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At least 433 records · Page 24Linked to original sources
PubMed2000

Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon.

Nonsense-mediated decay (NMD) rids eukaryotic cells of aberrant mRNAs containing premature termination codons. These are discriminated from true termination codons by downstream cis-elements, such as exon-exon junctions. We describe three novel human proteins involved in NMD, hUpf2, hUpf3a, and hUpf3b. While in HeLa cell extracts these proteins are complexed with hUpf1, in intact cells hUpf3a and hUpf3b are nucleocytoplasmic shuttling proteins, hUpf2 is perinuclear, and hUpf1 cytoplasmic. hUpf3a and hUpf3b associate selectively with spliced beta-globin mRNA in vivo, and tethering of any hUpf protein to the 3'UTR of beta-globin mRNA elicits NMD. These data suggest that assembly of a dynamic hUpf complex initiates in the nucleus at mRNA exon-exon junctions and triggers NMD in the cytoplasm when recognized downstream of a translation termination site.

3' Untranslated Regions↗
PubMed1998

Cell-type specific factors bind to regulatory elements located downstream of the TATA-box element in the mouse myelin basic protein (MBP) gene promoter.

Cell-type specific transcription of the myelin basic protein (MBP) gene in primary oligodendrocytes (OL) is regulated by cis-acting regulatory elements located at both upstream and downstream of the TATA-box region of the MBP promoter. To identify cell-type specific factors that bind to the downstream regulatory elements, we utilised DNase I footprinting analysis and gel retardation assays with nuclear extracts from myelin-forming OL as well as a non-myelin forming cell line, C6 glioma (C6) cells. Several regions of DNA were protected from DNAse I digestion by nuclear extracts of both cell types. However, two regions, from -17 to +17 and from +47 to +58 were protected specifically in OL, while three regions, from + 17 to + 22, from +43 to +49 and from +58 to +64 were protected only with C6 nuclear extracts. Inspection of the protected regions for homology with known transcription factor binding sites revealed that sequences at from +47 to +58 and from +56 to +68 showed extensive homology to the negative regulatory element (NRE1), of the mouse renin gene and to the interferon (IFN) consensus sequence of major histocompatibility complex class I genes (MHC I-ICS), respectively. Gel retardation assays using a MHC I-ICS oligonucleotide and transient transfection assays using MBP-CAT constructs were used to study the effect of IFNs on MBP promoter activity in OL and C6 cells. In OL, IFN-alpha/beta caused little induction of CAT activity, but IFN-gamma resulted in a 2-3.5-fold decrease in CAT activity. In contrast, in C6 cells both IFN-alpha/beta and IFN-gamma induced a 1.5-2.5-fold increase in CAT activity. The cooperative effects of factors binding to NREs and ICS may be responsible for the cell-type specific regulation of MBP gene transcription.

Animals↗
PubMed1998

The gene downstream of Streptomyces aureofaciens whiB encodes a large protein with proposed transmembrane localization, and is induced by glucose.

The sequence analysis of the region downstream of the Streptomyces aureofaciens whiB sporulation gene revealed a long open reading frame (1219 amino acids; Mr 128 209) encoding protein with potential transmembrane structure. By integrative transformation, via double cross-over, a stable null mutant of the gene, orf1219, was prepared. This mutation appeared to have no obvious effect on vegetative growth and differentiation. In vitro and in vivo transcriptional analysis of the downstream gene revealed a single apparent promoter induced by glucose.

Amino Acid Sequence↗
PubMed2001

Gene organization of bovine BCNT that contains a portion corresponding to an endonuclease domain derived from an RTE-1 (Bov-B LINE), non-LTR retrotransposable element: duplication of an intramolecular repeat unit downstream of the truncated RTE-1.

