Abstract
Thyroid hormone (T3) affects development and metabolism in vertebrates. We have been studying intestinal remodeling during T3-dependent Xenopus metamorphosis as a model for organ maturation and formation of adult organ-specific stem cells during vertebrate postembryonic development, a period characterized by high levels of plasma T3. T3 is believed to affect development by regulating target gene transcription through T3 receptors (TRs). While many T3 response genes have been identified in different animal species, few have been shown to be direct target genes in vivo, especially during development. Here we generated a set of genomic microarray chips covering about 8000 bp flanking the predicted transcription start sites in Xenopus tropicalis for genome wide identification of TR binding sites. By using the intestine of premetamorphic tadpoles treated with or without T3 and for chromatin immunoprecipitation assays with these chips, we determined the genome-wide binding of TR in the control and T3-treated tadpole intestine. We further validated TR binding in vivo and analyzed the regulation of selected genes. We thus identified 278 candidate direct TR target genes. We further provided evidence that these genes are regulated by T3 and likely involved in the T3-induced formation of adult intestinal stem cells during metamorphosis.
Highlights
Thyroid hormone (T3) regulates the formation and/or maturation of many organs into the adult form during vertebrate development and affects the homeostasis and physiological function of many adult organs/tissues, such as the heart and muscles[1,2,3,4,5,6,7,8]
To identify genes that are bound by T3 receptors (TRs) in the intestine, we treated premetamorphic, stage 54, Xenopus tropicalis tadpoles with 10 nM T3 for 2 days
The intestine was isolated from the control and T3 treated tadpoles and subjected to anti-TR antibody chromatin immunoprecipitation (ChIP)-on-chip assay by using genomic microarray chip set
Summary
Thyroid hormone (T3) regulates the formation and/or maturation of many organs into the adult form during vertebrate development and affects the homeostasis and physiological function of many adult organs/tissues, such as the heart and muscles[1,2,3,4,5,6,7,8]. Recent progress in genomic editing has made it possible to analyze the function of endogenous genes in Xenopus[16,17,18,19,20] These and other properties have made anuran metamorphosis an excellent model to study the molecular basis of T3 action during vertebrate development. Subtractive hybridization screening and subsequent gene expression microarray analyses have discovered many such genes in different organs/tissues during both natural and T3-induced metamorphosis[4, 21, 38,39,40,41,42,43,44,45] These studies have revealed complex but informative global gene regulation patterns underlying organ transformations during metamorphosis. Bioinformatics analyses suggest that these genes are regulated during T3-dependent intestinal remodeling, implicating a role in the formation of adult intestinal stem cells during Xenopus metamorphosis, a period equivalent to the postembryonic development in mammals[3, 4]
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