Sgs-3 chromatin structure and trans-activators: developmental and ecdysone induction of a glue enhancer-binding factor, GEBF-I, in Drosophila larvae

The transcription of the Drosophila melanogaster 68C salivary gland glue gene Sgs-3 involves the interaction of a distal and a proximal regulatory region. These are marked in vivo by a specific chromatin structure which is established sequentially during development, starting early in embryogenesis. The distal region is characterized by a stage- and tissue-specific DNase I hypersensitive site. A stage- and tissue-specific factor, GEBF-I, binds in this region and is missing in 2B5 mutant larvae which lack Sgs-3 transcripts. This binding involves the simultaneous interaction with two distinct DNA sequences which induces conformational changes in the protein. Salivary glands acquire competence to respond to ecdysone in the mid-third larval instar, whereafter the hormone rapidly induces both the GEBF-I protein and Sgs-3 transcription.

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Interaction of a tissue-specific factor with an essential rat growth hormone gene promoter element.

Molecular and Cellular Biology ◽

10.1128/mcb.7.3.1193 ◽

1987 ◽

Vol 7 (3) ◽

pp. 1193-1197 ◽

Cited By ~ 51

Author(s):

B L West ◽

D F Catanzaro ◽

S H Mellon ◽

P A Cattini ◽

J D Baxter ◽

...

Keyword(s):

Growth Hormone ◽

Dna Sequences ◽

Site Directed Mutagenesis ◽

Specific Factor ◽

Growth Hormone Gene ◽

Base Pairs ◽

Hybrid Gene ◽

Specific Expression ◽

Tissue Specific ◽

Rat Growth

Rat growth hormone (rGH) gene expression is normally restricted to the anterior pituitary. As a model of this tissue specificity, we compared the transient expression of an rGH-chloramphenicol acetyltransferase (CAT) hybrid gene in rGH-producing rat pituitary tumor (GC) cells and in non-rGH-producing rat fibroblast (rat-2) cells. Deletion analysis of the rGH portion of this hybrid gene demonstrated that DNA sequences within 140 base pairs 5' to the rGH gene were sufficient for correct cell type-specific expression. Deletion of an additional 35 base pairs of the rGH 5'-flanking DNA resulted in a loss of expression of the transfected hybrid gene and correlated with the interaction of a putative trans-acting factor with this region of the rGH promoter. This factor was detectable by DNase I footprinting in a crude nuclear extract from GC cells but not from rat-2 cells. Site-directed mutagenesis of the footprint region caused complete loss of expression of a hybrid gene containing 530 base pairs 5' to the rGH gene. Thus, the interaction of this factor, which we term GC2, is likely to be essential for the tissue-specific expression of the rGH gene.

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FoxA Proteins Regulate H19 Endoderm Enhancer E1 and Exhibit Developmental Changes in Enhancer Binding In Vivo

Molecular and Cellular Biology ◽

10.1128/mcb.24.21.9601-9609.2004 ◽

2004 ◽

Vol 24 (21) ◽

pp. 9601-9609 ◽

Cited By ~ 12

Author(s):

Lingyun Long ◽

Brett T. Spear

Keyword(s):

Chromatin Immunoprecipitation ◽

Binding Sites ◽

Fetal Liver ◽

Carcinoma Cells ◽

Specific Factor ◽

Specific Expression ◽

Tissue Specific ◽

Parietal Endoderm ◽

F9 Embryonal Carcinoma Cells

ABSTRACT Multiple enhancers govern developmental and tissue-specific expression of the H19-Igf2 locus, but factors that bind these elements have not been identified. Using chromatin immunoprecipitation, we have found two FoxA binding sites in the H19 E1 enhancer. Mutating these sites diminishes E1 activity in hepatoma cells. Additional chromatin immunoprecipitations show that FoxA binds to E1 in fetal liver, where H19 is abundantly expressed, but that binding decreases in adult liver, where H19 is no longer transcribed, even though FoxA proteins are present at both times. FoxA proteins are induced when F9 embryonal carcinoma cells differentiate into visceral endoderm (VE) and parietal endoderm (PE). We show that FoxA binds E1 in VE cells, where H19 is expressed, but not in PE cells, where H19 is silent. This correlation between FoxA binding and H19 expression indicates a role for FoxA in regulating H19, including developmental activation in the yolk sac and liver and postnatal repression in the liver. This is the first demonstration of a tissue-specific factor involved in developmental control of H19 expression. These data also indicate that the presence of FoxA proteins is not sufficient for binding but that additional mechanisms must govern the accessibility of FoxA proteins to their cognate binding sites within the H19 E1 enhancer.

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Transcription of the interleukin 4 gene is regulated by multiple promoter elements.

