RRBS in zebra finch brain after song playback
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB28656 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR2796520.fastq.gz | Fastqsanger.gz | |||
| ERR2796530.fastq.gz | Fastqsanger.gz | |||
| ERR2796540.fastq.gz | Fastqsanger.gz | |||
| ERR2796521.fastq.gz | Fastqsanger.gz | |||
| ERR2796531.fastq.gz | Fastqsanger.gz |
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Project description:Song learning in zebra finches is a prototypical example of a complex learned behavior, yet knowledge on the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 dph and 65 dph). We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA (hydroxy)methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing zebra finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age dependent gene expression was found for various transcription factors (i.a. OTX2, AR and FOS) involved in neurodevelopment. Additionally, genomic regions featured by age dependent differential methylation in differentially expressed genes were significantly enriched for specific transcription factor binding motifs. Incomplete dosage compensation was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life. In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in zebra finch telencephalon.
2021-04-07 | GSE147973 | GEO
Project description:Song learning in zebra finches is a prototypical example of a complex learned behavior, yet knowledge on the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 dph and 65 dph). We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA (hydroxy)methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing zebra finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age dependent gene expression was found for various transcription factors (i.a. OTX2, AR and FOS) involved in neurodevelopment. Additionally, genomic regions featured by age dependent differential methylation in differentially expressed genes were significantly enriched for specific transcription factor binding motifs. Incomplete dosage compensation was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life. In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in zebra finch telencephalon.
2021-04-07 | GSE147972 | GEO
Project description:Protein extraction of zebra finch testes and ovaries samples
2020-01-13 | PXD014692 | Pride
Project description:Like human speech, birdsong is a complex vocal behavior that is acquired by sensorimotor learning based on coordination of auditory input and vocal output to mimic memorized tutor song. Here we investigate neural circuits for vocal learning and production in deafened songbirds to elucidate how sensory-input regulate genetic and epigenetic property of vocal development and its associated gene expression dynamics. Compared with audition-intact birds, in deafened zebra finches, the vocal development is delayed but song crystallization is observed at more than three times later, producing individually different but structured vocal patterns. In contrast to the distinct difference of vocal ontogeny between audition (+) and (-), unexpectedly, developmental regulation of gene expression dynamics is strictly conserved with age-locked trend in vocal motor circuit in both intact and deafened birds, indicating sensory-input independent robustness of developmental gene expression dynamics in the motor circuit for sensorimotor learning. This discrepancy between outward vocal phenotype and inward gene expression dynamics provides new insight into neural regulation at closing of the critical period for vocal learning by two different forms: auditory inputs-dependent ‘active’ crystallization and gene expression dynamics-mediated ‘passive’ crystallization.
2014-03-21 | GSE56075 | GEO
Project description:A male zebra finch begins to learn to sing by memorizing a tutorM-bM-^@M-^Ys song during a sensitive period in juvenile development. Tutor song memorization requires molecular signaling within the auditory forebrain. Using microarray and in situ hybridizations, we tested whether the auditory forebrain at an age just before tutoring expresses a different set of genes compared with later life after song learning has ceased. Microarray analysis revealed differences in expression of thousands of genes in the male auditory forebrain at posthatch day 20 (P20) compared with adulthood. Furthermore, song playbacks had essentially no impact on gene expression in P20 auditory forebrain, but altered expression of hundreds of genes in adults. Most genes that were song-responsive in adults were expressed at constitutively high levels at P20. Using in situ hybridization with a representative sample of 44 probes, we confirmed these effects and found that birds at P20 and P45 were similar in their gene expression patterns. Additionally, eight of the probes showed maleM-bM-^@M-^Sfemale differences in expression. We conclude that the developing auditory forebrain is in a very different molecular state from the adult, despite its relatively mature gross morphology and electrophysiological responsiveness to song stimuli. Developmental gene expression changes may contribute to fine-tuning of cellular and molecular properties necessary for song learning. Post-hatch day 20 male zebra finches that had been raised in acoustic isolation with a foster female or adult male zebra finches were placed in a song playback chamber. The next day, birds heard either silence (control) or 30 minutes of novel song. All samples were hybridized against the universal SoNG RNA reference pool, 6 biological replicates per group in each of 4 groups.
2012-03-24 | E-GEOD-36657 | biostudies-arrayexpress
Project description:To investigate the cellular basis of parental species bias at birdsong, we performed single nuclei RNA-seq for six zebra finch and owl finch F1 hybrid juvenile birds.
2023-11-04 | GSE217341 | 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:A male zebra finch begins to learn to sing by memorizing a tutor’s song during a sensitive period in juvenile development. Tutor song memorization requires molecular signaling within the auditory forebrain. Using microarray and in situ hybridizations, we tested whether the auditory forebrain at an age just before tutoring expresses a different set of genes compared with later life after song learning has ceased. Microarray analysis revealed differences in expression of thousands of genes in the male auditory forebrain at posthatch day 20 (P20) compared with adulthood. Furthermore, song playbacks had essentially no impact on gene expression in P20 auditory forebrain, but altered expression of hundreds of genes in adults. Most genes that were song-responsive in adults were expressed at constitutively high levels at P20. Using in situ hybridization with a representative sample of 44 probes, we confirmed these effects and found that birds at P20 and P45 were similar in their gene expression patterns. Additionally, eight of the probes showed male–female differences in expression. We conclude that the developing auditory forebrain is in a very different molecular state from the adult, despite its relatively mature gross morphology and electrophysiological responsiveness to song stimuli. Developmental gene expression changes may contribute to fine-tuning of cellular and molecular properties necessary for song learning.
2012-03-24 | GSE36657 | GEO
Project description:To investigate the cellular basis of parental species bias at birdsong, we performed single nuclei RNA-seq for six zebra finch and owl finch F1 hybrid juvenile birds.
2023-11-04 | GSE217340 | GEO
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. The ZF exon-arrays analysis validated the RNA-seq expression result for 75% and 62%, of the down and up-regulated genes, respectively. A subset of genes was validated also 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
2016-02-22 | GSE71344 | GEO