DNA methylation is an epigenetic mark that occurs at cytosines throughout the genome, is involved in regulating gene expression, and can be altered in response to environmental signals. This study investigated DNA methylation and gene expression patterns in hippocampus samples from two studies observing reduced hippocampal-based spatial learning and memory in response to early life environmental insults (iron deficiency and PRRSv infection) in porcine biomedical models of cognitive development (Rytych et al. 2012; Elmore et al. 2014). Reduced representation bisulfite sequencing and RNA-seq was performed on 16 hippocampus samples (iron deficiency - 3 deficient, 4 control; PRRSv infection - 4 infected, 5 control). In total 192 and 455 differentially expressed genes (DEGs) were detected in the iron deficient and PRRSv infected groups, respectively. Of these, 53 were differentially expressed in both studies, including genes involved in neurodevelopment and function, such as CARTPT, NTNG1, PRSS12, GABRE, and HTR2C. Differential DNA methylation was assessed at over 600,000 CpG and 2.4 million non-CpG sites in both studies, identifying 853 differentially methylated (DM) CpG and 99 DM non-CpG sites in the iron deficient group, including 12 sites associated with 9 DEGs. 1,857 DM CpG and 153 DM non-CpG sites were identified in the PRRSv infected group, including 26 sites associated with 19 DEGs. Increased expression of VWF (log2 fold change > 1.8) and HTR2C (log2 fold change > 1.0) was associated with hypomethylation of the same genomic regions in the iron deficient and PRRSv infected groups. In addition, as HTR2C undergoes adenosine-to-inosine (A-to-I) RNA editing at 5 sites affecting human HTR2C receptor activity and brain function, HTR2C editing frequencies were determined. Increased editing was detected at the first site (site A) in both groups, although the difference was only significant for the iron deficient group (P = 0.019). In addition, one RNA isoform (IAAAI) and one protein isoform (V-S-I) were expressed exclusively in both the iron deficient and PRRSv infected groups. Together, these results provide evidence for altered hippocampal DNA methylation, gene expression, and HTR2C RNA editing in response to early life environmental insults in two independent studies of cognitive development.
Rytych et al. 2012. Early life iron deficiency impairs spatial cognition in neonatal piglets. J. Nutr. 142(11):2050-2056
Elmore et al. 2014. Respiratory viral infection in neonatal piglets causes marked microglia activation in the hippocampus and deficits in spatial learning. J. Neurosci. 34(6):2120-2129