BCNT (a protein named after Bucentaur or craniofacial development protein 1) has a unique structure in Ruminantia. Bovine BCNT contains a region of the endonuclease domain derived from a truncated RTE-1 (previously called Bov-B LINE), a non-LTR retrotransposable repetitive element, and two repeat units (intramolecular repeat, IR) each with 40 amino acids in the C-terminal region. In contrast the human and mouse BCNT proteins contain one repeat unit and lack the RTE-1-derived portion. The 3' UTR of bovine bcnt cDNA also contains an approximately 300-bp portion homologous to the 3'-part of RTE-1. We examined the bovine bcnt genomic DNA sequence to understand how the bovine bcnt gene has been organized. The sequence of 3' UTR homologous portion was found to more closely resemble the Art2 element than the bovine RTE-1. By PCR screening a bovine/hamster hybrid somatic cell panel, the bovine bcnt gene was mapped to chromosome 18, syntenic human chromosome 16q on which human BCNT is located. The bcnt genomic DNA sequence corresponding to the cDNA downstream of a RTE-1 derived portion reveals that each IR unit is flanked by both 5'-side and 3'-side introns and that 3'-UTR consists of one exon. The alignment of the above sequence with a bovine RTE-1 did not show any significant homology downstream of the endonuclease domain. On the other hand, the alignment of the intron sequences with each other revealed that the six sequential homologous segments ranging in size from 40 to 453 bp existed over a 1 kb long sequence between both the 5'- and 3'-side introns flanking each bovine IR unit. In addition, both the 174-bp of 5'-side intron and 80-bp of 3'-side intron neighboring each 120-bp IR exon are significantly homologous among the two bovine IRs, human IR and mouse IR. These results suggest that a truncated bovine RTE-1 was inserted into the intron upstream of an IR unit of an ancestor bcnt gene and that a duplication of a relatively long region that includes IR occurred in the bovine genome.

3' Untranslated Regions↗
PubMed1997

Gene coding for the transcription factor, SUG/proteasome, p45 is located nearly 40 kb downstream from the rat growth hormone gene.

About 40 kilobases (kb) downstream of the rat growth hormone gene, a gene was found to be expressed in the liver and placenta as 1.5 kb poly(A)-rich RNA. Using the genomic DNA fragment as a probe, the corresponding cDNA clone containing a 1.3 kb insert was isolated from the rat liver cDNA library. The deduced amino acid sequence having 406 residues was identical with that of the mouse transcription factor, SUG and human proteasome subunit, p45. The gene was thus identified as the rat SUG/p45 (rSUG/p45) gene. The 5' end of the gene was determined by the primer-extension analysis and the exon was noted to comprise 1409 bases. The rSUG/p45 gene, 6.0 kb in length and possessing 12 exons, started at 42.8 and ended at 36.8 kb downstream from the transcription start site of the GH gene. From exon 2 to 11, the size of each rSUG/p45 exon was identical with the corresponding exon of the 4.4 kb pig gene. Rat SUG/p45 mRNA was similarly expressed in seven different tissues and one cell line.

ATPases Associated with Diverse Cellular Activitie↗
PubMed1999

A sequence with homology to human HPFH-linked enhancer elements and to a family of G-protein linked membrane receptor genes is located downstream of the chicken beta-globin locus.

We report 5805bp of novel sequence (GenBank/EMBL Accession No. AJ012570) from a region starting approx. 11.5kb downstream of the chicken beta-globin locus (map position approx. +30.8 to +36.6kb), which contains a 945bp open reading frame (map position approx. +33 to +33.9kb). This is predicted to encode a 315-residue protein containing seven hydrophobic helical regions and a 17 amino acid motif characteristic of the R7G family of G-protein coupled membrane-bound receptors. The open reading frame and some surrounding sequence also have significant homology with the breakpoint enhancer elements, which also contain open reading frames, implicated in the HPFH-1/2 and HPFH-6 deletional forms of the human syndrome, hereditary persistence of foetal haemoglobin (HPFH). The existence of similar sequences at similar distances downstream of the beta-globin genes in chickens and HPFH patients is intriguing.

Amino Acid Sequence↗
PubMed2002

The efficacy of endocrine disruptor screening tests in detecting anti-estrogenic effects downstream of receptor-ligand interactions.

