Genetic effects on an index of wing shape on chromosome 2 of Drosophila melanogaster were mapped ... more Genetic effects on an index of wing shape on chromosome 2 of Drosophila melanogaster were mapped using isogenic recombinants with transposable element markers. At least 10 genes with small additive effects are dispersed evenly along the chromosome. Many interactions exist, with only small net effects in homozygous recombinants and little effect on phenotypic variance. Heterozygous chromosome segments show almost no dominance. Pleiotropic effects on leg shape are only minor. At first view, wing shape genes form a rather homogeneous class, but certain complexities remain unresolved.
Loci on the third chromosome of Drosophila melanogaster that affect an index of wing shape were m... more Loci on the third chromosome of Drosophila melanogaster that affect an index of wing shape were mapped, using recombinant isogenic lines, with transposable elements as markers. Many genes with small subequal effects are dispersed along the whole chromosome. Their alleles act nearly additively in heterozygotes. They have small correlated effects on leg shape, but no detectable effects on halteres. Small negative net interactions occur over most of the chromosome. The data set of 519 recombinant isogenic lines can be explained reasonably well by two models. One model posits an indefinitely large number of loci with no interactions. The other model posits 11 loci with additive effects whose sum equals the total phenotypic range and with large positive and negative interactions that nearly cancel each other.
We would like to thank Dr. Alan Templeton for the gift of the bisexual and parthenogenetic strain... more We would like to thank Dr. Alan Templeton for the gift of the bisexual and parthenogenetic strains of D. mercatorum. We also thank Kevin Cook for his thoughtful input and time spent reviewing the manuscript. We also would like to thank two semi-anonymous reviewers for their insightful comments that significantly improved the paper and prevented us from making a public spectacle of ourselves.
In Drosophila melanogaster a functional pericentriolar matrix (PCM) at mitotic centrosomes requir... more In Drosophila melanogaster a functional pericentriolar matrix (PCM) at mitotic centrosomes requires Centrosomin-Long Form (Cnn-LF) proteins. Moreover, tissue culture cells have shown that the centrosomal localization of both Cnn-LF and Polo kinase are co-dependent, suggesting a direct interaction. Our recent study found Cnn potentially binds to and is phosphorylated by Polo kinase at 2 residues encoded by Exon1A, the initiating exon of a subset of Cnn isoforms. These interactions are required for the centrosomal localization of Cnn-LF in syncytial embryos and a mutation of either phosphorylation site is sufficient to block localization of both mutant and wild-type Cnn when they are co-expressed. Immunoprecipitation experiments show that Cnn-LF interacts directly with mitotically activated Polo kinase and requires the 2 phosphorylation sites in Exon1A. These IP experiments also show that Cnn-LF proteins form multimers. Depending on the stoichiometry between functional and mutant peptides, heteromultimers exhibit dominant negative or positive trans-complementation (rescue) effects on mitosis. Additionally, following the completion of meiosis, Cnn-Short Form (Cnn-SF) proteins are required for polar body formation in embryos, a process previously shown to require Polo kinase. These findings, when combined with previous work, clearly demonstrate the complexity of cnn and show that a view of cnn as encoding a single peptide is too simplistic.
INTRODUCTION In a previous paper (Weber 1996), results were presented from the first 100 generati... more INTRODUCTION In a previous paper (Weber 1996), results were presented from the first 100 generations of an ongoing, exploratory selection experiment on Drosophila melanogaster. Each generation, in each of two populations, 30,000 to 60,000 flies are scored for performance in a wind tunnel, and 2000 parents are selected from the strongest fliers. In the prior report, large gains in windtunnel performance had occurred in the selected lines, with large genetic changes, but correlated fitness costs were not demonstrable. Large fitness costs have usually been associated with extreme trait gains in experimental selection and in selective breeding. These costs have generally been regarded as necessary correlates of major change in selected traits.
