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Results for “Enhancer mapping”

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PubMed1998

A mammalian scaffold complex that selectively mediates MAP kinase activation.

The c-Jun NH2-terminal kinase (JNK) group of mitogen-activated protein (MAP) kinases is activated by the exposure of cells to multiple forms of stress. A putative scaffold protein was identified that interacts with multiple components of the JNK signaling pathway, including the mixed-lineage group of MAP kinase kinase kinases (MLK), the MAP kinase kinase MKK7, and the MAP kinase JNK. This scaffold protein selectively enhanced JNK activation by the MLK signaling pathway. These data establish that a mammalian scaffold protein can mediate activation of a MAP kinase signaling pathway.

Animals↗

PubMed2003

Bi-directional migration of lens epithelial cells in a physiological electrical field.

An endogenous electric field (EF) exists in the vertebrate lens, but the influences of this on the functions of lens epithelial cells (LECs) are unclear. Because LECs from different regions experience different patterns of endogenous EFs and show striking differences in morphology and function, bovine LECs from different regions were cultured in an applied EF to mimic that occurring naturally. The migration of LECs from central and peripheral regions was both stimulated and directed by an applied EF. Field-directed cell migration required serum, or growth factors. Cells cultured in serum free medium lost directed migration completely and this was restored partially by the addition of basic fibroblast growth factor. The direction of cell migration depended on both EF-strength and the origin of the LECs. Both central and peripheral LECs moved anodally at 150-250mVmm(-1). In a low EF (50mVmm(-1)), peripheral LECs migrated in the opposite direction, cathodally, but central LECs did not respond. Peripheral LECs alone therefore showed field strength dependent, bi-directional migration. A physiological EF enhanced activation of ERK1/2, a signaling molecule in the MAP kinase pathway, and this also required serum. Interestingly, expression of active ERK1/2 was enhanced in peripheral LECs at both 50 and 200mVmm(-1), which stimulated migration in different directions. In central LECs, which showed directed migration only at higher EFs, active ERK1/2 was increased only at 200mVmm(-1). The MAP kinase inhibitor U0126 prevented activation of ERK1/2 in LECs and inhibited EF-directed migration, implicating MAP kinase signaling in directing the migration of LECs in a physiological EF.

Animals↗

PubMed1980

Modulatory effect of brain acetylcholine on reflex-induced bradycardia and tachycardia in conscious rats.

The effects of intracerebroventricular (i.c.v.) injection of physostigmine and hemicholinium-3 (HC-3) on reflex bradycardia and tachycardia have been studied in unanesthetized rats. The reflex increases and decreases in heart rate were elicited by i.v. injection of norepinephrine and sodium nitroprusside, respectively. Physostigmine (5-10 micrograms) increased basal mean arterial pressure (MAP), reduced basal heart rate (HR), enhanced the reflex bradycardia and reduced reflex tachycardia. Physostigmine did not modify either the pressor effect of norepinephrine, the depressor effect of sodium nitroprusside or the responsiveness of peripheral muscarinic receptors. Pretreatment (i.c.v.) with atropine (0.3 micrograms) completely abolished the effect of physostigmine on MAP, HR, reflex bradycardia and reflex tachycardia. Pretreatment (i.c.v.) with mecamylamine (50 micrograms) did not modify the effect of the cholinesterase inhibitor on MAP, HR and reflex tachycardia, but inverted its effect on reflex bradycardia. Injection of HC-3 (20 micrograms i.c.v.) did not modify MAP, but reduced HR and inhibited both reflex bradycardia and reflex tachycardia. The HC-3 bradycardic effect started within minutes and lasted for about 1 hr, while the depressor effect on the reflexes began only after 15 min and continued for several hours. In addition, i.c.v. pretreatment with HC-3 completely abolished all the effects of physostigmine on MAP, HR, reflex bradycardia and reflex tachycardia. These results suggest that brain acetylcholine has a modulatory effect on baroreceptor reflexes. This modulation operates through muscarinic receptors in reflex tachycardia and through both muscarinic and nicotinic receptors in reflex bradycardia.

Acetylcholine↗

PubMed2005

Development and validation of a whole-cell inhibition assay for bacterial methionine aminopeptidase by surface-enhanced laser desorption ionization-time of flight mass spectrometry.

