Gene expression is controlled through regulatory elements such as promoters and enhancers. Enhancers and other regulatory regions are usually bound by sequence-specific transcription factors that activate or repress transcription from promoters. The interactions, activities, and regulatory events that occur at and between enhancers and promoters are poorly understood.
We previously mapped the genome-wide landscape of RNA Polymerase II transcription initiation and elongation in C. elegans (Chen et al 2013). We identified ~75,000 sites of transcription initiation across the genome, most of which are bidirectional. In addition to transcription initiation sites at promoters, we also observed widespread bidirectional transcription initiation at enhancers. This pattern, which is also seen at mammalian enhancer regions, indicates a surprising similarity between enhancers and promoters.
We have been conducting transgenic assays to investigate and compare the activities of enhancers and promoters. We will present the results of these experiments, including findings showing that most tested core promoters contain extensive spatial and temporal information and that ~50% of tested enhancers can act as protein coding promoters, usually driving a subset of the associated gene’s expression pattern.