Genetics & Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, USA.
Department of Animal Science, Iowa State University, Ames, IA, USA.
BMC Genomics. 2022 Aug 11;23(1):575. doi: 10.1186/s12864-022-08773-5.
Genetics studies in the porcine immune system have enhanced selection practices for disease resistance phenotypes and increased the efficacy of porcine models in biomedical research; however limited functional annotation of the porcine immunome has hindered progress on both fronts. Among epigenetic mechanisms that regulate gene expression, DNA methylation is the most ubiquitous modification made to the DNA molecule and influences transcription factor binding as well as gene and phenotype expression. Human and mouse DNA methylation studies have improved mapping of regulatory elements in these species, but comparable studies in the pig have been limited in scope.
We performed whole-genome bisulfite sequencing to assess DNA methylation patterns in nine pig immune cell populations: CD21 and CD21 B cells, four T cell fractions (CD4, CD8, CD8CD4, and SWC6γδ), natural killer and myeloid cells, and neutrophils. We identified 54,391 cell differentially methylated regions (cDMRs), and clustering by cDMR methylation rate grouped samples by cell lineage. 32,737 cDMRs were classified as cell lowly methylated regions (cLMRs) in at least one cell type, and cLMRs were broadly enriched in genes and regions of intermediate CpG density. We observed strong correlations between differential methylation and expression across immune cell populations, with cell-specific low methylation disproportionately impacting genes exhibiting enriched gene expression in the same cell type. Motif analysis of cLMRs revealed cell type-specific enrichment of transcription factor binding motifs, indicating that cell-specific methylation patterns may influence accessibility by trans-acting factors. Lastly, cDMRs were enriched for immune capacity GWAS SNPs, and many such overlaps occurred within genes known to influence immune cell development and function (CD8B, NDRG1).
Our DNA methylation data improve functional annotation of the porcine genome through characterization of epigenomic regulatory patterns that contribute to immune cell identity and function, and increase the potential for identifying mechanistic links between genotype and phenotype.
猪免疫系统的遗传学研究增强了对疾病抗性表型的选择实践，并提高了猪模型在生物医学研究中的功效；然而，猪免疫基因组的有限功能注释阻碍了这两个方面的进展。在调节基因表达的表观遗传机制中，DNA 甲基化是对 DNA 分子进行的最普遍的修饰，它影响转录因子的结合以及基因和表型的表达。人类和小鼠的 DNA 甲基化研究已经改进了这些物种中调控元件的映射，但在猪中的类似研究在范围上受到限制。
我们进行了全基因组亚硫酸氢盐测序，以评估 9 种猪免疫细胞群体中的 DNA 甲基化模式：CD21 和 CD21 B 细胞、4 个 T 细胞亚群（CD4、CD8、CD8CD4 和 SWC6γδ）、自然杀伤细胞和髓细胞以及中性粒细胞。我们鉴定了 54391 个细胞差异甲基化区域（cDMR），并且基于 cDMR 甲基化率的聚类将样品按细胞谱系分组。32737 个 cDMR 被分类为至少一种细胞类型中细胞低甲基化区域（cLMR），并且 cLMR 在中间 CpG 密度的基因和区域中广泛富集。我们观察到免疫细胞群体中差异甲基化与表达之间存在很强的相关性，细胞特异性低甲基化不成比例地影响在同一细胞类型中表现出富集基因表达的基因。cLMR 的基序分析显示转录因子结合基序的细胞类型特异性富集，表明细胞特异性甲基化模式可能影响转录因子的可及性。最后，cDMR 富集了免疫能力 GWAS SNPs，并且许多此类重叠发生在已知影响免疫细胞发育和功能的基因（CD8B、NDRG1）内。
我们的 DNA 甲基化数据通过表征有助于免疫细胞身份和功能的表观基因组调控模式，改善了猪基因组的功能注释，并增加了在基因型和表型之间识别机制联系的潜力。
