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

 Sandra Steyaert1*, 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

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