Bacterial methionine aminopeptidase (MAP) is a protease that removes methionine from the N termini of newly synthesized bacterial proteins after the peptide deformylase enzyme cleaves the formyl group from the initiator formylmethionine. MAP is an essential bacterial gene product and thus represents a potential target for therapeutic intervention. A fundamental challenge in the antibacterial drug discovery field is demonstrating conclusively that compounds with in vitro enzyme inhibition activity produce the desired antibacterial effect by interfering with the same target in whole bacterial cells. One way to address the activity of inhibitor compounds is by profiling cellular biomarkers in whole bacterial cells using compounds that are known inhibitors of a particular target. However, in the case of MAP, no specific inhibitors were available for such studies. Instead, a genetically attenuated MAP strain was generated in which MAP expression was placed under the control of an inducible arabinose promoter. Thus, MAP inhibition in whole cells could be mimicked by growth in the absence of arabinose. This genetically attenuated strain was used as a benchmark for MAP inhibition by profiling whole-cell lysates for unprocessed proteins using surface-enhanced laser desorption ionization-time of flight mass spectrometry (MS). Eight proteins between 4 and 14 kDa were confirmed as being unprocessed and containing the initiator methionine by adding back purified MAP to the preparations prior to MS analysis. Upon establishing these unprocessed proteins as biomarkers for MAP inhibition, the assay was used to screen small-molecule chemical inhibitors of purified MAP for whole-cell activity. Fifteen compound classes yielded three classes of compound with whole-cell activity for further optimization by chemical expansion. This report presents the development, validation, and implementation of a whole-cell inhibition assay for MAP.

Aminopeptidases↗

PubMed2005

Characterization of micrometastatic disease in melanoma sentinel lymph nodes by enhanced pathology: recommendations for standardizing pathologic analysis.

Lymphatic mapping and sentinel lymph node (SLN) biopsy are widely used as a staging technique for patients with cutaneous malignant melanoma who are at risk for metastases. SLN status has been shown to be a strong predictor of prognosis, and a variety of techniques have been used to identify minimal metastatic disease in SLNs. However, there is no validated consensus method for the optimal histologic analysis of SLNs harvested from melanoma patients. This study was conducted: 1) to assess the yield of metastatic melanoma detected in SLNs deemed negative by initial routine pathologic analysis (RPA) by subjecting them (after review of the original slides) to enhanced pathologic analysis (EPA) that included complete step-sectioning and immunohistochemistry (IHC); 2) to characterize the distribution of metastatic melanoma deposits within the SLNs; 3) to determine a preferred method of pathologic analysis applicable to daily practice; and 4) to attempt to assess the clinical significance of disease detected by EPA. A total of 105 SLNs were harvested from 49 patients who underwent successful SLN biopsy procedures during the period of study. Ten SLNs from 10 patients were positive on initial RPA and were not analyzed further. Ninety-five SLNs from the remaining 39 patients were reviewed and processed with additional hematoxylin and eosin, S-100 protein, and HMB-45 stains at 50-microm intervals for 20 levels or until the SLN tissue was exhausted. A single pathologist reviewed all sections without knowledge of the results of the other stains. Overall, metastatic melanoma was discovered in SLNs from 20 of the 39 patients: SLNs from 6 patients were found to have melanoma on review of the original hematoxylin and eosin slides, and SLNs from 14 patients were positive only after EPA. Twenty-one individual positive SLNs from these 14 patients were detected by EPA; of these, 10 positive SLNs were identified solely by IHC, representing 12% of the patient cohort and 10% of all SLNs studied by EPA. Detection rates were significantly associated with the staining method and the number of levels performed (P < 0.01). S-100 protein staining resulted in the highest yield of SLN positivity (86%), followed by HMB-45 (81%) and hematoxylin and eosin (52%). No single method detected all of the micrometastases. A detailed topographic mapping of metastatic deposits in SLNs was carried out. When using all three staining techniques, all 20 levels were required to identify 100% of the micrometastases; 95% of positive SLNs were identified with 17 levels, 90% with 15 levels, 75% with 10 levels, and 42% with 3 levels. Projected rates of detection for various different sectioning strategies were determined, with alteration of either the number of levels examined, the interval between the levels, or both. Detection of SLN positivity can be increased to 71% by performing three levels at 250-mum intervals, each level being composed of a set of three sections stained with hematoxylin and eosin, S-100 protein, and HMB-45, respectively. Therefore, this is the methodology we propose for the study of SLNs in melanoma patients. After a median follow-up of 87 months (range, 9-134 months), patients with EPA-detected disease and those with negative SLNs by EPA demonstrated improved recurrence-free and disease-specific survival compared with patients with RPA-detected disease in SLNs. Sampling error introduced by variations in pathologic processing should be addressed by standardization of pathologic methods, and the clinical significance of minimal SLN disease should be addressed in prospective studies of homogeneously staged patients.

