Identification of two initiator elements in the bidirectional promoter of the human dihydrofolate reductase and mismatch repair protein 1 genes

The human dihydrofolate reductase (DHFR) gene and mismatch repair protein 1 (MRP1) genes are organized in a head-to-head configuration separated by an 90 base pair sequence. We have previously shown that as small as a 114 bp promoter sequences is sufficient for accurate and efficient initiation of divergent transcription. In this study, the mechanism of accurate transcription initiation in vivo from this short bidirectional promoter was analyzed by a newly developed highly sensitive primer extension assay. The GC boxes in the middle of this sequence were essential for bidirectional promoter activity, but not sufficient for accurate initiation. The sequences overlapping the transcription initiation sites of the DHFR and MRP1 genes were shown to function as the initiator, which directs transcription from an internal site. These initiators were strictly position dependent and were active only when located from 40 to 50 base pairs downstream from the GC box. Although there is no apparent sequence homology between two initiators, a common nuclear factor bound to these elements. Existence of two initiators located on both sides of the middle GC box seems to be the molecular basis of bidirectional activity of this short DNA sequence.