TABLE 1.

mRNAs enriched in pulldown and increased in knockdown of KSRPa

RefSeq accession no.DescriptionGene namemRNA statusARE classd
UnstablebStabilized in KSRP knockdownc
NM_001200 Bone morphogenetic protein 2 (BMP2), mRNA BMP2 ++
NM_000758 Colony stimulating factor 2 (granulocyte-macrophage) (CSF2), mRNA CSF2 ++II
NM_002089 Chemokine (C-X-C motif) ligand 2 (CXCL2), mRNA CXCL2 ++II
NM_002090 Chemokine (C-X-C motif) ligand 3 (CXCL3), mRNA CXCL3 ++II
NM_018948 ERBB receptor feedback inhibitor 1 (ERRFI1), mRNA ERRFI1 ++
NM_004864 Growth differentiation factor 15 (GDF15), mRNA GDF15 ++II
NM_002166 Inhibitor of DNA binding 2, dominant negative helix-loop-helix protein (ID2), mRNA ID2 ++I
NM_000600 Interleukin 6 (beta 2 interferon, beta 2) (IL6), mRNA IL6 ++I
NM_000584 Interleukin 8 (IL8), mRNA IL8 ++II
NM_000963 Prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) (PTGS2), mRNA PTGS2 ++II
NM_000024 Adrenergic beta-2-, receptor, surface (ADRB2), mRNA ADRB2 +
NM_016201 Angiomotin-like 2 (AMOTL2), mRNA AMOTL2 +
NM_025047 ADP-ribosylation factor-like 14 (ARL14), mRNA ARL14 +I
NM_006577 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2 (B3GNT2), mRNA B3GNT2 +I
NM_170735 Brain-derived neurotrophic factor (BDNF), transcript variant 1, mRNA BDNF +I
NM_001901 Connective tissue growth factor (CTGF), mRNA CTGF +
NM_001554 Cysteine-rich angiogenic inducer 61 (CYR61), mRNA CYR61 +
NM_012242 Dickkopf homolog 1 (Xenopus laevis) (DKK1), mRNA DKK1 +
NM_012266 DnaJ (Hsp40) homolog, subfamily B, member 5 (DNAJB5), mRNA DNAJB5 +
NM_004419 Dual specificity phosphatase 5 (DUSP5), mRNA DUSP5 +
NM_001946 Dual specificity phosphatase 6 (DUSP6), transcript variant 1, mRNA DUSP6 +
NM_004951 Epstein-Barr virus-induced gene 2 (lymphocyte-specific G protein-coupled receptor) (EBI2), mRNA EBI2 +
NM_001955 Endothelin 1 (EDN1), mRNA EDN1 +
NM_001956 Endothelin 2 (EDN2), mRNA EDN2 +I
NM_023037 Furry homolog (Drosophila) (FRY), mRNA FRY +
NM_005261 GTP binding protein overexpressed in skeletal muscle (GEM), transcript variant 1, mRNA GEM +
NM_005279 G protein-coupled receptor 1 (GPR1), mRNA GPR1 +
NM_005328 Hyaluronan synthase 2 (HAS2), mRNA HAS2 +
NM_001945 Heparin-binding EGF-like growth factor (HBEGF), mRNA HBEGF +II
NM_182757 IBR domain-containing 2 (IBRDC2), mRNA IBRDC2 +
NM_001547 Interferon-induced protein with tetratricopeptide repeats 2 (IFIT2), mRNA IFIT2 +
NM_005544 Insulin receptor substrate 1 (IRS1), mRNA IRS1 +
NM_000214 Jagged 1 (Alagille syndrome) (JAG1), mRNA JAG1 +II
NM_031419 Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor zeta (NFKBIZ), transcript variant 1, mRNA NFKBIZ +
NM_006186 Nuclear receptor subfamily 4, group A, member 2 (NR4A2), transcript variant 1, mRNA NR4A2 +I
NM_021127 Phorbol-12-myristate-13-acetate-induced protein 1 (PMAIP1), mRNA PMAIP1 +I