Adult↗

PubMed1985

Xenopus ribosomal gene enhancers function when inserted inside the gene they enhance.

The ribosomal DNA of Xenopus laevis contains repeated sequence elements in the intergenic spacer region that enhance transcription from the adjacent gene promoter (1,2). Previous work has shown that these RNA polymerase I enhancers influence the target promoter when they are in either orientation, at a distance of several kilobases, and only when they are in cis (3-5). In this work, we further show that enhancer activity is unaffected by inserting the enhancers within the transcription unit whose promoter is being enhanced. In addition, enhancer activity does not interfere with transcription through its sequences. The results suggest that the enhancers act at a point prior to the initiation of transcription and that they are likely to be dispensable once transcription has begun.

Animals↗

PubMed1997

[Evaluation of ischemic heart disease using the index of relative 99mTc-tetrofosmin uptake increase at exercise].

We calculated an increase of myocardial 99mTc-tetrofosmin uptake during exercise from resting condition, which was thought to reflect coronary flow reserve, and assessed whether this method enhanced the detection of coronary artery disease (CAD). Exercise myocardial SPECT was performed using 99mTc-tetrofosmin with one-day method (exercise-rest) in 26 patients. Twenty-one patients were suspected to have ischemic heart disease and 5 were control patients. A polar map was used to evaluate the increase in counts after exercise. The parameter of % uptake increase was obtained by the ratio of exercise and resting myocardial counts. The uptake was corrected for administration dose and time decay between the exercise and rest studies. The sensitivity for detecting patients with significant coronary stenosis by visual evaluation and % uptake increase map was 60% and 90%, respectively. In 5 patients, % uptake increase map detected stenosed coronary artery lesions that could not be detected by visual analysis. We concluded that the % uptake increase map combined with conventional SPECT images enhanced the detectability of coronary artery disease and the evaluation of the degree of coronary flow reserve.

Adult↗

PubMed1994

Mutation of the two carboxyl-terminal tyrosines in the insulin receptor results in enhanced activation of mitogen-activated protein kinase.

Activation of mitogen-activated protein (MAP) kinase represents an important mechanism in hormonal regulation. To clarify the role of MAP kinase activation in insulin action, we compared the activation of the enzyme in Rat-1 cells transfected with wild-type (Hirc) and mutant insulin receptors in which the 2 carboxyl-terminal tyrosines were substituted with phenylalanine (Y/F2). Expression of the Y/F2 mutant receptor enhanced the responsiveness of MAP kinase to insulin. Moreover, the insulin responsiveness of the activator of this enzyme, MAP kinase kinase, was also increased in these cells. To explore the early signaling events that might account for this increase in responsiveness, we evaluated the tyrosine phosphorylation of the insulin receptor substrate, IRS-1, and its subsequent association with phosphatidylinositol (PI)-3 kinase. In both cell types, insulin led to a dose-dependent increase in the association of tyrosine phosphorylated IRS-1 with the SH2 domain of the p85 regulatory subunit of PI-3 kinase, and also increased the amount of PI kinase activity detected in anti-IRS-1 immunoprecipitates. The effect of insulin was significantly greater in Y/F2 cells, as determined in both assays. In previous studies, cells bearing this receptor mutant exhibited an identical metabolic response but enhanced mitogenic response to insulin when compared with wild-type receptor. These data provide further evidence for divergence of the mitogenic and metabolic signaling pathways at or near the insulin receptor.

