Archaic structure of the gene encoding transcription factor USF

The upstream stimulatory factor (USF) is a helix-loop-helix transcription factor that interacts with specific sites on the DNA that are also recognized by the MYC oncoproteins. We isolated genomic clones to the murine 44-kDa form of USF (USF2 gene). This unique gene spans 13 kilobases of DNA and is composed of 10 exons. The gene seems to have maintained its archaic structure, since many of the exons encode discrete functional domains of the transcription factor originally identified by protein sequence comparisons. A particularly striking HpaII tiny fragment island, extending over nearly 2,000 base pairs, surrounds the USF2 translation initiation site. This region, which includes the USF2 promoter and the first four exons, is characterized by an overall GC content greater than 74%. Analysis by S1 mapping and transient transfection assays revealed that the USF2 transcripts originate from an initiator element located within a highly GC-rich region that is surrounded by two long polyadenylate stretches and functions as a bidirectional promoter. Different forms of USF2 messages result from the presence or absence of the fourth exon in the processed USF2 mRNA. Alternative splicing correlates with the lack of a consensus lariat branch point in the third intron. Transient cotransfection assays revealed that the presence or absence of the amino acid sequences encoded by exon 4 affects considerably the transcription activation properties of the USF2 protein.