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Y B Shi

Publications and source records attributed to Y B Shi.

At least 55 records · Page 3Linked to original sources
PubMed1997

Structural and functional features of a specific nucleosome containing a recognition element for the thyroid hormone receptor.

The Xenopus thyroid hormone receptor betaA (TRbetaA) gene contains an important thyroid hormone response element (TRE) that is assembled into a positioned nucleosome. We determine the translational position of the nucleosome containing the TRE and the rotational positioning of the double helix with respect to the histone surface. Histone H1 is incorporated into the nucleosome leading to an asymmetric protection to micrococcal nuclease cleavage of linker DNA relative to the nucleosome core. Histone H1 association is without significant consequence for the binding of the heterodimer of thyroid hormone receptor and 9-cis retinoic acid receptor (TR/RXR) to nucleosomal DNA in vitro, or for the regulation of TRbetaA gene transcription following microinjection into the oocyte nucleus. Small alterations of 3 and 6 bp in the translational positioning of the TRE in chromatin are also without effect on the transcriptional activity of the TRbetaA gene, whereas a small change in the rotational position of the TRE (3 bp) relative to the histone surface significantly reduces the binding of TR/RXR to the nucleosome and decreases transcriptional activation directed by TR/RXR. Our results indicate that the specific architecture of the nucleosome containing the TRE may have regulatory significance for expression of the TRbetaA gene.

Animals↗
PubMed1997

Determinants of chromatin disruption and transcriptional regulation instigated by the thyroid hormone receptor: hormone-regulated chromatin disruption is not sufficient for transcriptional activation.

Chromatin disruption and transcriptional activation are both thyroid hormone-dependent processes regulated by the heterodimer of thyroid hormone receptor and 9-cis retinoic acid receptor (TR-RXR). In the absence of hormone, TR-RXR binds to nucleosomal DNA, locally disrupts histone-DNA contacts and generates a DNase I-hypersensitive site. Chromatin-bound unliganded TR-RXR silences transcription of the Xenopus TRbetaA gene within a canonical nucleosomal array. On addition of hormone, the receptor directs the extensive further disruption of chromatin structure over several hundred base pairs of DNA and activates transcription. We define a domain of the TR protein necessary for directing this extensive hormone-dependent chromatin disruption. Particular TR-RXR heterodimers containing mutations in this domain are able to bind both hormone and their thyroid hormone receptor recognition element (TRE) within chromatin, yet are unable to direct the extensive hormone-dependent disruption of chromatin or to activate transcription. We distinguish the hormone-dependent disruption of chromatin and transcriptional activation as independently regulated events through the mutagenesis of basal promoter elements and by altering the position and number of TREs within the TRbetaA promoter. Chromatin disruption alone on a minichromosome is shown to be insufficient for transcriptional activation of the TRbetaA gene.

Amino Acid Sequence↗
PubMed1997

Thyroid hormone-dependent gene expression program for Xenopus neural development.

Although thyroid hormone (TH) plays a significant role in vertebrate neural development, the molecular basis of TH action on the brain is poorly understood. Using polymerase chain reaction-based subtractive hybridization we isolated 34 cDNAs for TH-regulated genes in the diencephalon of Xenopus tadpoles. Northern blots verified that the mRNAs are regulated by TH and are expressed during metamorphosis. Kinetic analyses showed that most of the genes are up-regulated by TH within 4-8 h and 13 are regulated by TH only in the brain. All cDNA fragments were sequenced and the identities of seven were determined through homology with known genes; an additional five TH-regulated genes were identified by hybridization with known cDNA clones. These include five transcription factors (including two members of the steroid receptor superfamily), a TH-converting deiodinase, two metabolic enzymes, a protein disulfide isomerase-like protein that may bind TH, a neural-specific cytoskeletal protein, and two hypophysiotropic neuropeptides. This is the first successful attempt to isolate a large number of TH-target genes in the developing vertebrate brain. The gene identities allow predictions about the gene regulatory networks underlying TH action on the brain, and the cloned cDNAs provide tools for understanding the basic molecular mechanisms underlying neural cell differentiation.

