Introduction
Epigenetic mechanisms can alter gene expression without variation in underlying DNA sequence (Bossdorf et al. 2008). Of the three molecular epigenetic mechanisms: DNA methylation, histone modification, and chromatin structure, only DNA methylation has received much attention in non-model organisms, especially vertebrates (Schrey et al. 2014; Sheldon et al. 2018).
Histones are highly conserved proteins that package DNA into the nucleosome (reviewed by Bartova et al. 2008). The ammino acid residues comprising histone tails can be covalently modified by up to 15 different subunits (i.e., methylation, acetylation, phosphorylation, ubiquitylation). Modifications to histone residues alter the reactivity of that histone-DNA complex and hence the conformation of DNA within the nucleus. Histone acetylation is generally an activating modification, promoting transcription by making the DNA more euchromatin like. By decreasing a histone’s affinity for DNA, transcription factor binding sites become more accessible, thus bolstering transcription (Bartova et al. 2008).
There are a limited number of histone acetylation studies on non-model organisms, and those that exist indicate that histone acetylation can have a major impact on gene expression, phenotypic plasticity, and plasticity of life history traits (Choppin et al. 2021, Reynolds et al. 2016). For instance, altered histone acetylation facilitated the shift in physiology of worker ants (Temnothorax rugatulus ) following the loss of a queen, increasing their fecundity, expression of immune genes, and longevity of the hive (Choppin et al. 2021). Changes in histone acetylation were also associated with pupal diapause (i.e., a period of dormancy that is induced by harsh environmental conditions) in the flesh fly (Sarcophaga bullata ; Reynolds et al. 2016).
Introduced species provide an excellent system to investigate the role of histone acetylation in variation in gene expression. Introduced individuals must rapidly adjust to new environments, a particularly fraught challenge because introduced populations tend to have low genetic variation and differentiation compared to native populations (Schrey et al. 2011; Liebl et al. 2015; Hanson et al. 2022). Ample evidence exists to support that DNA methylation, is important in this process (Liebl et al. 2013; Mounger et al. 2021). Indeed, the house sparrow (Passer domesticus ) has been successfully introduced throughout the world (Liebl et al. 2015), and DNA methylation is important at the individual level to variation in gene expression (Kilvitis et al. 2019) and at the population level in terms of success in colonizing new areas (Liebl et al. 2013; Sheldon et al. 2018; Swaegers et al. 2023). Partly, these population-level effects arise because individuals possess genomes with different dispositions to be epigenetically modified, a trait termed epigenetic potential (Kilvitis et al. 2017; Sheldon et al. 2023). One form of epigenetic potential has been estimated as the number of CpG sites in promoters. In past work, we have found that epigenetic potential varies among individuals (Hanson et al. 2020), is related to gene expression levels (Hanson et al. 2021), and is greater in house sparrows collected in more recently introduced areas than native ones (Hanson et al. 2022). We propose that histone modification is also important to introduced house sparrows, given that it has an impact on gene expression and phenotypic plasticity (Choppin et al. 2021, Reynolds et al. 2016).
Here, we screened histone modification in wild-collected house sparrows. Our goal was to facilitate investigations of histone acetylation and encourage the use of additional epigenetic markers beyond DNA methylation in ecological epigenetics. To do that we determined whether 1) histone acetylation can be measured in wild collected house sparrows using a commercially available assay developed for mammals, and 2) histone acetylation in house sparrows varies in an ecologically-intelligible manner. We measured histone acetylation in house sparrows that had been previously collected for a study on the response of individuals to Salmonella infection (Sheldon et al.in press ). These experimental samples provide us with the ecologically-relevant framework, in a controlled setting, to investigate relationships among epigenetic potential, acetylation and gene expression.