Core promoters in transcription: old problem, new insights

• In vivo experiments raise questions about the importance of core promoter elements in transcription.
• Genome-wide studies and pervasive transcription of the genome suggest that most genes lack defined core promoter elements, raising questions about the role of core promoter elements.
• Do noncoding RNAs utilize core promoter elements in the same fashion as protein coding genes?

Early studies established that transcription initiates within an approximately 50 bp DNA segment capable of nucleating the assembly of RNA polymerase II (Pol II) and associated general transcription factors (GTFs) necessary for transcriptional initiation; this region is called a core promoter. Subsequent analyses identified a series of conserved DNA sequence elements, present in various combinations or not at all, in core promoters. Recent genome-wide analyses have provided further insights into the complexity of core promoter architecture and function. Here we review recent studies that delineate the active role of core promoters in the transcriptional regulation of diverse physiological systems.