A genome-wide search for epigenetically 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.

Prenatal testosterone triggers long-term behavioral changes in male zebra finches: unravelling the neurogenomic mechanisms

“…The majority of DMRs found within 2 Kb of a gene were located in the gene body, specifically introns, for both mCG and mCH (Supplementary Fig. S1, Additional file 2 ), similar to past methylation work in zebra finches [ 21 ]. For the full list of genes with DMRs see Supplementary Tables S4, S5, Additional file 1 .…”

“…We used a LMM with adult ID as the random effect to determine if mCG or mCH levels differed between treatments within genomic features. We categorized genomic features using Ensembl (version 3.2.4), including 2 Kb upstream of the TSS (i.e., potential promoter) [ 21 ], gene body (exons and introns), and 2 Kb downstream of the transcription termination site (TTS).…”

“…Here, we explore the lasting effects of prenatal T on adult behavioral plasticity and genome-wide patterns of gene expression and methylation in male zebra finches ( Taeniopygia guttata ). Zebra finches are a good study system because they have numerous genes that are potential targets of epigenetic regulation [ 21 ]. Zebra finch embryos also express steroid receptors during early development (prior to endogenous T production) [ 22 ].…”

Avian ecological epigenetics: pitfalls and promises

“…It was hypothesized that certain environmental conditions could induce high DNMT expression in the hippocampus facilitating neural plasticity ). Furthermore, demethylation of nonneuronal tumour cells of Zebra Finches resulted in upregulation of genes that were neurobiologically relevant and under the putative control of DNA methylation (Steyaert et al 2016).…”

DNA Methylation Regulates Transcription Factor-Specific Neurodevelopmental but Not Sexually Dimorphic Gene Expression Dynamics in Zebra Finch Telencephalon

“…In brain cells, dynamic changes in DNA methylation occur in response to neuronal activity at specific loci in the genome ( Tognini et al, 2015 ), and recent studies also revealed the accumulation of non-CpG and hydroxymethylation during early postnatal neuronal development ( Kinde et al, 2015 ; Stroud et al, 2017 ; Price et al, 2019 ). DNA (promoter) methylation also regulates gene expression in zebra finches ( Steyaert et al, 2016 ), yet little is known about its function in song learning.…”