Introns in promoter - (May/16/2012 )
Recently I came across a PAPER which shows that there is methylation of exons in the promoter of glucocorticoid receptor gene in the brains of maternally cared rat pups. According to my concepts, introns (hence "exons") are present only in the coding regions of the genes, because RNA is made only from this coding region. If promoter regions, to the best of knowledge, are not transcribed, how can intron and exon regions be defined in promoters?
are you sure you are not mixing up introns and exons...?
Introns and exons can exist within the promoter. Exons are simply the mRNA, not just the protein coding sequence. So it somply means that some of the mRNA is produced within the promtoer region, but necessarily the coding sequence of hte mRNA.
Eukaryotes promoters are quite complex and some binding sites for proteins that activate the transcription may actually be downstream of the mRNA start position, or it may be that the presensce of the first intron/exon increases the promoters activity and is therefore considered part of the promoter region. Many of the strongest mammalian promoters have introns in them, Ubiquitin, Elongation factor alpha and chicken beta actin (full length) all have introns in them. In fact, many people add an intron upstream of their gene to prolong expression in vivo. It makes a gene more like a natural gene and decreases its chances of being methylated.