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The Darnell lab developed and validated a methodology to help those interested in the role of RNA binding proteins in biology and disease (Ule et al., Science 2003; Ule et al., Methods 2005). This method, termed Cross Linking and Immunoprecipitation (CLIP), was developed and validated by Kirk Jensen, Jernej Ule, and Aldo Mele in our laboratory.CLIP uses ultraviolet irradiation to induce covalent crosslinks between protein-RNA complexes in situ, allowing rigorous purification of RBPs along with small fragments of RNA, which can be amplified and quantitated. Our lab subsequently modernized this technology to enable identification of all RBP-bound RNA transcripts by performing HIgh-Throughput Sequencing of RNA isolated by CLIP (HITS-CLIP) (Licatalosi et al., Nature 2008; Chi et al., Nature 2009). The implementation of HITS-CLIP has established RNA binding proteins (RBPs) as key factors that localize and regulate RNA in the brain; however, the complexity of the mammalian brain has made it difficult to dissect the cell-specific functions of neuronal RBPs. To circumvent this challenge, our lab generated a platform that utilizes gene targeting to conditionally express GFP-tagged (cTag) RBPs in vivo in selected cell populations using the Cre/Lox system. This variation of CLIP has been used to study several RBPs in vivo, including: PAPB (Hwang et al., Neuron 2017), NOVA2 (Saito et al., Neuron 2019), and FMRP (Sawicka et al., Elife 2019).

Download CLIP Method (pdf) accompanying Science 2003
Download new CLIP Method (pdf) accompanying Methods 2005
Ago data and method can be found here.

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Laboratory of Molecular Neuro-oncology
Theobald Smith Hall
The Rockefeller University
1230 York Ave.
New York, NY 10065

Ms. Helen Marie Curry
Lab Administrator

Robert B. Darnell, M.D., Ph.D.
Robert and Harriet Heilbrunn Professor