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. 2007 Aug 6;27(19):6806–6817. doi: 10.1128/MCB.01036-07

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
a

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.