Genomic characterization of a gamma-interferon-inducible gene (IP-10) and identification of an interferon-inducible hypersensitive site

1987 ◽  
Vol 7 (10) ◽  
pp. 3723-3731
Author(s):  
A D Luster ◽  
J V Ravetch
Keyword(s):  
Gene Family ◽  
Transcriptional Activation ◽  
Protein A ◽  
Initiation Site ◽  
Gamma Interferon ◽  
Structural Basis ◽  
Hypersensitive Site ◽  
Platelet Factor ◽  
Platelet Protein ◽  
Inducible Gene

The genomic organization of a gamma-interferon-inducible gene, IP-10, reveals three introns that interrupt the transcribed sequence into four functional domains. Comparison of the intron-exon structure of this gene to the gene for an homologous chemotactic platelet protein, platelet factor 4, establishes that both genes are interrupted in precisely the same positions within homologous codons; this demonstrates that they belong to a gene family that evolved from a common ancestor. IP-10 and PF4 are two members of a newly described gene family that is likely to include the homologous chemotactic and mitogenic platelet basic proteins (connective tissue-activating protein III and beta-thromboglobulin), the transformation-related protein 9E3, and 310c, a mitogen-stimulated leukocyte protein. A DNase I-hypersensitive site has been found in responsive cells in a region upstream of the RNA initiation site. This hypersensitive site is induced by gamma interferon and thus provides a structural basis for the transcriptional activation seen for this gene by gamma interferon.

scholarly journals Genomic characterization of a gamma-interferon-inducible gene (IP-10) and identification of an interferon-inducible hypersensitive site.

1987 ◽  
Vol 7 (10) ◽  
pp. 3723-3731 ◽  
Author(s):  
A D Luster ◽  
J V Ravetch
Keyword(s):  
Gene Family ◽  
Transcriptional Activation ◽  
Protein A ◽  
Initiation Site ◽  
Gamma Interferon ◽  
Structural Basis ◽  
Hypersensitive Site ◽  
Platelet Factor ◽  
Platelet Protein ◽  
Inducible Gene

The genomic organization of a gamma-interferon-inducible gene, IP-10, reveals three introns that interrupt the transcribed sequence into four functional domains. Comparison of the intron-exon structure of this gene to the gene for an homologous chemotactic platelet protein, platelet factor 4, establishes that both genes are interrupted in precisely the same positions within homologous codons; this demonstrates that they belong to a gene family that evolved from a common ancestor. IP-10 and PF4 are two members of a newly described gene family that is likely to include the homologous chemotactic and mitogenic platelet basic proteins (connective tissue-activating protein III and beta-thromboglobulin), the transformation-related protein 9E3, and 310c, a mitogen-stimulated leukocyte protein. A DNase I-hypersensitive site has been found in responsive cells in a region upstream of the RNA initiation site. This hypersensitive site is induced by gamma interferon and thus provides a structural basis for the transcriptional activation seen for this gene by gamma interferon.

Rabbit lung surfactant protein A gene: identification of a lung-specific DNase I hypersensitive site

1992 ◽  
Vol 262 (6) ◽  
pp. L662-L671 ◽  
Author(s):  
Q. Chen ◽  
V. Boggaram ◽  
C. R. Mendelson
Keyword(s):  
Transcription Initiation ◽  
Regulatory Element ◽  
Protein A ◽  
Surfactant Protein ◽  
Initiation Site ◽  
Dnase I ◽  
Transcription Initiation Site ◽  
Hypersensitive Site ◽  
Rabbit Lung ◽  
Dnase I Hypersensitive Site

Expression of the gene encoding pulmonary surfactant protein A, SP-A, is lung specific and developmentally and hormonally regulated. Previously, we observed that SP-A gene transcription is initiated in fetal rabbit lung after day 21 of gestation and reaches maximal levels by day 28. In the present study, a cDNA specific for rabbit SP-A was used to isolate the SP-A gene from a rabbit genomic library. A 7.6-kb fragment containing the entire structural gene and approximately 380 bp of 5'-flanking DNA was isolated and characterized. The transcription initiation site, mapped by primer extension analysis, was localized 23 bp downstream of a putative TATA element. The structural gene is composed of five exons and four introns. The first exon encodes the 5'-untranslated region of the mRNA; the translation initiation site is in exon II, and exon V contains the two polyadenylation sites that give rise to the 2.0- and 3.0-kb species of SP-A mRNA. A potential adenosine 3',5'-cyclic monophosphate (cAMP)-regulatory element (CRE) was identified at -261 bp, and sequences with homology to glucocorticoid-regulatory element (GRE) half-sites were found at -150 and -190 bp upstream of the transcription initiation site and within the first intron. A DNase I hypersensitive site was identified in genomic DNA isolated from 21- and 28-day fetal and adult rabbit lung tissues. This site was mapped within the 5'-flanking region of the SP-A gene, at approximately -80 to -180 bp upstream of the transcription initiation site. The absence of this hypersensitive site in genomic DNA of liver, kidney, and heart tissues suggests that altered chromatin structure may serve a role in lung-specific SP-A gene expression. The presence of this tissue-specific DNase I hypersensitive site in lung nuclei from 21-day gestational age fetal rabbits suggests that the SP-A gene may exist in an accessible conformation prior to the time of transcription initiation.

