Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
Genome-wide identification of thyroid hormone receptor targets in the remodeling intestine during Xenopus tropicalis metamorphosis.
Fu L
,
Das B
,
Matsuura K
,
Fujimoto K
,
Heimeier RA
.
???displayArticle.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 tadpoleintestine. 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.
Figure 1. ChIP-on-chip assay identified putative TR targets in the tadpoleintestine. (A) Schematic representation of a gene in the genomic chips. About 5500 bp upstream and 2500 bp downstream of the 5′-end of the cDNA sequence in the databank for each putative gene in the Xenopus tropicalis genome database were used to design a 60 bp oligonucleotide probe at an average tiling distance of 205 bp, covering the entire 8000 bp. The probes were custom-printed onto the genomic chips. PSS: putative transcription start site. (B) Venn-diagram showing the genes with TR binding sites as identified from the ChIP-on-chip assay with the intestine samples from control and T3-treated stage 54 premetamorphic tadpoles. Note that vast majority of the genes bound by TR in the control tadpoles were also found in the T3-treated animals.
Figure 2. The ChIP signals across the 8000 bp promoter region for PGPEP1 and TFG1 from the control and T3 treated tadpoleintestine. Both the control and T3-treated groups had two independent samples as shown. The arrow points to the putative start site (PSS).
Figure 3. ChIP confirmation of the TR binding to target sites identified from the ChIP-on-chip assay. The intestine from stage 54 tadpoles treated with or without T3 was isolated and subjected to anti-TR antibody ChIP assay and the region around the putative TR binding sites as identified from the ChIP-on-chip assay was PCR amplified. Note that no TR binding was found in the control gene (exon 5 of the TRβ gene) while all three newly identified target genes had TR binding in the absence of T3 and this binding was enhanced upon T3 treatment, in agreement with the ChIP-on-chip data. * indicates pairs of samples with significant differences (pâ<â0.05).
Figure 4. RT-PCR analysis confirming the regulation of newly identified TR targets as T3 response genes. The RNA was isolated from the intestine of stage 54 tadpoles treated with or without T3 was isolated and subjected to RT-PCR analysis for gene expression. Note that all three genes were found to be induced by T3 treatment. *Indicates pairs of samples with significant differences (pâ<â0.05).
Figure 5. The putative TREs in the candidate TR target genes can mediate transcriptional activation by T3 in frog oocytes. The luciferase reporter construct containing the TREs of Dot1L, MBD3, PPM1B, PGPEP1, JUNB, BEND7, respectively, was co-injected with the control Renilla luciferase construct phRG-TK into the nuclei of Xenopus oocytes with or without prior cytoplasmic injection of Xenopus laevis TRα and RXRα mRNAs or GFP mRNA as negative control. The oocytes were incubated at 18â°C overnight in the presence or absence of 100ânM T3 and then used for dual luciferase assays. The relative activities of the firefly luciferase to Renilla luciferase were plotted. Note that all the reporters responded to T3 in the presence of TR/RXR.
Figure 6. Venn diagram showing overlap of the TR target genes identified by ChIP-on-chip assay with known developmentally regulated genes identified from an early expression microarray study. Of the 278 TR target genes identified by ChIP-on-chip assay, 95 or 34% were also found on the microarray used for the expression study (Note that the actually overlap might be higher as most genes may have different names on the microarray chips used in the expression study and on the genomic chips used here, therefore showing up as non-overlapping). Of the 95 genes present in the gene expression microarray, 38 were found to be regulated during metamorphosis in the intestine in either the epithelium (EP, 13 genes), non-epithelium (Non-EP, 14 genes) or both (11 genes), suggesting that about 40% of the genes identified here are regulated by T3 during intestinal metamorphosis.
Amano,
Isolation of genes involved in intestinal remodeling during anuran metamorphosis.
1998, Pubmed,
Xenbase
Amano,
Isolation of genes involved in intestinal remodeling during anuran metamorphosis.
1998,
Pubmed
,
Xenbase
Anselmo,
Fetal loss associated with excess thyroid hormone exposure.
