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Background  The  pericarp color1  ( p1 ) gene encodes for a myb-homologous protein that regulates the biosynthesis of brick-red flavonoid pigments called phlobahpenes. The pattern of pigmentation on the pericarp and cob glumes depends upon the allelic constitution at the  p1  locus.  p1  alleles have unique gene structure and copy number which have been proposed to influence the epigenetic regulation of tissue-specific gene expression. For example, the presence of tandem-repeats has been correlated with the suppression of pericarp pigmentation though a mechanism associated with increased DNA methylation.    Methodology/Principal Findings  Herein, we extensively characterize a  p1  allele called  P1-mosaic  ( P1-mm ) that has mosaic pericarp and light pink or colorless cob glumes pigmentation. Relative to the  P1-wr  (white pericarp and red cob glumes), we show that the tandem repeats of  P1-mm  have a modified gene structure containing a reduced number of repeats. The  P1-mm  has reduced DNA methylation at a distal enhancer and elevated DNA methylation downstream of the transcription start site.    Conclusions/Significance  Mosaic gene expression occurs in many eukaryotes. Herein we use maize  p1  gene as model system to provide further insight about the mechanisms that govern expression mosaicism. We suggest that the gene structure of  P1-mm  is modified in some of its tandem gene repeats. It is known that repeated genes are susceptible to chromatin-mediated regulation of gene expression. We discuss how the modification to the tandem repeats of  P1-mm  may have disrupted the epigenetic mechanisms that stably confer tissue-specific expression.

Gene Structure Induced Epigenetic Modifications of pericarp color1 Alleles of Maize Result in Tissue-Specific Mosaicism