Several predictive test methods for endocrine disrupters have been evaluated by international organizations. In this study, we performed a series of predictive tests for endocrine disrupters, i.e. the receptor binding assay, reporter gene assay, and immature rat uterotrophic assay, on all-trans retinoic acid (tRA), which may cause antiestrogenic activity via their receptors, interfere with estrogenic action at estrogen responsive element level, and we examine the efficacy of endocrine disruptor screening tests in detecting anti-estrogenic effects downstream of receptor-ligand interactions. Despite showing complete lack of binding affinity to ER in the receptor binding assay, tRA exhibited clear antagonist activity without any agonist activity in the reporter gene assay. In the in vivo test, tRA was subcutaneously administered to immature Crj:CD (SD) IGS rats at doses of 5 and 25 mg/kg per day for 3 days, beginning at 20 days of age. Additional groups of rats given tRA at the above doses were also subcutaneously injected with ethinyl estradiol (EE) at a dose of 0.6 microg per rat per day. A vehicle control group given olive oil alone and a positive control group given EE alone were also established. Although no uterotrophic activity was detected in any of the rats given only tRA, co-treatment with 5 and 25 mg/kg tRA and EE reduced the EE-induced increases in uterine weight. We confirmed that the ER antagonist activity of tRA may be mediated by transcriptional interference after ER-ligand complex binding to an estrogen responsive element of the gene by the gel mobility shift analysis. These findings suggest the reporter gene assay and uterotrophic assay can detect anti-estrogenic effects downstream of receptor-ligand interactions, but the receptor binding assay can not detect this type of interference. In any case, a screening strategy for endocrine disrupters, especially the primary screening battery for prioritizing the chemicals to be tested in the higher screening stages, should be designed to detect various kinds of chemicals possessing endocrine modulating activity including a retinoid-like endocrine modulator. Accordingly, reporter gene assay or uterotrophic assay should be conducted in the early stage of screening process for endocrine disrupting chemicals, because they can detect antagonist activity caused by both inhibition of receptor-ligand interaction and transcriptional interference. Particularly, the reporter gene assay may be a promising prescreening procedure, because it can be adopted in the high throughput screening process for thousands of chemicals and it requires no use of experimental animals.

Animals↗
PubMed2001

Identification of the gene immediately downstream of the murine INK4a/ARF locus.

The tumor suppressor gene ARF is formed by three exons, namely exons 1 beta, 2 and 3. Here, we show that embryo fibroblasts from mice genetically deficient in exons 2 and 3 (Delta 2,3) express a transcript formed by exon 1 beta followed by the 3'-terminal exon of the gene immediately downstream of the INK4a/ARF locus, which we have called NTp16 (Next-To-p16). The chimeric ARF-NTp16 transcript is not detectable in wild-type fibroblasts but its expression level in Delta 2,3 fibroblasts is 30% compared to the level of the normal ARF transcript in wild-type cells. Expression of the ARF-NTp16 transcript in Delta 2,3 cells is subject to normal regulatory features, such as upregulation by the accumulation of cell doublings, and by the presence of oncogenic Ras or E1a. The chimeric ARF-NTp16 transcript has the potential to encode a 17kDa peptide; however, this peptide is not accumulated in cells at detectable levels, probably reflecting poor codon usage or protein instability. We conclude that Delta 2,3 cells do not retain ARF functionality, at least to a significant extent. Interestingly, the expression pattern of the full-length NTp16 gene is altered in several tissues by the presence of the Delta 2,3 mutation. Finally, these data identify the gene immediately downstream of the INK4a/ARF locus, a region that has been previously proposed to contain another tumor suppressor different from the INK4a/ARF genes.

Amino Acid Sequence↗
PubMed1995

Isolation of genes differentially expressed at the downstream anastomosis of prosthetic arterial grafts with use of mRNA differential display.

