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. Examination of gene expression in liver of animals with Liver-specific Dio2 inactivation (Alb-D2KO).在新生小鼠肝脏中，Ⅱ型脱碘酶（type 2 deiodinase，D2）活性峰值可加速局部三碘甲状腺原氨酸（T3）的生成，并上调甲状腺激素（thyroid hormone，TH）应答基因的表达。本研究证实，T3信号通路的这一急性升高会永久性改变肝脏基因表达谱。肝脏特异性Dio2敲除（Alb-D2KO）模型中，出生后第1至5天（P1-P5）的离散染色质区域内H3K9me3水平出现一过性升高，同时成年小鼠肝脏中存在1508个被甲基化的DNA位点（H位点）。这些位点与1551个核心启动子区域染色质开放度降低（RCA；ATAC-seq）区域、以及2426个基因间区染色质开放度降低区域相关，同时伴随1525个基因的表达下调（RNA测序，RNA-seq）。H位点与RCA位点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联。对染色体构象捕获（Hi-C）数据的分析显示，57个受抑制基因的启动子区域存在染色质开放度降低，且与相距约300千碱基对（kbp）的基因间区染色质开放度降低区域存在紧密相互作用，其中包括在发育过程中发挥重要作用的叉头框蛋白A2（Foxa2）。综上，肝脏D2活性与TH信号通路的出生后骤增，可避免离散DNA位点发生甲基化，并重塑成年小鼠肝脏的转录组。这阐明了全身性T3激素如何在发育阶段通过局部作用，决定成年后染色质开放度与关键肝脏基因的表达模式。本研究同时对肝脏特异性Dio2敲除（Alb-D2KO）动物的肝脏基因表达进行了检测分析。