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1 . expression that plays a role in many cellular processes affecting a variety of traits. In this study DNA methylation was assessed in neuronal tissue from three pigs (frontal lobe) and one great tit (whole brain) using reduced representation and whole genome bisulfite sequencing, respectively. In addition, gene transcription patterns were profiled using RNA-seq. In total over 1.5 and 10.2 million CpG, and 5.5 and million non-cpg sites were covered in the porcine and great tit samples, respectively. The observed genomewide DNA methylation patterns in both species were consistent with previous mammalian findings, including low but significant non-cpg methylation that occurred predominantly at CpA dinucleotides. Both CpG and non-cpg methylation were negatively correlated with gene expression in porcine (Spearman s rho < , P < 1x10-15) and great tit brain (Spearman s rho < -0.22, P < ). In addition, increased CpG and decreased non-cpg methylation was found within transposable elements (TEs) compared to surrounding regions in the great tit brain. TE activity was negatively correlated with non-cpg methylation both within TEs (Spearman s rho -0.12, P < 1x10-15) and the surrounding 2 kb regions (Spearman s rho < -0.19, P < 1x10-15). These findings provide the first evidence for conservation of non-cpg methylation in mammalian and avian neuronal tissue, and suggest a functional role for non-cpg methylation in avian neuronal tissue. These results raise interesting questions regarding the universal role of non-cpg methylation in neuronal epigenetic regulation and its potential role in learning and memory.
2 Introduction. expression that plays a role in many cellular processes affecting a variety of traits. DNA methylation mainly occurs at CpG sites in animals. Non-CpG methylation is observed in embryonic stem cells, oocytes, and neurons of humans and mice. Both CpG and non-cpg methylation are negatively correlated with gene expression at transcription start sites (TSS) and gene bodies in human and mouse DNA methylation also suppresses transposable element (TE) activity, and TEs are highly active in neuronal tissue. Little is known about the regulatory role of non-cpg methylation in porcine and avian (Day et al., 2010; Guo et al., 2014)
3 . Frontal lobe DNA methylation patterns were assessed in three pigs using reduced representation bisulfite sequencing (RRBS) Alignment and methylation calling using BSseeker2 Whole brain DNA methylation patterns were assessed in one great tit using whole genome bisulfite sequencing (WGBS) Alignment and methylation calling using BSseeker2 Gene and TE transcription patterns were profiled using RNA-seq Alignments performed using Tophat2 Expression quantification performed using Cufflinks
4 . Distribution of methylated (>10%) cytosines in (a) great tit brain and (c) pig frontal lobe. Differences between (a) great tit and (c) pig neuronal patterns are due to differences between (a) WGBS and (b) RRBS techniques. Occurrence of nucleotides are given relative to the distance from the methylated (>10%) C nucleotide for (a) mouse, (b) pig, and (c) great tit brain.
5 . (a) Great tit brain and (b) pig frontal lobe CpG methylation is negatively correlated with gene expression at TSS (Spearman s Rho = and -0.16, respectively, P < 1x10-15) and gene bodies (Spearman s Rho = and -0.08, respectively, P < 1x10-15). (c) Great tit brain and (d) pig frontal lobe non-cpg methylation is negatively at TSS (Spearman s Rho = and -0.05, respectively, P < 1x10-14) and gene bodies (Spearman s Rho = and -0.11, respectively, P < 1x10-15).
6 . associated with TE activity in great tit brain (a) TE CpG methylation is not correlated with TE activity in great tit brain (Spearman s Rho TE body = 0.033, upstream = , downstream = ). (b) TE non-cpg methylation is negatively correlated with TE activity in great tit brain (Spearman s Rho TE body = -0.11, upstream = -0.20, downstream = -0.19, P < 1x10-15). Both CpG and non-cpg methylation are negatively correlated with gene expression in great tit and pig Non-CpG methyation is negatively correlated with TE activity in great tit conservation of non-cpg methylation between
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