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

Autor: Kees van Oers, Irene Verhagen, Arild Husby, Heidi M. Viitaniemi, Veronika N. Laine, Melanie Lindner, Marcel E. Visser
Přispěvatelé: Hut lab, Neurobiology, Animal Ecology (AnE), Organismal and Evolutionary Biology Research Programme, Finnish Museum of Natural History
Jazyk: angličtina
Rok vydání: 2021
Předmět:
0106 biological sciences
01 natural sciences
accessible and inaccessible tissues
Songbirds
Behavioral Ecology
Gene expression
Tissue-specific and tissue-general temporal changes
Passeriformes
skin and connective tissue diseases
0303 health sciences
DNA methylation
Reproduction
RNA expression
Methylation
PE&RC
Cell biology
Gedragsecologie
CpG site
great tit
Reduced representation bisulfite sequencing
international
1181 Ecology
evolutionary biology
Accessible and inaccessible tissues
Female
DNA microarray
Plan_S-Compliant_OA
Biotechnology
Research Article
Great tit
lcsh:QH426-470
Period (gene)
lcsh:Biotechnology
Biology
Animal Breeding and Genomics
010603 evolutionary biology
03 medical and health sciences
lcsh:TP248.13-248.65
tissue-specific and tissue-general temporal changes
Genetics
Animals
Fokkerij en Genomica
Genetik
Gene
030304 developmental biology
lcsh:Genetics
WIAS
RNA
CpG Islands
sense organs
Zdroj: BMC Genomics
BMC Genomics, 22(1). BioMed Central Ltd.
BMC Genomics, 22
BMC Genomics, 22(1):36. BioMed Central
BMC Genomics 22 (2021)
BMC Genomics, Vol 22, Iss 1, Pp 1-16 (2021)
ISSN: 1471-2164
DOI: 10.1186/s12864-020-07329-9
Popis: 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.
Databáze: OpenAIRE
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