Dataset Information

Avian reproductive tissue proteome (zebra finch)

ABSTRACT: Protein extraction of zebra finch testes and ovaries samples

INSTRUMENT(S): Q Exactive

ORGANISM(S): Taeniopygia Guttata (zebra Finch) (poephila Guttata)

TISSUE(S): Testis, Oocyte

SUBMITTER: Toni Gossmann

LAB HEAD: Dennis Kappei

PROVIDER: PXD014692 | Pride | 2020-01-13

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20170902_LAB_DK_TG_13P033_ZF10_a.raw	Raw
	20170902_LAB_DK_TG_13P033_ZF10_b.raw	Raw
	20170902_LAB_DK_TG_13P033_ZF10_c.raw	Raw
	20170902_LAB_DK_TG_13P033_ZF10_d.raw	Raw
	20170902_LAB_DK_TG_14R041_ZF07_a.raw	Raw

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Publications

Programmed DNA elimination of germline development genes in songbirds.

Kinsella Cormac M CM Ruiz-Ruano Francisco J FJ Dion-Côté Anne-Marie AM Charles Alexander J AJ Gossmann Toni I TI Cabrero Josefa J Kappei Dennis D Hemmings Nicola N Simons Mirre J P MJP Camacho Juan Pedro M JPM Forstmeier Wolfgang W Suh Alexander A

Nature communications 20191129 1

In some eukaryotes, germline and somatic genomes differ dramatically in their composition. Here we characterise a major germline-soma dissimilarity caused by a germline-restricted chromosome (GRC) in songbirds. We show that the zebra finch GRC contains >115 genes paralogous to single-copy genes on 18 autosomes and the Z chromosome, and is enriched in genes involved in female gonad development. Many genes are likely functional, evidenced by expression in testes and ovaries at the RNA and protein ...[more]

PMID: 31784533

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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 Within the overall project, we performed a set of microarrays to validate RNAseq data (Series accession number GSE61060) . DMSO- and AZA-treated zebra finch cell lines, i.e. G266 and ZFTMA. ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided for individual Sample records. Processed data is available on Series record.