2004,
Pubmed
Bilesimo,
Specific histone lysine 4 methylation patterns define TR-binding capacity and differentiate direct T3 responses.
2011,
Pubmed
,
Xenbase
Blitz,
Biallelic genome modification in F(0) Xenopus tropicalis embryos using the CRISPR/Cas system.
2013,
Pubmed
,
Xenbase
Brown,
Amphibian metamorphosis.
2007,
Pubmed
,
Xenbase
Buchholz,
A dominant-negative thyroid hormone receptor blocks amphibian metamorphosis by retaining corepressors at target genes.
2003,
Pubmed
,
Xenbase
Buchholz,
Gene-specific changes in promoter occupancy by thyroid hormone receptor during frog metamorphosis. Implications for developmental gene regulation.
2005,
Pubmed
,
Xenbase
Buchholz,
Pairing morphology with gene expression in thyroid hormone-induced intestinal remodeling and identification of a core set of TH-induced genes across tadpole tissues.
2007,
Pubmed
,
Xenbase
Buchholz,
Molecular and developmental analyses of thyroid hormone receptor function in Xenopus laevis, the African clawed frog.
2006,
Pubmed
,
Xenbase
Buchholz,
Transgenic analysis reveals that thyroid hormone receptor is sufficient to mediate the thyroid hormone signal in frog metamorphosis.
2004,
Pubmed
,
Xenbase
Buisine,
Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis.
2015,
Pubmed
,
Xenbase
Cai,
Changing a limb muscle growth program into a resorption program.
2007,
Pubmed
,
Xenbase
Chatonnet,
Genome-wide analysis of thyroid hormone receptors shared and specific functions in neural cells.
2013,
Pubmed
Choi,
Unliganded thyroid hormone receptor α regulates developmental timing via gene repression in Xenopus tropicalis.
2015,
Pubmed
,
Xenbase
Das,
Identification of direct thyroid hormone response genes reveals the earliest gene regulation programs during frog metamorphosis.
2009,
Pubmed
,
Xenbase
Das,
Gene expression changes at metamorphosis induced by thyroid hormone in Xenopus laevis tadpoles.
2006,
Pubmed
,
Xenbase
de Escobar,
Maternal thyroid hormones early in pregnancy and fetal brain development.
2004,
Pubmed
de Escobar,
Iodine deficiency and brain development in the first half of pregnancy.
2007,
Pubmed
Denver,
Thyroid hormone-dependent gene expression program for Xenopus neural development.
1997,
Pubmed
,
Xenbase
Dong,
Identification of thyroid hormone receptor binding sites and target genes using ChIP-on-chip in developing mouse cerebellum.
2009,
Pubmed
Freake,
Thermogenesis and thyroid function.
1995,
Pubmed
Fu,
Transcriptional regulation of the Xenopus laevis Stromelysin-3 gene by thyroid hormone is mediated by a DNA element in the first intron.
2006,
Pubmed
,
Xenbase
Furlow,
The transcription factor basic transcription element-binding protein 1 is a direct thyroid hormone response gene in the frog Xenopus laevis.
2002,
Pubmed
,
Xenbase
Furlow,
In vitro and in vivo analysis of the regulation of a transcription factor gene by thyroid hormone during Xenopus laevis metamorphosis.
1999,
Pubmed
,
Xenbase
Grimaldi,
High-throughput sequencing will metamorphose the analysis of thyroid hormone receptor function during amphibian development.
2013,
Pubmed
,
Xenbase
Grøntved,
Transcriptional activation by the thyroid hormone receptor through ligand-dependent receptor recruitment and chromatin remodelling.
2015,
Pubmed
Harper,
The transcriptional repressor Blimp1/Prdm1 regulates postnatal reprogramming of intestinal enterocytes.
2011,
Pubmed
Hasebe,
Epithelial-connective tissue interactions induced by thyroid hormone receptor are essential for adult stem cell development in the Xenopus laevis intestine.
2011,
Pubmed
,
Xenbase
Hasebe,
Thyroid hormone-induced cell-cell interactions are required for the development of adult intestinal stem cells.