PURPOSE: Downstream anastomotic intimal hyperplasia in prosthetic arterial grafts remains a major cause of delayed graft failure. The new method of messenger RNA (mRNA) differential display was used to screen numerous genes to gain insight into the molecular mechanisms of intimal hyperplasia. METHODS: Fifty-centimeter-long 8 mm expanded polytetrafluoroethylene grafts were placed in four mongrel dogs from the carotid artery to the distal abdominal aorta. At 3 months the distal anastomoses and adjacent normal aortas were harvested; a portion was taken for histologic examination, and total RNA was isolated from the remainder. Differential mRNA display was used to identify candidate cDNA clones whose expression differed in anastomotic intimal hyperplasia as compared with adjacent unaffected aorta. The clones were sequenced, and national gene databases were searched. Northern blot analysis confirmed alteration of gene expression. RESULTS: Approximately 5000 mRNA species were screened, and 11 candidate clones were obtained. DNA sequence revealed homology of five clones to known gene sequences. Homologous genes included an interferon-gamma-induced human gene, (IGUP I-5111), alpha-1 protease inhibitor gene, human retinoblastoma susceptibility gene, and human creatine kinase gene (two clones). Northern blot analysis revealed altered gene expression in 4 of 11, nonregulation in 1 of 11, and undetectable signals in 6 of 11. Expression of the clone representing IGUP I-5111 in the segment of intimal hyperplasia was found to be decreased over threefold to only 31% +/- 16.4% SE of the level seen in normal aorta. CONCLUSIONS: The technique of mRNA differential display has identified differences in gene expression in an in vivo model of anastomotic intimal hyperplasia. Expression of RNA with homology to an interferon-gamma-induced human gene was consistently decreased within the hyperplastic region at the downstream polytetrafluoroethylene arterial anastomosis.

Anastomosis, Surgical↗
PubMed1995

Detection of two groups of 25.2 MDa Tet M plasmids by polymerase chain reaction of the downstream region.

Forty-four Neisseria gonorrhoeae, 12 N. meningitidis, four Kingella denitrificans and one Eikenella corrodens carrying 25.2 MDa Tet M plasmids were analysed using polymerase chain reaction (PCR) to the downstream region of the incomplete Tet M transposon. From each isolate, one of two different PCR fragments of approximately 700 or 1600 bp were obtained. The two different sized PCR fragments had > or = 90% DNA sequence identity with Ureaplasma urealyticum Tet M downstream sequences. The difference between the large PCR fragment and the smaller PCR fragment was a deletion of over 800 bp in the smaller fragment. Both PCR fragments were found in plasmids isolated from N. gonorrhoeae and K. denitrificans. The smaller PCR fragment was found in N. meningitidis plasmids and the larger PCR fragment was found in the E. corrodens plasmid.

Bacterial Proteins↗
PubMed2000

Local and downstream effects of excitotoxic lesions in the rat medial prefrontal cortex on In vivo 1H-MRS signals.

The rat medial prefrontal cortex (mPFC) regulates subcortical dopamine transmission via projections to the striatum and ventral tegmental area. We used in vivo proton magnetic resonance spectroscopy (1H-MRS) at 4.7 T to determine whether excitotoxic lesions of the mPFC result in alterations of N-acetylaspartate (NAA), a marker of neuronal integrity, both locally and downstream in the striatum. Lesioned rats exhibited persistent reductions of NAA and other metabolites within the prefrontal cortex; selective reductions of NAA were seen in the striatum, but not in the parietal cortex. Consistent with earlier reports, lesioned rats exhibited a transient enhancement in amphetamine-induced hyperlocomotion. Prefrontal NAA losses correlated with lesion extent. In the striatum, while there was no change in tissue volume, expression of striatal glutamic acid decarboxylase-67 mRNA was significantly reduced. In vivo NAA levels thus appear sensitive to both local and downstream alterations in neuronal integrity, and may signal meaningful effects at cellular and behavioral levels.

Amphetamine↗
PubMed2003

An extracellular matrix-specific microarray allowed the identification of target genes downstream of discoidin domain receptors.

The two discoidin domain receptors, DDR1 and DDR2, are tyrosine kinases that are activated by collagen and are essential regulators of cell-matrix communication. However, the target genes downstream of activated DDRs and their physiological significance are largely unknown. Here, we describe a novel method to dissect signaling pathways induced by extracellular matrix (ECM) receptors. Using the doxycycline-inducible repression system (tet-off), we generated human fibrosarcoma and mouse fibroblast cell lines over-expressing DDR1 or DDR2. These cell lines were employed for gene expression analysis using microarrays specific for human and mouse genes coding for ECM proteins or ECM-interacting factors. We found that approximately 10% of the genes studied were up- or down-regulated more than twofold in response to signals generated by over-expressing DDRs. A common event downstream of DDR1 and DDR2 in human and mouse cells was the up-regulation of P-selectin glycoprotein ligand. Key target genes repressed upon DDR activation were agrin, syndecan-1 and alpha3 integrin. ECM-specific microarrays were found a valuable tool to dissect gene expression changes induced by collagen-receptor signaling pathways.

