Sandra Steyaert^1*, Jolien Diddens², Jeroen Galle¹, Ellen De Meester¹, Sarah De Keulenaer¹, Antje Bakker³, Nina Sohnius-Wilhelmi³, Carolina Frankl-Vilches³, Annemie Van der Linden⁴, Wim Van Criekinge¹, Wim Vanden Berghe² and Tim De Meyer¹

ABSTRACT

 Currently under peer review by Scientific Reports

 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.

Presented data

The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus ¹ and are accessible through GEO Series accession numbers GSE61060 and GSE71344 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61060 , http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71344).

Next to these files, RRBS data has also been made available in BAM-format which can be downloaded from the link below.

ZFTMA_UT_RRBS_bt2_unique.bam