Two interesting papers related to our research October 30, 2008

Pat Brown (the inventor of microarrays) just published a paper in PLoS Biology in which he described the identification of mRNA targets for 40 RNA-binding proteins. Not only it’s a very interesting study that emphasizes the extent of post-transcriptional regulation, but they also extensively use FIRE for motif discovery ( along with their homebrewed approach)

Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO (2008) Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System. PLoS Biol 6(10): e255

The other paper in Nature by Ruschlow and colleagues describes a protein that binds to a putative reglatory element (CAGGTAG) that we identified in our collaboration with Eric Wieschaus as highly over-represented upstream of the earliest zygotic genes in the Drosophila embryo (De Renzis, Elemento et al, PLoS Biology, 2007).They used one-hybrid assay to identify the zinc finger protein called Zelda.

Liang HL, Nien CY, Liu HY, Metzstein MM, Kirov N, Rushlow C. The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila. Nature.