2013,
Pubmed
,
Xenbase
Havis,
Metamorphic T3-response genes have specific co-regulator requirements.
2003,
Pubmed
,
Xenbase
Heimeier,
Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult.
2010,
Pubmed
,
Xenbase
Helbing,
Expression profiles of novel thyroid hormone-responsive genes and proteins in the tail of Xenopus laevis tadpoles undergoing precocious metamorphosis.
2003,
Pubmed
,
Xenbase
Howdeshell,
A model of the development of the brain as a construct of the thyroid system.
2002,
Pubmed
Hsu,
Thyroid hormone receptor gene knockouts.
1998,
Pubmed
Ishizuya-Oka,
Evolutionary insights into postembryonic development of adult intestinal stem cells.
2011,
Pubmed
Ishizuya-Oka,
Origin of the adult intestinal stem cells induced by thyroid hormone in Xenopus laevis.
2009,
Pubmed
,
Xenbase
Lazar,
Thyroid hormone receptors: multiple forms, multiple possibilities.
1993,
Pubmed
Lei,
Generation of gene disruptions by transcription activator-like effector nucleases (TALENs) in Xenopus tropicalis embryos.
2013,
Pubmed
,
Xenbase
Luu,
Differential regulation of two histidine ammonia-lyase genes during Xenopus development implicates distinct functions during thyroid hormone-induced formation of adult stem cells.
2013,
Pubmed
,
Xenbase
Luu,
Direct Regulation of Histidine Ammonia-Lyase 2 Gene by Thyroid Hormone in the Developing Adult Intestinal Stem Cells.
2017,
Pubmed
,
Xenbase
Machuca,
Analysis of structure and expression of the Xenopus thyroid hormone receptor-beta gene to explain its autoinduction.
1995,
Pubmed
,
Xenbase
Mangelsdorf,
The nuclear receptor superfamily: the second decade.
1995,
Pubmed
Matsuda,
An essential and evolutionarily conserved role of protein arginine methyltransferase 1 for adult intestinal stem cells during postembryonic development.
2010,
Pubmed
,
Xenbase
Matsuda,
Novel functions of protein arginine methyltransferase 1 in thyroid hormone receptor-mediated transcription and in the regulation of metamorphic rate in Xenopus laevis.
2009,
Pubmed
,
Xenbase
Matsuura,
Histone H3K79 methyltransferase Dot1L is directly activated by thyroid hormone receptor during Xenopus metamorphosis.
2012,
Pubmed
,
Xenbase
Matsuura,
Liganded thyroid hormone receptor induces nucleosome removal and histone modifications to activate transcription during larval intestinal cell death and adult stem cell development.
2012,
Pubmed
,
Xenbase
Muncan,
Blimp1 regulates the transition of neonatal to adult intestinal epithelium.
2011,
Pubmed
Nakajima,
Dual mechanisms governing muscle cell death in tadpole tail during amphibian metamorphosis.
2003,
Pubmed
,
Xenbase
Nakayama,
Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis.
2013,
Pubmed
,
Xenbase
Okada,
Molecular and cytological analyses reveal distinct transformations of intestinal epithelial cells during Xenopus metamorphosis.
2015,
Pubmed
,
Xenbase
Okada,
Direct Activation of Amidohydrolase Domain-Containing 1 Gene by Thyroid Hormone Implicates a Role in the Formation of Adult Intestinal Stem Cells During Xenopus Metamorphosis.
2015,
Pubmed
,
Xenbase
Paul,
Tissue- and gene-specific recruitment of steroid receptor coactivator-3 by thyroid hormone receptor during development.
2005,
Pubmed
,
Xenbase
Paul,
Distinct expression profiles of transcriptional coactivators for thyroid hormone receptors during Xenopus laevis metamorphosis.
2003,
Pubmed
,
Xenbase
Paul,
Coactivator recruitment is essential for liganded thyroid hormone receptor to initiate amphibian metamorphosis.
2005,
Pubmed
,
Xenbase
Porterfield,
The role of thyroid hormones in prenatal and neonatal neurological development--current perspectives.
