TABLE 1.
TRANSCRIPTS MODULATED IN RSV TRANSFORMED CHICKEN CELLS
| RSV (V-SRC) INDUCED GENES$ | |||||
| GENE SYMBOL | ACCESSION# | MW | GENE NAME | ARRAY(n=3) | RT-PCR(n=2) |
| PLAU | NM_205443 | 49 | plasminogen activator, urokinase | 196 ± 69 | 42 ± 11 |
| VIP | NM_205366 | 22 | vasoactive intestinal peptide | 124 ± 60 | 54 ± 0.5 |
| LOC423497 | XM_421400 | 353 | *AHNAK 1 & 2 related protein | 26 ± 5 | 8 ± 5 |
| LOC421581 | XM_419619 | 20 | *EMT organic cation transporter 3 | 18 ± 15 | N.C. |
| LOC423769 | XM_421641 | 65 | *arachidonate 5-lipoxygenase | 13 ± 6 | 7 ± 3.5 |
| LOC421692 | XM_419729 | 86 | *cAMP-specific phosphodiesterase 7B | 10 ± 5 | 10 ± 1.5 |
| FST | NM_205200 | 38 | follistatin | 9 ± 5 | 4 ± 0.5 |
| LOC423890 | XM_421754 | 75 | *dual specificity phosphatase 5 | 7 ± 4 | 7 ± 1.5 |
| NES | NM_205033 | 202 | Nestin | 7 ± 1 | 1 ± 0.2 |
| MKP-2 | NM_204838 | 41 | MAP kinase phosphatase 2 | 6 ± 2 | 26 ± 15 |
| RSV (V-SRC) REPRESSED GENES | |||||
| NPC2 | NM_001004393 | 21 | stathmin-like 3 | 45 ± 52 | 2 ± 0.2 |
| NOV | NM_205268 | 38 | nephroblastoma-overexpressed gene | 42 ± 39 | 18 ± 15 |
| TGFBI | NM_205036 | 74 | TGF beta-induced protein, 68 kDa | 28 ± 31 | 7 ± 4 |
| LOC418180 | XM_416411 | 23 | *RAB, estrogen-regulated growth inhibitor | 18 ± 8 | 2 ± 0.3 |
| LOC428711 | XM_426269 | 61 | four and a half LIM domains 1 protein | 15 ± 1 | 3 ± 0.5 |
| DIO2 | NM_204114 | 31 | deiodinase | 15 ± 6 | 5 ± 1 |
| C1QTNF3 | XP_425002 | 34 | C1q and TNF-related protein 3 | 13 ± 6 | 3 ± 0.5 |
| CPEB1 | XM_413713 | 80 | cytoplasmic polyadenylation element BP1 | 8 ± 3 | 0.3 ± 0.1 |
| TFPI | XM_421849 | 35 | tissue factor pathway inhibitor | 5 ± 2 | 3 ± 1 |
| TGFB3 | NM_205454 | 47 | TGF beta 3 | 5 ± 0.8 | 5 ± 2.5 |
v-src oncogene was upregulated 265 (+/−45) fold in RSV-SR transformed CEF compared to CEF infected with the non-transforming derivative of RSV-SR td106 mutant. Since there is no v-src gene expressed in the control, non-transformed cells, the over-expression value for the v-src transcript reflects a comparison with the endogenous level of c-src transcript. The value is derived from three independent experiments (n=3) in which chicken genome arrays were screened with cRNA probes derived from independent sets of transformed and infected cells.
“MW” represents molecular weight in kiloDaltons of the unprocessed protein product calculated from the translated cDNA of the predicted gene product with the aid of ExPASy tools.
denotes “similar” in most cases based on the annotation of the sequence provided by Affymetrix. For all the sequences, which we marked here with ‘*’ and therefore termed as “similar” to known mammalian genes, we performed BLASTP analysis and compared them to human proteins. The sequences were from 60 to 80% identical over the main portions of proteins and most likely represent bona fide orthologs. However, a caution is advised, as there are examples of avian-specific genes that share a significant degree of sequence identity with mammalian genes but do not represent their orthologs, e.g., chicken yrk and human yes (Sudol et al., 1993).
N.C. stands for “not confirmed”. It applies to one transcript for which we could not obtain a single size DNA product with the real time PCR, in spite of trying three sets of primers spanning different regions of the sequence.