500 putative eukaryotic translation initiation factor 2-alpha kinase … Tb927.4.24903; UTR conserved hypothetical |
| 28N6 | 2.30 | 1.11 | Tb927.4.1910 hypothetical conserved, noncoding repeats |
| 17K17 | 2.00 | 2.28 | Tb927.4.500 conserved hypothetical, forkhead domain |
| 22F9 | 2.38 | 1.09 | Tb927.4.1000 hypothetical conserved, Tb927.4.1010 hypothetical, Tb927.4.1020 serine-palmitoyl-coenzyme A transferase (putative) (very short overlap) |
| 50F22 | 3.26 | 2.22 | Tb927.7.3590 hypothetical conserved … Tb927.7.3600 hypothetical conserved |
| 06K14 | 2.24 | 1.97 | Tb09.211.3040 DNA-repair (putative) … Tb09.211.3050 hypothetical conserved |
| 06D20 | 2.11 | 1.41 | Tb10.6k15.2720 l-isoaspartate O-methyltransferase (putative) and 3′-UTR of hypothetical |
| 05M11 | 2.09 | 1.70 | Tb10.70.2020, conserved hypothetical, two Zn fingers; predicted RNA about 10 kb |
| 17G18 | 2.39 | 1.82 | Tb10.70.2020 (see 05M11) |
| 13O16 | 2.00 | 1.37 | Tb10.70.4080 hypothetical conserved |
| 19F16 | 5.06 | 2.08 | Tb11.01.0820 hypothetical conserved |
| 12D23 | 2.06 | 1.62 | Tb11.01.2580 hypothetical conserved |
| 21K4 | 2.33 | 1.53 | Tb11.01.3390 DNA topoisomerase II (putative) (predicted 4.9-kb RNA); Tb11.01.3380 histone acetyltransferase (putative) (very short overlap, predicted 2.5-kb mRNA); clone hybridizes with both RNAs, the larger one is upregulated by UBP1/2 overexpression; predicted 3′-UTR about 700 nt, several poly(U) tracts |
| 12F14 | 2.03 | 1.11 | Tb11.02.5190 pantothenate kinase subunit (putative) … Tb11.02.5180 DNA-directed RNA polymerase II subunit 9 (putative) (both clone sequences identical) |
| 14F1 | 2.05 | 1.73 | Tb11.02.5190 (see 12F14) |
| 31M3 | 5.63 | 2.61 | Tb11.03.069 hypothetical conserved |
a
See Materials and Methods. The results here were reproduced for three different biological replicates, each with dye-swap. The effect of overexpression of TcUBP1 is also shown. Annotations were performed as previously described (7); the identities of the open reading frames given correspond to the mRNAs that are predicted to hybridize with the clone.
b
GPI, glycosyl phosphatidylinositol anchor.