title: A genome-wide search for epigenetically [corrected] regulated genes in zebra finch using MethylCap-seq and RNA-seq.
abstract: 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.
authors: Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent, Belgium.
authors: Sandra
authors: S
authors: Steyaert
authors: Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
authors: Jolien
authors: J
authors: Diddens
authors: Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent, Belgium.
authors: Jeroen
authors: J
authors: Galle
authors: Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent, Belgium.
authors: Ellen
authors: E
authors: De Meester
authors: Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent, Belgium.
authors: Sarah
authors: S
authors: De Keulenaer
authors: Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.
authors: Antje
authors: A
authors: Bakker
authors: Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.
authors: Nina
authors: N
authors: Sohnius-Wilhelmi
authors: Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany.
authors: Carolina
authors: C
authors: Frankl-Vilches
authors: Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
authors: Annemie
authors: A
authors: Van der Linden
authors: Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent, Belgium.
authors: Wim
authors: W
authors: Van Criekinge
authors: Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
authors: Wim
authors: W
authors: Vanden Berghe
authors: Department of Mathematical Modelling, Statistics and Bioinformatics, University of Ghent, Ghent, Belgium.
authors: Tim
authors: T
authors: De Meyer
mesh_terms: D000818:Animals; D030161:Avian Proteins / Q000235:genetics* / Q000378:metabolism; D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D045744:Cell Line, Tumor; D018899:CpG Islands; D019175:DNA Methylation / Q000187:drug effects; D000077209:Decitabine; D044127:Epigenesis, Genetic; D005260:Female; D046369:Finches / Q000235:genetics* / Q000378:metabolism; D053263:Gene Regulatory Networks; D016678:Genome; D007858:Learning / Q000502:physiology; D008297:Male; D008568:Memory / Q000502:physiology; D009419:Nerve Tissue Proteins / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
chemical_list: D030161:Avian Proteins; D009419:Nerve Tissue Proteins; D000077209:Decitabine; D001374:Azacitidine