Cis-Acting Transcriptional Regulatory Elements

Abstract Although it is impossible to discuss the cis-acting DNA sequence elements without reference to the trans-acting factors that bind to these sequences, this chapter will primarily focus on defining the different types of positive and negative cis-acting transcriptional regulatory elements. The trans-acting factors will be described in considerable detail in Chapter 3. All the cis-acting elements that affect transcription are defined on the basis of functional criteria. Therefore, none of these elements can be definitively identified solely by the examination of nucleotide sequence data. In general cis-acting elements are DNA sequences containing binding sites for several different transcription factors that are required en bloc for the element to function fully. The first defining criterion is whether the putative element has a positive or negative effect on transcription. In general, positive cis-acting elements contain binding sites for positive trans-acting factors (transcriptional activators) and negative cis-acting elements contain binding sites for negative trans-acting factors (transcriptional repressors). Examples of positive cis-regulatory elements include promoters and enhancers, whereas silencers and transcription-arrest sites represent examples of negative regulatory elements.