scholarly journals FoxA2, Nkx2.2, and PDX-1 Regulate Islet β-Cell-Specific mafA Expression through Conserved Sequences Located between Base Pairs −8118 and −7750 Upstream from the Transcription Start Site

2006 ◽  
Vol 26 (15) ◽  
pp. 5735-5743 ◽  
Author(s):  
Jeffrey C. Raum ◽  
Kevin Gerrish ◽  
Isabella Artner ◽  
Eva Henderson ◽  
Min Guo ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Cell Function ◽  
Specific Activity ◽  
Regulatory Region ◽  
Start Site ◽  
Cell Type ◽  
Transcription Start ◽  
Β Cell ◽  
Pancreatic Cell ◽  
Cell Type Specific

ABSTRACT The MafA transcription factor is both critical to islet β-cell function and has a unique pancreatic cell-type-specific expression pattern. To localize the potential transcriptional regulatory region(s) involved in directing expression to the β cell, areas of identity within the 5′ flanking region of the mouse, human, and rat mafA genes were found between nucleotides −9389 and −9194, −8426 and −8293, −8118 and −7750, −6622 and −6441, −6217 and −6031, and −250 and +56 relative to the transcription start site. The identity between species was greater than 75%, with the highest found between bp −8118 and −7750 (∼94%, termed region 3). Region 3 was the only upstream mammalian conserved region found in chicken mafA (88% identity). In addition, region 3 uniquely displayed β-cell-specific activity in cell-line-based reporter assays. Important regulators of β-cell formation and function, PDX-1, FoxA2, and Nkx2.2, were shown to specifically bind to region 3 in vivo using the chromatin immunoprecipitation assay. Mutational and functional analyses demonstrated that FoxA2 (bp −7943 to −7910), Nkx2.2 (bp −7771 to −7746), and PDX-1 (bp −8087 to −8063) mediated region 3 activation. Consistent with a role in transcription, small interfering RNA-mediated knockdown of PDX-1 led to decreased mafA mRNA production in INS-1-derived β-cell lines (832/13 and 832/3), while MafA expression was undetected in the pancreatic epithelium of Nkx2.2 null animals. These results suggest that β-cell-type-specific mafA transcription is principally controlled by region 3-acting transcription factors that are essential in the formation of functional β cells.

scholarly journals Lysine Represses Transcription of the Escherichia coli dapB Gene by Preventing Its Activation by the ArgP Activator

2008 ◽  
Vol 190 (15) ◽  
pp. 5224-5229 ◽  
Author(s):  
Jean Bouvier ◽  
Patrick Stragier ◽  
Violette Morales ◽  
Elisabeth Rémy ◽  
Claude Gutierrez
Keyword(s):  
Escherichia Coli ◽  
Transcription Start Site ◽  
Biosynthetic Pathway ◽  
Genomic Library ◽  
Regulatory Region ◽  
Null Mutation ◽  
Start Site ◽  
Transcription Start ◽  
Gene Encoding ◽  
Gel Retardation Assay

ABSTRACT The Escherichia coli dapB gene encodes one of the enzymes of the biosynthetic pathway leading to lysine and its immediate precursor, diaminopimelate. Expression of dapB is repressed by lysine, but no trans-acting regulator has been identified so far. Our analysis of the dapB regulatory region shows that sequences located in the −81/−118 interval upstream of the transcription start site are essential for full expression of dapB, as well as for lysine repression. Screening a genomic library for a gene that could alleviate lysine repression when present in multicopy led to the recovery of argP, a gene encoding an activating protein of the LysR-type family, known to use lysine as an effector. An argP null mutation strongly decreases dapB transcription that becomes insensitive to lysine. Purified His6-tagged ArgP protein binds with an apparent K d of 35 nM to the dapB promoter in a gel retardation assay, provided that sequences up to −103 are present. In the presence of l-lysine and l-arginine, the binding of ArgP to dapB is partly relieved. These results fit with a model in which ArgP contributes to enhanced transcription of dapB when lysine becomes limiting.

