Tissue-specific expression from a compound TATA-dependent and TATA-independent promoter.

We have found that the mouse metallothionein-I (MT-I) gene promoter functions in an unusual, compound manner. It directs both TATA-dependent and TATA-independent modes of transcription in vivo. The TATA-dependent message is initiated at the previously characterized +1 transcription start site and is the predominant species in most tissues. In many cell types it is metal inducible. The TATA-independent initiation sites are distributed over the 160 bp upstream of the previously characterized +1 start site, and the RNA products are present in all tissues examined. Only in testis, however, do the TATA-independent transcripts predominate, accumulating to highest levels in pachytene-stage meiotic cells and early spermatids. Unlike the TATA-dependent +1 transcript, these RNAs are not induced by metal, even in cultured cells in which the +1 species is induced. Transfection studies of site-directed mutants show that destruction of the TATA element drastically alters the ratio of the two RNA classes in cells in which the +1 transcripts normally dominates. In TATA-minus mutants, the TATA-independent RNAs become the most prevalent, although they remain refractory to metal induction. Thus, the MT-I promoter utilizes two different types of core promoter function within a single cell population. The two different types of core promoter respond very differently to environmental stimuli, and the choice between them appears to be regulated in a tissue-specific fashion.

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Human glucagon gene promoter sequences regulating tissue-specific versus nutrient-regulated gene expression

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00215.2001 ◽

2002 ◽

Vol 282 (1) ◽

pp. R173-R183 ◽

Cited By ~ 23

Author(s):

Min Nian ◽

Jun Gu ◽

David M. Irwin ◽

Daniel J. Drucker

Keyword(s):

Gene Expression ◽

Gene Promoter ◽

Regulatory Sequences ◽

Dependent Manner ◽

Specific Expression ◽

Tissue Specific ◽

High Fiber ◽

Fiber Diet ◽

Regulated Gene Expression

The glucagon-like peptides (GLPs) are synthesized and secreted in a nutrient-dependent manner in rodents; however, the factors regulating human GLP-1 and GLP-2 biosynthesis remain unclear. To understand how nutrients regulate human proglucagon gene expression, we studied the expression of a human proglucagon promoter-growth hormone (GH) transgene in 1.6 human glucagon-GH transgenic mice. Fasting-refeeding significantly decreased and increased the levels of circulating mouse insulin and transgene-derived hGH ( P < 0.05 fasting vs. refeeding) and decreased and upregulated, respectively, the levels of endogenous mouse proglucagon RNA in the ileum but not in the jejunum or colon. High-fiber feeding significantly increased the levels of glucose-stimulated circulating hGH and upregulated levels of mouse intestinal proglucagon gene expression in the jejunum, ileum, and colon ( P < 0.05, 0 vs. 30% fiber diet). In contrast, neither fasting-refeeding nor a high-fiber diet upregulated the expression of the human proglucagon promoter-hGH transgene. These findings demonstrate that human proglucagon gene regulatory sequences specifying tissue-specific expression in gut endocrine cells are not sufficient for recognition of energy-derived signals regulating murine glucagon gene expression in enteroendocrine cells in vivo.

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Expression of small cytoplasmic transcripts of the rat identifier element in vivo and in cultured cells.

Molecular and Cellular Biology ◽

10.1128/mcb.7.6.2148 ◽

1987 ◽

Vol 7 (6) ◽

pp. 2148-2154 ◽

Cited By ~ 36

Author(s):

R D McKinnon ◽

P Danielson ◽

M A Brow ◽

F E Bloom ◽

J G Sutcliffe

Keyword(s):

Rat Brain ◽

Cell Lines ◽

Mammalian Cells ◽

Cultured Cells ◽

Cell Types ◽

Culture Conditions ◽

Specific Expression ◽

Peripheral Tissues ◽

Primate Cell

We examined the level of expression of small RNA transcripts hybridizing to a rodent repetitive DNA element, the identifier (ID) sequence, in a variety of cell types in vivo and in cultured mammalian cells. A 160-nucleotide (160n) cytoplasmic poly(A)+ RNA (BC1) appeared in late embryonic and early postnatal rat brain development, was enriched in the cerebral cortex, and appeared to be restricted to neural tissue and the anterior pituitary gland. A 110n RNA (BC2) was specifically enriched in brain, especially the postnatal cortex, but was detectable at low levels in peripheral tissues. A third, related 75n poly(A)- RNA (T3) was found in rat brain and at lower levels in peripheral tissues but was very abundant in the testes. The BC RNAs were found in a variety of rat cell lines, and their level of expression was dependent upon cell culture conditions. A rat ID probe detected BC-like RNAs in mouse brain but not liver and detected a 200n RNA in monkey brain but not liver at lower hybridization stringencies. These RNAs were expressed by mouse and primate cell lines. Thus, tissue-specific expression of small ID-sequence-related transcripts is conserved among mammals, but the tight regulation found in vivo is lost by cells in culture.