Journal of Experimental Medicine ◽

10.1084/jem.177.6.1663 ◽

1993 ◽

Vol 177 (6) ◽

pp. 1663-1674 ◽

Cited By ~ 69

Author(s):

M D Todd ◽

M J Grusby ◽

J A Lederer ◽

E Lacy ◽

A H Lichtman ◽

...

Keyword(s):

Gene Transcription ◽

Dna Sequences ◽

Interleukin 2 ◽

Regulatory Elements ◽

Inducible Expression ◽

Interleukin 4 ◽

Upstream Sequence ◽

Tissue Specific ◽

Cytokine Genes

Activation of T helper cell 1 (Th1) and Th2 results in transcription of the interleukin 2 (IL-2) and IL-4 cytokine genes, respectively. Whereas many of the regulatory elements and factors responsible for IL-2 transcription in T cells are well defined, little is known about parallel mechanisms that drive transcription of the IL-4 gene. Here we have analyzed the murine IL-4 promoter, both in vivo and in a Th2 clone. 3 kb of IL-4 upstream sequence is shown to be sufficient to achieve tissue-specific and inducible expression of a thymidine kinase reporter gene in vivo in a manner that mirrors the expression of endogenous IL-4. Tissue-specific and inducible expression is also demonstrated in a Th2 clone, but not in a B cell line. Deletional and mutational analysis of the IL-4 promoter demonstrated that sequences from -100 to -28 were necessary for a transcriptional response to Concanavalin A or anti-CD3 monoclonal antibody. An overlapping, yet smaller region, spanning the sequences from -60 to -28 bp was shown to be required for the response to ionomycin. Mutation of an 8-bp region from -43 to -35 of the IL-4 promoter completely abrogated IL-4 gene transcription in response to all stimuli tested. In addition, our results show that the effects of the immunosuppressive agent Cyclosporin A map to the same DNA sequences as the positive control elements. These results identify DNA sequences that are functionally important for the control of IL-4 gene transcription both in vivo and in vitro. Although these sequences are highly conserved in the human and murine IL-4 genes, they are largely not present in the IL-2 enhancer complex. Thus, cytokine-specific cis-acting elements may be one mechanism by which these two cytokine genes are differentially regulated.

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Trithorax- and Polycomb-Group Response Elements within an Ultrabithorax Transcription Maintenance Unit Consist of Closely Situated but Separable Sequences

Molecular and Cellular Biology ◽

10.1128/mcb.19.7.5189 ◽

1999 ◽

Vol 19 (7) ◽

pp. 5189-5202 ◽

Cited By ~ 70

Author(s):

Sergei Tillib ◽

Svetlana Petruk ◽

Yurii Sedkov ◽

Alexander Kuzin ◽

Miki Fujioka ◽

...

Keyword(s):

Dna Sequences ◽

Protein Complexes ◽

Expression Patterns ◽

Regulatory Region ◽

Protein Product ◽

Polycomb Group ◽

Response Elements ◽

Complex Element ◽

Group Response

ABSTRACT In Drosophila, two classes of genes, thetrithorax group and the Polycomb group, are required in concert to maintain gene expression by regulating chromatin structure. We have identified Trithorax protein (TRX) binding elements within the bithorax complex and have found that within thebxd/pbx regulatory region these elements are functionally relevant for normal expression patterns in embryos and confer TRX binding in vivo. TRX was localized to three closely situated sites within a 3-kb chromatin maintenance unit with a modular structure. Results of an in vivo analysis showed that these DNA fragments (each ∼400 bp) contain both TRX- and Polycomb-group response elements (TREs and PREs) and that in the context of the endogenousUltrabithorax gene, all of these elements are essential for proper maintenance of expression in embryos. Dissection of one of these maintenance modules showed that TRX- and Polycomb-group responsiveness is conferred by neighboring but separable DNA sequences, suggesting that independent protein complexes are formed at their respective response elements. Furthermore, we have found that the activity of this TRE requires a sequence (∼90 bp) which maps to within several tens of base pairs from the closest neighboring PRE and that the PRE activity in one of the elements may require a binding site for PHO, the protein product of the Polycomb-group genepleiohomeotic. Our results show that long-range maintenance of Ultrabithorax expression requires a complex element composed of cooperating modules, each capable of interacting with both positive and negative chromatin regulators.

