Aneuploidy causes tissue-specific qualitative changes in global gene expression patterns in maize

Abstract

Segmental aneuploidy refers to the relative excess or deficiency of specific chromosome regions. This condition results in gene dosage imbalance and often causes severe phenotypic alterations in plants and animals. The mechanisms by which gene dosage imbalance affects gene expression and phenotype are not completely clear. The effects of aneuploidy on the transcriptome may depend on the types of cells analyzed and on the developmental stage. We performed global gene expression profiling to determine the effects of segmental aneuploidy on gene expression levels in two different maize (Zea mays) tissues and a detailed analysis of expression of 30 genes affected by aneuploidy in multiple maize tissues. Different maize tissues varied in the frequency at which genes located outside of the aneuploid regions are positively or negatively regulated as well as in the degree of gene dosage compensation. Multiple genes demonstrated qualitative changes in gene expression due to aneuploidy, when the gene became ectopically expressed or completely silenced in aneuploids relative to wild-type plants. Our data strongly suggested that quantitative changes in gene expression at developmental transition points caused by variation in gene copy number progressed through tissue development and resulted in stable qualitative changes in gene expression patterns. Thus, aneuploidy in maize results in alterations of gene expression patterns that differ between tissues and developmental stages of maize seedlings.

Figure 1.

Different sets of genes are affected by aneuploidy in two different tissues. The expression ratios of the DpDf versus wild-type tissues were compared for meristem-enriched and green seedling tissues in order to assess whether genes were differentially expressed in both genotypes or just one of the genotypes. Only genes differentially expressed in at least one of the aneuploid tissues and expressed in both tissues are shown. Genes equally affected in both tissues are expected to fall on the diagonal line, while genes affected only in one tissue are expected to be located along the axes. Shades and shapes indicate gene behavior in two tissues: black circles designate genes with significant changes in expression levels in both tissues; gray triangles and white squares indicate genes with significant changes in total seedling tissue or meristem-enriched tissue, respectively.

Figure 2.

Aneuploidy causes both cis- and trans-variation of gene expression levels. Distribution of genes with significant expression changes across maize chromosomes is shown. Chromosome 1 is shown as a representative for chromosomes other than 5, since no clear preferences in gene distribution along nonaffected chromosomes were detected. Each transcript is represented by a mark. The x axes correspond to the gene location on a maize contig along the chromosomes, and the y axes show expression ratios with positive values indicating increased expression in DpDf plants. Shades report on relative significance (white is highest, black is lowest). Genes on chromosome 5 that are dosage compensated are at the zero line; any gene significantly above is not dosage compensated.

Figure 3.

Trisomic genes demonstrate different patterns of expression changes. Trisomic genes from a representative 15-Mb region of chromosome 5 are shown. The x axis corresponds to the chromosomal location of a gene along chromosome 5 (in Mb), and the y axis shows expression ratios with positive values indicating increased expression in DpDf plants. Each trisomic transcript is represented by two marks: a square shows expression change in meristem-enriched tissues, while a circle shows expression change in seedlings. Color indicates gene behavior in two tissues: black refers to genes with significant changes in expression levels in both tissues; blue and red indicate genes with significant changes in meristem-enriched and seedling tissue, respectively; while white shows genes with no significant changes in either tissue. Genes on chromosome 5 that are dosage compensated are at the zero line; any gene significantly above is not dosage compensated. The horizontal line (y = 0.32) indicates the log₂ value of the cutoff ratio used in this study (log₂ 1.25 = 0.32).

Figure 4.

Aneuploidy causes progressive qualitative changes in gene expression patterns. A, Average ratios of gene expression detected by qRT-PCR and normalized to expression in meristem of wild-type (Wt) plants. Error bars denote se values for each experiment. B, Semiquantitative RT-PCR was performed for 40 cycles. The mez1 gene served as a normalization control for cDNA concentration. All RNAs were tested without reverse transcriptase enzyme and showed negative results (data not shown). Lanes are as follows: 1, wild-type (w/t) meristem tissue; 2, wild-type young leaf; 3, wild-type developing leaf; 4, wild-type mature leaf; 5, DpDf meristem; 6, DpDf young leaf; 7, DpDf developing leaf; 8, DpDf mature leaf; 9, negative control (water).