A novel promoter in the mouse rDNA spacer is active in vivo and in vitro

We have identified a novel RNA polymerase I (pol I) transcription initiation site within the 'non-transcribed' spacer of mouse rDNA. This spacer promoter is located about 2 kb upstream of the 45S pre-rRNA promoter and directs specific transcription initiations both in a cell-free system using truncated templates and in vivo after transfection into mouse cells. The spacer promoter contains an 11 out of 16 bases match to the core element of the major ribosomal gene promoter and is oriented in the same direction. It exerts a significantly lower transcriptional activity as compared to the 45S pre-rRNA promoter. The elongation of transcripts initiated at the spacer promoter is stopped at a termination signal located 170 bp upstream of the pre-rRNA start site. Since it has been previously shown that, in addition to its terminator function, the same sequence motif acts as an upstream element of the adjacent gene promoter, the function of the spacer promoter may be to capture free pol I molecules and drive them to the gene promoter in order to achieve the high level of transcription characteristic of eukaryotic rRNA genes.