Animal studies were done as approved byEunice Kennedy ShriverNational Institute of Child Health and Human Development Animal Use and Care Committee. == Quantitative RT-PCR (qRT-PCR) == Total RNA was isolated from the intestine of tadpoles at premetamorphic stage 54, early metamorphic climax (stage 58), metamorphic climax (stages 6062), and the end of metamorphosis (stage 66). number of histone activation and repression marks have been defined based on correlations with mRNA levels in cell cultures. Most but not all correlate with gene expression induced by liganded TR during development, suggesting that tissue and developmental context influences the roles of histone modifications in gene regulation. Our findings provide important mechanistic insights on how chromatin remodeling affects developmental gene regulationin vivo. Thyroid hormone (T3) plays a critical role Timonacic in adult organ function and development in mammals (15). In humans, the most important period of T3action responsible for cretinism appears to be the so-called postembryonic period, a few months before and several months after birth, which is critical for growth and maturation of many organs, including the brain (35). Unfortunately, the difficulty in manipulating uterus-enclosed mammalian embryos has severely limited molecular and functional studies of T3action during this critical late embryonic developmental period. Metamorphosis in amphibians serves as an excellent model to study Timonacic T3function during postembryonic development in vertebrate due to its total dependence on T3(35). All changes during metamorphosis in amphibians such asXenopus laevisandX. tropicalis, two highly related species, are initiated and controlled by T3through gene regulation by T3receptor (TR) (4,6,7). During this period, the endogenous T3peaks at the climax of metamorphosis to induce the metamorphic changes and organ maturation, similar to the high levels of T3present in human fetal plasma during the postembryonic period of extensive organ development and maturation (3,4). Molecular and genetic studies have demonstrated that the metamorphic effects of T3are mediated by TR (6,812). TR forms heterodimers with 9-cis retinoic acid receptors (RXR), and these dimers bind to T3response element (TRE) in TR target genes (1,2,13,14). In the absence of T3, TR/RXR functions as a repressor, whereas in the presence of T3, TR/RXR functions as an activator. FRAP2 In both transcriptional activation and repression, different cofactor complexes are recruited by TR to TRE to affect transcription (2,1523). Using the metamorphosis model system, we and others have provided strongin vivoevidence to support the importance of histone modifying cofactor complexes in mediating gene regulation by liganded or unliganded TR and in regulatingXenopusdevelopment (8,2430). On the other hand, relatively little is known on whether the recruitment of the histone modifying cofactor complexes by TR is associated with changes in histone modifications and chromatin remodeling at target genes during developmentin vivo. Eukaryotic DNA is wrapped around nucleosomes, composed of an octamer of four core histones (H2A, H2B, H3, and H4), which form the primary units of the chromatin. The histones, particularly their N-terminal tails, are subject to a large number of posttranslational modifications, including acetylation, methylation, phosphorylation, and ubiquitylation (31). These histone modifications seem to have a substantial influence on chromatin structure and gene function. Transcription initiation by RNA polymerase II (Pol II) involves the coordinated action of the general transcription machinery with chromatin modifying and remodeling enzymes (32). In particular, di- and trimethylation of H3 lysine 9 (H3K9me2, H3K9me3) and trimethylation of H3K27 (H3K27me3) Timonacic can elicit the formation of repressive heterochromatin through the recruitment of heterochromatin protein 1 (33) and polycomb group proteins, respectively (3436). In contrast, histone modifications that are associated with active transcription, such as acetylation of histone 3 and histone 4 (H3 and H4) or di- or trimethylation of H3K4 (H3K4me2, H3K4me3), are commonly referred to as euchromatin modifications (37,38). Most modifications are distributed in distinct patterns within the upstream region, the core promoter, the 5 end of the open reading frame and the 3 end of the open reading frame (38,39). Although extensive studies in cell cultures have provided strong evidence to suggest that histone modifications function in a combinatorial fashion to regulate the diverse activities associated with chromatin, whether these patterns of histone modifications are associated with gene regulation by nuclear receptors during vertebrate development remains.