Analysis of the Promoter from an Expanding Mouse Retrotransposon Subfamily

Abstract

The mouse genome contains several subfamilies of the retrotransposon L1. One subfamily, TF, contains 4000–5000 full-length members and is expanding due to retrotransposition of a large number of active elements. Here we studied the TF5′ untranslated region (UTR), which contains promoter activity required for subfamily expression. Using reporter assays, we show that promoter activity is derived from TF-specific monomer sequences and is proportional to the number of monomers in the 5′ UTR. These data suggest that nearly all full-length TFelements in the mouse genome are currently competent for expression. We aligned the sequences of 53 monomers to generate a consensus TFmonomer and determined that most TFelements are truncated near a potential binding site for a transcription initiation factor. We also determined that much of the sequence variation among TFmonomers results from transition mutations at CpG dinucleotides, suggesting that genomic TF5′ UTRs are methylated at CpGs.