Skip to main content

Table 3 Intersection between potential and experimentally defined target genes related to miRNAs in TIA-depleted HeLa cells

From: Identification of a set of miRNAs differentially expressed in transiently TIA-depleted HeLa cells by genome-wide profiling

Gene symbol Description Associated miRNA TIA-iCLIP
Up-regulated genes  
CNR1 Cannabinoid receptor 1 (brain) miR-30b-3p +
EIF4A2 Eukaryotic translation initiation factor 4A, isoform 2 miR-586 +++
EREG Epiregulin miR-586 +
F2RL2 Coagulation factor II (thrombin) receptor-like 2 miR-30b-3p +
IL1R1 Interleukin 1 receptor, type I miR-498 ++
IRAK2 Interleukin-1 receptor-associated kinase 2 miR-503-5p ++
SELI Selenoprotein I miR-197-3p ++
Down-regulated genes  
ACADSB Acyl-Coenzyme A dehydrogenase, short/branched chain miR-203 ++
ACOX1 Acyl-Coenzyme A oxidase 1, palmitoyl miR-373-5p ++
ALS2CR4 Amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 4 miR-203 +++
ANKH Ankylosis, progressive homolog (mouse) miR-203 +++
AP1S2 Adaptor-related protein complex 1, sigma 2 subunit miR-203 ++
AP2B1 Adaptor-related protein complex 2, beta 1 subunit miR-203 +++
APPBP2 Amyloid beta precursor protein (cytoplasmic tail) binding protein 2 miR-612 ++
BBS1 Bardet-Biedl syndrome 1 miR-612 +
BRIP1 BRCA1 interacting protein C-terminal helicase 1 miR-373-5p +
C16orf72 Chromosome 16 open reading frame 72 miR-671-5p +++
C18orf54 Chromosome 18 open reading frame 54 miR-625-5p ++
C1orf96 Chromosome 1 open reading frame 96 miR-373-5p ++
C20orf108 Chromosome 20 open reading frame 108 miR-30b-3p +
CCDC50 Coiled-coil domain containing 50 miR-203 +
CENPH Centromere protein H miR-612 +
CLCC1 Chloride channel CLIC-like 1 miR-373-5p and 30b-3p ++
COL4A4 Collagen, type IV, alpha 4 miR-203 +++
CTDSPL2 CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2 miR-203 +++
CTSC Cathepsin C miR-203 ++
DAB2 Disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila) miR-203 +++
DDIT4 DNA-damage-inducible transcript 4 miR-30b-3p ++
EEF1A1 Eukaryotic translation elongation factor 1 alpha 1 miR-373-5p +
EIF4EBP2 Eukaryotic translation initiation factor 4E binding protein 2 miR-373-5p ++
ELMOD2 ELMO/CED-12 domain containing 2 miR-30b-3p ++
EPHA7 EPH receptor A7 miR-503-5p +++
FAM129A Family with sequence similarity 129, member A miR-373-5p and 586 ++
FBXO9 F-box protein 9 miR-203 ++
IQCE IQ motif containing E miT-483-5p +
KCTD12 Potassium channel tetramerisation domain containing 12 miR-373-5p and 586 +
KLF9 Kruppel-like factor 9 miR-373-5p ++
KRIT1 KRIT1, ankyrin repeat containing miR-373-5p +
LAMP2 Lysosomal-associated membrane protein 2 miR-373-5p ++
MCM4 Minichromosome maintenance complex component 4 miR-373-5p ++
MECP2 Methyl CpG binding protein 2 (Rett syndrome) miR-203 +
MIB1 Mindbomb homolog 1 (Drosophila) miR-373-5p, 503 and 203 ++
MOBKL2B MOB1, Mps One Binder kinase activator-like 2B (yeast) miR-503-5p and 203 +++
MTAP Methylthioadenosine phosphorylase miR-125a-3p ++
MTHFD2L Methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like miR-373-5p ++
NAV1 Neuron navigator 1 miR-503-5p ++
NDRG3 NDRG family member 3 miR-203 ++
NDST1 N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1 miR-30b-3p +
NHLRC2 NHL repeat containing 2 miR-373-5p ++
NID1 Nidogen 1 miR-30b-3p ++
PAWR PRKC, apoptosis, WT1, regulator miR-30b-3p +++
PCGF6 Polycomb group ring finger 6 miR-203 +
PDE1A Phosphodiesterase 1A, calmodulin-dependent miR-373-5p +++
PGM2 Phosphoglucomutase 2 miR-498 +++
PLD1 Phospholipase D1, phosphatidylcholine-specific miR-203 +++
RAB22A RAB22A, member RAS oncogene family miR-498 ++
RBM8A RNA binding motif protein 8A miR-373-5p +
RECK Reversion-inducing-cysteine-rich protein with kazal motifs miR-503-5p ++
RGC32 Regulator of cell cycle miR-30b-5p ++
SFPQ Splicing factor proline/glutamine-rich (polypyrimidine tract binding protein associated) miR-586 ++
SGPL1 Sphingosine-1-phosphate lyase 1 miR-373-5p ++
SLC12A2 Solute carrier family 12 (sodium/potassium/chloride transporters), member 2 miR-503-5p, 586 and 203 +
SLC35B3 Solute carrier family 35, member B3 miR-203 ++
SNAPC3 Small nuclear RNA activating complex, polypeptide 3, 50kDa miR-373-5p and 671 +++
STXBP4 Syntaxin binding protein 4 miR-625-5p +
SUDS3 Suppressor of defective silencing 3 homolog (S. cerevisiae) miR-203 +++
SYNC1 Syncoilin, intermediate filament 1 miR-203 ++
TFDP2 Transcription factor Dp-2 (E2F dimerization partner 2) miR-30b-3p and 203 +++
TIA1 TIA1 cytotoxic granule-associated RNA binding protein miR-30b3p +++
TNFRSF19 Tumor necrosis factor receptor superfamily, member 19 miR-125a-3p ++
TNRC6B Trinucleotide repeat containing 6B miR-503-5p, 586 and 203 ++
TSEN2 tRNA splicing endonuclease 2 homolog (S. cerevisiae) miR-197-3p +
VAMP1 Vesicle-associated membrane protein 1 (synaptobrevin 1) miR-203 ++
VGLL3 Vestigial like 3 (Drosophila) miR-373-5p ++
VPS13A Vacuolar protein sorting 13 homolog A (S. cerevisiae) miR-586 ++
WDFY3 WD repeat and FYVE domain containing 3 miR-203 +
ZBTB44 Zinc finger and BTB domain containing 44 miR-203 ++
ZNF169 Zinc finger protein 169 miR-125a-3p ++
  1. Gene cluster defining a molecular signature of up- (highlighted in red in Figure 3) and down-regulated (highlighted in green in Figure 3) genes linked to up-regulated miRNAs in TIA-depleted HeLa cells. Gene symbol, gene title as description and associated miRNAs are indicated. Estimation of the density of binding sites of TIA proteins on up- and down-regulated target genes by iCLIP analysis is shown. The relative quantification estimated as low (+), medium (++) and high (+++) density is indicated.