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Ksp-cadherin gene promoter. II. Kidney-specific activity in transgenic mice

AJP Renal Physiology ◽

10.1152/ajprenal.1999.277.4.f599 ◽

1999 ◽

Vol 277 (4) ◽

pp. F599-F610 ◽

Cited By ~ 22

Author(s):

Peter Igarashi ◽

Cooduvalli S. Shashikant ◽

R. Brent Thomson ◽

Dilys A. Whyte ◽

Shuxian Liu-Chen ◽

...

Keyword(s):

Epithelial Cells ◽

Transgenic Mice ◽

Collecting Duct ◽

Gene Promoter ◽

Regulatory Elements ◽

Developmental Expression ◽

Tubular Epithelial Cells ◽

Specific Expression ◽

Tissue Specific

Kidney-specific cadherin (Ksp-cadherin, cadherin 16) is a tissue-specific member of the cadherin superfamily that is expressed exclusively in the basolateral membrane of tubular epithelial cells in the kidney. To determine the basis for tissue-specific expression of Ksp-cadherin in vivo, we evaluated the activity of the promoter in transgenic mice. Transgenic mice containing 3.3 kb of the mouse Ksp-cadherin promoter and an Escherichia coli lacZ reporter gene were generated by pronuclear microinjection. Assays of β-galactosidase enzyme activity showed that the transgene was expressed exclusively in the kidney in both adult and developing mice. Within the kidney, the transgene was expressed in a subset of renal tubular epithelial cells that endogenously expressed Ksp-cadherin and that were identified as collecting ducts by colabeling with Dolichos biflorus agglutinin. In the developing metanephros, expression of the transgene in the branching ureteric bud correlated with the developmental expression of Ksp-cadherin. Identical patterns of expression were observed in multiple founder mice, indicating that kidney specificity was independent of transgene integration site. However, heterocellular expression was observed consistent with repeat-induced gene silencing. We conclude that the Ksp-cadherin gene promoter directs kidney-specific expression in vivo. Regulatory elements that are sufficient to recapitulate the tissue- and differentiation-specific expression of Ksp-cadherin in the renal collecting duct are located within 3.3 kb upstream to the transcriptional start site.

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Tissue-Specific and Inducer-Specific Differential Induction of ISG56 and ISG54 in Mice

Journal of Virology ◽

10.1128/jvi.00322-07 ◽

2007 ◽

Vol 81 (16) ◽

pp. 8656-8665 ◽

Cited By ~ 49

Author(s):

Fulvia Terenzi ◽

Christine White ◽

Srabani Pal ◽

Bryan R. G. Williams ◽

Ganes C. Sen

Keyword(s):

Cultured Cells ◽

Cell Types ◽

Type I Interferons ◽

Specific Cell ◽

Type I ◽

Mrna Levels ◽

Tissue Specific ◽

Interferon Stimulated Genes ◽

Differential Pattern

ABSTRACT The interferon-stimulated genes (ISGs) ISG56 and ISG54 are strongly induced in cultured cells by type I interferons (IFNs), viruses, and double-stranded RNA (dsRNA), which activate their transcription by various signaling pathways. Here we studied the stimulus-dependent induction of both genes in vivo. dsRNA, which is generated during virus infection, induced the expression of both genes in all organs examined. Induction was not seen in STAT1-deficient mice, indicating that dsRNA-induced gene expression requires endogenous IFN. We further examined the regulation of these ISGs in several organs from mice injected with dsRNA or IFN-β. Both ISG56 and ISG54 were widely expressed and at comparable levels. However, in organs isolated from mice injected with IFN-α the expression of ISG54 was reduced and more restricted in distribution compared with the expression level and distribution of ISG56. When we began to study specific cell types, splenic B cells showed ISG54 but not ISG56 expression in response to all agonists. Finally, in livers isolated from mice infected with vesicular stomatitis virus, the expression of ISG56, but not ISG54, was induced; this difference was observed at both protein and mRNA levels. These studies have revealed unexpected complexity in IFN-stimulated gene induction in vivo. For the first time we showed that the two closely related genes are expressed in a tissue-specific and inducer-specific manner. Furthermore, our findings provide the first evidence of a differential pattern of expression of ISG54 and ISG56 genes by IFN-α and IFN-β.