Animals↗
PubMed1997

Temporal and spatial expression of an intestinal Na+/PO4 3- cotransporter correlates with epithelial transformation during thyroid hormone-dependent frog metamorphosis.

The amphibian intestine has two morphologically distinct structures during development. Early embryogenesis generates a simple, tube-like intestine in the tadpole whereas after thyroid hormone (T3)-dependent metamorphosis a newly remodeled adult intestine is formed similar to that of higher vertebrates. This change requires a drastic transformation of the epithelial layer We have isolated a Na+/PO4 3- cotransporter gene that may contribute to this transformation. The deduced amino acid sequence of this gene shows a high degree of homology to the mammalian renal Na+/PO4 3- cotransporters, which have little or no expression in organs other than the kidney. The frog gene is highly expressed and regulated by T3 in the intestine with little expression and/or regulation by T3 in most other organs. Its mRNA is restricted to the differentiated epithelial cells both in tadpoles and postmetamorphic frogs. Interestingly, its expression is low in premetamorphic tadpoles, but up-regulated when metamorphosis is initiated by endogenous T3. As the larval epithelium undergoes programmed cell death (apoptosis), the mRNa level drops to a minimum. Subsequently, the gene is reactivated at the tip region of the newly formed adult intestinal folds and a crest-trough polarity of expression is established by the end of metamorphosis. This temporal regulation profile is also reproduced when premetamorphic tadpoles are treated with T3 to induce precocious intestinal remodeling. These results suggest a possible role of the Na+/PO 4 3- cotransporter during metamorphosis and demonstrate that the adult epithelial cell differentiation pattern is established in the direction of crest-to-trough of the intestinal fold, concurrent with the epithelial morphogenic process.

Amino Acid Sequence↗
PubMed1997

Temporal and spatial regulation of a putative transcriptional repressor implicates it as playing a role in thyroid hormone-dependent organ transformation.

Thyroid hormone (T3) induces both larval cell death and adult cell proliferation and differentiation during amphibian metamorphosis. We have previously isolated a bZip transcription factor (TH/bZip) as a T3 response gene in the metamorphosing Xenopus intestine. We demonstrate that the Xenopus TH/bZip gene is a direct T3-response gene and ubiquitously regulated by T3 in tadpoles. Developmental in situ hybridization analyses have shown that TH/bZip gene is regulated in a cell-type-specific manner that correlates with tissue transformation. In particular, it is found to be expressed in the larval intestinal epithelial cells prior to their apoptotic degeneration and in the proliferating adult cell types. However, the gene is repressed again upon adult cell differentiation. This regulation pattern mimics that of the thyroid hormone receptor (TR)beta genes. Since the TH/bZip gene is a direct T3-response gene, such a correlation suggests that TR beta may be involved in the regulation of the TH/bZip gene. More importantly, in situ hybridization reveals a strong spatiotemporal correlation of TH/bZip expression with the tissue-specific remodeling in the intestine, suggesting that TH/bZip gene may participate, depending on the cell types, in both inducing apoptosis and stimulating cell proliferation. A similar role has been reported for the proto-oncogene c-myc, another leucine-zipper-containing transcription factor, in tissue culture cell systems.

Animals↗
PubMed1997

Characterization of the Xenopus homolog of an immediate early gene associated with cell activation: sequence analysis and regulation of its expression by thyroid hormone during amphibian metamorphosis.

