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

Abstract

Background DNA 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. Results We 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. Conclusion Temporal 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.

Epigenetics and Early Life Stress: Experimental Brood Size Affects DNA Methylation in Great Tits (Parus major)

“…Most of the genes were functional in tissues other than blood and this may affect how gene expression is related to a trait, due to tissue differentiation. However, multiple studies have shown that gene expression levels in the blood were related to the processes associated with that gene (Roulin et al, 2011;Zhu et al, 2017;Lindner et al, 2021b), suggesting that gene expression levels in blood in our study could explain plasticity in phenotypic traits related to brood size variation. Although these results demonstrate that early life stress affects epigenetic regulation of genes related to brood size, namely genes that are known to affect development, growth, metabolism, behavior and cognition, future work is needed.…”

“…Promoter regions were defined as 2000 bp upstream to 200 bp downstream of the annotated gene start site (Lindner et al, 2021a). Upstream and downstream regions were defined as 10 K bp up-and downstream regions adjacent to the gene body, respectively (Laine et al, 2016;Lindner et al, 2021b). Since DNA methylation is reciprocal on both strands, annotation was not directional (i.e., each DMS could overlap with the Watson and Crick strands).…”

Does Arsenic Contamination Affect DNA Methylation Patterns in a Wild Bird Population? An Experimental Approach

“… 59 Nevertheless, tissue-specific methylation differences were larger for genes that are expressed in a tissue-specific way 48 and measuring methylation levels from red blood cells might therefore miss tissue-dependent genes whose expression is expected to change. 59 …”

Does arsenic contamination affect DNA methylation patterns in a wild bird population? An experimental approach

“…Studies have shown that absolute methylation values between e.g. blood and liver or kidney and brain are highly correlated (48,58), just like changes in methylation in red blood cells and liver are correlated (59). Nevertheless tissuespecific methylation differences were larger for genes that are expressed in a tissue-specific way (48) and measuring methylation levels from red blood cells might therefore miss tissuedependent genes whose expression is expected to change (59).…”

“…Absolute methylation values between e.g. blood and liver or kidney and brain are highly correlated (48,58,59), just like changes in methylation in red blood cells and liver are correlated (59) and thus blood can be used as a proxy. Ten samples from the arsenic and ten from control treatment were selected for the DNA methylation analyses.…”