TABLE 1.
Top TIAR target mRNAs identified on MGC arrays after RNP IPa
Name | Symbol | RefSeq accession no. | Unigene no. | Z ratio |
---|---|---|---|---|
Nucleolar protein family A3 (H/ACA small nucleolar RNPs) | NOLA3 | NM_018648 | Hs#S2294033 | 3.38 |
ADP-ribosylation factor 3 | ARF3 | NM_001659 | Hs#S1726280 | 3.13 |
Metallothionein 1H | MT1H | NM_005951 | Hs#S3219010 | 3.06 |
Small nuclear ribonucleoprotein D3 polypeptide 18 kDa | SNRPD3 | NM_004175 | Hs#S1729293 | 2.90 |
Metallothionein 1L | MT1L | NM_002450 | Hs#S1727187 | 2.88 |
Phospholipid scramblase 3 | PLSCR3 | NM_020360 | Hs#S2294612 | 2.66 |
Serine hydroxymethyltransferase 2 (mitochondrial) | SHMT2 | NM_005412 | Hs#S1730829 | 2.61 |
Cystatin B (stefin B) | CSTB | NM_000100 | Hs#S1730514 | 2.52 |
F11 receptor | JAM1 | NM_144503 | Hs#S4554561 | 2.42 |
Laminin, alpha 5 | LAMA5 | NM_005560 | Hs#S3619103 | 2.40 |
Adenylosuccinate lyase | ADSL | NM_000026 | Hs#S1728269 | 2.26 |
H3 histone, family 3B (H3.3B) | H3F3B | NM_005324 | Hs#S1730616 | 2.26 |
3-Hydroxybutyrate dehydrogenase (heart, mitochondrial) | BDH | NM_004051 | Hs#S4001852 | 2.24 |
SWI/SNF related, matrix associated, regulator of chromatin | SMARCE1 | NM_003079 | Hs#S1730834 | 2.23 |
Long-chain fatty-acyl elongase | LCE | NM_024090 | Hs#S3355556 | 2.16 |
H2A histone family, member Y2 | H2AFY2 | NM_018649 | Hs#S2294022 | 2.16 |
Non-SMC (structural maintenance of chromosomes) 1 | NSE1 | NM_145080 | Hs#S4554546 | 2.14 |
CHK1 checkpoint homolog (Schizosaccharomyces pombe) | CHEK1 | NM_001274 | Hs#S1726468 | 2.13 |
Transforming growth factor beta 1-induced transcript 1 | TGFB1I1 | NM_015927 | Hs#S2140275 | 2.13 |
MAD1 mitotic arrest-deficient-like 1 (yeast) | MAD1L1 | NM_003550 | Hs#S1731867 | 2.12 |
Amplified in osteosarcoma | OS-9 | NM_006812 | Hs#S1731315 | 2.12 |
Fibrinogen-like 1 | FGL1 | NM_004467 | Hs#S1732393 | 2.11 |
Cytochrome c oxidase subunit IV isoform 1 | COX4I1 | NM_001861 | Hs#S1730504 | 2.10 |
Mevalonate (diphospho) decarboxylase | MVD | NM_002461 | Hs#S1731983 | 2.10 |
Ubiquitin-conjugating enzyme E2C | UBE2C | NM_007019 | Hs#S1731533 | 2.06 |
Wiskott-Aldrich syndrome protein-interacting protein | WASPIP | NM_003387 | Hs#S1728188 | 2.02 |
Dihydropyrimidine dehydrogenase | DPYD | NM_000110 | Hs#S1728556 | 1.98 |
Small nuclear ribonucleoprotein polypeptide F | SNRPF | NM_003095 | Hs#S1727894 | 1.96 |
Ribosomal protein L5 | RPL5 | NM_000969 | Hs#S1727704 | 1.94 |
Malic enzyme 2, NAD+-dependent, mitochondrial | ME2 | NM_002396 | Hs#S1727151 | 1.92 |
G protein-coupled receptor 56 | GPR56 | NM_005682 | Hs#S1729809 | 1.91 |
COX10 homolog, cytochrome c oxidase assembly protein | COX10 | NM_001303 | Hs#S1732347 | 1.91 |
Whole-cell lysates prepared from untreated RKO cells were used for IP assays by employing either IgG or anti-TIAR antibodies. RNA was subsequently extracted from the RNP complexes present in the IP material and was reverse transcribed; the resulting radiolabeled molecules were used to hybridize a cDNA array (32). The most enriched transcripts found in association with TIAR (TIAR IP material compared with IgG IP material) are listed. The top 179 enriched transcripts with complete 3′UTR sequences, the experimental dataset (see Table S1 in the supplemental material), were used to derive the TIAR motif. The Z ratio column reflects the differences in signal intensity when comparing TIAR IP with IgG IP array signals (32). Transcripts were deemed TIAR targets if Z ratios are >1.