NM_005398 Protein phosphatase 1, regulatory (inhibitor) subunit 3C (PPP1R3C), mRNA PPP1R3C +
NM_000958 Prostaglandin E receptor 4 (subtype EP4) (PTGER4), mRNA PTGER4 +I
NM_198965 Parathyroid hormone-like hormone (PTHLH), transcript variant 1, mRNA PTHLH +I
NM_144593 Ras homolog enriched in brain-like 1 (RHEBL1), mRNA RHEBL1 +
NM_014575 Schwannomin interacting protein 1 (SCHIP1), mRNA SCHIP1 +
NM_000450 Selectin E (endothelial adhesion molecule 1) (SELE), mRNA SELE +II
NM_005842 Sprouty homolog 2 (Drosophila) (SPRY2), mRNA SPRY2 +I
NM_003222 Transcription factor AP-2 gamma (activating enhancer binding protein 2 gamma) (TFAP2C), mRNA TFAP2C +
NM_000594 Tumor necrosis factor (TNF, superfamily, member 2) (TNF), mRNA TNF +II
NM_001003818 Tripartite motif-containing 6 (TRIM6), transcript variant 1, mRNA TRIM6 +
NM_033035 Thymic stromal lymphopoietin (TSLP), transcript variant 1, mRNA TSLP +I
NM_024640 yrdC domain-containing (E. coli) (YRDC), mRNA YRDC +
NM_023039 Ankyrin repeat, family A (RFXANK-like), 2 (ANKRA2), mRNA ANKRA2
NM_001233 Caveolin 2 (CAV2), transcript variant 1, mRNA CAV2 I
NM_025214 Coiled-coil domain-containing 68 (CCDC68), mRNA CCDC68 I
NM_004591 Chemokine (C-C motif) ligand 20 (CCL20), mRNA CCL20
NM_012129 Claudin 12 (CLDN12), mRNA CLDN12
NM_030627 Cytoplasmic polyadenylation element binding protein 4 (CPEB4), mRNA CPEB4 II
NM_001912 Cathepsin L (CTSL), transcript variant 1, mRNA CTSL
NM_001565 Chemokine (C-X-C motif) ligand 10 (CXCL10), mRNA CXCL10
NM_005409 Chemokine (C-X-C motif) ligand 11 (CXCL11), mRNA CXCL11
NM_000782 Cytochrome P450, family 24, subfamily A, polypeptide 1 (CYP24A1), nuclear gene encoding mitochondrial protein, mRNA CYP24A1
NM_019885 Cytochrome P450, family 26, subfamily B, polypeptide 1 (CYP26B1), mRNA CYP26B1
AK026768 cDNA: FLJ23115 fis, clone LNG07933 DPY19L1P1
NM_022726 Elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4 (ELOVL4), mRNA ELOVL4 I
NM_001432 Epiregulin (EREG), mRNA EREG I
NM_144503 F11 receptor (F11R), transcript variant 4, mRNA F11R
NM_001993 Coagulation factor III (thromboplastin, tissue factor) (F3), mRNA F3 II
NM_020066 Formin 2 (FMN2), mRNA FMN2
NM_013409 Follistatin (FST), transcript variant FST344, mRNA FST
NM_013372 Gremlin 1, cysteine knot superfamily, homolog (Xenopus laevis) (GREM1), mRNA GREM1
NM_001548 Interferon-induced protein with tetratricopeptide repeats 1 (IFIT1), transcript variant 2, mRNA IFIT1
NM_016584 Interleukin 23, alpha subunit p19 (IL23A), mRNA IL23A
NM_002192 Inhibin, beta A (activin A, activin AB alpha polypeptide) (INHBA), mRNA INHBA I
NM_000210 Integrin, alpha 6 (ITGA6), mRNA ITGA6
NM_005574 LIM domain only 2 (rhombotin-like 1) (LMO2), mRNA LMO2
NM_033049 Mucin 13, cell surface-associated (MUC13), mRNA MUC13
NM_021229 Netrin 4 (NTN4), mRNA NTN4
NM_002581 Pregnancy-associated plasma protein A, pappalysin 1 (PAPPA), mRNA PAPPA
