Structure and Functions of the Rodent Identifier Retroposon Located in the c-Ha-ras Oncogene Far Upstream Regulatory Region

Retrotransposition is developmentally programmed and such events regulate host genes creating a new trait. A ~120 bp identifier (ID) retroposon insertion was detected in the 161 bp rat c-Ha-ras oncogene far upstream regulatory element. The designed oligonucleotides was probed using gel electrophoresis mobility shift assay to assess transcription factors. The ID retroposon derived Avr1 oligonucleotide binds a nuclear protein complex present in all carcinoma cell lines tested, but not in nuclear extract from normal liver cells. However, Avr2 and Avr3 oligonucleotides (conserved Ha-ras repressor motifs) bind to protein factors found in both normal and carcinoma cells. Also, the Avr3 oligonucleotide binds a small protein in normal cells verses a large complex in carcinoma cells. Each oligonucelotide-protein binding is strong and specific. BLAST sequence analysis has demonstrated that the transposed ID sequence is conserved in too many genes. Avr1 sequence is also a part of the highly expressed HaSV and VL30-retroelements, suggesting that Avr1 factor acts as an activator of transcription. The differential expression of Avr1 trans-activator factor and ubiquitous nature of Avr1 sequence could be used as a marker in cancer diagnostics. This study supports the multiple functions of the smallest ID retroposon shaping the genomic evolution and could be studied further to understand the molecular mechanisms of transposition in cancer, stress and drug resistance.