Animals↗
PubMed2002

Zebrafish Rho kinase 2 acts downstream of Wnt11 to mediate cell polarity and effective convergence and extension movements.

BACKGROUND: During vertebrate gastrulation convergence and extension (CE), movements narrow and lengthen embryonic tissues. In Xenopus and zebrafish, a noncanonical Wnt signaling pathway constitutes the vertebrate counterpart to the Drosophila planar cell polarity pathway and regulates mediolateral cell polarization underlying CE. Despite the identification of several signaling molecules required for normal CE, the downstream transducers regulating individual cell behaviors driving CE are only beginning to be elucidated. Moreover, how defective mediolateral cell polarity impacts CE is not understood. RESULTS: Here, we show that overexpression of zebrafish dominant-negative Rho kinase 2 (dnRok2) disrupts CE without altering cell fates, phenocopying noncanonical Wnt signaling mutants. Moreover, Rho kinase 2 (Rok2) overexpression partially suppresses the slb/wnt11 gastrulation phenotype, and ectopic expression of noncanonical Wnts modulates Rok2 intracellular distribution. In addition, time-lapse analyses associate defective dorsal convergence movements with impaired cell elongation, mediolateral orientation, and consequently failure to migrate along straight paths. Transplantation experiments reveal that dnRok2 cells in wild-type hosts neither elongate nor orient their axes. In contrast, wild-type cells are able to elongate their cell bodies in dnRok2 hosts, even though they fail to orient their axes. CONCLUSIONS: During zebrafish gastrulation, Rok2 acts downstream of noncanonical Wnt11 signaling to mediate mediolateral cell elongation required for dorsal cell movement along straight paths. Furthermore, elongation and orientation of the cell body are independent properties that require both cell-autonomous and nonautonomous Rok2 function.

Animals↗
PubMed1992

Injection characteristics and downstream contrast material distribution of flush aortography catheters: in vitro study.

Performance of 11 commercially available 4- and 5-F aortic flush catheters was evaluated with respect to the extent of upstream injection, catheter motion, and downstream homogeneity of a 10-, 15-, and 20-mL/sec bolus of 76% meglumine sodium diatrizoate at room temperature. Tests were made in a pulsatile aortic flow model containing circulating fluid isoviscous to blood. The injection process was recorded on videotape. Homogeneity of the contrast material bolus was determined spectrophotometrically from samples collected from the center and each of the four quadrants of the vessel lumen. Upstream contrast material injection between 1.5 and 7 cm in length emerged from all catheters; it was lowest with one of the "tennis racket" designs from one and a new spiral end-loop design (Halo) from another manufacturer. All catheters, except the most rigid and largest-caliber catheter (5.8 F) showed considerable shaft motion at the higher injection rates. Downstream contrast material mixing homogeneity was always best at the highest injection rate but altogether was better for the Halo catheter than for any other catheter tested. It is concluded that all tested 4- and 5-F aortic flush catheters show some undesirable features, but certain design modifications improve performance and comparative testing is helpful to distinguish such features.

Aortography↗
PubMed1998

Granzyme B directly and efficiently cleaves several downstream caspase substrates: implications for CTL-induced apoptosis.

Caspase-mediated proteolysis of downstream substrates is a critical element of the execution pathway common to all forms of apoptosis studied to date. While this caspase-dependent pathway is activated during cytotoxic lymphocyte granule-induced cell death, recent studies have also provided evidence for caspase-independent pathways. However, the mechanisms mediating these additional pathways have not been defined. The current study demonstrates that DNA-PKcs and NuMA are directly and efficiently cleaved by granzyme B in vitro and in vivo, generating unique substrate fragments not observed during other forms of apoptosis. This direct, caspase-independent ability of granzyme B to cleave downstream death substrates constitutes an apoptotic effector mechanism that is insensitive to inhibitors of the signaling or execution components of the endogenous apoptotic cascade.

