Developmental stage-specific regulation of Xenopus tRNA genes by an upstream promoter element

Typically the internal promoter elements of tRNA genes are necessary and sufficient to support transcription. Here a sequence element preceding a Xenopus tRNA gene is shown to be required for transcription in late stage, but not early stage oocyte extracts. The constitutive tyrD gene is expressed in both early and late oocyte extracts, whereas the early oocyte-specific tyrCooc gene is only expressed in early extracts. An upstream promoter element (URR), between positions -42 and -14 of the tyrD gene, mediates this differential expression. The URR is required for tyrD transcription in late oocyte extracts. Placing the URR upstream of the tyrCooc gene allows this gene to be transcribed in late extracts. The URR is irrelevant to transcription in early extracts; transcription of tyrD or tyrCooc requires only the internal promoter sequences. This indicates the polymerase III transcriptional machinery changes during oogenesis, resulting in a stringent upstream sequence requirement. Mutations within the URR are shown to alter the preferred site of initiation by RNA polymerase III. Shifting the position of the URR upstream by one-half helical turn also repositioned the site of initiation, suggesting the URR directs the placement of the initiation factor complex or polymerase itself.