Table 3 Intersection between potential and experimentally defined target genes related to miRNAs in TIA-depleted HeLa cells
Gene symbol | Description | Associated miRNA | TIA-iCLIP |
|---|---|---|---|
Up-regulated genes | Â | ||
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 | Â | ||
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 | ++ |