The last few decades has seen the discovery of a number of transcription factors (TFs) that bind RNA as well as DNA. Although the functional effects of RNA binding by a subset of these TFs has been elucidated to some degree, little is known about the molecular mechanisms of such interactions. Only one structure of a TF bound to RNA has been published, that of TFIIIA of Xenopus laevis bound to its cognate RNA.

 The Drosophila protein Bicoid acts as both a transcription and translation factor in early embryos, binding RNA with the same homeodomain it uses to bind DNA. Bicoid regulates multiple genes at the DNA level, but the only known RNA target of bicoid is the 3’ UTR of the posterior determinant gene caudal. Binding of Bicoid to the caudal mRNA represses translation of caudal.

 The current study aims to elucidate the nature of RNA binding by Bicoid. Gel electrophoretic mobility shift assays (EMSAs) have been carried out, demonstrating that Bicoid binds to the BRE with similar affinity to which it binds the full length caudal 3’UTR. Currently, EMSAs using truncations of the BRE are being carried out in order to more closely define the RNA recognition sequence. Once this is achieved, structural approaches will be utilised to determine the nature of the interaction.

 A molecular picture of the bicoid:caudal interaction will enhance our understanding of the dual function of TFs and more broadly of cross talk between different levels of gene regulation.