scholarly journals A catalog of transcription start sites across 115 human tissue and cell types

2021 ◽  
Author(s):  
Jill E Moore ◽  
Xiao-Ou Zhang ◽  
Shaimae I Elhajjajy ◽  
Kaili Fan ◽  
Fairlie Reese ◽  
...  
Keyword(s):  
Gene Expression ◽  
Disease Gene ◽  
Cell Types ◽  
Start Site ◽  
Valuable Resource ◽  
Cell Type ◽  
Transcription Start ◽  
Transcription Start Sites ◽  
Cell Type Specific ◽  
Gwas Catalog

Accurate transcription start site (TSS) annotations are essential for understanding transcriptional regulation and its role in human disease. Gene collections such as GENCODE contain annotations for tens of thousands of TSSs, but not all of these annotations are experimentally validated nor do they contain information on cell type-specific usage. Therefore, we sought to generate a collection of experimentally validated TSSs by integrating RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression (RAMPAGE) data from 115 cell and tissue types, which resulted in a collection of approximately 50 thousand representative RAMPAGE peaks. These peaks were primarily proximal to GENCODE-annotated TSSs and were concordant with other transcription assays. Because RAMPAGE uses paired-end reads, we were then able to connect peaks to transcripts by analyzing the genomic positions of the 3' ends of read mates. Using this paired-end information, we classified the vast majority (37 thousand) of our RAMPAGE peaks as verified TSSs, updating TSS annotations for 20% of GENCODE genes. We also found that these updated TSS annotations were supported by epigenomic and other transcriptomic datasets. To demonstrate the utility of this RAMPAGE rPeak collection, we intersected it with the NHGRI/EBI GWAS catalog and identified new candidate GWAS genes. Overall, our work demonstrates the importance of integrating experimental data to further refine TSS annotations and provides a valuable resource for the biological community.

Drosophila OVO regulates ovarian tumor transcription by binding unusually near the transcription start site

Development ◽  
2001 ◽  
Vol 128 (9) ◽  
pp. 1671-1686 ◽  
Author(s):  
J. Lu ◽  
B. Oliver
Keyword(s):  
Transcription Start Site ◽  
Ovarian Tumor ◽  
Core Promoter ◽  
Regulatory Region ◽  
Start Site ◽  
Loss Of Function ◽  
Transcription Start ◽  
Germline Expression ◽  
Promoter Swapping

Evolutionarily conserved ovo loci encode developmentally regulated, sequence-specific, DNA-binding, C(2)H(2)-zinc-finger proteins required in the germline and epidermal cells of flies and mice. The direct targets of OVO activity are not known. Genetic experiments suggest that ovo acts in the same regulatory network as ovarian tumor (otu), but the relative position of these genes in the pathway is controversial. Three OVO-binding sites exist in a compact regulatory region that controls germline expression of the otu gene. Interestingly, the strongest OVO-binding site is very near the otu transcription start, where basal transcriptional complexes must function. Loss-of-function, gain-of-function and promoter swapping constructs demonstrate that OVO binding near the transcription start site is required for OVO-dependent otu transcription in vivo. These data unambiguously identify otu as a direct OVO target gene and raise the tantalizing possibility that an OVO site, at the location normally occupied by basal components, functions as part of a specialized core promoter.

scholarly journals Regulation of the EDG84A gene by FTZ-F1 during metamorphosis in Drosophila melanogaster.

