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: 11.77). 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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Available from: Eric P Spana, Aug 24, 2015
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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.
    Molecular Biology and Evolution 06/2015; DOI:10.1093/molbev/msv147 · 14.31 Impact Factor
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    • "To our knowledge, this is the first demonstration of condensin regulation by ubiquitination and Slimb association with chromatin to actively modulate interphase chromosome organization. These results Slimb suppresses condensin II activity • Buster et al. autosomes, where each autosome is present in four copies (Zhang et al., 2010). If each discrete globular domain arose from a distinct major chromosome (not including the minute fourth chromosomes), then 10 gumballs per cell would be expected, which is consistent with our measurements. "
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    ABSTRACT: Condensin complexes play vital roles in chromosome condensation during mitosis and meiosis. Condensin II uniquely localizes to chromatin throughout the cell cycle and, in addition to its mitotic duties, modulates chromosome organization and gene expression during interphase. Mitotic condensin activity is regulated by phosphorylation, but mechanisms that regulate condensin II during interphase are unclear. Here, we report that condensin II is inactivated when its subunit Cap-H2 is targeted for degradation by the SCF(Slimb) ubiquitin ligase complex and that disruption of this process dramatically changed interphase chromatin organization. Inhibition of SCF(Slimb) function reorganized interphase chromosomes into dense, compact domains and disrupted homologue pairing in both cultured Drosophila cells and in vivo, but these effects were rescued by condensin II inactivation. Furthermore, Cap-H2 stabilization distorted nuclear envelopes and dispersed Cid/CENP-A on interphase chromosomes. Therefore, SCF(Slimb)-mediated down-regulation of condensin II is required to maintain proper organization and morphology of the interphase nucleus.
    The Journal of Cell Biology 03/2013; 201(1). DOI:10.1083/jcb.201207183 · 9.69 Impact Factor
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    • "The S2 tissue culture line of Drosophila cells is popularly used for cellular level studies. Zhang et al. found that it is highly aneuploidy in the context of having two X chromosomes and four sets of autosomes (and thus male) and studied the gene expression globally [52]. Within the varied regions, genes displayed the range of expression that would qualify them as compensated or exhibiting a dosage effect. "
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    ABSTRACT: The early principles of the impact of aneuploidy were determined in plants and Drosophila. Here we summarize the classical results and then relate them to more current studies of gene expression in these taxa. As a general rule, aneuploidy is detrimental, even to the point of lethality, compared to changes in the dosage of the whole genome. Gene expression studies demonstrate an analogous relationship, namely that changes in dosage of chromosomes or chromosomal segments will modulate many genes but changes in whole ploidy have much less of an effect. One of the most common trans-acting effects is an inverse response of a gene to the altered dosage of a chromosomal segment. This effect can produce dosage compensation when it occurs for a gene that is also present in the varied region. Some open questions in the field of aneuploidy research are discussed.
    Seminars in Cell and Developmental Biology 02/2013; 24(4). DOI:10.1016/j.semcdb.2013.02.004 · 5.97 Impact Factor
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