Broad shifts in gene expression during early postnatal life are associated with shifts in histone methylation patterns

During early postnatal life, extensive changes in gene expression occur concomitantly in multiple major organs, indicating the existence of a common core developmental genetic program. This program includes hundreds of growth-promoting genes that are downregulated with age in liver, kidney, lung, and heart, and there is evidence that this component of the program drives the widespread decline in cell proliferation that occurs in juvenile life, as organs approach adult sizes. To investigate epigenetic changes that might orchestrate this program, we performed chromatin immunoprecipitation-promoter tiling array to assess temporal changes in histone H3K4 and H3K27 trimethylation (me3) at promoter regions throughout the genome in kidney and lung, comparing 1- to 4-wk-old mice. We found extensive genome-wide shifts in H3K4me3 and H3K27me3 occurring with age in both kidney and lung. The number of genes with concordant changes in the two organs was far greater than expected by chance. Temporal changes in H3K4me3 showed a strong, positive association with changes in gene expression, assessed by microarray, whereas changes in H3K27me3 showed a negative association. Gene ontology analysis indicated that shifts in specific histone methylation marks were associated with specific developmental functions. Of particular interest, genes with decreases in H3K4me3 with age in both organs were strongly implicated in cell cycle and cell proliferation functions. Taken together, the findings suggest that the common core developmental program of gene expression which occurs in multiple organs during juvenile life is associated with a common core developmental program of histone methylation. In particular, declining H3K4me3 is strongly associated with gene downregulation and occurs in the promoter regions of many growth-regulating genes, suggesting that this change in histone methylation may contribute to the component of the genetic program that drives juvenile body growth deceleration. Tissues samples were collect from Lung (1 and 4 week old) and Kidney (1 and 4 week old) respectively with four biological replications of mice that were collected, frozen in liquid nitrogen, and stored at -70 °C在出生后早期阶段，多种主要器官的基因表达均发生广泛变化，提示存在一套共有的核心发育遗传程序。该程序包含数百个随年龄增长在肝、肾、肺和心脏中表达下调的促生长基因，且有证据表明，该程序的这一组分会驱动幼年阶段随着器官趋近成年尺寸时出现的细胞增殖广泛下降。 为探究可能调控该程序的表观遗传变化，我们采用染色质免疫沉淀-启动子平铺微阵列（chromatin immunoprecipitation-promoter tiling array）技术，评估了1至4周龄小鼠肾与肺组织全基因组启动子区域内组蛋白H3K4及H3K27三甲基化（me3）的时序变化。 我们发现，在肾与肺组织中，H3K4me3与H3K27me3均随年龄发生广泛的全基因组水平变化。两个器官中变化趋势一致的基因数量远高于随机概率下的预期值。 通过微阵列检测的基因表达变化与H3K4me3的时序变化呈显著正相关，而H3K27me3的变化则呈负相关。 基因本体（Gene Ontology, GO）分析显示，特定组蛋白甲基化修饰的变化与特定发育功能相关。 尤为值得关注的是，在两个器官中随年龄增长H3K4me3水平下降的基因，显著富集于细胞周期与细胞增殖相关功能通路。 综上，本研究结果表明，幼年阶段多种器官中共有的核心基因表达发育程序，与一套共有的核心组蛋白甲基化发育程序相关。 具体而言，H3K4me3水平的下降与基因表达下调显著相关，且该修饰变化发生于众多生长调控基因的启动子区域，提示组蛋白甲基化的这一变化可能参与调控驱动幼年机体生长减速的遗传程序组分。 本研究分别采集了1周龄与4周龄小鼠的肺与肾组织样本，每组均设置4次生物学重复；采集后的样本经液氮速冻后保存于-70℃环境中。