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Expression of small cytoplasmic transcripts of the rat identifier element in vivo and in cultured cells

Molecular and Cellular Biology ◽

10.1128/mcb.7.6.2148-2154.1987 ◽

1987 ◽

Vol 7 (6) ◽

pp. 2148-2154

Author(s):

R D McKinnon ◽

P Danielson ◽

M A Brow ◽

F E Bloom ◽

J G Sutcliffe

Keyword(s):

Rat Brain ◽

Cell Lines ◽

Mammalian Cells ◽

Cultured Cells ◽

Cell Types ◽

Culture Conditions ◽

Specific Expression ◽

Peripheral Tissues ◽

Primate Cell

We examined the level of expression of small RNA transcripts hybridizing to a rodent repetitive DNA element, the identifier (ID) sequence, in a variety of cell types in vivo and in cultured mammalian cells. A 160-nucleotide (160n) cytoplasmic poly(A)+ RNA (BC1) appeared in late embryonic and early postnatal rat brain development, was enriched in the cerebral cortex, and appeared to be restricted to neural tissue and the anterior pituitary gland. A 110n RNA (BC2) was specifically enriched in brain, especially the postnatal cortex, but was detectable at low levels in peripheral tissues. A third, related 75n poly(A)- RNA (T3) was found in rat brain and at lower levels in peripheral tissues but was very abundant in the testes. The BC RNAs were found in a variety of rat cell lines, and their level of expression was dependent upon cell culture conditions. A rat ID probe detected BC-like RNAs in mouse brain but not liver and detected a 200n RNA in monkey brain but not liver at lower hybridization stringencies. These RNAs were expressed by mouse and primate cell lines. Thus, tissue-specific expression of small ID-sequence-related transcripts is conserved among mammals, but the tight regulation found in vivo is lost by cells in culture.

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Transcriptional and morphological profiling of parvalbumin interneuron subpopulations in the mouse hippocampus

Nature Communications ◽

10.1038/s41467-020-20328-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Lin Que ◽

David Lukacsovich ◽

Wenshu Luo ◽

Csaba Földy

Keyword(s):

Large Scale ◽

Cell Types ◽

Rna Seq ◽

Neuronal Identity ◽

Parvalbumin Interneurons ◽

Different Types ◽

Parvalbumin Interneuron ◽

Cam Profile ◽

Developmental Domains

AbstractThe diversity reflected by >100 different neural cell types fundamentally contributes to brain function and a central idea is that neuronal identity can be inferred from genetic information. Recent large-scale transcriptomic assays seem to confirm this hypothesis, but a lack of morphological information has limited the identification of several known cell types. In this study, we used single-cell RNA-seq in morphologically identified parvalbumin interneurons (PV-INs), and studied their transcriptomic states in the morphological, physiological, and developmental domains. Overall, we find high transcriptomic similarity among PV-INs, with few genes showing divergent expression between morphologically different types. Furthermore, PV-INs show a uniform synaptic cell adhesion molecule (CAM) profile, suggesting that CAM expression in mature PV cells does not reflect wiring specificity after development. Together, our results suggest that while PV-INs differ in anatomy and in vivo activity, their continuous transcriptomic and homogenous biophysical landscapes are not predictive of these distinct identities.