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Binding of a factor to an enhancer element responsible for the tissue-specific expression of the chicken alpha A-crystallin gene

Development ◽

10.1242/dev.113.2.539 ◽

1991 ◽

Vol 113 (2) ◽

pp. 539-550 ◽

Cited By ~ 2

Author(s):

I. Matsuo ◽

M. Kitamura ◽

K. Okazaki ◽

K. Yasuda

Keyword(s):

Gene Expression ◽

Dna Sequences ◽

Nuclear Protein ◽

Fusion Gene ◽

Regulatory Region ◽

Binding Activity ◽

Flanking Sequence ◽

Specific Expression ◽

Enhancer Element

We have characterized a regulatory region of the chicken alpha A-crystallin gene using transfection assays, which revealed that a 84 base pair element (−162 to −79) in the 5′ flanking sequence is necessary and sufficient for lens-specific expression. A multimer of this element functions as lens-specific enhancer and synergistically activates transcription from chicken alpha A-crystallin or beta-actin basal promoters fused to the CAT gene. In vivo competition experiments demonstrated that DNA sequences containing the 84 bp element reduced alpha A-crystallin-CAT fusion gene expression. A nuclear factor present exclusively in lens cells binds to the 84 bp element in the region between positions −165 and −140. Southwestern blot analysis showed that 61,000 Mr (61 × 10(3) Mr) lens nuclear protein exhibited DNA-binding activity specific to the 84 bp element. Our data suggested that the 61 × 10(3) Mr nuclear protein, and the 84 bp element that it interacts with, may be involved in regulating the alpha A-crystallin gene expression in vivo.

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Interaction of a tissue-specific factor with an essential rat growth hormone gene promoter element

Molecular and Cellular Biology ◽

10.1128/mcb.7.3.1193-1197.1987 ◽

1987 ◽

Vol 7 (3) ◽

pp. 1193-1197

Author(s):

B L West ◽

D F Catanzaro ◽

S H Mellon ◽

P A Cattini ◽

J D Baxter ◽

...

Keyword(s):

Growth Hormone ◽

Dna Sequences ◽

Site Directed Mutagenesis ◽

Specific Factor ◽

Growth Hormone Gene ◽

Base Pairs ◽

Hybrid Gene ◽

Specific Expression ◽

Tissue Specific ◽

Rat Growth

Rat growth hormone (rGH) gene expression is normally restricted to the anterior pituitary. As a model of this tissue specificity, we compared the transient expression of an rGH-chloramphenicol acetyltransferase (CAT) hybrid gene in rGH-producing rat pituitary tumor (GC) cells and in non-rGH-producing rat fibroblast (rat-2) cells. Deletion analysis of the rGH portion of this hybrid gene demonstrated that DNA sequences within 140 base pairs 5' to the rGH gene were sufficient for correct cell type-specific expression. Deletion of an additional 35 base pairs of the rGH 5'-flanking DNA resulted in a loss of expression of the transfected hybrid gene and correlated with the interaction of a putative trans-acting factor with this region of the rGH promoter. This factor was detectable by DNase I footprinting in a crude nuclear extract from GC cells but not from rat-2 cells. Site-directed mutagenesis of the footprint region caused complete loss of expression of a hybrid gene containing 530 base pairs 5' to the rGH gene. Thus, the interaction of this factor, which we term GC2, is likely to be essential for the tissue-specific expression of the rGH gene.

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Histone Modifications, but Not Nucleosomal Positioning, Correlate with Major Histocompatibility Complex Class I Promoter Activity in Different Tissues In Vivo

Molecular and Cellular Biology ◽

10.1128/mcb.00889-08 ◽

2008 ◽

Vol 28 (24) ◽

pp. 7323-7336 ◽

Cited By ~ 10

Author(s):

Aparna S. Kotekar ◽

Jocelyn D. Weissman ◽

Anne Gegonne ◽

Helit Cohen ◽

Dinah S. Singer

Keyword(s):

Major Histocompatibility Complex ◽

Mhc Class I ◽

Histone Modifications ◽

Nucleosome Occupancy ◽

Regulatory Region ◽

Class I ◽

Major Histocompatibility ◽

Tissue Specific ◽

Histocompatibility Complex

ABSTRACT To examine the role of chromatin in transcriptional regulation of the major histocompatibility complex (MHC) class I gene, we determined nucleosome occupancy and positioning, histone modifications, and H2A.Z occupancy across its regulatory region in murine tissues that have widely different expression levels. Surprisingly, nucleosome occupancy and positioning were indistinguishable between the spleen, kidney, and brain. In all three tissues, the 200 bp upstream of the transcription start site had low nucleosome occupancy. In contrast, nuclease hypersensitivity, histone modifications, and H2A.Z occupancy showed tissue-specific differences. Thus, tissue-specific differences in MHC class I transcription correlate with histone modifications and not nucleosomal organization. Further, activation of class I transcription by gamma interferon or its inhibition by α-amanitin did not alter nucleosome occupancy, positioning, nuclease hypersensitivity, histone modifications, or H2A.Z occupancy in any of the tissues examined. Thus, chromatin remodeling was not required to dynamically modulate transcriptional levels. These findings suggest that the MHC class I promoter remains poised and accessible to rapidly respond to infection and environmental cues.