We analyzed the usage and consequences of alternative cleavage and polyadenylation (APA) in Droso... more We analyzed the usage and consequences of alternative cleavage and polyadenylation (APA) in Drosophila melanogaster by using >1 billion reads of stranded mRNA-seq across a variety of dissected tissues. Beyond demonstrating that a majority of fly transcripts are subject to APA, we observed broad trends for 3 0 untranslated region (UTR) shortening in the testis and lengthening in the central nervous system (CNS); the latter included hundreds of unannotated extensions ranging up to 18 kb. Extensive northern analyses validated the accumulation of full-length neural extended transcripts, and in situ hybridization indicated their spatial restriction to the CNS. Genes encoding RNA binding proteins (RBPs) and transcription factors were preferentially subject to 3 0 UTR extensions. Motif analysis indicated enrichment of miRNA and RBP sites in the neural extensions, and their termini were enriched in canonical cis elements that promote cleavage and polyadenylation. Altogether, we reveal broad tissue-specific patterns of APA in Drosophila and transcripts with unprecedented 3 0 UTR length in the nervous system.
The formation of the pericentriolar matrix (PCM) and a fully functional centrosome in syncytial D... more The formation of the pericentriolar matrix (PCM) and a fully functional centrosome in syncytial Drosophila melanogaster embryos requires the rapid transport of Cnn during initiation of the centrosome replication cycle. We show a Cnn and Polo kinase interaction is apparently required during embryogenesis and involves the exon 1A-initiating coding exon, suggesting a subset of Cnn splice variants is regulated by Polo kinase. During PCM formation exon 1A Cnn-Long Form proteins likely bind Polo kinase before phosphorylation by Polo for Cnn transport to the centrosome. Loss of either of these interactions in a portion of the total Cnn protein pool is sufficient to remove native Cnn from the pool, thereby altering the normal localization dynamics of Cnn to the PCM. Additionally, Cnn-Short Form proteins are required for polar body formation, a process known to require Polo kinase after the completion of meiosis. Exon 1A Cnn-LF and Cnn-SF proteins, in conjunction with Polo kinase, are required at the completion of meiosis and for the formation of functional centrosomes during early embryogenesis.
The ease of genetic manipulation in Drosophila melanogaster using the Gal4/UAS system has been be... more The ease of genetic manipulation in Drosophila melanogaster using the Gal4/UAS system has been beneficial in addressing key biological questions. Current modifications of this methodology to temporally induce transgene expression require temperature changes or exposure to exogenous compounds, both of which have been shown to have detrimental effects on physiological processes. The recently described auxin-inducible gene expression system (AGES) utilizes the plant hormone auxin to induce transgene expression and is proposed to be the least toxic compound for genetic manipulation, with no obvious effects on Drosophila development and survival in one wild-type strain. Here we show that auxin delays larval development in a widely-used fly strain, and auxin exposure in adult Drosophila induces observable changes in physiology and feeding behavior. We found that there is a dosage response to adult survival upon auxin exposure and low auxin concentrations alter feeding activity. Furthermor...
<p>A-D) One copy versus two copy gene expression levels plotted at the centers of each gene... more <p>A-D) One copy versus two copy gene expression levels plotted at the centers of each gene model (labeled below). Observations made in the isogenic genetic background (filled) and the hybrid genetic background (open) are shown. Genes whose expression is below the expression cutoff (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006295#sec015" target="_blank">Methods</a>) are not shown. A, B) One copy gene expression of the genes between chr2L:12,545,800 and 12,975,028, which is uncovered by five different <i>Dfs</i>. C, D) One copy gene expression of the genes between chr2L:19,003,398 and 19,158,447 region that is uncovered by four different <i>Dfs</i>. E, F) Sashimi plots that display normalized numbers of mapped reads across <i>RpL30</i> and <i>RpL7-like</i> gene body regions. Expression in <i>Df(2L)ED1202/+</i> for <i>RpL30</i> and <i>Df(2L)ED761/+</i> for <i>RpL7-like</i> was compared to expression in <i>Df(2L)ED774/+</i>, which was the shortest deletion in our study and is <i>+/+</i> for both genes. Exons (black bars) in the gene models and transcription direction (chevrons) are show below. G, H) Dosage responses (y-axis) of one copy genes when uncovered by deletions of indicated length (x-axis). Results from the isogenic genetic background (top) and from the hybrid genetic background (bottom) are shown.</p
