Ploidy Regulation of Gene Expression

Galitski, Timothy; Saldanha, Alok J.; Styles, Cora A.; Lander, Eric S.; Fink, Gerald R.

doi:10.1126/science.285.5425.251

Cited by 608 publications

(518 citation statements)

References 21 publications

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“…(86) Few genes were upregulated or downregulated in the Arabidopsis autotetraploids, consistent with the findings in yeast, in which a dozen genes were expressed differently in response to ploidy changes in a series of haploid, diploid, triploid and autotetraploid. (88) The data suggest that during autopolyploid formation the dosage-dependent regulatory mechanisms prevail. (89) In another study, Hegarty et al (2005) found dramatic differences in floral gene expression between the allohexaploid hybrid, Senecio cambrensis, its parental taxa Senecio squalidus (diploid) and Senecio vulgaris (tetraploid), and the intermediate triploid (sterile) hybrid Senecio Â baxteri.…”

Section: Activation Of Transposons and Changes In Dna Methylation In mentioning

confidence: 98%

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 In mentioning

confidence: 98%

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

2006

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“…NIH-PA Author Manuscript NIH-PA Author Manuscript which might allow them to reach a higher metabolic rate to support nitrogen fixation 65,68 . The intensive DNA synthesis that is required for endoreduplication within bacteroids requires a large quantity of dNTPs that must be supplied by ribonucleotide reductase (RNR) 89 .…”

Section: Nih-pa Author Manuscriptmentioning

confidence: 99%

“…Plant cell endoreduplication is required for the formation of functional nodules, and is dependent on the degradation of mitotic cyclins by anaphase-promoting complex (APC), an E3 ubiquitin ligase 66,67 . The advantages of cellular polyploidy are a higher transcription rate and a higher metabolic rate than cells with the normal 2n DNA content 68 -characteristics that might be important for the invaded plant cells to support bacterial nitrogen fixation (discussed later).…”

Section: Box 2 Mesorhizobium Loti and Lotus Japonicus: Model System Fmentioning

confidence: 99%

“…Surprisingly, plants that form indeterminate nodules impose a programme of genomic endoreduplication on the invading bacterial cells 65 . Bacteroids within indeterminate nodules increase their DNA content and cell size, which might allow them to reach a higher metabolic rate to support nitrogen fixation 65,68 . The intensive DNA synthesis that is required for endoreduplication within bacteroids requires a large quantity of dNTPs that must be supplied by ribonucleotide reductase (RNR) 89 .…”

Section: Box 3 Host Invasion Parallels Between Rhizobia and Animal Pamentioning

confidence: 99%

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How rhizobial symbionts invade plants: the Sinorhizobium–Medicago model

et al. 2007

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Nitrogen-fixing rhizobial bacteria and leguminous plants have evolved complex signal exchange mechanisms that allow a specific bacterial species to induce its host plant to form invasion structures through which the bacteria can enter the plant root. Once the bacteria have been endocytosed within a host-membrane-bound compartment by root cells, the bacteria differentiate into a new form that can convert atmospheric nitrogen into ammonia. Bacterial differentiation and nitrogen fixation are dependent on the microaerobic environment and other support factors provided by the plant. In return, the plant receives nitrogen from the bacteria, which allows it to grow in the absence of an external nitrogen source. Here, we review recent discoveries about the mutual recognition process that allows the model rhizobial symbiont Sinorhizobium meliloti to invade and differentiate inside its host plant alfalfa (Medicago sativa) and the model host plant barrel medic (Medicago truncatula).The recent completion of the Sinorhizobium meliloti genome sequence, and the progress towards the completion of the Medicago truncatula genome sequence, have led to a surge in the molecular characterization of the determinants that are involved in the development of the symbiosis between rhizobial bacteria and leguminous plants. Aromatic compounds from legumes called flavonoids first signal the rhizobial bacteria to produce lipochitooligosaccharide compounds called Nod factors 1 . Nod factors that are secreted by the bacteria activate multiple responses in the host plant that prepare the plant to receive the invading bacteria. Nod factors and symbiotic exopolysaccharides induce the plant to form infection threads, which are thin tubules filled with bacteria that penetrate into the plant cortical tissue and deliver the bacteria to their target cells. Plant cells in the inner cortex internalize the invading bacteria in host-membrane-bound compartments that mature into structures known Correspondence to G.C.W. gwalker@mit.edu. Competing interests statementThe authors declare no competing financial interests. DATABASES Invasion of plant rootsAlthough plant roots are exposed to various micro-organisms in the soil, their cell walls form a strong protective barrier against most harmful species. The early steps in the invasion of barrel medic (M. truncatula) and alfalfa (Medicago sativa) roots by S. meliloti are characterized by the reciprocal exchange of signals that allow the bacteria to use the plant root hair cells as a means of entry. Initial signal exchangeFlavonoid compounds (2-phenyl-1,4-benzopyrone derivatives) produced by leguminous plants are the first signals to be exchanged by host-rhizobial symbiont pairs 1 (FIG. 1). Flavonoids bind bacterial NodD proteins, which are members of the LysR family of transcriptional regulators, and activate these proteins to induce the transcription of rhizobial genes 1,2 . For example, the M. sativa-derived flavonoid luteolin stimulates binding of an active form of NodD1 to an S. meliloti 'nod-box' p...

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“…In a genome-wide transcription analysis, Galitski et al could show that yeast (S. cerevisiae) cells with different ploidy exhibit different patterns of gene expression, providing evidence for a ploidy-driven mechanism of gene regulation. 2 An increase in ploidy strongly correlates with increased cell size, as observed in bacteria, yeast, plants, and animals. [1][2][3] The expression of specific G 1 cyclins is repressed with increasing ploidy, which eventually results in a retarded passage through START (the entry point into the cell cycle) and therefore a larger cell size.…”

Section: Introductionmentioning

confidence: 99%

Depletion of Endonuclease G Selectively Kills Polyploid Cells

Büttner¹,

Carmona-Gutiérrez²,

Vitale³

et al. 2007

Cell Cycle

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Endonuclease G is a mitochondrio-nuclear located nuclease with dual-vital and lethal-functions. Besides its role in apoptosis execution, we have recently shown that depletion of endonuclease G leads to necrotic cell death in yeast. Here, we present further mechanistic elucidation of endonuclease G's vital functions. The deletion of the yeast Endonuclease G gene causes the complete elimination of tetraploid cells during exponential growth. Consistently, conditional knockdown of mammalian endonuclease G selectively kills tetraploid but not diploid clones of the human HCT116 colon carcinoma cell line. We conclude that endonuclease G is important for the viability of polyploid mammalian and yeast cells.

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Ploidy Regulation of Gene Expression

Cited by 608 publications

References 21 publications

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

How rhizobial symbionts invade plants: the Sinorhizobium–Medicago model

Depletion of Endonuclease G Selectively Kills Polyploid Cells

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