scholarly journals Metabolic Regulation of IMD2 Transcription and an Unusual DNA Element That Generates Short Transcripts

2007 ◽  
Vol 27 (8) ◽  
pp. 2821-2829 ◽  
Author(s):  
Katarzyna A. Kopcewicz ◽  
Thomas W. O'Rourke ◽  
Daniel Reines
Keyword(s):  
Dna Sequences ◽  
Metabolic Regulation ◽  
Regulatory Region ◽  
Initiation Site ◽  
Transcription Start ◽  
Heterologous Promoter ◽  
Short Rnas ◽  
Nucleotide Pools ◽  
Blocking Activity ◽  
Nuclear Exosome

ABSTRACT Transcriptional regulation of IMD2 in yeast (Saccharomyces cerevisiae) is governed by the concentration of intracellular guanine nucleotide pools. The mechanism by which pool size is measured and transduced to the transcriptional apparatus is unknown. Here we show that DNA sequences surrounding the IMD2 initiation site constitute a repressive element (RE) involved in guanine regulation that contains a novel transcription-blocking activity. When this regulatory region is placed downstream of a heterologous promoter, short poly(A)+ transcripts are generated. The element is orientation dependent, and sequences within the normally transcribed and nontranscribed regions of the element are required for its activity. The promoter-proximal short RNAs are unstable and serve as substrates for the nuclear exosome. These findings support a model in which intergenic short transcripts emanating from upstream of the IMD2 promoter are terminated by a polyadenylation/terminator-like signal embedded within the IMD2 transcription start site.

scholarly journals 5' regulatory region of a novel cytokine gene mediates selective activation by interferon gamma.

1991 ◽  
Vol 173 (2) ◽  
pp. 417-422 ◽  
Author(s):  
T M Wright ◽  
J M Farber
Keyword(s):  
Interferon Gamma ◽  
Regulatory Region ◽  
Raw 264.7 Cells ◽  
Raw 264.7 ◽  
Genomic Fragment ◽  
Transcription Start ◽  
Heterologous Promoter ◽  
Platelet Factor ◽  
Ifn Gamma ◽  
Ifn Alpha

A newly described member of the platelet factor 4 family of cytokine genes, mig, is selectively induced by interferon gamma (IFN-gamma), and not IFN-alpha, in the mouse macrophage-like cell line RAW 264.7. Treatment of RAW 264.7 cells with IFN-gamma activated mig gene transcription as determined by nuclear run-on assays. mig genomic clones were isolated, and constructs containing genomic fragments that included the mig promoter region and the CAT reporter gene were prepared. In RAW 264.7 cells transfected with these constructs, CAT activity was found to be selectively induced by IFN-gamma. A 278-bp genomic fragment containing 235 nucleotides 5' of the transcription start site was sufficient for IFN-gamma-selective induction of CAT activity. Analysis of 5' deletion mutants localized a region essential for activation by IFN-gamma to within 64 nucleotides extending from -235 to -172. A genomic fragment containing this sequence was capable of conferring IFN-gamma inducibility to constructs with a heterologous promoter.

scholarly journals The manganese-responsive repressor Mur of Rhizobium leguminosarum is a member of the Fur-superfamily that recognizes an unusual operator sequence

Microbiology ◽  
2005 ◽  
Vol 151 (12) ◽  
pp. 4071-4078 ◽  
Author(s):  
Edit Díaz-Mireles ◽  
Margaret Wexler ◽  
Jonathan D. Todd ◽  
Dominico Bellini ◽  
Andrew W. B. Johnston ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Rhizobium Leguminosarum ◽  
Regulatory Protein ◽  
Regulatory Region ◽  
Initiation Site ◽  
Recognition Sequence ◽  
Transcription Analysis ◽  
Similar Affinity

