GENE REGULATION BY TR. Based on TR expression profiles and its molecular properties, we have previously proposed a dual function model for TR during frog development. That is, the heterodimers between TR and RXR (9-cis retinoic acid receptor) bind to target genes in vivo. In premetamorphic tadpoles, they repress gene expression in the absence of TH to prevent metamorphosis, thus ensuring a proper tadpole growth period. When TH is present either from endogenous synthesis during development or exogenous addition to the raring water of premetamorphic tadpoles, TR/RXR heterodimers activate TH-inducible genes to initiate metamorphosis. Our studies in the last several years have provided molecular and genetic support for this model. Furthermore, we have revealed important roles of corepressor and coactivator complexes in TR action during metamorphosis. To understand the molecular pathways induced by TR during this process, it is critical to identify and characterize the immediate early, direct target genes of TH, i.e., genes regulated by TH in the absence of new protein synthesis. We took advantage of the ability to easily induce metamorphosis with physiological levels of TH and to carry out microarray analysis in Xenopus laevis and genome-wide sequence analysis in Xenopus tropicalis. This allowed us to identify 188 up-regulated and 249 down-regulated genes by TH in the absence of new protein synthesis in whole animals. We further provide evidence to show that these genes contain functional TH response elements (TREs) that are bound by TR in tadpoles and that their promoters are regulated by TR in vivo. More importantly, gene ontology analysis showed that the direct up-regulated genes are enriched in categories important for transcriptional regulation and protein degradation-dependent signaling processes but not DNA replication. Our findings thus revealed the existence of interesting pathways induced by TH at the earliest step of metamorphosis. ANALYZING THE GENE EXPRESSION PROGRAMS UNDERLYING THE TEMPORAL TRANSFORMATIONS DURING METAMORPHOSIS. The complexity of metamorphic changes in different organs argues for the presence of different gene regulation programs regulated by TR. Knowledge on this systematic gene regulation will help to identify not only molecular markers but also important cellular pathways or critical genes for future mechanistic studies. Thus, we have begun to use the recently developed Xenopus laevis cDNA array to analyze genome-wide gene expression changes associated with TH-induced intestinal remodeling, a process that involves selective degeneration of the larval epithelium through apoptosis and de novo development of the adult epithelium. Clustering of the expression patterns revealed co-expressed genes involved in essential cell processes such as apoptosis and proliferation. Furthermore, we showed that most of the genes highly induced at metamorphic climax were also upregulated in the mouse intestine around birth, the postembryonic period resembling metamorphosis, supporting conservation in the underlying molecular pathways. Moreover, our genome-wide analysis identified many larval/embryo- and adult-specific genes. Detailed analysis revealed 17 larval specific genes that may represent molecular markers for human colonic cancers, while many adult specific genes are associated with dietary enzymes. This global developmental expression study provides the first detailed molecular description of intestinal remodeling and maturation during postembryonic development, which should help improve our understanding of intestinal organogenesis and human diseases.
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