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

Abstract

BackgroundThe 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 FindingsHerein, 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/SignificanceMosaic 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.

Early flowering and genetic containment studies in transgenic poplar

“…However, a low activity of this promoter in some cells, due to variable gene expression level, may be a possible reason for presence of viable pollen grains in some catkins. Epigenetic modifications may result in a mosaic gene expression (Bastar et al 2004, Robbins et al 2009, Freeman et al 2011. T-DNA positional effects may be playing an important role too (Kumar & Fladung 2001).…”

Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation

“…Paramutation can clearly result in epigenetic variation, but only certain alleles at a particular locus are subject to regulation by paramutation (Chandler and Stam, 2004), which may reflect the need for certain genetic elements to create an environment that is permissive for a role of epigenetics for the regulation of facilitated epialleles. Similarly, there are many examples of potential chromatin-based regulation that may be linked to genetic changes, such as transposon insertions (Kinoshita et al, 2007;Saze and Kakutani, 2007;Martin et al, 2009;Robbins et al, 2009).…”

Mosaic patterns of transgene expression in plants

“…MANIFESTATION IN PLANTS One of illustrative example of mosaic gene expres sion in plants is the unequal pigmentation of different organs (seeds in maize, flowers in snapdragon) caused by abnormal pigment formation as a result of allelic interactions upon paramutations [45][46][47][48][49].…”

“…Plants with P1 wr allele, represented by six tandem arrayed copies, have colorless pericarp and red ear cob. The plants with P1 mosaic (P1 mm) allele have variegated pericarp pigmentation and either colorless or light pink cob [45]. Within a single ear, unequal lev els of kernel pigmentation were demonstrated.…”

“…These fea tures affected the gene expression resulting in varie gated pigmentation of pericarp and the ear cob. It is sug gested that the P1 mm mosaic expression pattern results from the interaction of epigenetic mechanisms of the gene expression activation (hypomethylated enhancer) and suppression (the р1 hypermethylatyon) [45].…”