The manganese uptake regulator Mur of Rhizobium leguminosarum is a close homologue of the global iron regulatory protein Fur. Mur represses the sitABCD operon, which encodes a Mn2+ transport system, specifically in response to Mn2+ but not Fe2+. In previous work the authors mapped the 5′ ends of two sit operon transcripts, termed TS1 and TS2, which were co-ordinately regulated by Mn2+-Mur, but this paper now shows that only TS1 is a primary transcript. DNase I protection analyses showed that purified Mur bound, with similar affinity, to two sites in the regulatory region of sitABCD, but only when Mn2+ was present in the reaction buffer. These Mn2+-Mur-binding sites, termed MRS1 and MRS2 (Mur-responsive sequence), were closely related in sequence to each other and were separated by 16 bp, spanning the transcription initiation site TS1. The extent of the protected DNA was 34 and 31 bp for MRS1 and MRS2, respectively, which is in accord with other members of the Fur family. The DNA sequences recognized by Mn2+-Mur are wholly different from conventional Fur boxes, but some similarities to a recognition sequence for the Fur regulator from Bradyrhizobium japonicum were noted. Transcription analysis of the R. leguminosarum mur gene showed its expression to be independent of Mn2+-Mur. Thus, Mur is a sequence-specific DNA-binding protein that responds in vitro to manganese, and thus can occlude RNA polymerase access to the sitABCD promoter. Moreover, Mur recognizes a DNA sequence atypical for the Fur superfamily and, like Fur from B. japonicum, defines a new subclass of Fur-like transcriptional regulators.

scholarly journals Transvection at the End of the Truncated Chromosome in Drosophila melanogaster

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1375-1387
Author(s):  
Mikhail Savitsky ◽  
Tatyana Kahn ◽  
Ekaterina Pomerantseva ◽  
Pavel Georgiev
Keyword(s):  
Drosophila Melanogaster ◽  
Homologous Chromosome ◽  
Regulatory Region ◽  
Proximal Region ◽  
The Other ◽  
Upstream Region ◽  
Upstream Sequence ◽  
Transcription Start ◽  
Promoter Proximal Region

Abstract The phenomenon of transvection is well known for the Drosophila yellow locus. Thus enhancers of a promoterless yellow locus in one homologous chromosome can activate the yellow promoter in the other chromosome where the enhancers are inactive or deleted. In this report, we examined the requirements for trans-activation of the yellow promoter at the end of the deficient chromosome. A number of truncated chromosomes ending in different areas of the yellow regulatory region were examined in combination with the promoterless y alleles. We found that trans-activation of the yellow promoter at the end of a deficient chromosome required ∼6 kb of an additional upstream sequence. The nature of upstream sequences affected the strength of transvection: addition of gypsy sequences induced stronger trans-activation than addition of HeT-A or yellow sequences. Only the promoter proximal region (within -158 bp of the yellow transcription start) was essential for trans-activation; i.e., transvection did not require extensive homology in the yellow upstream region. Finally, the yellow enhancers located on the two pairing chromosomes could cooperatively activate one yellow promoter.

Transcriptional and posttranscriptional regulation of maize mitochondrial gene expression

1991 ◽  
Vol 11 (1) ◽  
pp. 533-543
Author(s):  
R M Mulligan ◽  
P Leon ◽  
V Walbot
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Posttranscriptional Regulation ◽  
Rank Order ◽  
Mitochondrial Gene ◽  
Initiation Site ◽  
Gene Copy ◽  
Promoter Strength ◽  
Protein Coding

Lysed maize mitochondria synthesize RNA in the presence of radioactive nucleoside triphosphates, and this assay was utilized to compare the rates of transcription of seven genes. The rates of incorporation varied over a 14-fold range, with the following rank order: 18S rRNA greater than 26S rRNA greater than atp1 greater than atp6 greater than atp9 greater than cob greater than cox3. The products of run-on transcription hybridized specifically to known transcribed regions and selectively to the antisense DNA strand; thus, the isolated run-on transcription system appears to be an accurate representation of endogenous transcription. Although there were small differences in gene copy abundance, these differences cannot account for the differences in apparent transcription rates; we conclude that promoter strength is the main determinant. Among the protein coding genes, incorporation was greatest for atp1. The most active transcription initiation site of this gene was characterized by hybridization with in vitro-capped RNA and by primer extension analyses. The DNA sequences at this and other transcription initiation sites that we have previously mapped were analyzed with respect to the apparent promoter strengths. We propose that two short sequence elements just upstream of initiation sites form at least a portion of the sequence requirements for a maize mitochondrial promoter. In addition to modulation at the level of transcription, steady-state abundance of protein-coding mRNAs varied over a 20-fold range and did not correlate with transcriptional activity. These observations suggest that posttranscriptional processes are important in the modulation of mRNA abundance.

