全基因组范围内牛 H3K27me3 修饰及其对外周血淋巴细胞基因表达的调控作用。
Genome-wide bovine H3K27me3 modifications and the regulatory effects on genes expressions in peripheral blood lymphocytes.
机构信息
Key Laboratory of Agricultural Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, PR China.
出版信息
PLoS One. 2012;7(6):e39094. doi: 10.1371/journal.pone.0039094. Epub 2012 Jun 28.
BACKGROUND
Gene expression of lymphocytes was found to be influenced by histone methylation in mammals and trimethylation of lysine 27 on histone H3 (H3K27me3) normally represses genes expressions. Peripheral blood lymphocytes are the main source of somatic cells in the milk of dairy cows that vary frequently in response to the infection or injury of mammary gland and number of parities.
METHODS
The genome-wide status of H3K27me3 modifications on blood lymphocytes in lactating Holsteins was performed via ChIP-Seq approach. Combined with digital gene expression (DGE) technique, the regulation effects of H3K27me3 on genes expressions were analyzed.
RESULTS
The ChIP-seq results showed that the peaks of H3K27me3 in cows lymphocytes were mainly enriched in the regions of up20K (50%), down20K (30%) and intron (~28%) of the genes. Only ~3% peaks were enriched in exon regions. Moreover, the highest H3K27me3 modification levels were mainly around the 2 Kb upstream of transcriptional start sites (TSS) of the genes. Using conjoint analysis with DGE data, we found that H3K27me3 marks tended to repress target genes expressions throughout whole gene regions especially acting on the promoter region. A total of 53 differential expressed genes were detected in third parity cows compared to first parity, and the 25 down-regulated genes (PSEN2 etc.) were negatively correlated with H3K27me3 levels on up2Kb to up1Kb of the genes, while the up-regulated genes were not showed in this relationship.
CONCLUSIONS
The first blueprint of bovine H3K27me3 marks that mediates gene silencing was generated. H3K27me3 plays its repressed role mainly in the regulatory region in bovine lymphocytes. The up2Kb to up1Kb region of the down-regulated genes in third parity cows could be potential target of H3K27me3 regulation. Further studies are warranted to understand the regulation mechanisms of H3K27me3 on somatic cell count increases and milk losses in latter parities of cows.
背景
在哺乳动物中，淋巴细胞的基因表达受组蛋白甲基化的影响，组蛋白 H3 赖氨酸 27 三甲基化（H3K27me3）通常抑制基因表达。奶牛的外周血淋巴细胞是乳腺感染或损伤以及胎次变化时乳汁中体细胞的主要来源。
方法
采用 ChIP-Seq 方法检测泌乳荷斯坦奶牛血液淋巴细胞中 H3K27me3 修饰的全基因组状态。结合数字基因表达（DGE）技术，分析 H3K27me3 对基因表达的调控作用。
结果
ChIP-seq 结果表明，奶牛淋巴细胞中 H3K27me3 的峰主要富集在基因的 up20K（50%）、down20K（30%）和内含子（~28%）区域。只有约 3%的峰富集在外显子区域。此外，H3K27me3 修饰水平最高的区域主要位于基因转录起始位点（TSS）上游的 2Kb 左右。通过与 DGE 数据的联合分析，我们发现 H3K27me3 标记倾向于在整个基因区域抑制靶基因的表达，特别是在启动子区域。与第一胎相比，第三胎奶牛共检测到 53 个差异表达基因，其中 25 个下调基因（如 PSEN2 等）与基因 up2Kb 到 up1Kb 区域的 H3K27me3 水平呈负相关，而上调基因则没有表现出这种关系。
结论
生成了介导基因沉默的牛 H3K27me3 标记的第一张图谱。在牛淋巴细胞中，H3K27me3 主要在调控区域发挥其抑制作用。第三胎奶牛下调基因的 up2Kb 到 up1Kb 区域可能是 H3K27me3 调控的潜在靶点。需要进一步研究以了解 H3K27me3 对奶牛后期胎次体细胞数增加和产奶量减少的调控机制。
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