Table 2.
Experimental data supporting interactions between lncRNAs and RNA-binding proteins (RBPs) that are commonly associated with cancer.
| LncRNAs commonly associated with cancer | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Most common RNA-binding proteins (RBPs) | HOTAIR | HULC | H19 | MALAT1 | LINC00152 (CYTOR) | UCA1 | PVT1 | NEAT1 | HNF1A-AS1 |
| eIF4A3 | CLIP-seq / HITS-CLIP (NPInter, POSTAR3)143 | CLIP-Seq / HITS-CLIP; iCLIP (NPInter, POSTAR3)143 | CLIP-seq / HITS-CLIP; iCLIP (NPInter, POSTAR3)143 | CLIP-Seq / HITS-CLIP (NPInter, POSTAR3)143 | |||||
| PTB (PTBP1) | iCLIP (POSTAR3) | Affinity Capture Mass Spectrometry (BioGRID)142 | PAR-CLIP; HITS-CLIP (NPInter, lncRNome, POSTAR3) | PAR-CLIP; HITS-CLIP; iCLIP (NPInter, lncRNome, POSTAR3) | PAR-CLIP; HITS-CLIP; iCLIP; eCLIP (NPInter, lncRNome, POSTAR3) | eCLIP (POSTAR3) | PAR-CLIP; HITS-CLIP; iCLIP (NPInter, lncRNome, POSTAR3) | PAR-CLIP; HITS-CLIP; iCLIP (NPInter, lncRNome, POSTAR3) | |
| FUS | CLIP-seq (NPInter)144 | CLIP-Seq (NPInter)144 | ,CLIP-Seq; PAR-CLIP (NPInter, POSTAR3)150,144,153 | CLIP-seq / HITS-CLIP; eCLIP (NPInter, POSTAR3)144 | CLIP-Seq; PAR-CLIP (NPInter, POSTAR3)150,144 | ,RIP; CHART-seq CLIP-Seq; PAR-CLIP (NPInter, POSTAR3)150,144,145,156 | PAR-CLIP (POSTAR3) | ||
| DGCR8 | eCLIP (NPInter, POSTAR3)154 | eCLIP; HITS-CLIP (NPInter, POSTAR3)154 | eCLIP (NPInter)154 | eCLIP (POSTAR3) | eCLIP (NPInter)154 | ,eCLIP; CHART-seq; HITS-CLIP (NPInter, POSTAR3)154,156 | eCLIP (NPInter)154 | ||
| IGF2BP1/2/3 | PAR-CLIP (NPInter, lncRNome, POSTAR3)151 | Affinity Chromatography (NPInter)157 | ,iCLIP; PAR-CLIP; RT-PCR In situ Hybridization Northern Blot (NPInter, POSTAR3)165,166 | ,eCLIP; PAR-CLIP; iCLIP (NPInter, lncRNome, POSTAR3)151,154,155 | PAR-CLIP (POSTAR3) | iCLIP; eCLIP (POSTAR3) | PAR-CLIP; eCLIP; iCLIP (NPInter, lncRNome, POSTAR3)154 | ,eCLIP; PAR-CLIP; iCLIP; CHART-Seq (NPInter, POSTAR3)151,154–156 | eCLIP (NPInter)154 |
| UPF1 | PAR-CLIP; HITS-CLIP (NPInter, POSTAR3)152 | HITS-CLIP (POSTAR3) | ,eCLIP; PAR-CLIP; HITS-CLIP; iCLIP (NPInter, POSTAR3)154,146,152 | eCLIP; HITS-CLIP; iCLIP (NPInter, POSTAR3)154 | iCLIP (POSTAR3) | ,eCLIP; PAR-CLIP; iCLIP; HITS-CLIP (NPInter, POSTAR3)154,146,152 | ,eCLIP; PAR-CLIP; HITS-CLIP (NPInter, POSTAR3)154,146,152 | PAR-CLIP (NPInter)152 | |
| U2AF65 | iCLIP (POSTAR3) | iCLIP (POSTAR3) | iCLIP (POSTAR3) | iCLIP (POSTAR3) | iCLIP (POSTAR3) | ||||
| SFRS1 | iCLIP (POSTAR3) | PAR-CLIP; iCLIP (POSTAR3) | ,iCLIP; Microarray eCLIP; CLIP-Seq CHART-seq; PAR-CLIP (NPInter, POSTAR3)147–149,154,156 | eCLIP; iCLIP (NPInter, POSTAR3)154 | ,eCLIP; CLIP-Seq; PAR-CLIP; iCLIP (NPInter, POSTAR3)147,154 | ,eCLIP; CLIP; PAR-CLIP CLIP-Seq; CHART-seq (NPInter, POSTAR3)147,154,156 | eCLIP (NPInter)154 | ||
| Other RBPs of interest | ,AGO2, ELAVL1, EZH2. Affinity Capture-RNA; Protein-RNA (BioGRID, POSTAR3)160–164 | AGO2. PAR-CLIP; HITS-CLIP Affinity Capture - RNA (POSTAR3, BioGRID)158 | AGO2, ELAVL1, EZH2. PAR-CLIP; HITS-CLIP; iCLIP Affinity Capture - RNA (POSTAR3, BioGRID)158 | AGO2, ELAVL1. PAR-CLIP; HITS-CLIP; iCLIP (POSTAR3) | AGO2, ELAVL1. PAR-CLIP; HITS-CLIP (POSTAR3) | AGO2, ELAVL1. PAR-CLIP; HITS-CLIP; iCLIP (POSTAR3) | AGO2, ELAVL1. PAR-CLIP Affinity Capture - RNA (POSTAR3, BioGRID)159 | ||
Information extracted from several databases including NPInter136–139, BioGRID140, lncRNome134 and POSTAR3141. CLIP UV Cross-Linking and Immunoprecipitation, PAR-CLIP Photoactivatable Ribonucleoside-enhanced Crosslinking and Immunoprecipitation, eCLIP Enhanced CLIP, iCLIP Individual-nucleotide resolution UV Crosslinking and Immunoprecipitation, CHART-seq Capture Hybridization Analysis of RNA Targets, RIP RNA Immunoprecipitation.