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Quantitative Studies of Fibronectin Adsorption on Submicron Scaffolds

ASME 2012 Summer Bioengineering Conference, Parts A and B ◽

10.1115/sbc2012-80633 ◽

2012 ◽

Author(s):

Shawn Regis ◽

Manisha Jassal ◽

Sina Youssefian ◽

Nima Rahbar ◽

Sankha Bhowmick

Keyword(s):

Surface Functionalization ◽

Cultured Cells ◽

Cell Attachment ◽

Md Simulations ◽

Cell Types ◽

Biological Processes ◽

Integrin Receptors ◽

Tissue Engineering Scaffolds ◽

Quantitative Studies

Fibronectin plays a crucial role in adhesion of several cell types, mainly due to the fact that it is recognized by at least ten different integrin receptors. Since most cell types can bind to fibronectin, it becomes involved in many various biological processes. The interaction of cells with ECM proteins such as fibronectin provides the signals affecting morphology, motility, gene expression, and survival of cells [1]. Fibronectin exists in both soluble and insoluble forms; soluble fibronectin is secreted by cells and exits in cell media or body fluids, whereas insoluble fibronectin exists in tissues or the extracellular matrix of cultured cells [2]. The ability to control adsorption of fibronectin on tissue engineering scaffolds would therefore play a huge role in controlling cell attachment and survival in vivo. This can be achieved through surface functionalization of the scaffolds. The goal of these studies is to use molecular dynamics (MD) simulations to mechanistically understand how fibronectin adsorption is enhanced by surface functionalization of submicron scaffolds.

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Human globin gene promoter sequences are sufficient for specific expression of a hybrid gene transfected into tissue culture cells

Molecular and Cellular Biology ◽

10.1128/mcb.7.1.398-402.1987 ◽

1987 ◽

Vol 7 (1) ◽

pp. 398-402

Author(s):

T Rutherford ◽

A W Nienhuis

Keyword(s):

Gene Expression ◽

Globin Gene ◽

Gene Promoter ◽

Gene Promoters ◽

Globin Genes ◽

Specific Expression ◽

Tissue Specific ◽

Promoter Sequences ◽

Erythroleukemia Cells ◽

Murine Erythroleukemia

The contribution of the human globin gene promoters to tissue-specific transcription was studied by using globin promoters to transcribe the neo (G418 resistance) gene. After transfection into different cell types, neo gene expression was assayed by scoring colony formation in the presence of G418. In K562 human erythroleukemia cells, which express fetal and embryonic globin genes but not the adult beta-globin gene, the neo gene was expressed strongly from a fetal gamma- or embryonic zeta-globin gene promoter but only weakly from the beta promoter. In murine erythroleukemia cells which express the endogenous mouse beta genes, the neo gene was strongly expressed from both beta and gamma promoters. In two nonerythroid cell lines, human HeLa cells and mouse 3T3 fibroblasts, the globin gene promoters did not allow neo gene expression. Globin-neo genes were integrated in the erythroleukemia cell genomes mostly as a single copy per cell and were transcribed from the appropriate globin gene cap site. We conclude that globin gene promoter sequences extending from -373 to +48 base pairs (bp) (relative to the cap site) for the beta gene, -385 to +34 bp for the gamma gene, and -555 to +38 bp for the zeta gene are sufficient for tissue-specific and perhaps developmentally specific transcription.

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Stable transfer and restricted expression of a cloned class I gene encoding a secreted transplantation-like antigen

Molecular and Cellular Biology ◽

10.1128/mcb.5.6.1295-1300.1985 ◽

1985 ◽

Vol 5 (6) ◽

pp. 1295-1300

Author(s):

Y Barra ◽

K Tanaka ◽

K J Isselbacher ◽

G Khoury ◽

G Jay

Keyword(s):

Molecular Mechanisms ◽

Cell Types ◽

Class I ◽

Regulatory Sequences ◽

Transcriptional Enhancer ◽

Gene Encoding ◽

Specific Expression ◽

Tissue Specific ◽

Functional Studies ◽

I Gene

The identification of a unique major histocompatibility complex class I gene, designated Q10, which encodes a secreted rather than a cell surface antigen has led to questions regarding its potential role in regulating immunological functions. Since the Q10 gene is specifically activated only in the liver, we sought to define the molecular mechanisms which control its expression in a tissue-specific fashion. Results obtained by transfection of the cloned Q10 gene, either in the absence or presence of a heterologous transcriptional enhancer, into a variety of cell types of different tissue derivations are consistent with the Q10 gene being regulated at two levels. The first is by a cis-dependent mechanism which appears to involve site-specific DNA methylation. The second is by a trans-acting mechanism which would include the possibility of an enhancer binding factor. The ability to efficiently express the Q10 gene in certain transfected cell lines offers an opportunity to obtain this secreted class I antigen in quantities sufficient for functional studies; this should also make it possible to define regulatory sequences which may be responsible for the tissue-specific expression of Q10.

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