Article

Expression in Aneuploid Drosophila S2 Cells

Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
PLoS Biology (Impact Factor: 9.34). 02/2010; 8(2):e1000320. DOI: 10.1371/journal.pbio.1000320
Source: PubMed

ABSTRACT

Extensive departures from balanced gene dose in aneuploids are highly deleterious. However, we know very little about the relationship between gene copy number and expression in aneuploid cells. We determined copy number and transcript abundance (expression) genome-wide in Drosophila S2 cells by DNA-Seq and RNA-Seq. We found that S2 cells are aneuploid for >43 Mb of the genome, primarily in the range of one to five copies, and show a male genotype ( approximately two X chromosomes and four sets of autosomes, or 2X;4A). Both X chromosomes and autosomes showed expression dosage compensation. X chromosome expression was elevated in a fixed-fold manner regardless of actual gene dose. In engineering terms, the system "anticipates" the perturbation caused by X dose, rather than responding to an error caused by the perturbation. This feed-forward regulation resulted in precise dosage compensation only when X dose was half of the autosome dose. Insufficient compensation occurred at lower X chromosome dose and excessive expression occurred at higher doses. RNAi knockdown of the Male Specific Lethal complex abolished feed-forward regulation. Both autosome and X chromosome genes show Male Specific Lethal-independent compensation that fits a first order dose-response curve. Our data indicate that expression dosage compensation dampens the effect of altered DNA copy number genome-wide. For the X chromosome, compensation includes fixed and dose-dependent components.

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    • "One important scenario for adaptive regulation of gene expression is when there are changes or differences in gene dose (Veitia et al. 2008, 2013). Maintaining ancestral protein levels to sustain stoichiometric relationships in networks and pathways might in such cases be critical for proper function of protein–protein interactions (Zhang et al. 2010). A classical question in genetics to which this applies is the potential need for sex-linked dosage compensation upon sex chromosome evolution and the concomitant degeneration of nonrecombining genes (Ohno 1967; Disteche 2012). "
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    DESCRIPTION: Quantitative mass spectrometry reveals partial translational regulation for dosage compensation in chicken. Proteomics and RNAseq in chicken embryos.
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    • "One important scenario for adaptive regulation of gene expression is when there are changes or differences in gene dose (Veitia et al. 2008, 2013). Maintaining ancestral protein levels to sustain stoichiometric relationships in networks and pathways might in such cases be critical for proper function of protein–protein interactions (Zhang et al. 2010). A classical question in genetics to which this applies is the potential need for sex-linked dosage compensation upon sex chromosome evolution and the concomitant degeneration of nonrecombining genes (Ohno 1967; Disteche 2012). "
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    ABSTRACT: There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has mainly studied transcriptional regulation of sex-linked genes, which may not reflect expression at the protein level. Here we used liquid chromatography - tandem mass spectrometry (LC-MS/MS) to detect and quantify expressed levels of more than 2,400 proteins in 10 different tissues of male and female chicken embryos. For comparison, transcriptome sequencing was performed in the same individuals, five of each sex. The proteomic analysis revealed that dosage compensation was incomplete, with a mean male-to-female (M:F) expression ratio of Z-linked genes of 1.32 across tissues, similar to that at the RNA level (1.29). The mean Z chromosome-to-autosome expression ratio was close to one in males and lower than one in females, consistent with partly reduced Z chromosome expression in females. While our results exclude a general mechanism for chromosome-wide dosage compensation at translation, 30% of all proteins encoded from Z-linked genes showed a significant change in the M:F ratio compared to the corresponding ratio at the RNA level. This resulted in a pattern where some genes showed balanced expression between sexes and some close to twofold higher expression in males. This suggests that proteomic analyses will be necessary to reveal a more complete picture of gene regulation and sex chromosome evolution. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Full-text · Article · Jun 2015 · Molecular Biology and Evolution
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    • "Through comparison of diploid and polyploid plants of the same species (Coate and Doyle, 2010), or across the genome of a Drosophila cell line with heterogeneous ploidy (Zhang et al., 2010), it was found that a simple linear relationship does not universally exist between chromosome ploidy and transcript levels. As discussed next, many polyploid transcriptional changes are a result of increased cell size, and not caused by ploidy per se, and thus are not proportional to gene copy number (Wu et al., 2010; Miettinen et al., 2014). "
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    ABSTRACT: Polyploid cells, which contain more than two genome copies, occur throughout nature. Beyond well-established roles in increasing cell size/metabolic output, polyploidy can also promote nonuniform genome, transcriptome, and metabolome alterations. Polyploidy also frequently confers resistance to environmental stresses not tolerated by diploid cells. Recent progress has begun to unravel how this fascinating phenomenon contributes to normal physiology and disease. © 2015 Shoenfelder and Fox.
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