SELEX to identify gene targets

We have been looking at ways to identify genes that are regulated by FGFR3, specifically in the growth plate. To do so, we are working on a modified version of a technique called as SELEX (Systematic Evolution of Ligands by Exponential Enrichment). This method is typically used to screen for DNA aptamers/sequences that are preferentially bound by a protein/ligand of interest. Briefly, a library of DNA sequences is generated which contains at least some DNA sequences that will potentially bind the protein of interest.  The DNA sequences and the protein of interest are incubated together to let the protein bind to those DNA that present a preferred sequence for the protein to bind. The protein bound to the DNA is then isolated through several wash steps, and finally the specific DNA that was bound to the protein is identified by regular sequencing. 

Further reading:

1. Roulet, Emmanuelle, Stéphane Busso, Anamaria A Camargo, Andrew J G Simpson, Nicolas Mermod, and Philipp Bucher. “High-throughput SELEX SAGE Method for Quantitative Modeling of Transcription-factor Binding Sites.” Nature Biotechnology 20, no. 8 (August 2002): 831–835.
2. Jolma, Arttu, Teemu Kivioja, Jarkko Toivonen, Lu Cheng, Gonghong Wei, Martin Enge, Mikko Taipale, et al. “Multiplexed Massively Parallel SELEX for Characterization of Human Transcription Factor Binding Specificities.” Genome Research 20, no. 6 (June 1, 2010): 861–873.
3. Stower, Hannah. “Gene Regulation: Resolving Transcription Factor Binding.” Nature Reviews Genetics 13, no. 2 (December 29, 2011): 71–71.