Animals↗

PubMed1997

Differential effects of a mitogen-activated protein kinase kinase inhibitor on human neutrophil responses to chemotactic factors.

Chemotactic factors, i.e., an N-formyl peptide, C5a, interleukin-8, and leukotriene B4, induced neutrophils to activate mitogen-activated protein (MAP) kinases, as defined by the tyrosine phosphorylation and decrease in electrophoretic mobility of immunodetected 44-, 42-, and 40-kDa proteins. PD 98059, an inhibitor of MAP kinase kinase activation, blocked these changes. The drug likewise blocked neutrophil chemotaxis but did not alter superoxide anion production and paradoxically enhanced degranulation responses to the stimuli. The MAP kinase pathway appears to have a highly selective role in mediating motility but not other cellular responses.

Chemotactic Factors↗

PubMed2001

Epstein-Barr virus primes human polymorphonuclear leucocytes for the biosynthesis of leukotriene B4.

In the present study, we have investigated the effect of the short-term incubation of polymorphonuclear leucocytes (PMN) with infectious Epstein-Barr virus (EBV) on leukotriene B(4) (LTB(4)) biosynthesis. Pre-exposure of PMN to EBV led to an increased production of LTB(4) upon stimulation with either the ionophore A23187, the chemotactic peptide fMLP, or phagocytic particles (zymosan). Experiments performed with viral particles pretreated with a neutralizing antibody raised against the gp350 of the viral envelope revealed that a specific interaction between the PMN surface and the viral glycoprotein gp350 is required for the priming effect of EBV. Preincubation of PMN with EBV resulted in an increased release of arachidonic acid upon stimulation with a second agonist. Moreover, LTB(4) biosynthesis in EBV/A23187-treated PMN was greatly diminished in the presence of an inhibitor of the cytosolic phospholipase A2 (cPLA(2)), suggesting that cPLA(2) plays a critical role in the priming effect of EBV. Accordingly, EBV by itself promoted Ser-505 phosphorylation of cPLA(2) and strongly enhanced fMLP-induced phosphorylation of p38 MAP kinase, an enzyme known to phosphorylate cPLA(2) in human PMN. Furthermore, fMLP-induced translocation of cPLA(2) was strongly enhanced when PMN were previously exposed to EBV. These data indicate that binding of EBV to human PMN results in the activation of intracellular events involved in the release of pro-inflammatory lipid mediators.

Arachidonic Acid↗

PubMed1996

A 700 bp cis-acting region controls mating-type dependent recombination along the entire left arm of yeast chromosome III.

Homothallic switching of the mating-type MATa gene in Saccharomyces cerevisiae results from replacement by gene conversion of MAT-Ya DNA with Y(alpha) sequences copied from one of two unexpressed donors. MATa preferentially recombines with HML(alpha), located near the left end of chromosome III, but can use HMR(alpha), near the right chromosome end. MATa donor preference depends on a 700 bp orientation-independent cis-acting recombination enhancer, located 17 kb proximal to HML. Deletion of this element markedly reduces MATa's use of a donor inserted at any of four different locations along the leftmost 92 kb of chromosome III. This enhancer is sufficient for donor activation, since it stimulates use of the "wrong" donor, when it is inserted 7 kb proximal to HMR.

Base Sequence↗

PubMed2004

Enhancement of central dopaminergic activity in the kainate model of temporal lobe epilepsy: implication for the mechanism of epileptic psychosis.

There is an increased incidence of schizophrenia-like psychosis in temporal lobe epilepsy (TLE), and several risk factors have been implicated, including the duration of epilepsy and temporal lobe neuropathology. To investigate the biological mechanism of epileptic psychosis, we examined alterations of central dopaminergic systems in the kainate model of TLE. In adult rats, kainate was microinjected into the left amygdala to induce status epilepticus. An indirect dopamine agonist methamphetamine (MAP, 2 mg/kg, i.p.) was administered before and 1 month after the kainate treatment. MAP-induced locomotor activity was significantly enhanced in the kainate group compared with the baseline (pre-kainate) level, which was antagonized by pretreatment with haloperidol. The enhancement of locomotor activity in the kainate group was significantly correlated with the density of hippocampal CA1 neurons. Although the basal extracellular dopamine concentration was significantly lower in the striatum in the kainate group than in the control group (5.5 vs 39.2 fmol/20-min sample), the maximal concentration following MAP administration did not differ between the two groups. These results clearly demonstrate that hypersensitivity of the dopamine systems develops in the chronic phase of the kainate-induced TLE model, which may be responsible for the mechanism of epileptic psychosis.

