Mutator transposon insertions within maize genes often provide a novel outward reading promoter

The highly active family of Mutator (Mu) DNA transposons has been widely used for forward and reverse genetics in maize. There are examples of Mu-suppressible alleles which result in conditional phenotypic effects based on the activity of Mu. Phenotypes from these Mu- suppressible mutations are observed in Mu-active genetic backgrounds, but absent when Mu activity is lost. For some Mu-suppressible alleles, phenotypic suppression likely results from an outward-reading promoter within Mu that is only active when the autonomous Mu element is silenced or lost. We isolated 35 Mu alleles from the UniformMu population that represent insertions in 24 different genes. Most of these mutant alleles are due to insertions within gene coding sequences, but several 5 UTR and intron insertions were included. RNA-seq and de novo transcript assembly were utilized to document the transcripts produced from 33 of these Mu insertion alleles. For 20 of the 33 alleles, there was evidence of transcripts initiating within the Mu sequence reading through the gene. This outward-reading promoter activity was detected in multiple types of Mu elements and doesnt depend on the orientation of Mu. 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, and more broadly highlights a strategy for transposons to co-exist with their host. Article SummaryMutator (Mu) transposable elements are a widely used tool for insertional mutagenesis in maize and often insert in the 5 regions of genes. The characterization of transcripts for Mu insertion alleles reveals complex transcripts. These often result in one transcript that covers the first portion of the gene terminating in Mu and a second transcript initiating within Mu covering the latter portion of the gene. This may reflect a strategy for Mu to minimize the consequences of insertions within genes.