NM_002607 Platelet-derived growth factor alpha polypeptide (PDGFA), transcript variant 1, mRNA PDGFA
NM_016205 Platelet-derived growth factor C (PDGFC), mRNA PDGFC
NM_006823 Protein kinase (cyclic AMP-dependent, catalytic) inhibitor alpha (PKIA), transcript variant 6, mRNA PKIA
NM_001005377 Plasminogen activator, urokinase receptor (PLAUR), transcript variant 3, mRNA PLAUR I
NM_000959 Prostaglandin F receptor (FP) (PTGFR), transcript variant 1, mRNA PTGFR
NM_003020 Secretogranin V (7B2 protein) (SCG5), mRNA SCG5
NM_002998 Syndecan 2 (heparan sulfate proteoglycan 1, cell surface-associated, fibroglycan) (SDC2), mRNA SDC2
NM_002999 Syndecan 4 (amphiglycan, ryudocan) (SDC4), mRNA SDC4
NM_006216 Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 (SERPINE2), mRNA SERPINE2
NM_005025 Serpin peptidase inhibitor, clade I (neuroserpin), member 1 (SERPINI1), mRNA SERPINI1
NM_203349 SHC (Src homology 2 domain-containing) family, member 4 (SHC4), mRNA SHC4
NM_003759 Solute carrier family 4, sodium bicarbonate cotransporter, member 4 (SLC4A4), mRNA SLC4A4
NM_032229 SLIT and NTRK-like family, member 6 (SLITRK6), mRNA SLITRK6 I
NM_006714 Sphingomyelin phosphodiesterase, acid-like 3A (SMPDL3A), mRNA SMPDL3A
NM_003122 Serine peptidase inhibitor, Kazal type 1 (SPINK1), mRNA SPINK1
NM_030964 Sprouty homolog 4 (Drosophila) (SPRY4), mRNA SPRY4 I
NM_015000 Serine/threonine kinase 38-like (STK38L), mRNA STK38L
NM_018423 Serine/threonine/tyrosine kinase 1 (STYK1), mRNA STYK1 I
NM_003236 Transforming growth factor alpha (TGFA), mRNA TGFA I
NM_003243 Transforming growth factor beta receptor III (betaglycan, 300 kDa) (TGFBR3), mRNA TGFBR3
NM_024847 Transmembrane channel-like 7 (TMC7), mRNA TMC7
NM_003304 Transient receptor potential cation channel, subfamily C, member 1 (TRPC1), mRNA TRPC1 I
NM_016061 Yippee-like 5 (Drosophila) (YPEL5), mRNA YPEL5
NM_019006 Zinc finger, AN1-type domain 6 (ZFAND6), mRNA ZFAND6
NM_003407 Zinc finger protein 36, C3H type, homolog (mouse) (ZFP36), mRNA ZFP36 II
  • a Listed are mRNAs with >2-fold signal intensities in stKSRP pulldown compared to those in stGFP pulldown and >2-fold signal intensities in KSRP knockdown cells compared to those in GFP knockdown cells in two independent assays (for details, see Materials and Methods). Boldface indicates mRNAs destabilized by KSRP.

  • b mRNAs labeled “unstable” (+) decreased to 50% or less at 3 h after actinomycin D addition in GFP knockdown cells in both assays.

  • c For mRNAs labeled “stabilized” (+), the ratio of signal intensities for 3 h of actinomycin D treatment to those at 0 h is >1.33-fold higher for KSRP knockdown than for GFP knockdown cells.

  • d ARE classification was done using the ARED3.0 database search tool (http://rc.kfshrc.edu.sa/ared ). ARE-containing as well as unstable mRNAs are highly significantly overrepresented (P < 0.0001, Fisher's exact test).