Antigens, Nuclear↗
PubMed1995

Effect of a main renal artery stenosis on the downstream Doppler waveform in dogs.

RATIONALE AND OBJECTIVES: We evaluated the changes in the down-stream Doppler waveforms caused by a proximal stenosis in the main renal artery of dogs. METHODS: Renal parenchymal arterial waveforms downstream from mild (< 50%), moderate (50-75%), and severe (76-95%) stenoses were compared with nonstenotic baseline waveforms in five mongrel dogs. Waveform shapes were categorized as biphasic or monophasic. The percentage of biphasic and monophasic waveforms was determined for each stenosis. The acceleration index (AI) and the acceleration time (AT) were determined using traditional and modified calculations (AI' and AT'). Late systolic deceleration (DS), diastolic deceleration (DD), and the resistive index (RI) also were measured. RESULTS: AT, AI', and AT' demonstrated significant differences between the severe stenoses and nonstenotic baselines (p < .05); however, there was no difference between the mild and moderate stenoses versus baselines. The percentage distribution of monophasic and biphasic waveforms was highly correlated with the degree of stenosis. Monophasic waveforms increased on average from 22.5% of baseline waveforms to 76.5% of waveforms in the severe stenoses. Biphasic waveforms decreased on average from 69.9% of baseline waveforms to 18.7% of waveforms in the severe stenoses. CONCLUSION: Quantitative evaluation of the downstream waveform parameters (AI, AT, AI', AT', DS, DD, and RD in the dog kidney is not sufficiently accurate, but calculation of the percentage of the monophasic and biphasic waveforms present may be useful to predict a hemodynamically significant renal artery stenosis (> or = 50%).

Animals↗
PubMed2002

E2F transcriptional repressor complexes are critical downstream targets of p19(ARF)/p53-induced proliferative arrest.

The p16(INK4a)/pRB/E2F and p19(ARF)/p53 tumor suppressor pathways are disrupted in most human cancers. Both p19(ARF) and p53 are required for the induction of senescence in primary mouse embryonic fibroblasts (MEFs), but little is known about their downstream targets. Disruption of E2F-mediated transcriptional repression in MEFs caused a general increase in the expression of E2F target genes, including p19ARF. We detected no contribution of E2F-mediated transactivation in this setting, indicating that a predominant role of endogenous E2F in asynchronously growing primary MEFs is to repress its target genes. Moreover, relief of transcriptional repression by E2F rendered MEFs resistant to senescence induced by either p19(ARF), p53, or RAS(V12). Thus, E2F transcriptional repressor complexes are critical downstream targets of antiproliferative p19(ARF)/p53 signaling.

3T3 Cells↗
PubMed2000

Translation during cold adaptation does not involve mRNA-rRNA base pairing through the downstream box.

The downstream box (DB) has been proposed to enhance translation of several mRNAs and to be a key element controlling the expression of cold-shocked mRNAs. However, the proposal that the DB exerts its effects through a base pairing interaction with the complementary anti-downstream box (antiDB) sequence (nt 1469-1483) located in the penultimate stem (helix 44) of 16S rRNA remains controversial. The existence of this interaction during initiation of protein synthesis under cold-shock conditions has been investigated in the present work using an Escherichia coli strain whose ribosomes lack the potential to base pair with mRNA because of a 12 bp inversion of the antiDB sequence in helix 44. Our results show that this strain is capable of cold acclimation, withstands cold shock, and its ribosomes translate mRNAs that contain or lack DB sequences with similar efficiency, comparable to that of the wild type. The structure of helix 44 in 30S ribosomal subunits from cells grown at 37 degrees C and from cells subjected to cold shock was also analyzed by binding a 32P-labeled oligonucleotide complementary to the antiDB region and by chemical probing with DMS and kethoxal. Both approaches clearly indicate that this region is in a double-stranded conformation and therefore not available for base pairing with mRNA.

Adaptation, Physiological↗