Table 1.
Representative RNA-binding proteins studied by CLIP
| RNABP | Method | Tissue/cell type | Principal findings | Reference(s) |
|---|---|---|---|---|
| Nova | CLIP and HITS-CLIP | Mouse brain | Binding motif Biologically coherent targets Map of RNA splicing Regulation of poly(A) usage 3′-UTR localization elements Focused analysis of RNA splicing in the Reelin pathway | Ule et al. 2003; Licatalosi et al. 2008; Racca et al. 2010; Yano et al. 2010 |
| PTB | HITS-CLIP; reanalysis of published CLIP data | HeLa cells | Binding motif Map of RNA splicing | Xue et al. 2009; Llorian et al. 2010 |
| Tagged-Khd1 | HITS-CLIP | Saccharomyces cerevisiae | Binding motif Biologically coherent targets Discovery of role in translational regulation | Wolf et al. 2010 |
| hnRNP A1 | CLIP | HeLa cells | Discovery of role in regulating pri-mRNA processing | Guil and Caceres 2007 |
| TIA1 | HITS-iCLIP | HeLa cells | Map of RNA splicing | Wang et al. 2010 |
| Fox2 | HITS-CLIP | Human embryonic stem cells | Biologically coherent targets Map of RNA splicing | Yeo et al. 2009 |
| SFRS1 | CLIP and HITS-CLIP | HEK293T cells | Binding motif Sites relevant to disease | Sanford et al. 2008, 2009 |
| Tagged-Rrm4 | CLIP | Filamentous fungus Ustilago maydis | Binding motif Localization of rrm4-RNPs | Becht et al. 2006 |
| CUGBP1 | CLIP | Mouse hindbrain | Binding motif Validation of splicing target | Daughters et al. 2009 |
| Tagged-snRNPs | HITS-CLIP | S. cerevisiae | Detailed mapping of protein–rRNA and snoRNA interaction sites | Granneman et al. 2009; Bohnsack et al. 2009 |
| Ro homolog Rsr | CLIP | Eubacterium Deinococcus radiodurans | Discovery of interaction with rRNA | Wurtmann and Wolin 2010 |
| hnRNP C | HITS-iCLIP | HeLa cells | Binding motif Map of RNA splicing Discovery of hnRNP particle organization related to splicing | Konig et al. 2010 |
| Ago; Tagged-Ago | HITS-CLIP; PAR-CLIP | Mouse brain; HeLa; HEK293 cells | Ago-miRNA-binding sites defined | Chi et al. 2009; Hafner et al. 2010; Leung et al. 2011 |
| Alg-1 | HITS-CLIP | Caenorhabditis elegans | Alg-1-miRNA-binding sites defined | Zisoulis et al. 2010 |
| Msy2 | CLIP | Mouse seminiferous tubules | Discovery of interaction with piRNAs, other small RNAs | Xu et al. 2009 |
| HuR | PAR-CLIP | HEK293 cells | Role in mRNA stability and processing | Lebedeva et al. 2011; Mukherjee et al. 2011 |
| FMRP | HITS-CLIP | Mouse brain | Discovery of mechanism of translational inhibition and link with autism | Darnell et al. 2011 |
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Modified from Darnell 2010.