Analysis of Variance↗

PubMed2004

Fluorescence resonance energy transfer reports properties of syntaxin1a interaction with Munc18-1 in vivo.

Syntaxin1A, a neural-specific N-ethylmaleimide-sensitive factor attachment protein receptor protein essential to neurotransmitter release, in isolation forms a closed conformation with an N-terminal alpha-helix bundle folded upon the SNARE motif (H3 domain), thereby limiting interaction of the H3 domain with cognate SNAREs. Munc18-1, a neural-specific member of the Sec1/Munc18 protein family, binds to syntaxin1A, stabilizing this closed conformation. We used fluorescence resonance energy transfer (FRET) to characterize the Munc18-1/syntaxin1A interaction in intact cells. Enhanced cyan fluorescent protein-Munc18-1 and a citrine variant of enhanced yellow fluorescent protein-syntaxin1A, or mutants of these proteins, were expressed as donor and acceptor pairs in human embryonic kidney HEK293-S3 and adrenal chromaffin cells. Apparent FRET efficiency was measured using two independent approaches with complementary results that unambiguously verified FRET and provided a spatial map of FRET efficiency. In addition, enhanced cyan fluorescent protein-Munc18-1 and a citrine variant of enhanced yellow fluorescent protein-syntaxin1A colocalized with a Golgi marker and exhibited FRET at early expression times, whereas a strong plasma membrane colocalization, with similar FRET values, was apparent at later times. Trafficking of syntaxin1A to the plasma membrane was dependent on the presence of Munc18-1. Both syntaxin1A(L165A/E166A), a constitutively open conformation mutant, and syntaxin1A(I233A), an H3 domain point mutant, demonstrated apparent FRET efficiency that was reduced approximately 70% from control. In contrast, the H3 domain mutant syntaxin1A(I209A) had no effect. By using phosphomimetic mutants of Munc18-1, we also established that Ser-313, a Munc18-1 protein kinase C phosphorylation site, and Thr-574, a cyclin-dependent kinase 5 phosphorylation site, regulate Munc18-1/syntaxin1A interaction in HEK293-S3 and chromaffin cells. We conclude that FRET imaging in living cells may allow correlated regulation of Munc18-1/syntaxin1A interactions to Ca(2+)-regulated secretory events.

Animals↗

PubMed2002

Tracing odor-induced activation in the olfactory bulbs of mice using manganese-enhanced magnetic resonance imaging.

Ithas previously been demonstrated that it is possible to map active regions of the brain using MRI relying on the fact that Mn(2+) ion enters excitable cells through voltage-gated calcium channels and is an excellent relaxation agent. In addition, Mn(2+) has been shown to trace neuronal connections in the mouse olfactory and visual systems, enabling MRI neuronal tract tracing. The purpose of the present studies was to determine if these two properties could be combined to trace Mn(2+) from sites of activation in the olfactory epithelium to the olfactory bulb thereby localizing regions within the olfactory bulb that respond to a particular odor. Mice were exposed to an aerosolized solution containing either a high pheromone content odor (male mouse urine) or amyl acetate plus MnCl(2). In both cases the odors caused a localized T(1) MRI enhancement in the olfactory epithelium and bulb that was dependent upon the presence of Mn(2+). The high pheromone containing solution caused enhancement in the anatomically correct location of the accessory olfactory bulb. Amyl acetate also caused T(1)-weighted MRI enhancement in specific regions of the olfactory bulb. These areas showing activation agree well with previous 2-deoxyglucose and BOLD fMRI results in the rat. Using manganese-enhanced MRI (MEMRI) it should be possible to rapidly map a variety of odors. Furthermore, since the effects of activation are imaged after the activation protocol it should be possible to take the time to obtain very high resolution images and make MEMRI maps from awake behaving animals.

