Stochastic and Epigenetic Changes of Gene Expression in Arabidopsis Polyploids

Wang, Jianlin; Tian, Lili; Madlung, Andreas; Lee, Hyeon-Se; Chen, Meng; Lee, Jinsuk J.; Watson, Brian; Kagochi, Trevor; Comai, Luca; Chen, Z. Jeffrey

doi:10.1534/genetics.104.027896

Cited by 327 publications

(379 citation statements)

References 88 publications

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“…Among them, $4% were from A. thaliana parent, $5% from A. arenosa parent, $1% from both parents, and $1% from neither parents (or novel gene expression patterns). (43) Similar levels of changes were found in three independent allotetraploid lineages, suggesting that those genes are subjected to similar regulation during allopolyploid evolution.…”

Section: Activation Of Transposons and Changes In Dna Methylation Inmentioning

confidence: 58%

“…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.…”

Section: Activation Of Transposons and Changes In Dna Methylation Inmentioning

confidence: 99%

“…(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.…”

Section: Activation Of Transposons and Changes In Dna Methylation Inmentioning

confidence: 99%

“…AtRAD54 is a putative homolog of SNF2/RAD54 subfamily that is involved in both DNA repair and transcriptional regulation. (65) AtRAD54 is activated in synthetic Arabidopsis auto-and allotetraploids but not in diploid parents and natural allotetraploids (A. suecica), (43) suggesting a role of DNA recombination and repair in the maintenance of genomic stability during early stages of polyploidy formation. Types of genomic and gene expression changes documented in the polyploids.…”

mentioning

confidence: 99%

“…1C) as demonstrated in the production of new Arabidopsis allotetraploids. (42)(43)(44) Fusion of unreduced gametes may be the predominate mode because almost every plant species produces a variable but small amount of unreduced gametes via first or second division meiotic restitution, (45) and many plant species are autotetraploids. (24,41) It is notable that autopolyploids may be formed via either model, except that a single species is involved.…”

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Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

2006

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SummaryPolyploidy is produced by multiplication of a single genome (autopolyploid) or combination of two or more divergent genomes (allopolyploid). The available data obtained from the study of synthetic (newly created or human-made) plant allopolyploids have documented dynamic and stochastic changes in genomic organization and gene expression, including sequence elimination, inter-chromosomal exchanges, cytosine methylation, gene repression, novel activation, genetic dominance, subfunctionalization and transposon activation. The underlying mechanisms for these alterations are poorly understood. To promote a better understanding of genomic and gene expression changes in polyploidy, we briefly review origins and forms of polyploidy and summarize what has been learned from genome-wide gene expression analyses in newly synthesized autoand allopolyploids. We show transcriptome divergence between the progenitors and in the newly formed allopolyploids. We propose models for transcriptional regulation, chromatin modification and RNA-mediated pathways in establishing locus-specific expression of orthologous and homoeologous genes during allopolyploid formation and evolution. Polyploidy and its formsPolyploidy occurs throughout the evolutionary history of all eukaryotes, (1,2) predominately in flowering plants (3,4) including many important agricultural crops. (5) Compared to plants, polyploidy occurs rarely in animals, but clearly exists in some invertebrates (e.g. insects) and vertebrates (e.g. fish, amphibians and reptiles). (4,6) The relative paucity of polyploidy in animals is attributed to the delicate schemes of sex determination and animal development, which are disrupted by polyploidization. (7,8) Therefore, polyploid animals rarely exist. (9) Moreover, aneuploid and polyploid cells in animals and human are often associated with malignant cell proliferation or carcinogenesis. (10) However, endopolyploidy (somatic polyploid cells within a diploid individual) appears to be a physiological response to developmental changes in plants and some animals, (11,12) indicating plasticity of plant and animal genomes. In the post-sequencing era, polyploidy is proving to be a fascinating and challenging field of plant biology, stimulating many research advances and insightful reviews. (2,13 -24) Here we attempt to update the views using genomic-scale results and provide new mechanistic insights.Historically, Winkler (1916) introduced the term polyploidy, (25) and Winge (1917) called attention to the general importance of polyploidy in the evolution of angiosperms. (26) At that time, research in polyploidy was somewhat limited by the plant and animal materials that were available in nature. In 1937, Blakeslee and Avery induced polyploidy in plants using colchicine, a chemical inhibitor of mitotic cell divisions. (27) The technique has been successfully used to induce chromosome doubling in meristemic cells of diploids and interspecific hybrids. Doubling a single 'diploid' genome results in an autotetraploid, while doubling c...

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Section: Activation Of Transposons and Changes In Dna Methylation Inmentioning

confidence: 58%

Section: Activation Of Transposons and Changes In Dna Methylation Inmentioning

confidence: 99%

Section: Activation Of Transposons and Changes In Dna Methylation Inmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

2006

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Epigenetic inheritance and plant evolution

Miryeganeh

Saze

2019

Population Ecology

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Being sessile organisms, plants show a high degree of developmental plasticity to cope with a constantly changing environment. While plasticity in plants is largely controlled genetically, recent studies have demonstrated the importance of epigenetic mechanisms, especially DNA methylation, for gene regulation and phenotypic plasticity in response to internal and external stimuli. Induced epigenetic changes can be a source of phenotypic variations in natural plant populations that can be inherited by progeny for multiple generations. Whether epigenetic phenotypic changes are advantageous in a given environment, and whether they are subject to natural selection is of great interest, and their roles in adaptation and evolution are an area of active research in plant ecology. This review is focused on the role of heritable epigenetic variation induced by environmental changes, and its potential influence on adaptation and evolution in plants.

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Ploidy Variation in Plants

Birchler

2009

Encyclopedia of Life Sciences

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Evidence from genome sequences of many plant species indicate that all plants have had a cyclical history of doubling of chromosome numbers, followed by gene deletions back to a near diploid level. Recent cases of increases in genome copy number are generally considered to comprise ploidy variation. Ploidy variation involves changes in the number of whole sets of chromosomes. Aneuploid variation involves changes in the number of individual chromosomes. The two types of chromosomal changes have different consequences for gene expression patterns. Key concepts: An increase in whole genome chromosome sets is a recurring process in plant evolution followed by deletion of genes back to a near diploid level. Recent genome doubling can consist of genomes from slightly diverged species and are referred to as allopolyploids. Recent genome doubling within a species is referred to as autopolyploids. Allopolyploids and autopolyploids have different genetic behaviours. Cell size increases with the number of genomes present, as does gene expression in general. Aneuploidy is the change in copy number of part of the genome. Aneuploidy produces greater changes in gene expression than does ploidy variation.

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Stochastic and Epigenetic Changes of Gene Expression in Arabidopsis Polyploids

Cited by 327 publications

References 88 publications

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

Epigenetic inheritance and plant evolution

Ploidy Variation in Plants

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