1996 ◽  
Vol 16 (11) ◽  
pp. 6509-6515 ◽  
Author(s):  
T Murata ◽  
Y Kageyama ◽  
S Hirose ◽  
H Ueda
Keyword(s):  
Drosophila Melanogaster ◽  
Binding Site ◽  
Transcription Start Site ◽  
Fusion Gene ◽  
Regulatory Region ◽  
Posterior Part ◽  
Nuclear Hormone Receptor ◽  
The Body ◽  
Start Site ◽  
Transcription Start

The transcription factor FTZ-F1 is a member of the nuclear hormone receptor superfamily and is transiently expressed during the mid- and late prepupal periods in Drosophila melanogaster. A putative pupal cuticle gene, EDG84A, is expressed slightly following FTZ-F1 expression during the prepupal period and carries a strong FTZ-F1 binding site between bases 100 and 92 upstream of its transcription start site. In this study, EDG84A mRNA was found to be prematurely expressed upon heat induction of FTZ-F1 in prepupae carrying the heat shock promoter-FTZ-F1 cDNA fusion gene construct. Transgenic fly lines having the 0.8-kb region of the EDG84A promoter fused to lacZ expressed the reporter gene in a tissue- and stage-specific manner. Base substitutions in the FTZ-F1 binding site within the 0.8-kb promoter abolished expression of lacZ. These results strongly suggest that the EDG84A gene is a direct target of FTZ-F1. Deletion studies of the cis-regulatory region of the EDG84A gene revealed that space-specific expression in imaginal disc-derived epidermis is controlled by the region between bp -408 and -104 from the transcription start site. The region between bp -408 and -194 is necessary to repress expression in a posterior part of the body, while the region between bp -193 and -104 carries a positive element for activation in an anterior part of the body. These results suggest that FTZ-F1 governs expression of the EDG84A gene in conjunction with putative tissue-specific regulators.

scholarly journals Hepatocyte-stimulating factor, beta 2 interferon, and interleukin-1 enhance expression of the rat alpha 1-acid glycoprotein gene via a distal upstream regulatory region.

1988 ◽  
Vol 8 (1) ◽  
pp. 42-51 ◽  
Author(s):  
K R Prowse ◽  
H Baumann
Keyword(s):  
Transcription Start Site ◽  
Interleukin 1 ◽  
Regulatory Region ◽  
Regulatory Sequence ◽  
Start Site ◽  
Transcription Start ◽  
Acid Glycoprotein ◽  
Beta 2 ◽  
Chloramphenicol Acetyltransferase Gene ◽  
Stimulating Factor

The rat alpha 1-acid glycoprotein (AGP) gene is transcriptionally regulated by dexamethasone, interleukin 1 (IL-1), hepatocyte-stimulating factor, and beta 2 interferon. The steroid and peptide hormones stimulate expression of the AGP gene synergistically as well as independently. The regulatory sequence responsible for dexamethasone-stimulated expression has been localized previously to a region that is 120 to 64 base pairs (bp) upstream of the transcription start site (H. Baumann and L. E. Maquat, Mol. Cell. Biol. 6:2551-2561, 1986). To identify the regulatory sequence that is responsive to the peptide hormones, different lengths of the AGP gene 5'-flanking DNA were linked to the chloramphenicol acetyltransferase gene and then assayed for hormone-inducible chloramphenicol acetyltransferase gene expression in transiently transfected HepG2 cells. We demonstrate that an enhancer region that is responsive to IL-1, hepatocyte-stimulating factor, and beta 2 interferon lies within a 142-bp sequence located 5,300 to 5,150 bp upstream of the transcription start site. This distal regulatory region can confer hormone inducibility to a heterologous promoter; exert its affect in either orientation; and function, to a lesser degree, in nonhepatic but IL-1-responsive cells.

scholarly journals Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

2018 ◽  
Author(s):  
Christoph S. Börlin ◽  
Nevena Cvetesic ◽  
Petter Holland ◽  
David Bergenholm ◽  
Verena Siewers ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Start Site ◽  
Environmental Conditions ◽  
Transcription Initiation ◽  
Core Promoter ◽  
Regulatory Region ◽  
Laboratory Strain ◽  
Start Site ◽  
Transcription Start ◽  
Strong Negative Correlation