Short repeated elements in the upstream regulatory region of the SUC2 gene of Saccharomyces cerevisiae

1986 ◽  
Vol 6 (7) ◽  
pp. 2324-2333
Author(s):  
L Sarokin ◽  
M Carlson
Keyword(s):  
Carbon Catabolite Repression ◽  
Consensus Sequence ◽  
Regulatory Region ◽  
Lacz Fusion ◽  
Upstream Region ◽  
Upstream Regulatory Region ◽  
Heterologous Promoter ◽  
Suc2 Gene ◽  
High Level ◽  
Repeated Motif

Expression of secreted invertase from the SUC2 gene is regulated by carbon catabolite repression. Previously, an upstream regulatory region that is required for derepression of secreted invertase was identified and shown to confer glucose-repressible expression to the heterologous promoter of a LEU2-lacZ fusion. In this paper we show that tandem copies of a 32-base pair (bp) sequence from the upstream regulatory region activate expression of the same LEU2-lacZ fusion. The level of expression increased with the number of copies of the element, but was independent of their orientation; the expression from constructions containing four copies of the sequence was only twofold lower than that when the entire SUC2 upstream regulatory region was present. This activation was not significantly glucose repressible. The 32-bp sequence includes a 7-bp motif with the consensus sequence (A/C)(A/G)GAAAT that is repeated at five sites within the upstream regulatory region. Genetic evidence supporting the functional significance of this repeated motif was obtained by pseudoreversion of a SUC2 deletion mutant lacking part of the upstream region, including two copies of the 7-bp element. In three of five pseudorevertants, the mutations that restored high-level SUC2 expression altered one of the remaining copies of the 7-bp element.

Characterization of the inducer of short transcripts, a human immunodeficiency virus type 1 transcriptional element that activates the synthesis of short RNAs

1993 ◽  
Vol 13 (2) ◽  
pp. 1251-1263
Author(s):  
M Sheldon ◽  
R Ratnasabapathy ◽  
N Hernandez
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Regulatory Region ◽  
Short Rnas ◽  
Immunodeficiency Virus ◽  
R Region ◽  
Transcription Complexes ◽  
Hiv 1

The inducer of short transcripts, or IST, is an unusual transcriptional element located downstream of the human immunodeficiency virus type 1 (HIV-1) promoter. IST activates HIV-1 transcription, but the resulting RNAs are short and end at approximately position +59. IST, therefore, appears to promote the formation of transcription complexes that are unable to elongate efficiently. This activity contrasts with that of TAR, the target for Tat trans-activation, which upon binding of the viral protein Tat promotes the formation of transcription complexes capable of efficient elongation through the entire viral genome. We have localized and characterized the IST element. Our results indicate that IST is located mainly between positions -5 and +26, although the sequences from positions +40 to +59 also contribute to IST activity. Unlike TAR, which is an RNA element, IST appears to be a DNA element. Thus, the HIV-1 R region is a complex regulatory region with RNA and DNA elements that promote the formation of transcription complexes with different elongation properties.

Identification of a regulatory region that mediates glucose-dependent induction of the Saccharomyces cerevisiae enolase gene ENO2

1986 ◽  
Vol 6 (7) ◽  
pp. 2287-2297
Author(s):  
R Cohen ◽  
J P Holland ◽  
T Yokoi ◽  
M J Holland
Keyword(s):  
Gene Expression ◽  
Regulatory Region ◽  
Carbon Sources ◽  
Initiation Site ◽  
Deletion Mapping ◽  
Regulatory Regions ◽  
Coding Sequences ◽  
Flanking Region ◽  
Fused Gene ◽  
In Cells