The complex transformation of a tadpole to a frog during amphibian development is under the control of thyroid hormone (T3). T3 is known to regulate gene transcription through its nuclear receptors. We have previously isolated many genes which are up-regulated by T3 in the intestine of Xenopus laevis tadpoles. We have now cloned a full-length cDNA for one such gene (IU12). Sequence analysis shows that the IU12 cDNA encodes a plasma membrane protein with 12 transmembrane domains and homologous to a mammalian gene associated with cell activation and organ development. Similarly, we have found that IU12 is activated during intestinal remodeling when both cell death and proliferation take place. Furthermore, IU12 is an early T3-response gene and its expression in the intestine during T3-induced metamorphosis mimics that during normal development. These results argue for a role of IU12 in the signal transduction pathways leading to intestinal metamorphosis.

Amino Acid Sequence↗
PubMed1997

Cyclosporin A but not FK506 inhibits thyroid hormone-induced apoptosis in tadpole intestinal epithelium.

Amphibian metamorphosis and mammalian T cell development represent two of the best known systems where developmental programmed cell death through apoptosis takes place. Two immunosuppressants, cyclosporin A (CsA) and FK506, have been demonstrated to inhibit activation-induced cell death in immature T cells and T cell hybridomas. In this study, we have established an in vitro system in which isolated primary tadpole intestinal epithelial cells undergo typical apoptosis upon treatment with thyroid hormone (T3), the causative agent of metamorphosis. It is surprising that this T3-induced apoptosis was found to be inhibited only by CsA but not by FK506, whereas both immunosuppressants block activation-induced apoptosis in T cells. Since T3 exerts its effect primarily by regulating gene transcription through direct binding to nuclear thyroid hormone receptors, our results strongly suggest that except for their similarity in the T cell receptor-mediated signal transduction process, CsA, but not FK506, also blocks another yet-unidentified step during the induction of apoptosis. The identification of this novel function of CsA may provide an important clue toward the understanding of the mechanism of apoptosis and helps in designing better clinical applications of the immunosuppressants.

Animals↗
PubMed1997

Both thyroid hormone and 9-cis retinoic acid receptors are required to efficiently mediate the effects of thyroid hormone on embryonic development and specific gene regulation in Xenopus laevis.

Tissue culture transfection and in vitro biochemical studies have suggested that heterodimers of thyroid hormone receptors (TRs) and 9-cis retinoic acid receptors (RXRs) are the likely in vivo complexes that mediate the biological effects of thyroid hormone, 3,5,3'-triiodothyronine (T3). However, direct in vivo evidence for such a hypothesis has been lacking. We have previously reported a close correlation between the coordinated expression of TR and RXR genes and tissue-dependent temporal regulation of organ transformations during Xenopus laevis metamorphosis. By introducing TRs and RXRs either individually or together into developing Xenopus embryos, we demonstrate here that RXRs are critical for the developmental function of TRs. Precocious expression of TRs and RXRs together but not individually leads to drastic, distinct embryonic abnormalities, depending upon the presence or absence of T3, and these developmental effects require the same receptor domains as those required for transcriptional regulation by TR-RXR heterodimers. More importantly, the overexpressed TR-RXR heterodimers faithfully regulate endogenous T3 response genes that are normally regulated by T3 only during metamorphosis. That is, they repress the genes in the absence of T3 and activate them in the presence of the hormone. On the other hand, the receptors have no effect on a retinoic acid (RA) response gene. Thus, RA- and T3 receptor-mediated teratogenic effects in Xenopus embryos occur through distinct molecular pathways, even though the resulting phenotypes have similarities.

Animals↗
PubMed1996

Functional characterization of a mutant thyroid hormone receptor in Xenopus laevis.

