Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons

Melanie Lindner,Veronika N Laine,Arild Husby,Kees Van Oers,Irene Verhagen,Marcel E Visser,Heidi M Viitaniemi

doi:10.1186/s12864-020-07329-9

Abstract

BackgroundDNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of DNA methylation we need simultaneous within-individual assessment of methylation changes and gene expression changes over time. Within-individual repeated sampling of tissues, which are essential for trait expression is, however, unfeasible (e.g. specific brain regions, liver and ovary for reproductive timing). Here, we explore to what extend between-individual changes in DNA methylation in a tissue accessible for repeated sampling (red blood cells (RBCs)) reflect such patterns in a tissue unavailable for repeated sampling (liver) and how these DNA methylation patterns are associated with gene expression in such inaccessible tissues (hypothalamus, ovary and liver). For this, 18 great tit (Parus major) females were sacrificed at three time points (n = 6 per time point) throughout the pre-laying and egg-laying period and their blood, hypothalamus, ovary and liver were sampled.ResultsWe simultaneously assessed DNA methylation changes (via reduced representation bisulfite sequencing) and changes in gene expression (via RNA-seq and qPCR) over time. In general, we found a positive correlation between changes in CpG site methylation in RBCs and liver across timepoints. For CpG sites in close proximity to the transcription start site, an increase in RBC methylation over time was associated with a decrease in the expression of the associated gene in the ovary. In contrast, no such association with gene expression was found for CpG site methylation within the gene body or the 10 kb up- and downstream regions adjacent to the gene body.ConclusionTemporal changes in DNA methylation are largely tissue-general, indicating that changes in RBC methylation can reflect changes in DNA methylation in other, often less accessible, tissues such as the liver in our case. However, associations between temporal changes in DNA methylation with changes in gene expression are mostly tissue- and genomic location-dependent. The observation that temporal changes in DNA methylation within RBCs can relate to changes in gene expression in less accessible tissues is important for a better understanding of how environmental conditions shape traits that temporally change in expression in wild populations.

Highlights

DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions
Cytosine-phosphodiester bond-guanine (CpG) site methylation in Red blood cell (RBC) changes throughout the breeding season within individuals [6] and here we find that DNA methylation changes throughout this period in RBCs and liver based on between-individual samples in a similar way
This shows that general patterns of DNA methylation in any tissue cannot be taken as predictive values for gene expression changes in other tissues and the effects of methylation changes are likely very targeted

Summary

Introduction

DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. Many traits are phenotypically plastic and change with alterations in the environment This includes circannual traits such as seasonal reproduction in birds: every spring a seasonally breeding female responds to increasing photoperiod and temperature to gradually switch from an inactive state to an active reproductive state such that the specific timing of this response depends on the environmental conditions of the respective year (i.e. the trait is phenotypically plastic) [1]. It remains poorly understood how the translation of environmental conditions to a within-individual temporal response in trait value is mediated on the molecular level, i.e. how phenotypic plasticity works. The latter study demonstrated that short day length induced a temporal decrease in DNA methylation levels within the promoter region of type III deiodinase (DIO3), a gene involved in the photoperiodic regulation of reproduction, and established a causal link between reduced DIO3 promoter methylation and gonadal regression via increased transcription of DIO3 [5]

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