ABSTRACTOne of the fundamental processes that determine cellular fate is regulation of gene transcription. Understanding these regulatory processes is therefore essential for understanding cellular responses to changes in environmental conditions. At the core promoter, the regulatory region containing the transcription start site (TSS), all inputs regulating transcription are integrated. Here, we used Cap Analysis of Gene Expression (CAGE) to analyze the pattern of transcription start sites at four different environmental conditions (limited in ethanol, limited in nitrogen, limited in glucose and limited in glucose under anaerobic conditions) using the Saccharomyces cerevisiae strain CEN.PK113-7D. With this experimental setup we were able to show that the TSS landscape in yeast is stable at different metabolic states of the cell. We also show that the shape index, a characteristic feature of each TSS describing the spatial distribution of transcription initiation events, has a surprisingly strong negative correlation with the measured expression levels. Our analysis supplies a set of high quality TSS annotations useful for metabolic engineering and synthetic biology approaches in the industrially relevant laboratory strain CEN.PK113-7D, and provides novel insights into yeast TSS dynamics and gene regulation.

Functional Studies on the Promoter Region of the Human GTP Cyclohydrolase I Gene

Pteridines ◽  
1995 ◽  
Vol 6 (3) ◽  
pp. 108-111
Author(s):  
Markus Gütlich ◽  
Klaus Witter ◽  
Gerd Katzenmeier ◽  
Wolfgang Rödl ◽  
Thomas Wernert ◽  
...  
Keyword(s):  
Transcription Start Site ◽  
Promoter Region ◽  
Regulatory Region ◽  
Start Site ◽  
Gtp Cyclohydrolase I ◽  
Gtp Cyclohydrolase ◽  
Transcription Start ◽  
Functional Studies ◽  
First Intron ◽  
Rapid Amplification

Summary We have isolated genomic clones that contained the gene for human GTP cyclohydrolase I. One clone containing the 5'-regulatory region of this gene was further analysed. It encompassed the first exon, parts of the first intron and about 2.6kb of the promoter region. The transcription start site was localised by rapid amplification of cDNA ends (5'-RACE). The 2.6 kb region upstream of the transcription start site showed promoter activity when ligated upstream of a reporter gene. 5'-truncations of the promoter region increased its activity as long as the CAAT and TATA boxes remained unchanged. Several putative Spl responsive elements were located within a GC-rich region close to the transcription start site.

Hepatocyte-stimulating factor, beta 2 interferon, and interleukin-1 enhance expression of the rat alpha 1-acid glycoprotein gene via a distal upstream regulatory region

1988 ◽  
Vol 8 (1) ◽  
pp. 42-51
Author(s):  
K R Prowse ◽  
H Baumann
Keyword(s):  
Transcription Start Site ◽  
Interleukin 1 ◽  
Regulatory Region ◽  
Regulatory Sequence ◽  
Start Site ◽  
Transcription Start ◽  
Acid Glycoprotein ◽  
Beta 2 ◽  
Chloramphenicol Acetyltransferase Gene ◽  
Stimulating Factor

The rat alpha 1-acid glycoprotein (AGP) gene is transcriptionally regulated by dexamethasone, interleukin 1 (IL-1), hepatocyte-stimulating factor, and beta 2 interferon. The steroid and peptide hormones stimulate expression of the AGP gene synergistically as well as independently. The regulatory sequence responsible for dexamethasone-stimulated expression has been localized previously to a region that is 120 to 64 base pairs (bp) upstream of the transcription start site (H. Baumann and L. E. Maquat, Mol. Cell. Biol. 6:2551-2561, 1986). To identify the regulatory sequence that is responsive to the peptide hormones, different lengths of the AGP gene 5'-flanking DNA were linked to the chloramphenicol acetyltransferase gene and then assayed for hormone-inducible chloramphenicol acetyltransferase gene expression in transiently transfected HepG2 cells. We demonstrate that an enhancer region that is responsive to IL-1, hepatocyte-stimulating factor, and beta 2 interferon lies within a 142-bp sequence located 5,300 to 5,150 bp upstream of the transcription start site. This distal regulatory region can confer hormone inducibility to a heterologous promoter; exert its affect in either orientation; and function, to a lesser degree, in nonhepatic but IL-1-responsive cells.

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