<p>A) Boxplots of gene expression in two copy genes (open) or one copy genes (red and blue ... more <p>A) Boxplots of gene expression in two copy genes (open) or one copy genes (red and blue for females and males, respectively) from all <i>Df</i> lines used (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006295#pgen.1006295.g001" target="_blank">Fig 1</a> for boxplot parameters). B) Cumulative distribution function plots for female <i>Df</i>/+ (red), male <i>Df</i>/+ (blue), and +/+ gene expression (black, for both sexes). The grey line displays +/+ gene expression level shifted by -1 (log2). Arrowhead indicates Kolmogorov-Smirnov statistic (<i>D</i>), the largest vertical differences between two cumulative distributions (0.045 for isogenic and 0.051 for hybrid). A, B) Data from isogenic (top) and hybrid (bottom) genetic backgrounds are shown. C, D) Scatter plots that compare one copy gene expression relative to two copy gene expression between the isogenic genetic background and hybrid genetic background. A subset of genes in (C) represents “better compensated” genes identified in clustering analysis (Green). The grey numbers on the plots indicate the number of <i>Df</i>/+ genes appeared in each quadrant, divided by (-1, -1). The same genes that are deficient in multiple Df/+ flies were counted multiple times. Pearson’s correlation coefficient (<i>r</i>), slopes from linear regression and <i>p</i> values (F-tests) are shown. E) Barplots that display the proportion of male-biased or female-biased genes from all <i>Drosophila</i> genes, chromosome 2L genes, and the better compensation in females (C, green). ***<i>p</i> < 0.001 (Hypergeometric test).</p
<p>A) <i>Dfs</i> used in this study. The extent of the deleted DNA (bars) and p... more <p>A) <i>Dfs</i> used in this study. The extent of the deleted DNA (bars) and position along the first 25Mb of <i>2L</i> (bottom scale) are indicated. <i>Dfs</i> were tested in both the isogenic and hybrid background (except: * isogenic only, and ** hybrid only). B, C) Box plots of gene expression in two copy genes (open) and one copy genes (filled) relative to normalized global expression of the same genes in the rest of the dataset. Bottom, middle, and top lines of each box represent the 1<sup>st</sup>, 2<sup>nd</sup> (median), and 3<sup>rd</sup> quartile of the distribution, respectively. The maximum or minimum observation within 1.5 times of the interquartile range (3<sup>rd</sup> quartile– 1<sup>st</sup> quartile) from the 3<sup>rd</sup> or 1<sup>st</sup> quartile, respectively is indicated by whiskers. Notches indicate the 95% confidence interval for the medians. A 2-fold difference in expression is delimited by the solid and dotted horizontal lines. D, E) Normalized relative expression value distributions of two copy genes (dashed line, open), the projected distribution if gene expression was reduced by 50% in one copy genes (dotted line, filled), and observed one copy gene expression (solid line, open). F, G) Scatter plots that display one copy gene expression levels between males and females from same <i>Dfs</i>. Pearson’s correlation coefficient (<i>r</i>), regression slope, and <i>p</i> value for the correlation are indicated. B, D, F) Isogenic background. C, E, G) Hybrid background.</p
<p>A, B) One copy versus two copy gene expression levels plotted against the median express... more <p>A, B) One copy versus two copy gene expression levels plotted against the median expression levels of replicates in <u>F</u>ragments <u>P</u>er <u>K</u>ilobase of transcript per <u>M</u>illion mapped reads (FPKM). C, D) Boxplots that display different degree of autosomal dosage compensation of the genes that are classified as housekeeping, or non-housekeeping based on the Naïve Bayes Classifier [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006295#pgen.1006295.ref040" target="_blank">40</a>]. <i>p</i> values are from Mann-Whitney U tests. E-H) Gene expression levels of <i>Df</i>/+ genes were plotted based on Tissue Specificity Score (TSPS, E,G) and <i>tau</i> score (F,H). For both scores, larger values indicate more tissue specific. Dashed lines in scatter plots, their slopes and <i>p</i> values are from linear modeling and the F-test. A, C, E, F) Results from the isogenic genetic background. B, D, G, H) from hybrid genetic background.</p
<p>A, B) Adjusted <i>p</i> values of gene expression change is plotted in–log s... more <p>A, B) Adjusted <i>p</i> values of gene expression change is plotted in–log scale across the genome for females (A) and males (B) of <i>Df(2L)ED136/+</i> flies. The grey region on chromosome 2L indicates the deletion. The threshold adjusted <i>p</i> = 0.05 is shown (dotted lines). <i>CG18600</i> displayed significant changes in both genetic backgrounds and sexes. C, D) Gene expression changes of <i>Df</i>/+ genes (diamond) and their two dose 1° neighbors (circle) genes in the integrated gene network of female <i>Df(2L)ED778</i>/+ flies from isogenic (C) and hybrid (D) genetic backgrounds. E, F) Overlap of gene expression changes between <i>Df</i>/+ genes, and their two dose 1°, 2°, and 3° neighbors between two different genetic backgrounds in females (E) and males (F). We called genes whose changes are greater than 1.5 folds and show same directional changes (up or down) in both genetic backgrounds to be overlapped. For brevity, “<i>Df(2L)</i>” and “<i>/+</i>” are omitted in genotypes. E.g. <i>Df(2L)ED105/+</i> is shown as <i>ED105</i>.</p
<p>Density plots that display gene expression changes of two copy genes that are neighbors ... more <p>Density plots that display gene expression changes of two copy genes that are neighbors of <i>Df</i> genes in the integrative network by 1° (primary, top), 2° (secondary, middle) and 3° (tertiary, bottom) are collectively plotted from all used lines against the expression changes of <i>Df</i> genes (one copy, x-axis) in females (left), males (center) and combined (right). Results from both the A) isogenic and B) hybrid background are shown. Pearson’s correlation coefficient (<i>r</i>) and slopes from linear modeling are shown.</p
Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for... more Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies of the left arm of chromosome 2 and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of gene regulation due to altered nuclear architecture are r...
Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for... more Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies on the left arm of chromosome 2 and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of changes in gene regulation due to altered nuclear archite...
Centrosomin (Cnn) is a required core component in mitotic centrosomes during syncytial developmen... more Centrosomin (Cnn) is a required core component in mitotic centrosomes during syncytial development and the presence of Cnn at centrosomes has become synonymous with fully functional centrosomes in Drosophila melanogaster. Previous studies of Cnn have attributed this embryonic function to a single isoform or splice variant. In this study, we present new evidence that significantly increases the complexity of cnn. Rather than a single isoform, Cnn function can be attributed to two unique classes of proteins that comprise a total of at least 10 encoded protein isoforms. We present the initial characterization of a new class of Cnn short isoforms required for centrosome function during gametogenesis and embryogenesis. We also introduce new evidence for a complex mix of Cnn isoforms present during early embryogenesis. Finally, we reexamine cnn mutations, in light of the short isoforms, and find previously overlooked differences attributable to allele-specific mutant phenotypes. This stud...
Genetic effects on an index of wing shape on chromosome 2 of Drosophila melanogaster were mapped ... more Genetic effects on an index of wing shape on chromosome 2 of Drosophila melanogaster were mapped using isogenic recombinants with transposable element markers. At least 10 genes with small additive effects are dispersed evenly along the chromosome. Many interactions exist, with only small net effects in homozygous recombinants and little effect on phenotypic variance. Heterozygous chromosome segments show almost no dominance. Pleiotropic effects on leg shape are only minor. At first view, wing shape genes form a rather homogeneous class, but certain complexities remain unresolved.
Loci on the third chromosome of Drosophila melanogaster that affect an index of wing shape were m... more Loci on the third chromosome of Drosophila melanogaster that affect an index of wing shape were mapped, using recombinant isogenic lines, with transposable elements as markers. Many genes with small subequal effects are dispersed along the whole chromosome. Their alleles act nearly additively in heterozygotes. They have small correlated effects on leg shape, but no detectable effects on halteres. Small negative net interactions occur over most of the chromosome. The data set of 519 recombinant isogenic lines can be explained reasonably well by two models. One model posits an indefinitely large number of loci with no interactions. The other model posits 11 loci with additive effects whose sum equals the total phenotypic range and with large positive and negative interactions that nearly cancel each other.
We would like to thank Dr. Alan Templeton for the gift of the bisexual and parthenogenetic strain... more We would like to thank Dr. Alan Templeton for the gift of the bisexual and parthenogenetic strains of D. mercatorum. We also thank Kevin Cook for his thoughtful input and time spent reviewing the manuscript. We also would like to thank two semi-anonymous reviewers for their insightful comments that significantly improved the paper and prevented us from making a public spectacle of ourselves.