1993,
Pubmed
Ramadoss,
Novel mechanism of positive versus negative regulation by thyroid hormone receptor β1 (TRβ1) identified by genome-wide profiling of binding sites in mouse liver.
2014,
Pubmed
Ranjan,
Transcriptional repression of Xenopus TR beta gene is mediated by a thyroid hormone response element located near the start site.
1994,
Pubmed
,
Xenbase
Sato,
A role of unliganded thyroid hormone receptor in postembryonic development in Xenopus laevis.
2007,
Pubmed
,
Xenbase
Schreiber,
Remodeling of the intestine during metamorphosis of Xenopus laevis.
2005,
Pubmed
,
Xenbase
Schreiber,
Diverse developmental programs of Xenopus laevis metamorphosis are inhibited by a dominant negative thyroid hormone receptor.
2001,
Pubmed
,
Xenbase
Shi,
Heritable CRISPR/Cas9-mediated targeted integration in Xenopus tropicalis.
2015,
Pubmed
,
Xenbase
Shi,
Dual functions of thyroid hormone receptors in vertebrate development: the roles of histone-modifying cofactor complexes.
2009,
Pubmed
,
Xenbase
Shi,
Biphasic intestinal development in amphibians: embryogenesis and remodeling during metamorphosis.
1996,
Pubmed
,
Xenbase
Shi,
The development of the adult intestinal stem cells: Insights from studies on thyroid hormone-dependent amphibian metamorphosis.
2011,
Pubmed
,
Xenbase
Shi,
Unliganded thyroid hormone receptor regulates metamorphic timing via the recruitment of histone deacetylase complexes.
2013,
Pubmed
,
Xenbase
Silva,
Thyroid hormone control of thermogenesis and energy balance.
1995,
Pubmed
Sterling,
Cytological and morphological analyses reveal distinct features of intestinal development during Xenopus tropicalis metamorphosis.
2012,
Pubmed
,
Xenbase
Sun,
Epigenetic regulation of thyroid hormone-induced adult intestinal stem cell development during anuran metamorphosis.
2014,
Pubmed
,
Xenbase
Sun,
Spatio-temporal expression profile of stem cell-associated gene LGR5 in the intestine during thyroid hormone-dependent metamorphosis in Xenopus laevis.
2010,
Pubmed
,
Xenbase
Sun,
Expression profiling of intestinal tissues implicates tissue-specific genes and pathways essential for thyroid hormone-induced adult stem cell development.
2013,
Pubmed
,
Xenbase
Sun,
Thyroid hormone regulation of adult intestinal stem cell development: mechanisms and evolutionary conservations.
2012,
Pubmed
,
Xenbase
Tata,
Gene expression during metamorphosis: an ideal model for post-embryonic development.
1993,
Pubmed
Tsai,
Molecular mechanisms of action of steroid/thyroid receptor superfamily members.
1994,
Pubmed
van der Flier,
Stem cells, self-renewal, and differentiation in the intestinal epithelium.
2009,
Pubmed
Wang,
Targeted gene disruption in Xenopus laevis using CRISPR/Cas9.
2015,
Pubmed
,
Xenbase
Wang,
Developmental regulation and function of thyroid hormone receptors and 9-cis retinoic acid receptors during Xenopus tropicalis metamorphosis.
2008,
Pubmed
,
Xenbase
Wen,
Unliganded thyroid hormone receptor α controls developmental timing in Xenopus tropicalis.
2015,
Pubmed
,
Xenbase
Wong,
Coordinated regulation of and transcriptional activation by Xenopus thyroid hormone and retinoid X receptors.
1995,
Pubmed
,
Xenbase
Wong,
Determinants of chromatin disruption and transcriptional regulation instigated by the thyroid hormone receptor: hormone-regulated chromatin disruption is not sufficient for transcriptional activation.
1997,
Pubmed
,
Xenbase
Yen,
Unliganded TRs regulate growth and developmental timing during early embryogenesis: evidence for a dual function mechanism of TR action.
2015,
Pubmed
,
Xenbase
Yen,
Physiological and molecular basis of thyroid hormone action.
2001,
Pubmed
