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...
Amplified differential gene expression (ADGE) is a novel technique, designed to profile gene expression of the whole transcriptome or to compare expression of a set of genes between two samples. ADGE employs hybridization to quadratically amplify the ratio of an expressed gene between control and tester samples before displaying. The subtle structures of adapters and primers are designed for displaying the amplified ratio of an expressed gene between two samples. Four selective nucleotides at the 3' end of primers are used to increase PCR efficiency for targeted molecules and to improve detection of PCR products. Double PCR with the same pair of primers expands the detection range, especially for genes of low abundance. Integration of these steps makes ADGE sensitive and accurate. Application to drug resistant human tumor cell lines showed that ADGE accurately profiled expression levels for induced, repressed or unchanged genes. The qualitative expression patterns for ADGE were verified with RT-PCR.
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