In Drosophila melanogaster a functional pericentriolar matrix (PCM) at mitotic centrosomes requir... more In Drosophila melanogaster a functional pericentriolar matrix (PCM) at mitotic centrosomes requires Centrosomin-Long Form (Cnn-LF) proteins. Moreover, tissue culture cells have shown that the centrosomal localization of both Cnn-LF and Polo kinase are co-dependent, suggesting a direct interaction. Our recent study found Cnn potentially binds to and is phosphorylated by Polo kinase at 2 residues encoded by Exon1A, the initiating exon of a subset of Cnn isoforms. These interactions are required for the centrosomal localization of Cnn-LF in syncytial embryos and a mutation of either phosphorylation site is sufficient to block localization of both mutant and wild-type Cnn when they are co-expressed. Immunoprecipitation experiments show that Cnn-LF interacts directly with mitotically activated Polo kinase and requires the 2 phosphorylation sites in Exon1A. These IP experiments also show that Cnn-LF proteins form multimers. Depending on the stoichiometry between functional and mutant peptides, heteromultimers exhibit dominant negative or positive trans-complementation (rescue) effects on mitosis. Additionally, following the completion of meiosis, Cnn-Short Form (Cnn-SF) proteins are required for polar body formation in embryos, a process previously shown to require Polo kinase. These findings, when combined with previous work, clearly demonstrate the complexity of cnn and show that a view of cnn as encoding a single peptide is too simplistic.
INTRODUCTION In a previous paper (Weber 1996), results were presented from the first 100 generati... more INTRODUCTION In a previous paper (Weber 1996), results were presented from the first 100 generations of an ongoing, exploratory selection experiment on Drosophila melanogaster. Each generation, in each of two populations, 30,000 to 60,000 flies are scored for performance in a wind tunnel, and 2000 parents are selected from the strongest fliers. In the prior report, large gains in windtunnel performance had occurred in the selected lines, with large genetic changes, but correlated fitness costs were not demonstrable. Large fitness costs have usually been associated with extreme trait gains in experimental selection and in selective breeding. These costs have generally been regarded as necessary correlates of major change in selected traits.
We analyzed the usage and consequences of alternative cleavage and polyadenylation (APA) in Droso... more We analyzed the usage and consequences of alternative cleavage and polyadenylation (APA) in Drosophila melanogaster by using >1 billion reads of stranded mRNA-seq across a variety of dissected tissues. Beyond demonstrating that a majority of fly transcripts are subject to APA, we observed broad trends for 3 0 untranslated region (UTR) shortening in the testis and lengthening in the central nervous system (CNS); the latter included hundreds of unannotated extensions ranging up to 18 kb. Extensive northern analyses validated the accumulation of full-length neural extended transcripts, and in situ hybridization indicated their spatial restriction to the CNS. Genes encoding RNA binding proteins (RBPs) and transcription factors were preferentially subject to 3 0 UTR extensions. Motif analysis indicated enrichment of miRNA and RBP sites in the neural extensions, and their termini were enriched in canonical cis elements that promote cleavage and polyadenylation. Altogether, we reveal broad tissue-specific patterns of APA in Drosophila and transcripts with unprecedented 3 0 UTR length in the nervous system.
The formation of the pericentriolar matrix (PCM) and a fully functional centrosome in syncytial D... more The formation of the pericentriolar matrix (PCM) and a fully functional centrosome in syncytial Drosophila melanogaster embryos requires the rapid transport of Cnn during initiation of the centrosome replication cycle. We show a Cnn and Polo kinase interaction is apparently required during embryogenesis and involves the exon 1A-initiating coding exon, suggesting a subset of Cnn splice variants is regulated by Polo kinase. During PCM formation exon 1A Cnn-Long Form proteins likely bind Polo kinase before phosphorylation by Polo for Cnn transport to the centrosome. Loss of either of these interactions in a portion of the total Cnn protein pool is sufficient to remove native Cnn from the pool, thereby altering the normal localization dynamics of Cnn to the PCM. Additionally, Cnn-Short Form proteins are required for polar body formation, a process known to require Polo kinase after the completion of meiosis. Exon 1A Cnn-LF and Cnn-SF proteins, in conjunction with Polo kinase, are required at the completion of meiosis and for the formation of functional centrosomes during early embryogenesis.
The ease of genetic manipulation in Drosophila melanogaster using the Gal4/UAS system has been be... more The ease of genetic manipulation in Drosophila melanogaster using the Gal4/UAS system has been beneficial in addressing key biological questions. Current modifications of this methodology to temporally induce transgene expression require temperature changes or exposure to exogenous compounds, both of which have been shown to have detrimental effects on physiological processes. The recently described auxin-inducible gene expression system (AGES) utilizes the plant hormone auxin to induce transgene expression and is proposed to be the least toxic compound for genetic manipulation, with no obvious effects on Drosophila development and survival in one wild-type strain. Here we show that auxin delays larval development in a widely-used fly strain, and auxin exposure in adult Drosophila induces observable changes in physiology and feeding behavior. We found that there is a dosage response to adult survival upon auxin exposure and low auxin concentrations alter feeding activity. Furthermor...
