In Nature early online this week, scientists used an RNAi screen in Drosophila to study the Notch signaling pathway during external sensory organ development. Their work identified six new genes involved in asymmetric cell division and 23 novel genes regulating the Notch pathway. Bioinformatic analysis allowed them to construct an interaction network map for Notch signaling and asymmetric cell division.
MIT researchers used computational methods and protein microarrays to design peptide ligands for human basic-region leucine zipper (bZIP) transcription factors. Their framework gave binding partners with high specificity and selectivity for the oncoproteins c-Jun, c-Fos and c-Maf over all 19 other bZIP families. "The proteins we design now are not likely to become drugs or therapeutics, but can be used in order to figure out the basic mechanisms of these interactions, which could be extremely valuable," senior author Amy Keating says in a press release.
Columbia scientists studied dopamine pathway gene expression patterns, finding that one cis-regulatory element, the dopamine (DA) motif, controls the expression of all dopamine pathway genes in all dopaminergic cell types in C. elegans. If the transcription factor encoded by ast-1 is lost, all dopaminergic neuronal subtypes fail to terminally differentiate.
In the April issue of Nature Biotechnology, two groups have used a combination of padlock probes and massively parallel sequencing to characterize cytosine methylation in targeted regions of the human genome. Their work is summed up in a review co-authored by Peter Laird. In one study they compared methylation in three human fibroblast lines and eight human pluripotent stem cell lines, finding, among others, that 288 regions were methylated differently in fibroblasts and pluripotent cells. A second paper used the alternate method to find a pattern of low promoter methylation and high gene-body methylation in highly expressed genes.