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Title
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A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq
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Author
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Abstract
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| 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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Language
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English
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Source (journal)
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Scientific reports. - London, 2011, currens
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Publication
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London
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Nature Publishing Group
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2016
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ISSN
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2045-2322
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DOI
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10.1038/SREP20957
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Volume/pages
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6
(2016)
, 16 p.
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Article Reference
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20957
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ISI
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000369924800001
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Pubmed ID
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26864856
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Note
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Corrigendum
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Medium
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E-only publicatie
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Full text (Publisher's DOI)
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Full text (open access)
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