Ayers Stephen, Switnicki Michal Piotr, Angajala Anusha, Lammel Jan, Arumanayagam Anithachristy S, Webb Paul
The Methodist Hospital Research Institute, Genomic Medicine Program, Houston, Texas, United States of America.
The Methodist Hospital Research Institute, Genomic Medicine Program, Houston, Texas, United States of America ; Tecnologico de Monterrey School of Medicine, Monterrey, NL, Mexico.
PLoS One. 2014 Feb 18;9(2):e81186. doi: 10.1371/journal.pone.0081186. eCollection 2014.
Thyroid hormone (TH) receptors (TRs) play central roles in metabolism and are major targets for pharmaceutical intervention. Presently, however, there is limited information about genome wide localizations of TR binding sites. Thus, complexities of TR genomic distribution and links between TRβ binding events and gene regulation are not fully appreciated. Here, we employ a BioChIP approach to capture TR genome-wide binding events in a liver cell line (HepG2). Like other NRs, TRβ appears widely distributed throughout the genome. Nevertheless, there is striking enrichment of TRβ binding sites immediately 5' and 3' of transcribed genes and TRβ can be detected near 50% of T3 induced genes. In contrast, no significant enrichment of TRβ is seen at negatively regulated genes or genes that respond to unliganded TRs in this system. Canonical TRE half-sites are present in more than 90% of TRβ peaks and classical TREs are also greatly enriched, but individual TRE organization appears highly variable with diverse half-site orientation and spacing. There is also significant enrichment of binding sites for TR associated transcription factors, including AP-1 and CTCF, near TR peaks. We conclude that T3-dependent gene induction commonly involves proximal TRβ binding events but that far-distant binding events are needed for T3 induction of some genes and that distinct, indirect, mechanisms are often at play in negative regulation and unliganded TR actions. Better understanding of genomic context of TR binding sites will help us determine why TR regulates genes in different ways and determine possibilities for selective modulation of TR action.
甲状腺激素（TH）受体（TRs）在新陈代谢中发挥核心作用，是药物干预的主要靶点。然而，目前关于TR结合位点的全基因组定位信息有限。因此，TR基因组分布的复杂性以及TRβ结合事件与基因调控之间的联系尚未得到充分认识。在这里，我们采用生物芯片免疫沉淀法（BioChIP）来捕获肝细胞系（HepG2）中TR的全基因组结合事件。与其他核受体一样，TRβ似乎广泛分布于整个基因组。尽管如此，在转录基因的5'端和3'端紧邻区域，TRβ结合位点显著富集，并且在近50%的T3诱导基因附近可检测到TRβ。相比之下，在该系统中，负调控基因或对未结合配体的TRs有反应的基因处，未观察到TRβ的显著富集。超过90%的TRβ峰中存在典型的甲状腺激素反应元件（TRE）半位点，经典的TREs也大量富集，但单个TRE的组织形式似乎高度可变，半位点的方向和间距各不相同。在TR峰附近，与TR相关的转录因子（包括AP-1和CTCF）的结合位点也显著富集。我们得出结论，T3依赖的基因诱导通常涉及近端TRβ结合事件，但某些基因的T3诱导需要远距离结合事件，并且在负调控和未结合配体的TR作用中，往往存在不同的间接机制。更好地理解TR结合位点的基因组背景将有助于我们确定TR以不同方式调控基因的原因，并确定选择性调节TR作用的可能性。