scholarly journals Loss of 111Indium as indicator of platelet injury

Blood ◽  
1981 ◽  
Vol 58 (2) ◽  
pp. 350-353 ◽  
Author(s):  
JH Joist ◽  
RK Baker
Keyword(s):  
Small Molecules ◽  
Adenine Nucleotides ◽  
Human Platelets ◽  
Metabolic Energy ◽  
Platelet Factor ◽  
Platelet Protein ◽  
Threshold Rate ◽  
Immune Injury ◽  
Triton X

Abstract We previously demonstrated that platelets can be labeled with 111Inoxine with high labeling efficiency and that 111In is not liberated from labeled platelets during the platelet release reaction or prolonged in vitro storage. In view of these findings, we examined the potential usefulness of loss of 111In from labeled platelets as an indicator or platelet damage by comparing the loss of 111In with that of 51Cr and LDH (in some experiments also with platelet factor 3 availability) under different conditions of platelet injury. When washed human platelets labeled with either 51Cr-chromate or 111In-oxine were exposed to increasing concentrations of detergents (Triton X-100, lysolecithin), threshold, rate, and extent of loss of 111In, 51Cr and, LDH were similar. In contrast, when labeled platelets were depleted of metabolic energy by incubation in glucose-free Tyrode albumin solution or glucose-depleted plasma in the presence of antimycin A and 2-deoxy-D- glucose, loss of 51Cr (and PF3a) occurred earlier and progressed at a faster rate than that of 111In or LDH. Similar results were obtained when platelets were exposed to increasing concentrations of PlA1 antibody, causing complement-mediated immune injury. The findings indicate that with certain agents that cause rapid platelet disruption (lysis), different platelet constituents are lost at similar rates. However, under conditions of more subtle or slowly progressive platelet injury, small molecules such as adenine nucleotides (51Cr) may escape earlier and at faster rates than larger molecules such as LDH or 111In- binding platelet protein. Thus, neither 111In loss nor LDH loss appear to be suitable indicators for sublytic or prelytic platelet injury.

scholarly journals Sir Proteins, Rif Proteins, and Cdc13p BindSaccharomyces Telomeres In Vivo

1998 ◽  
Vol 18 (9) ◽  
pp. 5600-5608 ◽  
Author(s):  
Brenda D. Bourns ◽  
Mary Kate Alexander ◽  
Andrew M. Smith ◽  
Virginia A. Zakian
Keyword(s):  
Reporter Gene ◽  
Transcriptional Activation ◽  
Binding Proteins ◽  
Position Effect ◽  
Initiation Site ◽  
Telomeric Sequence ◽  
Transcriptional Activation Domain ◽  
Amino Terminal ◽  
Sir Proteins

ABSTRACT Although a surprisingly large number of genes affect yeast telomeres, in most cases it is not known if their products act directly or indirectly. We describe a one-hybrid assay for telomere binding proteins and use it to establish that six proteins that affect telomere structure or function but which had not been shown previously to bind telomeres in vivo are indeed telomere binding proteins. A promoter-defective allele of HIS3 was placed adjacent to a chromosomal telomere. Candidate proteins fused to a transcriptional activation domain were tested for the ability to activate transcription of the telomere-linked HIS3 gene. Using this system, Rif1p, Rif2p, Sir2p, Sir3p, Sir4p, and Cdc13p were found to be in vivo telomere binding proteins. None of the proteins activated the same reporter gene when it was at an internal site on the chromosome. Moreover, Cdc13p did not activate the reporter gene when it was adjacent to an internal tract of telomeric sequence, indicating that Cdc13p binding was telomere limited in vivo. The amino-terminal 20% of Cdc13p was sufficient to target Cdc13p to a telomere, suggesting that its DNA binding domain was within this portion of the protein. Rap1p, Rif1p, Rif2p, Sir4p, and Cdc13p activated the telomeric reporter gene in a strain lacking Sir3p, which is essential for telomere position effect (TPE). Thus, the telomeric association of these proteins did not require any of the chromatin features necessary for TPE. The data support models in which the telomere acts as an initiation site for TPE by recruiting silencing proteins to the chromosome end.

