Core and region enriched networks of behaviorally regulated genes: the singing epigenome
Ontology highlight
ABSTRACT:
ORGANISM(S): Taeniopygia guttata
SUBMITTER: Andreas Pfenning
PROVIDER: E-GEOD-63936 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We queried a songbird brain to discover behaviorally regulated transcriptional mechanisms relevant for speech behavior. About 10% of zebra finch genes showed regulation during singing, and most were brain-region specific. We propose that the brain-regional diversity of the singing-regulated gene networks is derived both from differential combinatorial binding of transcription factors and the epigenetic state of these genes before singing begins. To test this hypothesis, we measured H3K27ac two brain regions that participate in song production.
2014-12-08 | GSE63936 | GEO
Project description:This study was part of a larger study on the zebra finch genome (Warren et al 2010. Nature). Here we present a summary of the specific experiment on singing-regulated gene expression. To evaluate the genomic landscape of learned vocal communication, we profiled gene expression in the zebra finch song nucleus, Area X, with custom Agilent oligoarrays for up to seven hours following initiation of singing. We developed algorithms to identify singing-regulated transcripts related to time spent singing, and discovered over 800 transcripts in Area X that are significantly regulated by singing. These included known increases of the egr1 and c-fos transcription factors, and a decrease in the FoxP2 transcription factor, a gene associated with spoken language development. We clusted the singing-regulated genes in Area X into 20 temporal dynamic expression patterns, which include rapidly up-regulated and transient, rapidly up-regulated and sustained, slowly up-regulated and sustained, a late upregulated response, and equally diverse clusters of down-regulated patterns. Using promotor motif search algorithms, we found significant over-representation of transcription factor binding sites in the promoters of genes within specific clusters. These binding sites included those of transcription factors known to be activated by neural activity and plasticity, such as CREB, SRF, AP-1, NFKB1, CFOS, EGR1, and MEF2.
2010-01-16 | GSE19900 | GEO
Project description:This study was part of a larger study on the zebra finch genome (Warren et al 2010. Nature). Here we present a summary of the specific experiment on singing-regulated gene expression. To evaluate the genomic landscape of learned vocal communication, we profiled gene expression in the zebra finch song nucleus, Area X, with custom Agilent oligoarrays for up to seven hours following initiation of singing. We developed algorithms to identify singing-regulated transcripts related to time spent singing, and discovered over 800 transcripts in Area X that are significantly regulated by singing. These included known increases of the egr1 and c-fos transcription factors, and a decrease in the FoxP2 transcription factor, a gene associated with spoken language development. We clusted the singing-regulated genes in Area X into 20 temporal dynamic expression patterns, which include rapidly up-regulated and transient, rapidly up-regulated and sustained, slowly up-regulated and sustained, a late upregulated response, and equally diverse clusters of down-regulated patterns. Using promotor motif search algorithms, we found significant over-representation of transcription factor binding sites in the promoters of genes within specific clusters. These binding sites included those of transcription factors known to be activated by neural activity and plasticity, such as CREB, SRF, AP-1, NFKB1, CFOS, EGR1, and MEF2. Gene expression in Area X was measured before singing (0) or after singing for 0.5, 1, 2, 3, 4, 5, 6, and 7hours. Six independent experiments were performed at each of the 9 timepoints.
2010-05-15 | E-GEOD-19900 | biostudies-arrayexpress
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). e12: AL (auditory lobule) from post-hatch day 20 male zebra finches after 30 minutes of novel song playback or silence control, 6 biological replicates per group. All samples were hybridized against the SoNG universal RNA pool.
2012-05-30 | E-GEOD-36742 | biostudies-arrayexpress
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). e11: Auditory lobules (AL) were collected from adult male zebra finches (Taeniopygia guttata) after 30 minutes of novel or familiar song playback, or silence control.
