Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds

ABSTRACT: We have performed a comparison of global patterns of gene expression between two bird species, the chicken and zebra finch, especially with regard to sex bias of autosomal vs. Z chromosome genes, dosage compensation and evolution of sex bias. Both species appear to lack a Z chromosome-wide mechanism of dosage compensation, because both have a similar pattern of significantly higher expression of Z genes in males relative to females. Unlike the chicken Z chromosome, which has female-specific expression of the non-coding RNA MHM (male hypermethylated), and acetylation of histone 4 lysine 16 (H4K16) near MHM, the zebra finch Z chromosome appears to lack the MHM sequence and acetylation of H4K16. The zebra finch also does not show the reduced male to female (M:F) ratio of gene expression near MHM similar to that found in the chicken. Although the M:F ratios of Z chromosome gene expression are similar across tissues and ages within each species, they differ between the two species. Z genes showing the greatest species difference in M:F ratio were concentrated near the MHM region of the chicken Z chromosome. The current study shows that the zebra finch differs from the chicken because it lacks a specialized region of greater dosage compensation along the Z chromosome, and shows dosage compensation for a different set of Z genes than the chicken. These patterns suggest that different avian taxa may have evolved specific compensatory mechanisms. Experimental groups: Post-hatch Days 1, 25, 45, and 90+ for both Females and Males (d1_F, d1_M, d25_F, d25_M, d45_F, d45_M, adult_F, adult_M). Biological replicates: 6 per group. One test developmental stage subject and one universal SoNG reference (pooled Taeniopygia guttata brain) per array.

ORGANISM(S): Taeniopygia guttata

SUBMITTER: Juli Wade

PROVIDER: E-GEOD-20035 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Songbirds provide rich natural models for studying the relationships of brain anatomy, behavioral function, environmental signals and gene expression. Under the Songbird Neurogenomics Initiative, investigators from more than a dozen laboratories collected brain samples from six species of songbird under a range of experimental conditions, and 488 of these samples were analyzed systematically for gene expression by microarray. ANOVA was used to test 32 planned contrasts in the data, revealing the relative impact of different factors. The brain region from which tissue was taken had the greatest influence on gene expression profile, affecting the majority of signals measured by the 18,848 non-redundant cDNAs spotted on the microarray. Social and environmental manipulations had highly variable impact, ranging from nil in some cases to robust in others. Several specific genes were identified as points of interest in the evolution of mechanisms by which environmental signals influence behavior. The data were also analyzed using Weighted Gene Co-expression Network Analysis (WGCNA) followed by Gene Ontology (GO) analysis. This revealed modules of co-regulated genes that are also enriched for specific functional annotations such as M-bM-^@M-^\ribosomeM-bM-^@M-^] (expressed more highly in juvenile brain) and M-bM-^@M-^\dopamine metabolic processM-bM-^@M-^] (expressed more highly in striatal song control nucleus Area X). These results underscore the complexity of influences on neural gene expression and provide a resource for studying how these influences are integrated during natural experience. RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different M-bM-^@M-^\treatmentsM-bM-^@M-^], i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA). e04: Whole telencephalon of p1, p25, p45 and adult zebra finches, both males and females, 6 biological replicates per group. All samples were hybridized against the SoNG universal reference RNA pool.

Project description:Songbirds provide rich natural models for studying the relationships of brain anatomy, behavioral function, environmental signals and gene expression. Under the Songbird Neurogenomics Initiative, investigators from more than a dozen laboratories collected brain samples from six species of songbird under a range of experimental conditions, and 488 of these samples were analyzed systematically for gene expression by microarray. ANOVA was used to test 32 planned contrasts in the data, revealing the relative impact of different factors. The brain region from which tissue was taken had the greatest influence on gene expression profile, affecting the majority of signals measured by the 18,848 non-redundant cDNAs spotted on the microarray. Social and environmental manipulations had highly variable impact, ranging from nil in some cases to robust in others. Several specific genes were identified as points of interest in the evolution of mechanisms by which environmental signals influence behavior. The data were also analyzed using Weighted Gene Co-expression Network Analysis (WGCNA) followed by Gene Ontology (GO) analysis. This revealed modules of co-regulated genes that are also enriched for specific functional annotations such as M-bM-^@M-^\ribosomeM-bM-^@M-^] (expressed more highly in juvenile brain) and M-bM-^@M-^\dopamine metabolic processM-bM-^@M-^] (expressed more highly in striatal song control nucleus Area X). These results underscore the complexity of influences on neural gene expression and provide a resource for studying how these influences are integrated during natural experience. RNA samples were collected from six different songbird species (phylogeny in SI Appendix, Figure S1) and representing 80 different M-bM-^@M-^\treatmentsM-bM-^@M-^], i.e., combinations of species, brain region, sex, age, and behavioral state. The tissue samples were organized around 15 standalone experiments (Table 1 and SI Appendix, Table S1), contributed by investigators in a dozen different laboratories but analyzed under uniform conditions in a single laboratory as originally planned under the Songbird Neurogenomics Initiative. Each sample was hybridized to a zebra finch cDNA array along with a universal reference (a pool of zebra finch telencephalic RNA). e02: Area X of p35 zebra finch males who had been individually acoustically isolated at p30, then at p35 placed next to a stimulus female and exposed to no tutor, father tutor, or unfamiliar tutor for 2 hours then sacrificed, 5 biological replicates in the familiar tutor and no tutor treatment groups, 6 biological replicates in the unfamiliar tutor group. All samples were hybridized against the SoNG universal RNA reference pool.

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Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds

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