RNA Structure:  Control of Viral and Oncogene Expression

Edlind, Thomas

Abstract

The role of RNA secondary structure in the control of bacterial gene expression has been extensively documented, but this subject has been little studied in higher eukaryotes. Recently, though, two observations have been made which warrant investigation. 1) The late RNA molecules of papovaviruses SV40, polyoma, and BKV include two sequences capable of stable base pairing. This pairing has been evolutionarily conserved in a manner which argues for the formation of the structure in vivo. The 3' splice site for the major late RNA is included in this conserved pairing. A specific role for secondary structure in splicing of higher eukaryotic RNA has not yet been demonstrated. 2) The human c-myc oncogene includes two sequences with the potential to form a highly stable secondary structure. These sequences would pair exon 1, a non-coding leader, with exon 2, which encodes the first half of the c-myc protein. A correlation between the absence of exon 1 in some Burkitt's lymphomas and high levels of c-myc expression suggests the exon 1 - exon 2 pairing may have a regulatory role. To examine the role, if any, of these potential structures in gene expression, cloned copies of the papovavirus and c-myc genes will be deleted by exonuclease treatment or modified by oligonucleotide-directed mutagenesis so as to specifically eliminate the potential pairing. The mutated DNA molecules will be transfected into cultured cells, and the RNA products will be examined by several different hybridization techniques to quantitate the effects of the secondary structure. A technique will be developed (involving psoralen crosslinking and primer extension) to map c-myc RNA secondary structure in vivo. Evolutionary conservation of this structure will also be investigated by cloning and sequencing c-myc genes from bovine and simian genomic libraries.