Animals↗

PubMed1988

The late promoter of the human papovavirus BK is contained within the early promoter enhancer region.

We have analyzed the sequences necessary for late promoter function and mapped the late mRNA start sites of the human papovavirus BK (prototype). Our results show that, under both replicating and nonreplicating conditions, the BKV late promoter is contained within the same region defined as the enhancer for the early promoter. This region consists of three 68-bp repeats (the middle one of which has an 18-bp deletion) and a 66-bp region containing an enhancer element denoted as c, located to the late side of the 68-bp repeats. Deletions within the early enhancer domain indicate that elements of the late promoter are found throughout the entire region.

Antigens, Viral, Tumor↗

PubMed1999

Use of T(2)-weighted susceptibility contrast MRI for mapping the blood volume in the glioma-bearing rat brain.

The aim of this work was to evaluate the potential of T(2)-weighted, steady-state susceptibility-enhanced contrast magnetic resonance imaging (MRI), to characterize brain tumor heterogeneity and tumor vascularization. In vivo T(2)-weighted MRI experiments were carried out on normal rats (n = 11) and rats bearing C6 glioma (n = 17), before and after the injection of a remanent superparamagnetic contrast agent. The DeltaR(2) variations of the transverse relaxation rate due to the injection of the contrast agent were used to generate relative cerebral blood volume (CBV) maps. Contrast enhancement of the tumor was shown to reflect tissue vascularization rather than leakage of the blood-brain barrier. The quantitative results clearly show the heterogeneity of tumor vascularization and reveal a high vessel density in the peripheral area (CBV(per) approximately 17.2 +/- 2.3 sec(-1)) and a low vessel density in the central area of the tumor (CBV(cen) approximately 2.5 +/- 0.5 sec(-1)). Magn Reson Med 42:754-761, 1999.

Animals↗

PubMed2004

An additional copy of the homologous region (hr1) sequence in the Autographa californica multinucleocapsid polyhedrosis virus genome promotes hyperexpression of foreign genes.

The Autographa californica multinucleocapsid nuclear polyhedrosis virus genome contains nine homologous region (hr1, hr1a, hr2, hr2a, hr3, hr4a, hr4b, hr4c, and hr5) sequences that are thought to be involved in viral replication and activation of transcription. Our results show that the 750 bp hr1 sequence is capable of functioning as an enhancer of transcription of foreign genes from the homologous late polyhderin gene promoter and the heterologous Drosophila heat shock protein (hsp70) promoter in insect cells. Introduction of an additional copy of the complete hr1 element downstream to the polyhedrin locus in the viral genome, while not affecting the stability of the recombinant virus for at least 30 serial passages, led to hyperexpression of reporter genes. The enhancement in the expression levels of foreign genes varied from 40 to 90-fold depending on the promoter used.

Animals↗

PubMed2025

Enhancer-targeting CRISPR screens at coronary artery disease loci suggest shared mechanisms of disease risk.

To systematically identify causal genetic mechanisms that confer risk for coronary artery disease (CAD) in GWAS loci, we mapped genome-wide variant-to-enhancer-to-gene (V2E2G) links in vascular smooth muscle cells (SMC). Enhancers identified by active chromatin features, and further prioritized by base-resolution deep learning models of chromatin accessibility in 108 CAD loci, were studied with CRISPRi targeting and Direct-Capture Targeted Perturb-seq (DC-TAP-seq) evaluation of 470 genes. Seventy-six V2E2G links were identified for 59 candidate CAD genes representing gene programs including epithelial-mesenchymal transformation, ubiquitination, and protein folding as well as BMP and TGFB signaling. Similar methods employed with an independent focused screen targeting one candidate locus at 9p21.3 identified 10 enhancers regulating expression of multiple genes at this location. Detailed molecular studies revealed that two enhancers mediating transcription factor binding and transcriptional regulation contribute to ancestry-specific and sex-specific risk for CAD and the surrogate biomarker vascular calcification. Together, these studies advance our identification of GWAS CAD V2E2G links across the genome, and specific mechanisms of risk at the complex 9p21.3 locus.

Journal Article↗