Upstream elements required for efficient transcription of a human U6 RNA gene resemble those of U1 and U2 genes even though a different polymerase is used.
U6 small nuclear RNA is transcribed by a different polymerase than U1-U5 RNAs, likely to be RNA polymerase III. Transcription from human U6 gene deletion-substitution templates in a HeLa S100 extract delineated the 5' border of a control element lying between 67 and 43 bp upstream from the initiation site. This region matches the location of, and shows considerable sequence similarity with, the proximal control element of U1 and U2 RNA genes, which are transcribed by RNA polymerase II. Transfection of human 293 cells with 5'-flanking deletion-substitution mutants of a U6 maxigene revealed a dominant control element between 245 and 149 bp upstream of the transcription start site. An octamer motif was found in this region in an inverted orientation relative to that of the human U1 and U2 RNA gene enhancers but in the same orientation as a human U4 RNA gene, the transcript of which functions together with U6 RNA in a single small nuclear ribonucleoprotein (snRNP) particle. The human U2 gene enhancer joined to the U6 maxigene was able to functionally replace the U6 distal control element(s).