Magnitude of modulation of gene expression in aneuploid maize depends on the extent of genomic imbalance
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Abstract: Aneuploidy has profound effects on an organism, typically more so than polyploidy, and the basis of this contrast is not fully understood. A dosage series of the maize long arm of chromosome 1 (1L) was used to compare relative global gene expression in different types and degrees of aneuploidy to gain insights into how the magnitude of genomic imbalance as well as hypoploidy affects global gene expression. While previously available methods require a selective examination of specific genes, RNA sequencing provides a whole-genome view of gene expression in aneuploids. Most studies of global aneuploidy effects have concentrated on individual types of aneuploids because multiple dose aneuploidies of the same genomic region are difficult to produce in most model genetic organisms. The genetic toolkit of maize allows the examination of multiple ploidies and 1–4 doses of chromosome arms. Thus, a detailed examination of expression changes both on the varied chromosome arms and elsewhere in the genome is possible, in both hypoploids and hyperploids, compared with euploid controls. Previous studies observed the inverse trans effect, in which genes not varied in DNA dosage were expressed in a negative relationship to the varied chromosomal region. This response was also the major type of changes found globally in this study. Many genes varied in dosage showed proportional expression changes, though some were seen to be partly or fully dosage compensated. It was also found that the effects of aneuploidy were progressive, with more severe aneuploids producing effects of greater magnitude.
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Key words:
- Aneuploidy /
- Polyploidy /
- Inverse effect /
- Gene regulation /
- Dosage compensation /
- Gene balance hypothesis
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Fig. 1. Ratio distribution plots. For every gene, the ratio of expression in an aneuploid plant compared to a euploid plant was determined.A–D: Ratio distribution plots of the first dosage series. A haploid/diploid comparison was used as a control (A). Trisomy/diploid (B), tetrasomy/diploid (C), and disomy/haploid (D) comparisons were all generated with plants from the same set. E and F: Ratio distribution plots of the second dosage series. Comparison of gene expression in monosomy/diploid (E) and trisomy/diploid (F). The x-axis indicates the expression ratio, and the y-axis indicates the number of genes in each bin. In A and C‒E, the three vertical guide bars indicate an inverse relationship to dosage (0.50), a value unchanged from euploid (1.00), and a direct relationship to dosage (2.00), respectively. In B and F, three guide bars indicating an inverse relationship, an unchanged relationship, and a direct relationship to dosage are placed at 0.67, 1.00, and 1.50, respectively. All expressed genes were considered. If a gene has the same average expression in the aneuploid condition as in the euploid condition, its ratio will be 1.00; if expression decreases in an aneuploid, its ratio will fall to the left of 1.00; if expression increases, its ratio will fall to the right of 1.00. For genes with a locus on chromosome 1L, a rightward trend can be observed in hyperploids and a leftward trend in the hypoploid, indicating a direct (but often partial) correlation between gene dosage and RNA expression in cis. For the non-1L genes, a shoulder can be observed on the left side of the central peak in several plots, indicating that some genes show an inverse correlation between 1L gene dosage and non-1L RNA expression.
Fig. 2. Volcano plots. A–D: Volcano plots of the first dosage series. The plots are based on the same comparisons of gene expression shown in Fig. 1A–D. E and F: Volcano plots of the second dosage series. The plots are based on the same comparisons of gene expression shown in . The x-axis is fold change, with expression ratio displayed at a log2 scale. The central guide represents log2(fold change) of 0.0, equivalent to an expression ratio of 1.00 (no change). In A and C‒E, the guide bars at log2(fold change) of −1.0 and 1.0 represent expression ratios of 0.50 and 2.00, respectively. In B and F, the guide bars represent expression ratios of 0.67 and 1.50, respectively. The y-axis is the mean of RPKM value at a log2 scale in the diploid control. Green points on the left of the centerline represent genes with a statistically significant decrease in gene expression from euploid to aneuploid (FDR < 0.05, log2(fold change) < 0). Red points on the right represent an increase in gene expression (FDR < 0.05, log2(fold change) > 0). Incis, the prevalence of direct effects is apparent. In trans, the relationship of dosage to expression is often inverse rather than direct, shown by the relative prevalence of significant down-regulated genes in hyperploid and up-regulated genes in hypoploid.
Fig. 3. Comparisons of expression levels of genes representing different dosage reactions by RT-qPCR. Three expression ratios – trisomy/diploid, tetrasomy/diploid, and disomy/haploid – are provided for each representative gene. A: Direct cis dosage effect. B: Cis dosage compensation. C: Inverse trans effect. D: Direct trans effect. E: No trans effect. Expression ratios measured by RT-qPCR generally matched the RNA sequencing results. The progressive impact of aneuploidy on gene expression is apparent in the direct cis dosage effect and inverse trans effect examples.
Fig. 4. Ratio distribution plots for chloroplast-targeted genes. Ratio distributions of only chloroplast-targeted genes were prepared. Genotypes, analysis and presentation are as described in Fig. 1.
Fig. 5. Ratio distribution plots for ribosomal genes. Ratio distributions of only ribosomal protein encoding genes were prepared. Genotypes, analysis and presentation are as described in Fig. 1.
Table 1. Summary of the edgeR significance test results.
Comparison Total number of genes Fold change significance below 1 Fold change significance above 1 Cis comparison Haploid/diploid (set 1) 2346 18 91 Trisomy/diploid (set 1) 2365 33 179 Tetrasomy/diploid (set 1) 2350 11 1158 Disomy/haploid (set 1) 2342 18 261 Monosomy/diploid (set 2) 2368 380 4 Trisomy/diploid (set 2) 2390 14 353 Trans comparison Haploid/diploid (set 1) 26,598 128 1064 Trisomy/diploid (set 1) 26,826 55 308 Tetrasomy/diploid (set 1) 26,371 835 660 Disomy/haploid (set 1) 26,304 526 359 Monosomy/diploid (set 2) 27,417 89 489 Trisomy/diploid (set 2) 26,953 198 445 Summary table of gene expression effects generated by edgeR. Cis (1L) and trans (non-1L) effects are separated. Total number of genes differs due to removal of data points for which the summation of RPKM counts in both conditions is less than 3. Significance is defined by False discovery rate (FDR) less than 0.05. 
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