Trans-acting dosage effects on the expression of model gene systems in maize aneuploids

Does the intrinsic instability of aneuploid genomes have a causal role in cancer?

The role of aneuploidy in carcinogenesis has long been debated. We argue here that aneuploid genomes are naturally more susceptible to the types of chromosome rearrangement and epigenetic aberration that are found typically in tumor cells. In some cases, the formation of an aneuploid genome might be the initiating step in neoplastic conversion.

Understanding mechanisms of novel gene expression in polyploids

Polyploidy has long been recognized as a prominent force shaping the evolution of eukaryotes, especially flowering plants. New phenotypes often arise with polyploid formation and can contribute to the success of polyploids in nature or their selection for use in agriculture. Although the causes of novel variation in polyploids are not well understood, they could involve changes in gene expression through increased variation in dosage-regulated gene expression, altered regulatory interactions, and rapid genetic and epigenetic changes. New research approaches are being used to study these mechanisms and the results should provide a more complete understanding of polyploidy.

Developmental impact on trans-acting dosage effects in maize aneuploids

The reduction in vigor or viability caused by aneuploidy may be the result of trans-acting dosage effects that reduce gene expression. To investigate the molecular and developmental parameters of aneuploid syndromes, the expression of sucrose synthase1 (sus1) and shrunken1 (sh1) was studied in 2-week-old plants. Expression of sus1 and sh1 was first investigated in euploids, where it was found that both transcripts varied in a diurnal fashion. Chromosome arm number can be varied in a series from one to three doses in maize. In the 14 aneuploid dosage series examined, most caused changes in sus1 and sh1 RNA levels that were both gene and tissue specific. Results were compared to previous data from embryo and endosperm tissue. More dosage effects were detected and the magnitude of RNA level modulation was greater in 2-week-old plant tissue. These findings suggest that the molecular consequences of aneuploidy might become more severe as development progresses.

Dosage-dependent gene regulation in multicellular eukaryotes: implications for dosage compensation, aneuploid syndromes, and quantitative traits

Evidence from a variety of data suggests that regulatory mechanisms in multicellular eukaryotes have evolved in such a manner that the stoichiometric relationship of the components of regulatory complexes affects target gene expression. This type of mechanism sets the level of gene expression and, as a consequence, the phenotypic characteristics. Because many types of regulatory processes exhibit dosage-dependent behavior, they would impact quantitative traits and contribute to their multigenic control in a semidominant fashion. Many dosage-dependent effects would also account for the extensive modulation of gene expression throughout the genome that occurs when chromosomes are added to or subtracted from the karyotype (aneuploidy). Moreover, because the majority of dosage-dependent regulators act negatively, this property can account for the up-regulation of genes in monosomics and hemizygous sex chromosomes to achieve dosage compensation.

Nuclear gene dosage effects upon the expression of maize mitochondrial genes

Each mitochondrion possesses a genome that encodes some of its own components. The nucleus encodes most of the mitochondrial proteins, including the polymerases and factors that regulate the expression of mitochondrial genes. Little is known about the number or location of these nuclear factors. B-A translocations were used to create dosage series for 14 different chromosome arms in maize plants with normal cytoplasm. The presence of one or more regulatory factors on a chromosome arm was indicated when variation of its dosage resulted in the alteration in the amount of a mitochondrial transcript. We used quantitative Northern analysis to assay the transcript levels of three mitochondrially encoded components of the cytochrome c oxidase complex (cox1, cox2, and cox3). Data for a nuclearly encoded component (cox5b) and for two mitochondrial genes that are unrelated to cytochrome c oxidase, ATP synthase alpha-subunit and 18S rRNA, were also determined. Two tissues, embryo and endosperm, were compared and most effects were found to be tissue specific. Significantly, the array of dosage effects upon mitochondrial genes was similar to what had been previously found for nuclear genes. These results support the concept that although mitochondrial genes are prokaryotic in origin, their regulation has been extensively integrated into the eukaryotic cell.

The oxen gene of Drosophila encodes a homolog of subunit 9 of yeast ubiquinol-cytochrome c oxidoreductase complex: evidence for modulation of gene expression in response to mitochondrial activity

A P-element insertion in the oxen gene, ox(1), has been isolated in a search for modifiers of white gene expression. The mutation preferentially exerts a negative dosage effect upon the expression of three genes encoding ABC transporters involved in pigment precursor transport, white, brown, and scarlet. A precise excision of the P element reverts the mutant phenotype. Five different transcription units were identified around the insertion site. To distinguish a transcript responsible for the mutant phenotype, a set of deletions within the oxen region was generated. Analysis of gene expression within the oxen region in the case of deletions as well as generation of transgenic flies allowed us to identify the transcript responsible for oxen function. It encodes a 6.6-kD homolog of mitochondrial ubiquinol cytochrome c oxidoreductase (QCR9), subunit 9 of the bc(1) complex in yeast. In addition to white, brown, and scarlet, oxen regulates the expression of three of seven tested genes. Thus, our data provide additional evidence for a cellular response to changes in mitochondrial function. The oxen mutation provides a model for the genetic analysis in multicellular organisms of the effect of mitochondrial activity on nuclear gene expression.

