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Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana.

Huettel B, Kreil DP, Matzke M, Matzke AJ - PLoS Genet. (2008)

Bottom Line: The results indicate that trisomy 5 disrupts gene expression throughout the genome and supports the production and/or retention of truncated copies of chromosome 5.Although trisomy 5 does not grossly distort the interphase arrangement of fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations between transgene alleles.Our analysis reveals the complex genomic changes that can occur in aneuploids and underscores the importance of using multiple experimental approaches to investigate how chromosome numerical changes condition abnormal phenotypes and progressive genome instability.

View Article: PubMed Central - PubMed

Affiliation: Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria.

ABSTRACT
Aneuploidy refers to losses and/or gains of individual chromosomes from the normal chromosome set. The resulting gene dosage imbalance has a noticeable affect on the phenotype, as illustrated by aneuploid syndromes, including Down syndrome in humans, and by human solid tumor cells, which are highly aneuploid. Although the phenotypic manifestations of aneuploidy are usually apparent, information about the underlying alterations in structure, expression, and interphase organization of unbalanced chromosome sets is still sparse. Plants generally tolerate aneuploidy better than animals, and, through colchicine treatment and breeding strategies, it is possible to obtain inbred sibling plants with different numbers of chromosomes. This possibility, combined with the genetic and genomics tools available for Arabidopsis thaliana, provides a powerful means to assess systematically the molecular and cytological consequences of aberrant numbers of specific chromosomes. Here, we report on the generation of Arabidopsis plants in which chromosome 5 is present in triplicate. We compare the global transcript profiles of normal diploids and chromosome 5 trisomics, and assess genome integrity using array comparative genome hybridization. We use live cell imaging to determine the interphase 3D arrangement of transgene-encoded fluorescent tags on chromosome 5 in trisomic and triploid plants. The results indicate that trisomy 5 disrupts gene expression throughout the genome and supports the production and/or retention of truncated copies of chromosome 5. Although trisomy 5 does not grossly distort the interphase arrangement of fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations between transgene alleles. Our analysis reveals the complex genomic changes that can occur in aneuploids and underscores the importance of using multiple experimental approaches to investigate how chromosome numerical changes condition abnormal phenotypes and progressive genome instability.

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Chromosome breaks in trisomic and triploid plants.Array CGH detected truncated copies of chromosome 5 in two chromosome 5                            trisomics (6-5-22 [potentially a secondary trisomic or                            isochromosome (2)] and 6-7-10), and a chromosome 1 truncation                            in a triploid plant (11-5). Each dot represents a probe set matching a                            unique gene model in the Arabidopsis genome. Identical                            chromosome copy numbers are indicated by a log2 ratio close to 0, while                            trisomy is characterized by the shift above the 0 baseline. Centromeres                            and pericentromeric heterochromatic regions are apparent by the areas                            deficient in dots.
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pgen-1000226-g003: Chromosome breaks in trisomic and triploid plants.Array CGH detected truncated copies of chromosome 5 in two chromosome 5 trisomics (6-5-22 [potentially a secondary trisomic or isochromosome (2)] and 6-7-10), and a chromosome 1 truncation in a triploid plant (11-5). Each dot represents a probe set matching a unique gene model in the Arabidopsis genome. Identical chromosome copy numbers are indicated by a log2 ratio close to 0, while trisomy is characterized by the shift above the 0 baseline. Centromeres and pericentromeric heterochromatic regions are apparent by the areas deficient in dots.

Mentions: The first chromosome break we detected was in a triploid plant from the F2 generation (11-5; Table S1), which contained a truncated copy of chromosome 1 lacking part of the top arm (Figures 2A and 3). The two trisomic F2 plants, 6-5 and 6-7, had structurally intact genomes as assessed by array CGH. In the F3 generation, however, we detected chromosome breaks in two trisomic plants (out of 26 tested by array CGH; Table S1B), one from each trisomic F2 parent. Both of these breaks affected the triplicated chromosome 5. In one case essentially the entire top arm of chromosome 5 was deleted (plant 6-5-22), suggesting a break around the centromere. In the second case, the break occurred in the vicinity of the DsRed transgene locus, such that the tip of the bottom arm of chromosome 5 was lost (plant 6-7-10) (Figure 2A and Figure 3).


Effects of aneuploidy on genome structure, expression, and interphase organization in Arabidopsis thaliana.