<p>A-D) One copy versus two copy gene expression levels plotted at the centers of each gene... more <p>A-D) One copy versus two copy gene expression levels plotted at the centers of each gene model (labeled below). Observations made in the isogenic genetic background (filled) and the hybrid genetic background (open) are shown. Genes whose expression is below the expression cutoff (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006295#sec015" target="_blank">Methods</a>) are not shown. A, B) One copy gene expression of the genes between chr2L:12,545,800 and 12,975,028, which is uncovered by five different <i>Dfs</i>. C, D) One copy gene expression of the genes between chr2L:19,003,398 and 19,158,447 region that is uncovered by four different <i>Dfs</i>. E, F) Sashimi plots that display normalized numbers of mapped reads across <i>RpL30</i> and <i>RpL7-like</i> gene body regions. Expression in <i>Df(2L)ED1202/+</i> for <i>RpL30</i> and <i>Df(2L)ED761/+</i> for <i>RpL7-like</i> was compared to expression in <i>Df(2L)ED774/+</i>, which was the shortest deletion in our study and is <i>+/+</i> for both genes. Exons (black bars) in the gene models and transcription direction (chevrons) are show below. G, H) Dosage responses (y-axis) of one copy genes when uncovered by deletions of indicated length (x-axis). Results from the isogenic genetic background (top) and from the hybrid genetic background (bottom) are shown.</p
<p>A) Boxplots of gene expression in two copy genes (open) or one copy genes (red and blue ... more <p>A) Boxplots of gene expression in two copy genes (open) or one copy genes (red and blue for females and males, respectively) from all <i>Df</i> lines used (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006295#pgen.1006295.g001" target="_blank">Fig 1</a> for boxplot parameters). B) Cumulative distribution function plots for female <i>Df</i>/+ (red), male <i>Df</i>/+ (blue), and +/+ gene expression (black, for both sexes). The grey line displays +/+ gene expression level shifted by -1 (log2). Arrowhead indicates Kolmogorov-Smirnov statistic (<i>D</i>), the largest vertical differences between two cumulative distributions (0.045 for isogenic and 0.051 for hybrid). A, B) Data from isogenic (top) and hybrid (bottom) genetic backgrounds are shown. C, D) Scatter plots that compare one copy gene expression relative to two copy gene expression between the isogenic genetic background and hybrid genetic background. A subset of genes in (C) represents “better compensated” genes identified in clustering analysis (Green). The grey numbers on the plots indicate the number of <i>Df</i>/+ genes appeared in each quadrant, divided by (-1, -1). The same genes that are deficient in multiple Df/+ flies were counted multiple times. Pearson’s correlation coefficient (<i>r</i>), slopes from linear regression and <i>p</i> values (F-tests) are shown. E) Barplots that display the proportion of male-biased or female-biased genes from all <i>Drosophila</i> genes, chromosome 2L genes, and the better compensation in females (C, green). ***<i>p</i> < 0.001 (Hypergeometric test).</p
<p>A) <i>Dfs</i> used in this study. The extent of the deleted DNA (bars) and p... more <p>A) <i>Dfs</i> used in this study. The extent of the deleted DNA (bars) and position along the first 25Mb of <i>2L</i> (bottom scale) are indicated. <i>Dfs</i> were tested in both the isogenic and hybrid background (except: * isogenic only, and ** hybrid only). B, C) Box plots of gene expression in two copy genes (open) and one copy genes (filled) relative to normalized global expression of the same genes in the rest of the dataset. Bottom, middle, and top lines of each box represent the 1<sup>st</sup>, 2<sup>nd</sup> (median), and 3<sup>rd</sup> quartile of the distribution, respectively. The maximum or minimum observation within 1.5 times of the interquartile range (3<sup>rd</sup> quartile– 1<sup>st</sup> quartile) from the 3<sup>rd</sup> or 1<sup>st</sup> quartile, respectively is indicated by whiskers. Notches indicate the 95% confidence interval for the medians. A 2-fold difference in expression is delimited by the solid and dotted horizontal lines. D, E) Normalized relative expression value distributions of two copy genes (dashed line, open), the projected distribution if gene expression was reduced by 50% in one copy genes (dotted line, filled), and observed one copy gene expression (solid line, open). F, G) Scatter plots that display one copy gene expression levels between males and females from same <i>Dfs</i>. Pearson’s correlation coefficient (<i>r</i>), regression slope, and <i>p</i> value for the correlation are indicated. B, D, F) Isogenic background. C, E, G) Hybrid background.</p