2012-05-30 | E-GEOD-36740 | biostudies-arrayexpress
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). e01: Brain regions HVC and RA were collected from Gambel's White crowned sparrows (Zonotrichia leucophrys gambelii) from the following experimental groups: long-term Short Day (SD); Long Day (LD) with Testosterone (T) for 3, 7, and 21 days (3LD+T, 7LD+T, 21LD+T respectively); SD and removal of T at 1 and 2 days (1SD-T, 2SD-T). Six biological replicates per group, five biological replicates in 3LD+T.HVC group. All samples were hybridized against the SoNG universal reference RNA pool.
2012-05-30 | E-GEOD-36705 | biostudies-arrayexpress
Project description:We have conducted a Cross-Species Microarray analysis by hybridizing genomic DNA from the common whitethroat (Sylivia communis) on a newly developed Affymetrix costum array designed for the zebra finch (Taeniopygia guttata), the Lund-zf array. We have also quality tested the Lund-zf array by hybridizing zebra finch genomic DNA to the platform.
2007-09-30 | E-MEXP-1181 | biostudies-arrayexpress
Project description:DNA methylation is tightly linked with gene expression regulation and has long been regarded a stable epigenetic mark in postmitotic cells. However, it recently became clear that postnatal brains appear to show stimulus-induced de novo CpG methylation or active demethylation related to neuronal plasticity. Due to striking homologies between the brains of birds and mammals, songbirds, especially the zebra finch, propose an attractive model for investigating the genome-wide DNA methylation profile and DNA methylation reconfiguration during brain development. In order to obtain a first genome-wide compendium of genes under putative DNA methylation control, we performed MethyCap-seq experiments on two recently cultured zebra finch cell lines, G266 and ZFTMA, also upon AZA-induced demethylation. First, the MethylCap-seq methodology in zebra finch was validated by comparison with RRBS generated data. Subsequently, quantitative analysis identified 30,700 significantly demethylated loci upon AZA-treatment. Further examination revealed enrichment of these regions in exons and promoters. To assess the influence of methylation on gene expression, RNA-seq experiments were performed. Comparison of the RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed obvious enrichment for neurological networks. A subset of genes was validated using qPCR and CpG pyrosequencing. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control. MethylCap-seq and RNA-seq experiments were performed on DMSO- and AZA-treated zebra finch cell lines, i.e. G266 and ZFTMA. As a quality control, also an untreated ZFTMA sample was analyzed with MethylCap-seq and RRBS.
2015-12-10 | E-GEOD-61060 | biostudies-arrayexpress
Project description:Songbirds possess one of the most accessible neural systems for the study of brain mechanisms of behavior. However, neuroethological studies in songbirds have been limited by the lack of high-throughput molecular resources and gene manipulation tools. To overcome this limitation, here we generated a resource of full-length cDNAs for gene expression analyses and gene manipulation in songbirds. We constructed 21 regular, normalized, and subtracted full-length cDNA libraries from brains of songbirds in 57 behavioral and developmental conditions in an attempt to clone as much of the brain transcriptome as possible. From these libraries ~14,000 transcripts were isolated, representing an estimated 4,738 genes, or ~40% of the genes expressed in the brain. With these cDNAs, we created a novel draft transcriptome database and large scale songbird brain cDNA microarrays. We used the arrays to reveal a set of 33 genes regulated in brain vocal nuclei by singing behavior. These genes clustered into 4 anatomical and 6 temporal brain expression patterns. Their functions spanned broad range of cellular and molecular categories, including signal transduction, trafficking, structural, and synaptically released molecules. With the full-length cDNAs, we over-expressed proteins of representative singing-regulated genes in vocal nuclei in the absence of singing, using a lentiviral vector system. This resource now allows investigators to comprehensively study molecular neuroethological mechanisms of behavior. Keywords: songbird, zebra finch, transcriptome, learned vocalization, immediate early genes, lentivirus
2006-04-11 | GSE4629 | GEO
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). e14: Hypothalamus from adult male Song sparrows 30 minutes after Simulated Territorial Intrusion (STI) or control, in spring and fall, 8 biological replicates per group (only 7 biological replicates in Spring Control group). All samples were hybridized against the SoNG universal RNA reference pool.
2012-05-30 | E-GEOD-36746 | biostudies-arrayexpress