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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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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.
Keywords
BRAIN, SEQUENCING DATA, BDNF GENE, MEMORY, ALZHEIMERS-DISEASE, SYNAPTIC PLASTICITY, EPIGENETIC REGULATION, DIFFERENTIAL EXPRESSION ANALYSIS, DNA METHYLATION, CELL-LINES

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Chicago
Steyaert, Sandra, Jolien Diddens, Jeroen Galle, Ellen De Meester, Sarah De Keulenaer, Antje Bakker, Nina Sohnius-Wilhelmi, et al. 2016. “A Genome-wide Search for Epigenetically Regulated Genes in Zebra Finch Using MethylCap-seq and RNA-seq.” Scientific Reports 6.
APA
Steyaert, Sandra, Diddens, J., Galle, J., De Meester, E., De Keulenaer, S., Bakker, A., Sohnius-Wilhelmi, N., et al. (2016). A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq. SCIENTIFIC REPORTS, 6.
Vancouver
1.
Steyaert S, Diddens J, Galle J, De Meester E, De Keulenaer S, Bakker A, et al. A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq. SCIENTIFIC REPORTS. 2016;6.
MLA
Steyaert, Sandra et al. “A Genome-wide Search for Epigenetically Regulated Genes in Zebra Finch Using MethylCap-seq and RNA-seq.” SCIENTIFIC REPORTS 6 (2016): n. pag. Print.
@article{7154363,
  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.},
  articleno    = {20957},
  author       = {Steyaert, Sandra and Diddens, Jolien and Galle, Jeroen and De Meester, Ellen and De Keulenaer, Sarah and Bakker, Antje and Sohnius-Wilhelmi, Nina and Frankl-Vilches, Carolina and Van der Linden, Annemie and Van Criekinge, Wim and Vanden Berghe, Wim and De Meyer, Tim},
  issn         = {2045-2322},
  journal      = {SCIENTIFIC REPORTS},
  keywords     = {BRAIN,SEQUENCING DATA,BDNF GENE,MEMORY,ALZHEIMERS-DISEASE,SYNAPTIC PLASTICITY,EPIGENETIC REGULATION,DIFFERENTIAL EXPRESSION ANALYSIS,DNA METHYLATION,CELL-LINES},
  language     = {eng},
  pages        = {16},
  title        = {A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq},
  url          = {http://dx.doi.org/10.1038/srep20957},
  volume       = {6},
  year         = {2016},
}

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