Thyroid hormone plays a causative role during frog metamorphosis, and its effect is mediated by thyroid hormone receptors (TRs). To investigate the function of Xenopus TRs, we have recently developed a thyroid hormone dependent in vivo transcription system by introducing TRs and RXRs (9-cis-retinoic acid receptors) into Xenopus oocytes. Interestingly, using this system, we have found that the TRalphaB cloned previously is defective in transcriptional activation compared with TRalphaA. In vitro DNA binding experiments show that TRalphaB.RXR heterodimers have drastically reduced affinity for a thyroid hormone response element. Site-directed mutagenesis shows that two of the seven amino acid residues that differ between TRalphaA and TRalphaB are responsible for the defect in TRalphaB function. These two residues affect the DNA binding by both TR.RXR heterodimers and TR homodimers. In contrast, heterodimer formation with RXRs is not affected as demonstrated by coimmunoprecipitation and dominant-transcriptional inhibition experiments. By cDNA and genomic DNA sequence analysis, we have demonstrated that the residues, which affect TRalphaB function when mutated, are identical between the wild type TRalphaB and TRalphaA. Thus, our experiments have discovered the first amphibian TR mutant. The DNA binding and transcription activation functions of the mutant are discussed in relation to the recently published TR crystal structure.

Amino Acid Sequence↗
PubMed1996

Nuclear factor I as a potential regulator during postembryonic organ development.

Nuclear factor I (NFI) family members are transcription factors that are believed to also participate in DNA replication. We have cloned two Xenopus laevis NFIs that are up-regulated by thyroid hormone. They are 84-95% identical to their counterparts in birds and mammals. In contrast, the two Xenopus NFIs are much less homologous to each other, sharing only 58% homology, which largely resides in the DNA binding domain at the amino terminus. However, both NFIs can bind to a consensus NFI binding site and activate the transcription of a promoter bearing the site. Northern blot reveals that both NFI genes are regulated in tissue- and developmental stage-dependent manners. They are first activated, independently of thyroid hormone, to low levels at stages 23/24, around the onset of larval organogenesis. After stage 54, their mRNA levels are dramatically upregulated by endogenous thyroid hormone, and high levels of their expression correlate with organ-specific metamorphosis. Furthermore, gel mobility shift assay indicates that the NFI proteins are present in different organs and that their levels are regulated similarly to the mRNA levels. These results strongly suggest that NFIs play important roles during postembryonic organ development, in contrast to the general belief that NFIs are ubiquitous factors.

Amino Acid Sequence↗
PubMed1996

Tadpole competence and tissue-specific temporal regulation of amphibian metamorphosis: roles of thyroid hormone and its receptors.

Amphibian metamorphosis is a post-embryonic process that systematically transforms different tissues in a tadpole. Thyroid hormone plays a causative role in this complex process by inducing a cascade of gene regulation. While natural metamorphosis does not occur until endogenous thyroid hormone has been synthesized, tadpoles are competent to respond to exogenous thyroid hormone shortly after hatching. In addition, even though the metamorphic transitions of individual organs are all controlled by thyroid hormone, each occurs at distinct developmental stages. Recent molecular studies suggest that this competence of premetamorphic tadpoles to respond to the hormone and the developmental stage-dependent regulation of tissue-specific transformations are determined in part by the levels of thyroid hormone receptors and the concentrations of cellular free thyroid hormone. In addition, at least two genes, encoding a cytosolic thyroid hormone binding protein and a 5-deiodinase, respectively, are likely to be critical players in regulating cellular free thyroid hormone concentrations. This review discusses how all of these molecular components coordinate to induce amphibian metamorphosis in a correct spatial and temporal manner. These studies provide us with general clues as to how and why tissues become competent to respond to hormonal signals.

Amphibians↗
PubMed1996

Transient expression of stromelysin-3 mRNA in the amphibian small intestine during metamorphosis.

