Transposon sequences drive tissue-specific expression of the maize regulatory gene R-s

The R family of genes in maize encodes transcription factors that activate anthocyanin synthesis. The R-r complex at the r locus contains two components, of which one, the aleurone-pigmenting R-s subcomplex, is an unusual promoter flanked by two head-to-head, nearly identical coding regions. The central region of the promoter, designated sigma(r) contains inverted terminal repeats and subterminal repeats, both of which are features of the CACTA transposon family. Transcription from the R-s promoter was strongest in aleurone but transcripts had a surprisingly variable initiation site and splicing pattern. Microprojectile bombardment indicated that the sequences introduced by transposition act as an enhancer of transcription in aleurone but not in coleoptile or mesocotyl tissue. Moreover, the region containing the subterminal repeats was able to activate expression when fused to a minimal promoter, suggesting that a factor that binds to the repeats may be responsible. Regions downstream of sigma encode a leader containing three ORFs, two of which are variably removed by splicing. The results presented here show that transposons can mediate the rearrangement of genes and confer new splicing and expression patterns. In the case of the r complex, this has resulted in a new phenotype, the pigmentation of aleurone cells.