Protein-coding genes are epigenetically regulated in Arabidopsis polyploids

Abstract

The fate of redundant genes resulting from genome duplication is poorly understood. Previous studies indicated that ribosomal RNA genes from one parental origin are epigenetically silenced during interspecific hybridization or polyploidization. Regulatory mechanisms for protein-coding genes in polyploid genomes are unknown, partly because of difficulty in studying expression patterns of homologous genes. Here we apply amplified fragment length polymorphism (AFLP)-cDNA display to perform a genome-wide screen for orthologous genes silenced in Arabidopsis suecica, an allotetraploid derived from Arabidopsis thaliana and Cardaminopsis arenosa. We identified ten genes that are silenced from either A. thaliana or C. arenosa origin in A. suecica and located in four of the five A. thaliana chromosomes. These genes represent a variety of RNA and predicted proteins including four transcription factors such as TCP3. The silenced genes in the vicinity of TCP3 are hypermethylated and reactivated by blocking DNA methylation, suggesting epigenetic regulation is involved in the expression of orthologous genes in polyploid genomes. Compared with classic genetic mutations, epigenetic regulation may be advantageous for selection and adaptation of polyploid species during evolution and development.genome duplication ͉ epigenetics ͉ gene silencing ͉ evolution P olyploidy results from duplication of a whole genome (autopolyploid) or from combining two or more distinct but related genomes (allopolyploid). It occurs in many organisms, but predominantly in vertebrates and plants (1, 2), and estimates indicate that over 70% of flowering plants had at least one event of polyploidization in their evolutionary lineage (1, 3-7). Many important crops, including banana, canola, coffee, cotton, maize, potato, oat, soybean, sugarcane, and wheat, are polyploid (8). The common occurrence of polyploids in nature probably reflects an evolutionary advantage of having redundant genes, freeing some gene copies from certain constraints of natural selection, to allow accumulation of new mutations that improve fitness. Consistent with this notion, polyploid plants are more widely distributed over more habitats than their diploid progenitors (1).The most common form of polyploids is allopolyploidy, in which two or more different but related (homoeologous) genomes are brought together in a single-cell nucleus. It is unclear how the expression of homologous genes is regulated in the hybrid cell. The vast majority of genes retain their function during evolution (7, 9-12), whereas some duplicate genes are mutated or silenced within a few million years (13). However, ''genomic shock'' as predicted by McClintock (14) occurs rapidly, resulting in sequence elimination and rearrangement (15, 16), demethylation of retroelements (17, 18), and relaxation of imprinting genes (19) in polyploid genomes. Furthermore, in interspecific hybrids or allopolyploids of vertebrates, invertebrates, and plants, one parental set of rRNA genes is subjected to silencing (20,21). The ge...

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

“…(83) The initial survey of gene expression variation indicated $2.5% of gene expression differences in A. suecica relative to A. thaliana and A. arenosa. (70) The levels of differential gene expression are higher in synthetic Arabidopsis allotetraploids (43) than in A. suecica. Approximately 11% of the cDNA fragments displayed changes that may be related to gene repression, activation and subfunctionalization (Fig.…”

“…Sunfish is methylated in the autotetraploid parent, but demethylated and reactivated in the allotetraploids, suggesting that allopolyploidization provokes perturbation of genomic structure and chromatin remodeling, giving rise to the reactivation and silencing of transposons (44) and proteincoding genes. (43,70) It is conceivable that changes in DNA methylation detected in recent Spartina (60) polyploids and synthetic Arabidopsis (44) allotetraploids are associated with gene expression changes and phenotypic variation. Notably, synthetic Arabidopsis allotetraploids are more sensitive than their parents to treatments of aza-dC, (44) a chemical inhibitor for DNA methylation, indicating that DNA methylation and other chromatin modifications become sensitized in the allotetraploids, probably due to remodeling activities during allopolyploid formation.…”

“…(21) How are orthologous protein-coding genes regulated in synthetic interspecific hybrids and allotetraploids? To address this question, several groups took AFLP-cDNA display approaches to uncover novel gene expression patterns in synthetic Arabidopsis allotetraploids and natural A. seucica, (42,70) cotton (31) and wheat (68,82) allotetraploids. Synthetic Arabidopsis allotetraploids were produced by direct hybridization between an A. thaliana Ler autotetraploid and A. arenosa, a naturally outcrossing tetraploid.…”

“…Once the expression patterns are established, they are maintained by chromatin modifications such as DNA methylation. (95) Blocking DNA methylation by chemical inhibitors (70) or dominant negative regulation of DNA methyltransferase genes (43) leads to activation of the silenced genes. Here we are inspired to propose a few models for the initial determination of locusspecific expression patterns during allopolyploid formation and evolution.…”

“…One might elucidate the detailed mode of action in this regulatory system using the dominant-negative mutants in chromatin proteins and the upstream regulators, which may overcome genetic redundancy in allopolyploids. (43) Indeed, some silenced genes are reactivated in the A. suecica met1-RNAi lines (43) or by blocking DNA methylation, (70) which is correlated with promoter demethylation in these specific loci.…”