Histone acetylation and gene expression analysis of sex lethal mutants in Drosophila

The evolution of sex determination mechanisms is often accompanied by reduction in dosage of genes on a whole chromosome. Under these circumstances, negatively acting regulatory genes would tend to double the expression of the genome, which produces compensation of the single-sex chromosome and increases autosomal gene expression. Previous work has suggested that to reduce the autosomal expression to the female level, these dosage effects are modified by a chromatin complex specific to males, which sequesters a histone acetylase to the X. The reduced autosomal histone 4 lysine 16 (H4Lys16) acetylation results in lowered autosomal expression, while the higher acetylation on the X is mitigated by the male-specific lethal complex, preventing overexpression. In this report, we examine how mutations in the principal sex determination gene, Sex lethal (Sxl), impact the H4 acetylation and gene expression on both the X and autosomes. When Sxl expression is missing in females, we find that the sequestration occurs concordantly with reductions in autosomal H4Lys16 acetylation and gene expression on the whole. When Sxl is ectopically expressed in Sxl(M) mutant males, the sequestration is disrupted, leading to an increase in autosomal H4Lys16 acetylation and overall gene expression. In both cases we find relatively little effect upon X chromosomal gene expression.

Genome evolution in polyploids

Polyploidy is a prominent process in plants and has been significant in the evolutionary history of vertebrates and other eukaryotes. In plants, interdisciplinary approaches combining phylogenetic and molecular genetic perspectives have enhanced our awareness of the myriad genetic interactions made possible by polyploidy. Here, processes and mechanisms of gene and genome evolution in polyploids are reviewed. Genes duplicated by polyploidy may retain their original or similar function, undergo diversification in protein function or regulation, or one copy may become silenced through mutational or epigenetic means. Duplicated genes also may interact through inter-locus recombination, gene conversion, or concerted evolution. Recent experiments have illuminated important processes in polyploids that operate above the organizational level of duplicated genes. These include inter-genomic chromosomal exchanges, saltational, non-Mendelian genomic evolution in nascent polyploids, inter-genomic invasion, and cytonuclear stabilization. Notwithstanding many recent insights, much remains to be learned about many aspects of polyploid evolution, including: the role of transposable elements in structural and regulatory gene evolution; processes and significance of epigenetic silencing; underlying controls of chromosome pairing; mechanisms and functional significance of rapid genome changes; cytonuclear accommodation; and coordination of regulatory factors contributed by two, sometimes divergent progenitor genomes. Continued application of molecular genetic approaches to questions of polyploid genome evolution holds promise for producing lasting insight into processes by which novel genotypes are generated and ultimately into how polyploidy facilitates evolution and adaptation.

Rapid structural and epigenetic changes in polyploid and aneuploid genomes

Recent work with plants has demonstrated that genome instability can be triggered by a change in chromosome number arising from either whole genome duplications (polyploidy) or loss/gain of individual chromosomes (aneuploidy). This genome instability is manifested as rapid structural and epigenetic alterations that can occur somatically or meiotically within a few generations after heteroploid formation. The intrinsic instability of newly formed polyploid and aneuploid genomes has relevance for genome evolution and human carcinogenesis, and points toward recombinational and epigenetic mechanisms that sense and respond to chromosome numerical changes.

The influence of triploidy on gene expression in the silkworm, bombyx mori

In Bombyx mori, it is well established that polyploids are easily induced when newly laid eggs are exposed to a variety of conditions, such as high or low temperature, centrifugal force, or chemicals like colchicine. To investigate gene dosage effects by varying the ploidy, the transcription levels of six genes expressed in various tissues were analysed in the diploid and two different genetically produced triploids (PPC and CCP). In the PPC triploid, the transcription level per cell of two genes was directly proportional to the structural gene dosage, whereas two other genes showed the mRNA level expected if compensation occurred. In the CCP triploid, three genes displayed dose-dependent levels of expression, whereas one gene showed the same expression level as the diploid strains. In both triploids, exceptional cases showed a negative correlation of expression with ploidy or a positive correlation greater than expected from the structural gene dosage. Interestingly, the transcription levels of most tested genes were significantly different from the strains which were used as parents of the triploids, and also widely divergent expression patterns were found for some genes in the diploid offspring. In this study, the cause of the unexpected expression patterns observed in the euploid series is discussed in relation to the difference between the two parental strains in expression level of genes and in trans-acting regulatory effects on their target genes.

