Mutator transposon insertions in maize often provide a novel promoter

The highly active family of Mutator (Mu) DNA transposons has been widely used in maize for forward and reverse genetics. We isolated 35 Mu insertion alleles from the UniformMu population that represent 24 different genes. RNA-seq and de novo transcript assembly were utilized to document the transcripts produced from these Mu insertion alleles. For 20 of the 35 alleles there was evidence of transcripts initiating within the Mu sequence that read-through to the gene transcription termination site. This outward-reading promoter activity was detected in multiple types of Mu elements and does not depend on the orientation of the Mu insertion. Expression analyses of Mu initiated transcripts revealed the Mu promoter often provides gene expression levels and patterns that are similar to the wild-type gene. These results suggest the Mu promoter may represent a minimal promoter that can respond to gene cis-regulatory elements. Findings from this study have implications for maize researchers using the UniformMu population to isolate loss-of-function alleles, and more broadly highlights a strategy for transposons to co-exist with their host.