That probably will sound boring to a lot of people, but for people who have done motif analyses of yeast microarray data, that’s a significant finding: the yeast factor that binds to RRPE has finally been identified. The RRPE motif (AAA[AT]TTTT) was found some time ago upstream of many genes involved in ribosomal biogenesis. It is particularly easy to identify computationally because the genes that have it are tightly co-expressed in gene expression profiling experiments (microarrays). Because ribosomal genes (and other growth -involved genes) are down-regulated in response to stress, and many perturbation experiments trigger a stress response, the RRPE motif repeatedly comes up when looking for motifs in clusters of co-expressed genes in microarray experiments. But up to now, nobody had succeeded in identifying the binding factor. Now, using a library of GST-tagged ORFs, and a gel-shift assay, Heideman and colleagues have identified Stb3 as the factor that binds RRPE (and did some pretty convincing follow-up experiments to confirm it). It is by the way interesting that Stb3 does not have a known DNA-binding domain …
Connotea July 1, 2007
I have been using Connotea for a couple of weeks now to keep track of the papers I like. I am pretty happy about the service. It recognizes a significant number of journal formats (meaning it automatically grabs the title, authors’ names, etc from the web pages for you). I also like the fact that it lets me add my own comments to the papers. There is however room for improvement : it is not as well integrated to Firefox as Del.icio.us (which I use to keep track of my bookmark), it does not recognize some important journals (Cell, ScienceDirect among others). Also, it doesn’t have enough users to be useful as a discovery tool.
Link: my Connotea library.
Update 07/02/07: there is a way to make Connotea recognize articles from ScienceDirect (or from any article that has a DOI): select the DOI (e.g. doi:10.1016/S1535-6108(03)00132-6) using the mouse, than click on “Add to Connotea”.
