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:
- 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.
- 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.
- Stower, Hannah. “Gene Regulation: Resolving Transcription Factor Binding.” Nature Reviews Genetics 13, no. 2 (December 29, 2011): 71–71.