Binding of transcription factors to the promoter of the human U1 RNA gene studied by footprinting.

The promoter structure of the known small nuclear RNA (snRNA) genes contains two major effectors of transcriptional activity: a proximal sequence element and a distal sequence element. In addition to these two functional elements (called elements B and D), the human U1 snRNA gene contains at least three minor elements (elements A, C, and E) that contribute to overall transcriptional efficiency (Murphy, J.T., Skuzeski, J.M., Lund, E., Steinberg, T.H., Burgess, R.R., and Dahlberg, J.E. (1987) J. Biol. Chem. 262, 1795-1803). To elucidate further the function of these transcription elements, we carried out a computer search to look for sequences in the U1 gene homologous to known transcription factor consensus sequences. Where such homology was found, DNase I and MPE-Fe(II) (methidiumpropyl-EDTA-Fe(II] footprinting was employed to study the interactions of these promoter regions with proteins partially purified from extracts of HeLa cells or human placenta. Footprints were observed over element D (the distal element) corresponding to sequences homologous to the octanucleotide binding protein (OCTA) and activator protein 1 (AP1). Protection was also observed over element B (the proximal element) corresponding to possible sites for stimulatory protein 1 (Sp1), enhancer core, major late transcription factor (MLTF), and a U1-specific transcription factor. Prior to this study, no specific transcription factor footprints had been observed over proximal elements of any snRNA gene. Footprints were also found over elements A and E. The results of the computer search and the footprinting are discussed in light of what is known about snRNA promoter activity.