Mapping of Trans-Acting Factor Binding in the Nervous System

The complexity of neural gene expression results from an inter- play of a multitude of signal transduction pathways and trans -acting transcription factors interacting at cis-acting DNA elements (1 ). Clearly, a major challenge is to define the pathways and molecular mechanism(s) interposed between protein kinase activation (action from the cell surface) and the cis -acting DNA elements (controlling target gene expression, in the nucleus), via intermediary protein factors. In general, investigators performing similar studies on various genes use large amounts of nuclear extracts made from cultured established cell lines. Simplicity of preparation is the main reason for this, as opposed to the difficulty of handling small quantities of primary neural tissues. Unfortunately, if only cell line extracts are used, not only is the infor- mation passed in vivo between cells in their natural context lost, but also information gained from these related established lines may have little physiological relevance to normal cells growing in their normal tissues. The methods presented in this chapter have been used (2 ,3 ) and may further be used to permit resolution of complex patterns of DNA-protein interactions generated from behavioral changes occur- ring at the level of the whole animal in healthy or diseased states.