Complementary and additive functions of TRα and TRβ during intestinal remodeling as revealed by ChIP-Seq analysis on wild type and TR knockout animals.

Intestinal structure is drastically changed from fetal to adult form during postembryonic development, a period around birth in mammals. This process is regulated by thyroid hormone (T3) via its receptors, T3 receptor (TR) α and TRβ during anuran metamorphosis. Here, we used intestinal remodeling during Xenopus tropicalis metamorphosis, which serves as a model for human postembryonic development, to identify TR-bound genes and determine the relative contribution to target gene binding by TRα and TRβ. We first examined the localization of TRα and TRβ mRNA during metamorphosis in Xenopus tropicalis and found that TRα was broadly expressed in the intestinal tissues from premetamorphosis to the end of metamorphosis, while TRβ was expressed at low levels during premetamorphosis but was upregulated at the climax of metamorphosis when intestinal stem cells are formed and proliferate. Interestingly, both TR genes were co-expressed in different cell types, including stem cells. Chromatin immunoprecipitation (ChIP)-seq analyses of the intestine from wild type, TRα- or TRβ-knockout premetamorphic tadpoles treated with or without T3 for 18 h identified many TR-bound genes and revealed the effects of individual TR knockout on the binding of target genes by TR. We found that individual TR knockout reduced both the number of TR-bound genes and the extent of TR binding to target genes with TRα knockout had a much more dramatic effect than TRβ knockout. On the other hand, the TR-bound genes were largely common among the three genotypes. These findings suggest that both TRα and TRβ contribute to target binding with TRα having a bigger contribution in premetamorphic intestine.