Role of the male specific lethal (msl) genes in modifying the effects of sex chromosomal dosage in Drosophila

Immunostaining of chromosomes shows that the male-specific lethal (MSL) proteins are associated with all female chromosomes at a low level but are sequestered to the X chromosome in males. Histone-4 Lys-16 acetylation follows a similar pattern in normal males and females, being higher on the X and lower on the autosomes in males than in females. However, the staining pattern of acetylation and the mof gene product, a putative histone acetylase, in msl mutant males returns to a uniform genome-wide distribution as found in females. Gene expression on the autosomes correlates with the level of histone-4 acetylation. With minor exceptions, the expression levels of X-linked genes are maintained with either an increase or decrease of acetylation, suggesting that the MSL complex renders gene activity unresponsive to H4Lys16 acetylation. Evidence was also found for the presence of nucleation sites for association of the MSL proteins with the X chromosome rather than individual gene binding sequences. We suggest that sequestration of the MSL proteins occurs in males to nullify on the autosomes and maintain on the X, an inverse effect produced by negatively acting dosage-dependent regulatory genes as a consequence of the evolution of the X/Y sex chromosomal system.

Epigenetic allelic states of a maize transcriptional regulatory locus exhibit overdominant gene action

Using alleles of the maize purple plant locus (pl), which encodes a transcriptional regulator of anthocyanin pigment synthesis, we describe a case of single-locus heterosis, or overdominance, where the heterozygote displays a phenotype that is greater than either homozygote. The Pl-Rhoades (Pl-Rh) allele is subject to epigenetic changes in gene expression, resulting in quantitatively distinct expression states. Allelic states with low-expression levels, designated Pl'-mahogany (Pl'-mah), are dominant to the high-expression state of Pl-Rh. Pl'-mah states retain low-expression levels in subsequent generations when homozygous or heterozygous with Pl-Rh. However, Pl'-mah alleles frequently exhibit higher expression levels when heterozygous with other pl alleles; illustrating an overdominant allelic relationship. Higher expression levels are also observed when Pl'-mah is hemizygous. These results suggest that persistent allelic interactions between Pl'-mah and Pl-Rh are required to maintain the low-expression state and that other pl alleles are missing sequences required for this interaction. The Pl-Rh state can be sexually transmitted from Pl'-mah/pl heterozygotes, but not from Pl'-mah hemizygotes, suggesting that fixation of the high-expression state may involve synapsis. The existence of such allele-dependent regulatory mechanisms implicates a novel importance of allele polymorphisms in the genesis and maintenance of genetic variation.

Interactions among dosage-dependent trans-acting modifiers of gene expression and position-effect variegation in Drosophila

We have investigated the effect of dosage-dependent trans-acting regulators of the white eye color gene in combinations to understand their interaction properties. The consequences of the interactions will aid in an understanding of aneuploid syndromes, position-effect variegation (PEV), quantitative traits, and dosage compensation, all of which are affected by dosage-dependent modifiers. Various combinations modulate two functionally related transcripts, white and scarlet, differently. The overall trend is that multiple modifiers are noncumulative or epistatic to each other. In some combinations, developmental transitions from larvae to pupae to adults act as a switch for whether the effect is positive or negative. With position-effect variegation, similar responses were found as with gene expression. The highly multigenic nature of dosage-sensitive modulation of both gene expression and PEV suggests that dosage effects can be progressively transduced through a series of steps in a hierarchical manner.

DNA methylation and plant development

The development of genetic tools to alter DNA methylation has led to a deeper understanding of the importance of DNA modification in the life strategies of different eukaryotic organisms. This review focuses on recent findings that demonstrate a role for cytosine methylation in the development of higher plants. The effects of altering DNA modification are considered in the context of unique aspects of plant development.

Characterization of a sex-influenced modifier of gene expression and suppressor of position-effect variegation in Drosophila

Modifier of white (Mow), a dominant transacting gene, has been identified through a mutagenic screen for second-site loci that alter the level of expression of the white eye color locus. Mow reduces the expression of white in most developmental stages, but enhances its expression in the pupal stage, the time at which the major contribution to the adult phenotype is made. Tests with an Alcohol dehydrogenase promoter-white reporter and a series of white truncation constructs have shown that Mow fails to affect the reporter; cis-regulatory mutations of white also show no response, suggesting a requirement for white regulatory domains for interaction with Mow. A quantitative analysis of steady-state transcript levels reveals that the white mRNA level decreases in the presence of one dose of Mow in larvae and adults, but the reduction is greater in females than males. Two other functionally related genes, brown and scarlet, also exhibit a similar sexually dimorphic alteration in expression, mediated by Mow. In the mid-pupal stage, by contrast, the level of white and brown mRNA is increased by Mow. In addition, Mow acts as a weak suppressor of position effect variegation (PEV). These observations suggest a connection between dosage modulation of gene expression and suppression of position-effect variegation.

The evolution of chromosomal sex determination and dosage compensation

In many species, sex is determined by a system based on X and Y chromosomes, the latter having lost much of their genetic activity. Y chromosomes have evolved independently many times, and the associated change in gene dosage in the heterogametic (XY) sex is often compensated for by regulatory mechanisms which ensure equal amounts of gene products of X-linked loci in males and females. There have recently been substantial advances in our knowledge of the molecular biology and genetics of sex chromosomes and dosage compensation, and in our understanding of the population genetic processes which are involved in their evolution.