Unknown,Transcriptomics,Genomics,Proteomics

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Comparative genomic hybridization of zebra finch and common whitethroat samples using a Affymetrix custom array designed for the zebra finch

ABSTRACT: 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.

INSTRUMENT(S): GeneChip Scanner 3000 [Affymetrix]

ORGANISM(S): Sylvia communis

SUBMITTER: Sara Naurin

PROVIDER: E-MEXP-1181 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

Dataset Information

Comparative genomic hybridization of zebra finch and common whitethroat samples using a Affymetrix custom array designed for the zebra finch

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