There are two yeast enolase genes, designated ENO1 and ENO2, which are expressed differentially in vegetative cells grown on glucose and in cells grown on gluconeogenic carbon sources. ENO2 is induced more than 20-fold in cells grown on glucose, whereas ENO1 expression is similar in cells grown on glucose and in cells grown on gluconeogenic carbon sources. Sequences within the 5' flanking region of ENO2 which are required for glucose-dependent induction were identified by deletion mapping analysis. These studies were carried out by using a fused gene containing the ENO2 5' flanking sequences and the ENO1 coding sequences. This fused gene undergoes glucose-dependent induction and is expressed at the same level as the resident ENO2 gene in cells grown on glucose or gluconeogenic carbon sources. Expression of fused genes containing deletion mutations within the ENO2 5' flanking region was monitored after integration at the ENO1 locus of a strain carrying a deletion of the resident ENO1 coding sequences. This analysis showed that there are two upstream activation sites located immediately upstream and downstream from a position 461 base pairs upstream from the transcriptional initiation site. Either one of these upstream activation sites is sufficient for glucose-dependent induction and normal gene expression in the presence of gluconeogenic carbon sources. Deletion of both regulatory regions results in a complete loss of gene expression. The regulatory regions function normally in both orientations relative to the coding sequences. Mutant fused genes containing small deletions within the regulatory regions were constructed; these genes were expressed normally in gluconeogenic carbon sources but were not induced in the presence of glucose. Based on this analysis, ENO2 contains a cis-acting regulatory region which is required for gene expression and mediates glucose-dependent induction of gene expression.

Multiple functional motifs in the chicken U1 RNA gene enhancer

1987 ◽  
Vol 7 (12) ◽  
pp. 4185-4193
Author(s):  
K A Roebuck ◽  
R J Walker ◽  
W E Stumph
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Initiation Site ◽  
Sequence Motifs ◽  
Small Nuclear Rna ◽  
Multiple Sequence ◽  
Transcriptional Initiation ◽  
Transcription System ◽  
Cell Extracts ◽  
Gene Enhancer

The DNA sequence requirements of chicken U1 RNA gene expression have been examined in an oocyte transcription system. An enhancer region, which was required for efficient U1 RNA gene expression, is contained within a region of conserved DNA sequences spanning nucleotide positions -230 to -183, upstream of the transcriptional initiation site. These DNA sequences can be divided into at least two distinct subregions or domains that acted synergistically to provide a greater than 20-fold stimulation of U1 RNA synthesis. The first domain contains the octamer sequence ATGCAAAT and was recognized by a DNA-binding factor present in HeLa cell extracts. The second domain (the SPH domain) consists of conserved sequences immediately downstream of the octamer and is an essential component of the enhancer. In the oocyte, the DNA sequences of the SPH domain were able to enhance gene expression at least 10-fold in the absence of the octamer domain. In contrast, the octamer domain, although required for full U1 RNA gene activity, was unable to stimulate expression in the absence of the adjacent downstream DNA sequences. These findings imply that sequences 3' of the octamer play a major role in the function of the chicken U1 RNA gene enhancer. This concept was supported by transcriptional competition studies in which a cloned chicken U4B RNA gene was used to compete for limiting transcription factors in oocytes. Multiple sequence motifs that can function in a variety of cis-linked configurations may be a general feature of vertebrate small nuclear RNA gene enhancers.

sry h-1, a new Drosophila melanogaster multifingered protein gene showing maternal and zygotic expression

1988 ◽  
Vol 8 (10) ◽  
pp. 4459-4468
Author(s):  
A Vincent ◽  
J Kejzlarovà-Lepesant ◽  
L Segalat ◽  
C Yanicostas ◽  
J A Lepesant
Keyword(s):  
Dna Sequences ◽  
Subsequent Development ◽  
Initiation Site ◽  
Protein Product ◽  
Protein Coding ◽  
Finger Protein ◽  
Early Embryos ◽  
The Family ◽  
Genes Encoding ◽  
Internal Initiation

Low-stringency hybridization of the Drosophila serendipity (sry) finger-coding sequences revealed copies of homologous DNA sequences in the genomes of members of the family Drosophilidae and higher vertebrates. sry h-1, a new Drosophila finger protein-coding gene isolated on the basis of this homology, encodes a 3.2-kilobase (kb) mRNA accumulating in eggs and abundant in early embryos. The predicted sry h-1 protein product, starting at an internal initiation site of translation, is a 868-amino-acid basic polypeptide containing eight TFIIIA-like fingers encoded by three separate exons. Links separating individual fingers in the sry h-1 protein are variable in length and sequence, in contrast with the invariant H/C link found in most multi-fingered proteins. The similarity of the developmental pattern of transcription of sry h-1 with that of several other Drosophila finger protein genes suggests the existence of a complex set of such genes encoding an information which is, at least partly, maternally provided to the embryo and required for activation of gene transcription in early embryos or maintenance of gene activity during subsequent development.

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