Huettel B, Kreil DP, Matzke M, Matzke AJ - PLoS Genet. (2008)

Chromosome breaks in trisomic and triploid plants.Array CGH detected truncated copies of chromosome 5 in two chromosome 5                            trisomics (6-5-22 [potentially a secondary trisomic or                            isochromosome (2)] and 6-7-10), and a chromosome 1 truncation                            in a triploid plant (11-5). Each dot represents a probe set matching a                            unique gene model in the Arabidopsis genome. Identical                            chromosome copy numbers are indicated by a log2 ratio close to 0, while                            trisomy is characterized by the shift above the 0 baseline. Centromeres                            and pericentromeric heterochromatic regions are apparent by the areas                            deficient in dots.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2562519&req=5

pgen-1000226-g003: Chromosome breaks in trisomic and triploid plants.Array CGH detected truncated copies of chromosome 5 in two chromosome 5 trisomics (6-5-22 [potentially a secondary trisomic or isochromosome (2)] and 6-7-10), and a chromosome 1 truncation in a triploid plant (11-5). Each dot represents a probe set matching a unique gene model in the Arabidopsis genome. Identical chromosome copy numbers are indicated by a log2 ratio close to 0, while trisomy is characterized by the shift above the 0 baseline. Centromeres and pericentromeric heterochromatic regions are apparent by the areas deficient in dots.
Mentions: The first chromosome break we detected was in a triploid plant from the F2 generation (11-5; Table S1), which contained a truncated copy of chromosome 1 lacking part of the top arm (Figures 2A and 3). The two trisomic F2 plants, 6-5 and 6-7, had structurally intact genomes as assessed by array CGH. In the F3 generation, however, we detected chromosome breaks in two trisomic plants (out of 26 tested by array CGH; Table S1B), one from each trisomic F2 parent. Both of these breaks affected the triplicated chromosome 5. In one case essentially the entire top arm of chromosome 5 was deleted (plant 6-5-22), suggesting a break around the centromere. In the second case, the break occurred in the vicinity of the DsRed transgene locus, such that the tip of the bottom arm of chromosome 5 was lost (plant 6-7-10) (Figure 2A and Figure 3).

Bottom Line: The results indicate that trisomy 5 disrupts gene expression throughout the genome and supports the production and/or retention of truncated copies of chromosome 5.Although trisomy 5 does not grossly distort the interphase arrangement of fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations between transgene alleles.Our analysis reveals the complex genomic changes that can occur in aneuploids and underscores the importance of using multiple experimental approaches to investigate how chromosome numerical changes condition abnormal phenotypes and progressive genome instability.

View Article: PubMed Central - PubMed

Affiliation: Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria.

ABSTRACT
Aneuploidy refers to losses and/or gains of individual chromosomes from the normal chromosome set. The resulting gene dosage imbalance has a noticeable affect on the phenotype, as illustrated by aneuploid syndromes, including Down syndrome in humans, and by human solid tumor cells, which are highly aneuploid. Although the phenotypic manifestations of aneuploidy are usually apparent, information about the underlying alterations in structure, expression, and interphase organization of unbalanced chromosome sets is still sparse. Plants generally tolerate aneuploidy better than animals, and, through colchicine treatment and breeding strategies, it is possible to obtain inbred sibling plants with different numbers of chromosomes. This possibility, combined with the genetic and genomics tools available for Arabidopsis thaliana, provides a powerful means to assess systematically the molecular and cytological consequences of aberrant numbers of specific chromosomes. Here, we report on the generation of Arabidopsis plants in which chromosome 5 is present in triplicate. We compare the global transcript profiles of normal diploids and chromosome 5 trisomics, and assess genome integrity using array comparative genome hybridization. We use live cell imaging to determine the interphase 3D arrangement of transgene-encoded fluorescent tags on chromosome 5 in trisomic and triploid plants. The results indicate that trisomy 5 disrupts gene expression throughout the genome and supports the production and/or retention of truncated copies of chromosome 5. Although trisomy 5 does not grossly distort the interphase arrangement of fluorescent-tagged sites on chromosome 5, it may somewhat enhance associations between transgene alleles. Our analysis reveals the complex genomic changes that can occur in aneuploids and underscores the importance of using multiple experimental approaches to investigate how chromosome numerical changes condition abnormal phenotypes and progressive genome instability.

Show MeSH
Related in: MedlinePlus