A distant enhancer element is required for polymerase III transcription of a U6 RNA gene

U RNAs are highly abundant small nuclear RNAs involved in the processing of messenger RNA. Most U RNA genes are thought to be transcribed by RNA polymerase II (pol II). However, evidence has recently been presented that U6 RNA genes are transcribed by RNA polymerase III (pol III). In the light of these results it was surprising to find that the 5' flanking region of a mouse U6 RNA gene includes a perfect copy of the octamer sequence motif, ATTTGCAT, found in many RNA polymerase II transcription enhancer elements. In the present study we show that deletion of mouse U6 gene sequences upstream of nucleotide position -217, including the octanucleotide motif, reduces U6 transcription by 90% when assayed in Xenopus laevis oocytes, suggesting the presence of a distant control element. DNase I footprinting of the 5' flanking region of the U6 gene shows protection of the octanucleotide sequence. Moreover, the 5' flanking sequence from -217 to -315 can replace the enhancer of a human U2 RNA gene. We therefore conclude that although U6 RNA genes appear to be transcribed by pol III, they are preceeded by an enhancer-like element which can functionally substitute for the enhancer of a pol II-transcribed U RNA gene.