Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Prenatal Heat Calls Program DNA Methylation in the Embryonic Zebra Finch Brain

ABSTRACT: Zebra finch embryos can detect prenatal acoustic cues that may help prepare them for post-hatch environmental conditions, but the molecular mechanisms underlying this developmental programming remain poorly understood. We used reduced representation bisulfite sequencing (RRBS) to profile DNA methylation in whole brains of embryonic day 14 zebra finch embryos exposed prenatally to either heat call playback or control call playback from embryonic day 10 through embryonic day 13. The study included embryos from both treatment groups, and samples failing RRBS quality control were excluded before downstream analysis, resulting in a final cohort of 35 embryos. Differential methylation analysis identified CpG sites associated with prenatal heat call exposure in genes and pathways related to nuclear receptor signaling, protein phosphorylation, synaptic organization, and GABAergic signaling. A recurrent signal across analytical models was intronic hypermethylation in RBFOX2, a gene involved in RNA splicing and neuronal development. These data indicate that prenatal acoustic experience is associated with locus-specific epigenetic variation in the embryonic brain and provide a molecular framework for understanding acoustic developmental programming in a warming environment.

ORGANISM(S): Taeniopygia guttata

PROVIDER: GSE324175 | GEO | 2026/03/13

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Multiome Profiling Reveals Astrocyte and Neuroendocrine Targets of Prenatal Acoustic Programming in Zebra Finch Embryos

Project description:Prenatal sensory experience can program offspring phenotypes, yet the cell-type-specific regulatory mechanisms remain poorly understood. In zebra finches (Taeniopygia guttata), parental heat call vocalizations program offspring for thermal environments. To identify the cellular and epigenetic targets of this acoustic programming, we performed single-nucleus multiome sequencing (joint snRNA-seq and snATAC-seq) on medial hypothalamic punches from embryonic day 13 (E13) zebra finch embryos exposed to heat call or control call playback from E9–E13. We profiled 55,950 nuclei across 49 cell clusters representing 13 cell types. Differential chromatin accessibility analysis revealed a striking enrichment of chromatin remodeling in astrocytes (204 of 236 differentially accessible peaks), with Heat Call exposure predominantly increasing chromatin accessibility. chromVAR motif enrichment identified NFIC and AP-1 family transcription factors as top differentially active motifs in heat call embryos. Weighted gene co-expression network analysis identified an astrocyte module (Astro-M7) positively associated with heat call exposure, enriched for Notch signaling components. Cicero co-accessibility analysis revealed 9,502 heat call-specific chromatin loops involving 3,891 unique regulatory elements, concentrated at gliogenic regulators including NFIA, HES-5-like, and DLL1. Pseudotemporal trajectory analysis showed accelerated astrocyte developmental progression in heat call embryos. Additionally, transthyretin (TTR) showed sexually dimorphic, playback-associated expression in paraventricular nucleus glutamatergic neurons. Together, these findings reveal an epigenetic priming mechanism by which prenatal acoustic cues accelerate astrocyte maturation and reshape neuroendocrine programs in the developing hypothalamus.

2026-03-06 | GSE322480 | GEO

Multiome Profiling Reveals Astrocyte and Neuroendocrine Targets of Prenatal Acoustic Programming in Zebra Finch Embryos

Project description:Multiome Profiling Reveals Astrocyte and Neuroendocrine Targets of Prenatal Acoustic Programming in Zebra Finch Embryos

| PRJNA1429414 | ENA

Transcriptional Profiling of Zebra Finch Hypothalamus After Chronic Heat Call Exposure

Project description:Late-stage zebra finch embryos were exposed to chronic playback of parental heat calls or control sounds to test how acoustic cues of extreme heat reshape hypothalamic gene expression. RNA-seq of medial hypothalamic punches revealed modest changes in neuroendocrine genes but strong downregulation of muscle and cytoskeletal programs, with evidence of altered isoform usage and enrichment in neurovascular cell populations. These findings indicate that parental heat calls drive a non-neuroendocrine transcriptional program underlying early-life developmental plasticity and acoustic-mediated adaptation to environmental extremes in birds.

2025-12-22 | GSE313742 | GEO

DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon [RRBS]

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

DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon [RNA-Seq]

2021-04-07 | GSE147972 | GEO

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

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

Single-cell RNA sequencing of the CFS414 zebra finch cell line

Project description:The zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a cell line from zebra finch embryonic fibroblasts using the SV40 large and small T antigens, designated CFS414. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. This single-cell RNA sequencing experiment provided information on the gene expression landscape of the cell line, informing on its cell type, transcriptomic stability, and value to researchers utilizing the zebra finch as a model organism.

2022-02-04 | GSE195934 | GEO

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

2015-12-10 | GSE61060 | GEO

Validation of a genome-wide search for zebra finch epigenetically regulated genes using Zebra finch Exon Arrays

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

Prenatal Heat Calls Program DNA Methylation in the Embryonic Zebra Finch Brain

Project description:Prenatal Heat Calls Program DNA Methylation in the Embryonic Zebra Finch Brain

| PRJNA1433561 | ENA