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

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作者
Sandra Steyaert
Jolien Diddens
Jeroen Galle
Ellen De Meester
Sarah De Keulenaer
Antje Bakker
Nina Sohnius-Wilhelmi
Carolina Frankl-Vilches
Annemie Van der Linden
Wim Van Criekinge
Wim Vanden Berghe
Tim De Meyer
机构
[1] Statistics and Bioinformatics,Department of Mathematical Modelling
[2] University of Ghent,Department of Biomedical Sciences
[3] Laboratory of Protein Chemistry,Department of Behavioral Neurobiology
[4] Proteomics and Epigenetic Signalling (PPES),Department of Biomedical Sciences
[5] University of Antwerp,undefined
[6] Max Planck Institute for Ornithology,undefined
[7] Bio-Imaging Lab,undefined
[8] University of Antwerp,undefined
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Scientific Reports | / 6卷
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摘要
Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the zebra finch genome, a model organism in neuroscience, as well as identifying putatively epigenetically regulated genes. RNA- and MethylCap-seq experiments were performed on two zebra finch cell lines in presence or absence of 5-aza-2′-deoxycytidine induced demethylation. First, the MethylCap-seq methodology was validated in zebra finch by comparison with RRBS-generated data. To assess the influence of (variable) methylation on gene expression, RNA-seq experiments were performed as well. Comparison of 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 remarkable enrichment for neurological networks. A subset of genes was validated using Exon Arrays, quantitative RT-PCR and CpG pyrosequencing on bisulfite-treated samples. 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.
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