TiGER: A database for tissue-specific gene expression and regulation

Background  

Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation.     

Avian SERPINB11 gene: characteristics, tissue-specific expression, and regulation of expression by estrogen

Serpins, a group of proteins with similar structural and functional properties, were first identified based on their unique mechanism of action: their inhibition of proteases. While most serpins have inhibitory roles, certain serpins are not involved in canonical proteolytic cascades but perform diverse functions including storage of ovalbumin in egg white, transport of hormones (thyroxine- and cortisol-binding globulin), and suppression of tumors. Of these, serpin peptidase inhibitor, clade B, member 11 (SERPINB11) is not an inhibitor of known proteases in humans and mice, and its function is unknown. In the present study, the SERPINB11 gene was cloned, and its expression profile was analyzed in various tissues from chickens. The chicken SERPINB11 gene has an open reading frame of 1346 nucleotides that encode a protein of 388 amino acids that has moderate homology (38.8%-42.3%) to mammalian SERPINB11 proteins. Importantly, SERPINB11 mRNA is most abundant in the chicken oviduct, specifically luminal and glandular epithelia, but it was not detected in any other chicken tissues of either sex. We then determined effects of diethylstilbestrol (DES; a synthetic nonsteroidal estrogen) on SERPINB11 expression in the chicken oviduct. Treatment of young chicks with DES induced SERPINB11 mRNA and protein only in luminal and glandular epithelial cells of the oviduct. Collectively, these results indicate that the novel estrogen-induced SERPINB11 gene is expressed only in epithelial cells of the chicken oviduct and implicate SERPINB11 in regulation of oviduct development and differentiated functions.     

From laminin to lamin: regulation of tissue-specific gene expression by the ECM

Mammary epithelial cells need a laminin-rich extracellular matrix (ECM) to achieve a functionally differentiated phenotype that includes secretion of milk-specific proteins such as beta-casein. There is good evidence that ECM-induced expression of beta-casein involves an 'ECM-response element' in the promoter of the casein gene that is activated by integrin-mediated signalling. This article proposes that ECM-induced structural changes in the cytoskeleton, histone organization and the nuclear matrix contribute to this tissue-specific gene expression.     

Relationship of cell growth to the regulation of tissue-specific gene expression during osteoblast differentiation

The relationship of cell proliferation to the temporal expression of genes characterizing a developmental sequence associated with bone cell differentiation can be examined in primary diploid cultures of fetal calvarial-derived osteoblasts by the combination of molecular, biochemical, histochemical, and ultrastructural approaches. Modifications in gene expression define a developmental sequence that has 1) three principal periods: proliferation, extracellular matrix maturation, and mineralization; and 2) two restriction points to which the cells can progress but cannot pass without further signals. The first restriction point is when proliferation is down-regulated and gene expression associated with extracellular matrix maturation is induced, and the second when mineralization occurs. Initially, actively proliferating cells, expressing cell cycle and cell growth regulated genes, produce a fibronectin/type I collagen extracellular matrix. A reciprocal and functionally coupled relationship between the decline in proliferative activity and the subsequent induction of genes associated with matrix maturation and mineralization is supported by 1) a temporal sequence of events in which an enhanced expression of alkaline phosphatase occurs immediately after the proliferative period, and later an increased expression of osteocalcin and osteopontin at the onset of mineralization; 2) increased expression of a specific subset of osteoblast phenotype markers, alkaline phosphatase and osteopontin, when proliferation is inhibited; and 3) enhanced levels of expression of the osteoblast markers when collagen deposition is promoted, suggesting that the extracellular matrix contributes to both the shutdown of proliferation and development of the osteoblast phenotype. The loss of stringent growth control in transformed osteoblasts and in osteosarcoma cells is accompanied by a deregulation of the tightly coupled relationship between proliferation and progressive expression of genes associated with bone cell differentiation.     

