Samples Screened
We screened H3 histone acetylation in paired liver and spleen tissues
from house sparrows (n = 12) previously collected from Tampa, Florida
(Table 1). These samples were used in a separate study of house sparrow
response to Salmonella enterica infection (as described in
Sheldon et al. 2023). We screened only males with similar body masses
(Table 1). For each individual, we compared H3 acetylation to the level
of the Toll Like Receptor-4 (TLR-4 ) gene expression in the cecum
estimated by qRT-PCR from RNA extracts using primers targeting theTLR-4 transcript (Sheldon et al. 2023). Also, we compared H3
acetylation to EP of the putative TLR-4 promoter, estimated by
sequencing 500 bp upstream from the transcription start site, and
categorizing individuals as low EP if they had 7 or fewer CpG sites, or
high EP if they had 8 or more CpG sites (Sheldon et al. 2023). We usedTLR-4 expression and EP because they are ecologically relevant,
variable in the individuals screened, and differ in response to
infection (Sheldon et al. 2023).
We used TLR-4 expression as an indicator of change in gene
expression among individuals in response to infection, in an attempt to
link variation in histone acetylation to individual phenotype. Given
that our H3 acetylation estimates are genome-wide, and not localized to
particular genes, we do not expect there to be a direct causal
relationship between H3 acetylation and TLR-4 expression. Nor do
we expect there to be a direct causal relationship between H3
acetylation and EP, as EP was estimated based on the number of CpG
sites, which are directly relevant to DNA methylation. However, as
histone modification and DNA methylation are epigenetic mechanisms, it
may be reasonable to expect that individuals with higher EP for DNA
methylation might also have higher EP for histone modification. Our
intention in comparing histone acetylation to TLR-4 expression
and EP was to ground the global estimates of H3 acetylation to
ecologically relevant factors at the individual level.