It has been suggested that a matrix metalloproteinase, stromelysin-3 (ST3), is an important enzyme for epithelial transformation; the ST3 gene is known to be regulated by thyroid hormone during Xenopus metamorphosis. In this study, we have examined the distribution of ST3 mRNA in the small intestine of Xenopus during metamorphosis by using in situ hybridization. Around stage 58, ST3 mRNA is first detectable in larval fibroblasts near the muscular layer, and then increases in amount throughout the entire region of connective tissue. By stage 61, when connective tissue cells are rapidly increasing in number, ST3 mRNA is localized in fibroblasts just beneath the epithelium. This localization of ST3 mRNA is in good temporal accordance with modification of the basement membrane and epithelial transformation from the larval to adult form. Thereafter, ST3 mRNA gradually decreases and is no longer detected after stage 63 when the adult epithelium has completely replaced the larval type. The transient expression of ST3 mRNA in the fibroblasts of connective tissue during metamorphosis indicates that it plays an important role in epithelial transformation by changing the basement membrane.

Animals↗
PubMed1996

Biphasic intestinal development in amphibians: embryogenesis and remodeling during metamorphosis.

Intestinal development in anurans is a biphasic process. The embryogenesis of intestine resembles that in higher vertebrates. The subsequent remodeling process during metamorphosis to produce an adult organ is controlled by TH. Recent progress in studying TH action and its application to amphibian metamorphosis has provided considerable insights into the remodeling process. One possible model for the TH-induced gene regulation cascade of intestinal remodeling is presented in Fig. 9. It is assumed that TRs function as heterodimers with RXRs. In the absence of TH, the TR-RXR heterodimers can bind to TH response elements present in the target genes and repress the basal transcription of these genes (Fondell et al., 1993; Damm et al., 1989; Sap et al., 1989; Baniahmad et al., 1992; Ranjan et al., 1994). The binding of TH leads to conformational changes in the receptor complexes that in turn activate gene transcription. The products of these early response genes then participate in the activation of the remaining gene regulation cascade. Exactly how this occurs remains unknown. Interestingly, the early response genes include not only transcription factors but also other proteins such as metalloproteinases. The transcription factors could activate or repress downstream TH response genes directly. Other proteins are likely to assert their effect indirectly. For example, they could modify the ECM or cell surface. In addition, they could regulate and/or participate in signal transduction by growth factors. The cooperation between these complex intra- and extracellular processes eventually results in the degeneration of the larval organ and formation of the adult tissue. This simplified scheme immediately raises many questions. Although the mRNAs for TRs and RXRs are present in the intestine and the other tissues during metamorphosis (Yaoita and Brown, 1990; Kawahara et al., 1991; Y.-B. Shi, unpublished observations), it is unknown whether the mRNA levels reflect the protein levels. It also remains to be tested whether TR-RXR is indeed the functional complex in vivo and whether the heterodimer is responsible for the activation of the early response genes isolated to date. The majority of the early response genes are ubiquitous. Of the few intestine-specific genes, none of them have yet been identified by sequence analysis. It is of great interest to understand how the same genes expressed in tissues undergoing drastically different changes can exert their biological effects. It is likely that together with existing proteins in the intestine, these early genes regulate tissue-specific downstream genes, which in turn determine the tissue-specific transformation. An important issue is to establish the identity of these downstream genes.

Amphibians↗
PubMed1996

The etiology of lung cancer in nonsmoking females in Harbin, China.

A case-control study of female lung adenocarcinoma in Harbin, China involving interviews with 120 cases of nonsmoking females, matched 1:1 with controls, showed that high coal use, indoor air pollution, exposure to coal dust, frequent frying and deep frying food, and a history of lung cancer in the family were statistically significant risk factors for female adenocarcinoma. High personal income, spacious living quarters, and frequent consumption of carrots were protective factors for adenocarcinoma.

Adult↗
PubMed1996

Identification and characterization of a novel collagenase in Xenopus laevis: possible roles during frog development.