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Conserved Sequences in a Tissue-Specific Regulatory Region of the pdx-1 Gene Mediate Transcription in Pancreatic β Cells: Role for Hepatocyte Nuclear Factor 3β and Pax6

Molecular and Cellular Biology ◽

10.1128/mcb.22.13.4702-4713.2002 ◽

2002 ◽

Vol 22 (13) ◽

pp. 4702-4713 ◽

Cited By ~ 56

Author(s):

Susan E. Samaras ◽

Michelle A. Cissell ◽

Kevin Gerrish ◽

Christopher V. E. Wright ◽

Maureen Gannon ◽

...

Keyword(s):

Cell Function ◽

Regulatory Region ◽

Nuclear Factor ◽

Hepatocyte Nuclear Factor ◽

Β Cells ◽

Β Cell ◽

Tissue Specific ◽

Conserved Sequence

ABSTRACT Pancreas duodenum homeobox 1 (PDX-1) is absolutely required for pancreas development and the maintenance of islet β-cell function. Temporal and cell-type-specific transcription of the pdx-1 gene is controlled by factors acting upon sequences found within its 5′-flanking region. Critical cis-acting transcriptional control elements are located within a nuclease hypersensitive site that contains three conserved subdomains, termed areas I, II, and III. We show that area II acts as a tissue-specific regulatory region of the pdx-1 gene, directing transgene expression to a subpopulation of islet cells. Mutation of the area II hepatocyte nuclear factor 3 (HNF3) binding element in the larger area I- and area II- containing PstBst fragment also decreases PBhsplacZ transgene penetrance. These two results indicate possible ontogenetic and/or functional heterogeneity of the β-cell population. Several other potential positive- and negative-acting control elements were identified in area II after mutation of the highly conserved sequence blocks within this subdomain. Pax6, a factor essential for islet α-cell development and islet hormone gene expression, was shown to bind in area II in vitro. Pax6 and HNF3β were also found to bind to this region in vivo by using the chromatin immunoprecipitation assay. Collectively, these data suggest an important role for both HNF3β and Pax6 in regulating pdx-1 expression in β cells.

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CarR, a MarR-family regulator from Corynebacterium glutamicum, modulated antibiotic and aromatic compound resistance

Biochemical Journal ◽

10.1042/bcj20190320 ◽

2019 ◽

Vol 476 (21) ◽

pp. 3141-3159 ◽

Cited By ~ 2

Author(s):

Meiru Si ◽

Can Chen ◽

Zengfan Wei ◽

Zhijin Gong ◽

GuiZhi Li ◽

...

Keyword(s):

Stress Response ◽

Ligand Binding ◽

Corynebacterium Glutamicum ◽

Conformational Changes ◽

Cysteine Oxidation ◽

Transcriptional Regulatory ◽

Ligand Free ◽

Redox Sensing

Abstract MarR (multiple antibiotic resistance regulator) proteins are a family of transcriptional regulators that is prevalent in Corynebacterium glutamicum. Understanding the physiological and biochemical function of MarR homologs in C. glutamicum has focused on cysteine oxidation-based redox-sensing and substrate metabolism-involving regulators. In this study, we characterized the stress-related ligand-binding functions of the C. glutamicum MarR-type regulator CarR (C. glutamicum antibiotic-responding regulator). We demonstrate that CarR negatively regulates the expression of the carR (ncgl2886)–uspA (ncgl2887) operon and the adjacent, oppositely oriented gene ncgl2885, encoding the hypothetical deacylase DecE. We also show that CarR directly activates transcription of the ncgl2882–ncgl2884 operon, encoding the peptidoglycan synthesis operon (PSO) located upstream of carR in the opposite orientation. The addition of stress-associated ligands such as penicillin and streptomycin induced carR, uspA, decE, and PSO expression in vivo, as well as attenuated binding of CarR to operator DNA in vitro. Importantly, stress response-induced up-regulation of carR, uspA, and PSO gene expression correlated with cell resistance to β-lactam antibiotics and aromatic compounds. Six highly conserved residues in CarR were found to strongly influence its ligand binding and transcriptional regulatory properties. Collectively, the results indicate that the ligand binding of CarR induces its dissociation from the carR–uspA promoter to derepress carR and uspA transcription. Ligand-free CarR also activates PSO expression, which in turn contributes to C. glutamicum stress resistance. The outcomes indicate that the stress response mechanism of CarR in C. glutamicum occurs via ligand-induced conformational changes to the protein, not via cysteine oxidation-based thiol modifications.

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