TABLE 1.

Top TIAR target mRNAs identified on MGC arrays after RNP IPa

NameSymbolRefSeq accession no.Unigene no.Z ratio
Nucleolar protein family A3 (H/ACA small nucleolar RNPs)NOLA3NM_018648Hs#S22940333.38
ADP-ribosylation factor 3ARF3NM_001659Hs#S17262803.13
Metallothionein 1HMT1HNM_005951Hs#S32190103.06
Small nuclear ribonucleoprotein D3 polypeptide 18 kDaSNRPD3NM_004175Hs#S17292932.90
Metallothionein 1LMT1LNM_002450Hs#S17271872.88
Phospholipid scramblase 3PLSCR3NM_020360Hs#S22946122.66
Serine hydroxymethyltransferase 2 (mitochondrial)SHMT2NM_005412Hs#S17308292.61
Cystatin B (stefin B)CSTBNM_000100Hs#S17305142.52
F11 receptorJAM1NM_144503Hs#S45545612.42
Laminin, alpha 5LAMA5NM_005560Hs#S36191032.40
Adenylosuccinate lyaseADSLNM_000026Hs#S17282692.26
H3 histone, family 3B (H3.3B)H3F3BNM_005324Hs#S17306162.26
3-Hydroxybutyrate dehydrogenase (heart, mitochondrial)BDHNM_004051Hs#S40018522.24
SWI/SNF related, matrix associated, regulator of chromatinSMARCE1NM_003079Hs#S17308342.23
Long-chain fatty-acyl elongaseLCENM_024090Hs#S33555562.16
H2A histone family, member Y2H2AFY2NM_018649Hs#S22940222.16
Non-SMC (structural maintenance of chromosomes) 1NSE1NM_145080Hs#S45545462.14
CHK1 checkpoint homolog (Schizosaccharomyces pombe)CHEK1NM_001274Hs#S17264682.13
Transforming growth factor beta 1-induced transcript 1TGFB1I1NM_015927Hs#S21402752.13
MAD1 mitotic arrest-deficient-like 1 (yeast)MAD1L1NM_003550Hs#S17318672.12
Amplified in osteosarcomaOS-9NM_006812Hs#S17313152.12
Fibrinogen-like 1FGL1NM_004467Hs#S17323932.11
Cytochrome c oxidase subunit IV isoform 1COX4I1NM_001861Hs#S17305042.10
Mevalonate (diphospho) decarboxylaseMVDNM_002461Hs#S17319832.10
Ubiquitin-conjugating enzyme E2CUBE2CNM_007019Hs#S17315332.06
Wiskott-Aldrich syndrome protein-interacting proteinWASPIPNM_003387Hs#S17281882.02
Dihydropyrimidine dehydrogenaseDPYDNM_000110Hs#S17285561.98
Small nuclear ribonucleoprotein polypeptide FSNRPFNM_003095Hs#S17278941.96
Ribosomal protein L5RPL5NM_000969Hs#S17277041.94
Malic enzyme 2, NAD+-dependent, mitochondrialME2NM_002396Hs#S17271511.92
G protein-coupled receptor 56GPR56NM_005682Hs#S17298091.91
COX10 homolog, cytochrome c oxidase assembly proteinCOX10NM_001303Hs#S17323471.91
  • 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.