Transcription is mediated through a variety of protein complexes that are not only responsible
for the actual mechanism of transcription, but also are regulatory, in that their interactions at promoters can
be altered by modifications, additional proteins, or homolog/paralog substitution. One important aspect of
promoter recognition is mediated via proteins which can recognize and bind to DNA. Research in this area has
led to the identification and characterization of core promoter elements that function to stimulate transcription
in vitro and in vivo. One of the greatest revolutions in eukaryotic gene regulation is the discoveries that
promoters, including their cores, are not as simply explained by naming some of their elements that compose
them. This chapter looks at which core elements have been discovered, identified and characterized and places
them in the context of the recent genomic scale studies that are being currently made. Furthermore, some
insights into different known promoter classes concerning their architecture, regulation and classification are
addressed. Finally, we discuss and present data about a core promoter that sits downstream of the transcription
start site in plants, a likely case of intron-mediated enhancement. Many, if not all, of these new discoveries are
raising the questions about how gene regulation is managed in vivo under continually changing conditions.
Keywords: core promoter, eukaryotic transcription, core promoter elements, TATA-box, intron-mediated enhancement, spatial
distribution analysis, Y-tract, CpG islands, alternative promoters, GAGA, BPC, cis-regulatory element (CRE), DNAdependent
RNA Polymerase II, Pol II, RNAP II.