Analysis of Saccharomyces cerevisiae his3 transcription in vitro: biochemical support for multiple mechanisms of transcription

1990 ◽  
Vol 10 (6) ◽  
pp. 2832-2839
Author(s):  
A S Ponticelli ◽  
K Struhl
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcriptional Activation ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Initiation Site ◽  
Activator Proteins ◽  
Nuclear Extracts ◽  
Transcription In Vitro

The promoter region of the Saccharomyces cerevisiae his3 gene contains two TATA elements, TC and TR, that direct transcription initiation to two sites designated +1 and +13. On the basis of differences between their nucleotide sequences and their responsiveness to upstream promoter elements, it has previously been proposed that TC and TR promote transcription by different molecular mechanisms. To begin a study of his3 transcription in vitro, we used S. cerevisiae nuclear extracts together with various DNA templates and transcriptional activator proteins that have been characterized in vivo. We demonstrated accurate transcription initiation in vitro at the sites used in vivo, transcriptional activation by GCN4, and activation by a GAL4 derivative on various gal-his3 hybrid promoters. In all cases, transcription stimulation was dependent on the presence of an acidic activation region in the activator protein. In addition, analysis of promoters containing a variety of TR derivatives indicated that the level of transcription in vitro was directly related to the level achieved in vivo. The results demonstrated that the in vitro system accurately reproduced all known aspects of in vivo his3 transcription that depend on the TR element. However, in striking contrast to his3 transcription in vivo, transcription in vitro yielded approximately 20 times more of the +13 transcript than the +1 transcript. This result was not due to inability of the +1 initiation site to be efficiently utilized in vitro, but rather it reflects the lack of TC function in vitro. The results support the idea that TC and TR mediate transcription from the wild-type promoter by distinct mechanisms.

scholarly journals Molecular signatures of selection associated with host-plant differences in Pieris butterflies

2019 ◽  
Author(s):  
Yu Okamura ◽  
Ai Sato ◽  
Natsumi Tsuzuki ◽  
Masashi Murakami ◽  
Hanna Heidel-Fischer ◽  
...  
Keyword(s):  
Gene Family ◽  
Host Plant ◽  
Host Plants ◽  
Protein A ◽  
Functional Differentiation ◽  
Major Allergen ◽  
Arms Race ◽  
Defense System ◽  
Evolutionary Forces ◽  
Key Innovation

AbstractAdaptive traits that enable organisms to conquer novel niches and experience subsequent diversification are ecologically and evolutionarily important. The larvae of Pieris butterflies express nitrile-specifier proteins (NSPs), a key innovation for overcoming the glucosinolate (GLS)-myrosinase-based defense system of their Brassicales host-plants. NSPs are a member of the NSP-like gene family, which includes the major allergen (MA) protein, a paralog of NSP with a GLS-disarming function, and a single domain major allergen (SDMA) protein, whose function is unknown. The arms-race between a highly variable host-plant defense system and members of the NSP-like gene family is suggested to mediate diversification in both Pierid butterflies and Brassicales plants. Here, we combined feeding experiments using 25 Brassicaceae plants and five Pieris species with larval transcriptome data to investigate the evolutionary forces acting on NSP-like gene family members associated with patterns of host-plant usage. Although we observed significantly elevated nonsynonymous to synonymous substitution ratios in NSPs, no such pattern was observed in MAs or SDMAs. Furthermore, we found a signature of positive selection of NSP at a phylogenetic branch which reflects different host-plant preferences. Our data indicate that NSPs have evolved in response to shifting preferences for host plants among five Pieris butterflies, whereas MAs and SDMAs appear to have more conserved functions. Our results show that the evolution and functional differentiation of key genes used in host-plant adaptation play a crucial role in the chemical arms-race between Pieris butterflies and their Brassicales host-plants.

scholarly journals Growth-regulated expression of rhoG, a new member of the ras homolog gene family.

1992 ◽  
Vol 12 (7) ◽  
pp. 3138-3148 ◽  
Author(s):  
S Vincent ◽  
P Jeanteur ◽  
P Fort
Keyword(s):  
Gene Family ◽  
Transcriptional Activation ◽  
Small Gtpase ◽  
Lung Fibroblasts ◽  
Human Organs ◽  
Regulated Expression ◽  
Genes Encoding ◽  
Rna Stabilization ◽  
Rna Accumulation ◽  
High Level

Cellular transition from the resting state to DNA synthesis involves master switches genes encoding transcriptional factors (e.g., fos, jun, and egr genes), whose targets remain to be fully characterized. To isolate coding sequences specifically accumulated in late G1, a differential screening was performed on a cDNA library prepared from hamster lung fibroblasts stimulated for 5 h with serum. One of the positive clones which displayed a sevenfold induction, turned out to code for a protein sharing homology to Ras-like products. Cloning and sequence analysis of the human homolog revealed that this putative new small GTPase, referred to as rhoG, is more closely related to the rac, CDC42, and TC10 members of the rho (ras homolog) gene family and might have diverged very early during evolution. rhoG mRNA accumulates in proportion to the mitogenic strength of various purified growth factors used for the stimulation, as a consequence of transcriptional activation. G1-specific RNA accumulation is impaired upon addition of antimitogenic cyclic AMP and is enhanced when protein synthesis is inhibited, mainly as a result of RNA stabilization. rhoG mRNA expression is observed in a wide variety of human organs but reaches a particularly high level in lung and placental tissues.

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