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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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Record number 505299
Title Gene and transposable element methylation in great tit (Parus major) brain and blood
Author(s) Derks, M.F.L.; Schachtschneider, K.M.; Madsen, O.; Schijlen, E.G.W.M.; Verhoeven, Koen J.F.; Oers, K. van
Source BMC Genomics 17 (2016). - ISSN 1471-2164
Department(s) Animal Breeding and Genetics
PRI BIOS Applied Bioinformatics
Behavioural Ecology
Publication type Refereed Article in a scientific journal
Publication year 2016
Abstract Background: Studies on vertebrate DNA methylomes have revealed a regulatory role of tissue specific DNA
methylation in relation to gene expression. However, it is not well known how tissue-specific methylation varies
between different functional and structural components of genes and genomes. Using whole-genome bisulfite
sequencing data we here describe both CpG and non-CpG methylation profiles of whole blood and brain tissue in
relation to gene features, CpG-islands (CGIs), transposable elements (TE), and their functional roles in an ecological
model species, the great tit (Parus major).
Results: We show that hypomethylation at the transcription start site (TSS) is enriched in genes with functional
classes that relate directly to processes specific to each tissue type. We find that 6877 (~21 %) of the CGIs are
differentially methylated between blood and brain, of which 1186 and 2055 are annotated to promoter and
intragenic regions, respectively. We observe that CGI methylation in promoter regions is more conserved between
tissues compared to CGI methylation in intra and inter-genic regions. Differentially methylated CGIs in promoter
and intragenic regions are overrepresented in genomic loci linked to development, suggesting a distinct role for
CGI methylation in regulating expression during development. Additionally, we find significant non-CpG
methylation in brain but not in blood with a strong preference for methylation at CpA dinucleotide sites. Finally,
CpG hypermethylation of TEs is significantly stronger in brain compared to blood, but does not correlate with TE
activity. Surprisingly, TEs showed significant hypomethylation in non-CpG contexts which was negatively correlated
with TE expression.
Conclusion: The discovery that TSS methylation levels are directly linked to functional classes related to each tissue
provides new insights in the regulatory role of DNA-methylation patterns. The dominant sequence motifs for brain
non-CpG methylation, similar to those found in mammals, suggests that a conserved non-CpG regulatory
mechanism was already present in the amniote ancestor. The negative correlation between brain non-CpG
methylation and TE activity (not found for CpG methylation) suggests that non-CpG is the dominant regulatory
form of methylation in TE silencing.
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