Developmental regulation and tissue-specific differences of heat shock gene expression in transgenic tobacco and Arabidopsis plants

The heat shock (hs) response during plant growth and development was analyzed in tobacco and Arabidopsis using chimaeric -glucuronidase reporter genes (hs-Gus) driven by a soybean hs promoter. Fluorimetric measurements and histochemical staining revealed high Gus activities in leaves, roots, and flowers exclusively after heat stress. The highest levels of heat-inducible expression were found in the vascular tissues. Without heat stress, a developmental induction of hs-Gus was indicated by the accumulation of high levels of Gus in transgenic tobacco seeds. There was no developmental induction of hs-Gus in Arabidopsis seeds. In situ hybridization to the RNA of the small heat shock protein gene Athsp17.6 in tissue sections revealed an expression in heat-shocked leaves but no expression in control leaves of Arabidopsis. However, a high level of constitutive expression of hs gene was detected in meristematic and provascular tissues of the Arabidopsis embryo. The developmental and tissue-specific regulation of the hs response is discussed.Abbreviations hs heat shock - Hsp heat shock protein(s) - hs Gus: heat-inducible Gus gene(s) - HSE heat shock element(s) - HSF heat shock factor - X-gluc 5-bromo-4-chloro-3-indolyl--D-glucuronide - Gus -glucuronidase - DAF days after flowering - SAR scaffold attachment region     

Estrogen regulation of tissue-specific expression of complement C3

The administration of estradiol to immature rats results in the increased synthesis and secretion of a 180-kDa protein, composed of 115- and 65-kDa subunits, by the uterine luminal epithelial cells. A monoclonal antibody against the 180-kDa protein was utilized to isolate the corresponding cDNA (LE-1) from a rat uterine luminal epithelial cell cDNA lambda gt11 expression library. This LE-1 cDNA was sequenced and shown to be homologous to complement component C3. The sequence was approximately 81 and 90% homologous to human and mouse C3, respectively. The LE-1 cDNA sequence was homologous with the 3' portion of the C3 mRNA containing the alpha subunit (115 kDa). Uterine mRNA isolated from immature rats treated with 1 microgram of estradiol for 24 h demonstrated a 25-fold increase in the concentration of a 6.0-kilobase mRNA by Northern hybridization with either LE-1 or authentic human C3 cDNA probes. To further examine the possibility that the estradiol-regulated secretory protein was C3, an aliquot of radiolabeled media protein from control and estradiol-stimulated rat uteri was incubated with goat anti-rat C3 antibody. The immunoprecipitated radiolabeled protein from estradiol-treated animals was increased significantly (p less than 0.01) compared to media from control animals. Analysis of the immunoprecipitated proteins on nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed a single protein of 180 kDa from estradiol-stimulated uterine media, whereas no detectable proteins were immunoprecipitated from media obtained from control uteri. Also, when the immunoprecipitated protein was reduced (20 mM dithiothreitol) it dissociated into two subunits of 115 and 65 kDa. Immunohistochemical studies demonstrated the presence of C3 only in the epithelial cells of estrogen-stimulated rat uteri. In addition, the estradiol-stimulated mRNA was only detectable in uterine epithelial cell RNA. Analysis of liver RNA demonstrated a 6.0-kilobase mRNA, as in the uterus, when hybridized with LE-1. However, unlike the uterus, its concentration was not influenced by estrogen administration with up to three daily injections of 100 micrograms of diethylstilbestrol. Based on biophysical, DNA sequence, and antibody data we conclude that rat uterine epithelial cells produce C3 in response to estradiol whereas the expression in the liver was not modulated by estrogens.     

Rat corticotropin-releasing hormone gene: sequence and tissue-specific expression

The rat corticotropin releasing hormone (CRH) gene has been isolated and characterized by DNA sequence analysis. The gene exhibits a structural organization similar to that of the human CRH gene. The nucleotide sequence encoding the entire rat CRH precursor is located on the second exon, while exon I encodes the 5'-untranslated region of the mRNA. Analysis of the nucleotide sequence homology between the human and rat CRH genes reveals several highly conserved regions including the CRH peptide-encoding sequence and the 5'-flanking sequence. RNA blot analysis demonstrates that CRH mRNA can be observed in numerous regions of the rat brain as well as the spinal cord, adrenal gland, pituitary, and testis.