Neonatal Thyroxine Activation Modifies Epigenetic Programming Of The Liver [RNA-Seq]. Neonatal Thyroxine Activation Modifies Epigenetic Programming Of The Liver [RNA-Seq]

In the neonatal liver, a peak of type 2 deiodinase (D2) activity accelerates local T3 production and the expression of thyroid hormone (TH)-responsive genes. Here we show that this acute increase in T3 signaling permanently modifies hepatic gene expression. Liver-specific Dio2 inactivation (Alb-D2KO) transiently increased H3K9me3 levels during post-natal days 1-5 (P1-P5) in discrete chromatin areas, and methylation of 1,508 DNA sites (H-sites) that remained in the adult mouse liver. These sites were associated with 1,551 areas of reduced chromatin accessibility (RCA; Atac-seq) within core promoters and 2,426 within intergenic regions, with reduction in the expression of 1,525 genes (RNA-seq). There was strong correlation between H-sites and RCA sites (r=0.85; p<0.0002), suggesting a cause-effect relationship. The analysis of chromosome conformation capture (Hi-C) data revealed a set of 57 repressed genes that have a promoter RCA in close contact with an intergenic RCA ~300 Kbp apart, including Foxa2 that plays an important role during development. Thus, the post-natal surge in hepatic D2 activity and TH-signaling prevents discrete DNA methylation and modifies the transcriptome of the adult mouse. This explains how the systemic T3 hormone acts locally during development to define future chromatin accessibility and expression of critically relevant hepatic genes. Overall design: Examination of gene expression in liver of animals with Liver-specific Dio2 inactivation (Alb-D2KO).

在新生小鼠肝脏中，2型脱碘酶（type 2 deiodinase, D2）活性的峰值会加速局部T3的生成，并促进甲状腺激素（thyroid hormone, TH）应答基因的表达。本研究证实，T3信号通路的这种急性激活会永久改变肝脏的基因表达谱。针对肝脏特异性Dio2敲除小鼠（Alb-D2KO）的研究显示，在出生后1-5天（P1-P5），其肝脏离散染色质区域内的组蛋白H3赖氨酸9三甲基化（H3K9me3）水平出现一过性升高，同时有1508个DNA位点（H-sites）发生甲基化，且这些位点在成年小鼠肝脏中仍持续存在。上述H位点与1551个染色质可及性降低区域（reduced chromatin accessibility, RCA；ATAC-seq）存在关联，其中1551个区域位于核心启动子区域内，2426个区域位于基因间区；此外，RNA测序（RNA-seq）结果显示，共有1525个基因的表达水平出现下调。H位点与RCA区域之间存在极强的相关性（r=0.85；p<0.0002），提示二者存在因果关系。染色体构象捕获（Hi-C）数据分析显示，有57个受抑制的基因，其启动子区域的RCA区域与相距约300千碱基对（kbp）的基因间区RCA区域存在紧密相互作用，其中包含在发育过程中发挥重要调控功能的Foxa2。由此可见，出生后肝脏D2活性与TH信号通路的骤升，可避免离散区域发生DNA甲基化，并重塑成年小鼠肝脏的转录组。这一发现解释了全身性T3激素如何在发育过程中通过局部作用，决定成年后染色质的可及性以及关键肝脏基因的表达模式。整体实验设计：检测肝脏特异性Dio2敲除小鼠（Alb-D2KO）肝脏组织中的基因表达情况。