Unusual case of apparent hypermutation in Arabidopsis thaliana

The dms4 (defective in meristem silencing 4) mutant of Arabidopsis thaliana is unique in having defects in both RNA-directed DNA methylation (RdDM) and plant development. DMS4 is an evolutionarily conserved, putative transcription factor of the Iwr1 (interacts with RNA polymerase II) type. DMS4 interacts with Pol II and also with RNA polymerases IV and V, which function in RdDM. Interactions with multiple polymerases may account for the diverse phenotypic effects of dms4 mutations. To dissect further the roles of DMS4 in RdDM and development, we performed a genetic suppressor screen using the dms4-1 allele, which contains in the sixth intron a splice site acceptor mutation that alters splicing and destroys the open reading frame. Following mutagenesis of dms4-1 seeds using ethyl methanesulfonate (EMS), we retrieved four dominant intragenic suppressor mutations that restored DMS4 function and wild-type phenotypes. Three of the four intragenic suppressor mutations created new splice site acceptors, which resulted in reestablishment of the wild-type open reading frame. Remarkably, the intragenic suppressor mutations were recovered at frequencies ranging from 35 to 150 times higher than expected for standard EMS mutagenesis in Arabidopsis. Whole-genome sequencing did not reveal an elevated mutation frequency genome-wide, indicating that the apparent hypermutation was confined to four specific sites in the dms4 gene. The localized high mutation frequency correlated with restoration of DMS4 function implies an efficient mechanism for targeted mutagenesis or selection of more fit revertant cells in the shoot apical meristem, thereby rapidly restoring a wild-type phenotype that is transmitted to future generations.