<p>A, B) One copy versus two copy gene expression levels plotted against the median express... more <p>A, B) One copy versus two copy gene expression levels plotted against the median expression levels of replicates in <u>F</u>ragments <u>P</u>er <u>K</u>ilobase of transcript per <u>M</u>illion mapped reads (FPKM). C, D) Boxplots that display different degree of autosomal dosage compensation of the genes that are classified as housekeeping, or non-housekeeping based on the Naïve Bayes Classifier [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006295#pgen.1006295.ref040" target="_blank">40</a>]. <i>p</i> values are from Mann-Whitney U tests. E-H) Gene expression levels of <i>Df</i>/+ genes were plotted based on Tissue Specificity Score (TSPS, E,G) and <i>tau</i> score (F,H). For both scores, larger values indicate more tissue specific. Dashed lines in scatter plots, their slopes and <i>p</i> values are from linear modeling and the F-test. A, C, E, F) Results from the isogenic genetic background. B, D, G, H) from hybrid genetic background.</p
<p>A, B) Adjusted <i>p</i> values of gene expression change is plotted in–log s... more <p>A, B) Adjusted <i>p</i> values of gene expression change is plotted in–log scale across the genome for females (A) and males (B) of <i>Df(2L)ED136/+</i> flies. The grey region on chromosome 2L indicates the deletion. The threshold adjusted <i>p</i> = 0.05 is shown (dotted lines). <i>CG18600</i> displayed significant changes in both genetic backgrounds and sexes. C, D) Gene expression changes of <i>Df</i>/+ genes (diamond) and their two dose 1° neighbors (circle) genes in the integrated gene network of female <i>Df(2L)ED778</i>/+ flies from isogenic (C) and hybrid (D) genetic backgrounds. E, F) Overlap of gene expression changes between <i>Df</i>/+ genes, and their two dose 1°, 2°, and 3° neighbors between two different genetic backgrounds in females (E) and males (F). We called genes whose changes are greater than 1.5 folds and show same directional changes (up or down) in both genetic backgrounds to be overlapped. For brevity, “<i>Df(2L)</i>” and “<i>/+</i>” are omitted in genotypes. E.g. <i>Df(2L)ED105/+</i> is shown as <i>ED105</i>.</p
<p>Density plots that display gene expression changes of two copy genes that are neighbors ... more <p>Density plots that display gene expression changes of two copy genes that are neighbors of <i>Df</i> genes in the integrative network by 1° (primary, top), 2° (secondary, middle) and 3° (tertiary, bottom) are collectively plotted from all used lines against the expression changes of <i>Df</i> genes (one copy, x-axis) in females (left), males (center) and combined (right). Results from both the A) isogenic and B) hybrid background are shown. Pearson’s correlation coefficient (<i>r</i>) and slopes from linear modeling are shown.</p
Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for... more Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies of the left arm of chromosome 2 and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of gene regulation due to altered nuclear architecture are r...
Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for... more Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies on the left arm of chromosome 2 and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of changes in gene regulation due to altered nuclear archite...
Centrosomin (Cnn) is a required core component in mitotic centrosomes during syncytial developmen... more Centrosomin (Cnn) is a required core component in mitotic centrosomes during syncytial development and the presence of Cnn at centrosomes has become synonymous with fully functional centrosomes in Drosophila melanogaster. Previous studies of Cnn have attributed this embryonic function to a single isoform or splice variant. In this study, we present new evidence that significantly increases the complexity of cnn. Rather than a single isoform, Cnn function can be attributed to two unique classes of proteins that comprise a total of at least 10 encoded protein isoforms. We present the initial characterization of a new class of Cnn short isoforms required for centrosome function during gametogenesis and embryogenesis. We also introduce new evidence for a complex mix of Cnn isoforms present during early embryogenesis. Finally, we reexamine cnn mutations, in light of the short isoforms, and find previously overlooked differences attributable to allele-specific mutant phenotypes. This stud...
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