Matrix metalloproteinases (MMPs) participate in extracellular matrix remodeling and degradation and have been implicated in playing important roles during organ development and pathological processes. Although it has been hypothesized for > 30 years that collagenase activities are responsible for collagen degradation during tadpole tail resorption, none of the previously cloned amphibian MMPs have been biochemically demonstrated to be collagenases. Here, we report a novel matrix metalloproteinase gene from metamorphosing Xenopus laevis tadpoles. In vitro biochemical studies demonstrate that this Xenopus enzyme is an interstitial collagenase and has an essentially identical enzymatic activity toward a collagen substrate as the human interstitial collagenase. Sequence comparison of this enzyme to other known MMPs suggests that the Xenopus collagenase is not a homologue of any known collagenases but instead represents a novel collagenase, Xenopus collagenase-4 (xCol4, MMP-18). Interestingly, during development, xCol4 is highly expressed only transiently in whole animals, at approximately the time when tadpole feeding begins, suggesting a role during the maturation of the digestive tract. More importantly, during metamorphosis, xCol4 is regulated in a tissue-dependent manner. High levels of its mRNA are present as the tadpole tail resorbs. Similarly, its expression is elevated during hindlimb morphogenesis and intestinal remodeling. In addition, when premetamorphic tadpoles are treated with thyroid hormone, the causative agent of metamorphosis, xCol4 expression is induced in the tail. These results suggest that xCol4 may facilitate larval tissue degeneration and adult organogenesis during amphibian metamorphosis.

Amino Acid Sequence↗
PubMed1995

A role for nucleosome assembly in both silencing and activation of the Xenopus TR beta A gene by the thyroid hormone receptor.

We have assembled the thyroid hormone-inducible promoter of the Xenopus thyroid hormone receptor (TR)beta A gene into chromatin using replication-coupled and -independent assembly pathways in vivo. We establish that heterodimers of TR and 9-cis retinoic acid receptors (RXR) can bind to their recognition sites within chromatin both in vivo and in vitro and alternately repress or activate transcription dependent on the absence or presence of thyroid hormone. Maximal transcriptional repression requires the presence of unliganded TR/RXR heterodimers during replication-coupled chromatin assembly. We demonstrate an increase in transcription directed by the TR beta A promoter of over two orders of magnitude in vivo, following the addition of thyroid hormone. This increase in transcription involves the relief of the repressed state that is established by the unliganded TR/RXR heterodimer during replication-coupled chromatin assembly. The association of thyroid hormone with the chromatin-bound TR/RXR heterodimer leads to the disruption of local chromatin structure in a transcription-independent process. Thus, chromatin structure has multiple roles in the regulation of TR beta A gene expression in vivo: The TR/RXR heterodimer recognizes the response element within chromatin, TR/RXR makes use of the chromatin assembly process to silence transcription more efficiently, and TR/RXR directs the disruption of local chromatin structure in response to thyroid hormone.

Animals↗
PubMed1995

Coordinated regulation of and transcriptional activation by Xenopus thyroid hormone and retinoid X receptors.

Thyroid hormone (T3) plays a causative role in amphibian metamorphosis. This regulation is thought to be mediated by heterodimers of T3 receptors (TRs) and retinoid X receptors (RXRs). We report here that Xenopus TRs can indeed form strong heterodimers with Xenopus RXRs on the T3 response element (TRE) present in Xenopus TR beta genes. Using a T3-responsive in vivo transcription system established by introducing TRs and RXRs into Xenopus oocytes, we demonstrated that TR-RXR heterodimers repressed TR beta gene promoter in the absence of T3 and activated the promoter in the presence of the hormone. Furthermore, by analyzing the expression of TR and RXR genes, we showed that TR and RXR genes were coordinately regulated in different tissues during metamorphosis. Thus high levels of their mRNAs are present in the limb during early stages of limb development when morphogenesis occurs and in the tail toward the end of metamorphosis when it is being resorbed. Such correlations coupled with our TRE-binding and in vivo transcriptional activation experiments provide strong evidence that TRs and RXRs function together to mediate the effects of T3 during metamorphosis. These results further suggest a possible molecular basis for the temporal regulation of tissue-specific metamorphosis.

Animals↗