SEARCH · PubMed Health

Results for “Enhancer mapping”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 667 records · Page 37Linked to original sources

PubMed1989

The first intron of the 4F2 heavy-chain gene contains a transcriptional enhancer element that binds multiple nuclear proteins.

We utilized the human 4F2 heavy-chain (4F2HC) gene as a model system to study the regulation of inducible gene expression during normal human T-cell activation. Previous studies have demonstrated that 4F2HC gene expression is induced during normal T-cell activation and that the activity of the gene is regulated, at least in part, by the interaction of a constitutively active 5'-flanking housekeeping promoter and a phorbol ester-responsive transcriptional attenuator element located in the exon 1-intron 1 region of the gene. We now report that 4F2HC intron 1 contains a transcriptional enhancer element which is active on a number of heterologous promoters in a variety of murine and human cells. This enhancer element has been mapped to a 187-base-pair RsaI-AluI fragment from 4F2HC intron 1. DNase I footprinting and gel mobility shift analyses demonstrated that this fragment contains two nuclear protein-binding sites (NF-4FA and NF-4FB) which flank a consensus binding site for the inducible AP-1 transcription factor. Deletion analysis showed that the NF-4FA, NF-4FB, and AP-1 sequences are each necessary for full enhancer activity. Murine 4F2HC intron 1 displayed enhancer activity similar to that of its human counterpart. Comparison of the sequences of human and murine 4F2HC intron 1s demonstrated that the NF-4FA, NF-4FB, and AP-1 sequence motifs have been highly conserved during mammalian evolution.

Animals↗

PubMed1993

Hypermutation is observed only in antibody H chain V region transgenes that have recombined with endogenous immunoglobulin H DNA: implications for the location of cis-acting elements required for somatic mutation.

Mice with transgenes containing an antibody H chain V region (VHDJH) gene were used in an analysis of the cis-acting elements required for hypermutation of immunoglobulin (Ig) V genes. These transgenes can somatically recombine with endogenous IgH DNA, leading to the formation of functional heavy (H) chains partially encoded by the transgenic VHDJH. The transgenomes in the five different lines of mice analyzed contain as little as 150 bp, and as much as 2.8 kb of natural DNA flanking the 5' side of the VH and either 1.5 or 2.3 kb (including the intronic enhancer and 5' matrix attachment region [MAR]) flanking the 3' side of VH. Hybridomas were constructed from immunized transgenic mice, and transgenes present in these hybridomas that had or had not recombined to form functional H chain loci were sequenced. The data obtained show that: (a) the recombined transgenes contain hypermutated VH genes; and (b) among such transgenes, even those containing only 150 bp of natural VH 5' flanking sequence and several kilobases of 5' plasmid vector sequence display a frequency, distribution, and type of mutation characteristic of conventional IgH loci. The data also indicate that transgenic VHDJH genes that have not recombined with endogenous IgH DNA are not substrates for hypermutation, even if they are flanked by 2.8 kb of natural 5' DNA, and 2.3 kb of natural 3' DNA, including the JH2-JH4 region, a MAR, and the intronic enhancer. Collectively, the data suggest that sequences 5' of the VH promoter are dispensable, a VH promoter and the intronic IgH enhancer region are not sufficient, and a region(s) within or 3' of the IgH constant region locus is requisite, for hypermutation of Ig VH transgenes.

Animals↗

PubMed2004

Mapping high-dimensional data onto a relative distance plane--an exact method for visualizing and characterizing high-dimensional patterns.

We introduce a distance (similarity)-based mapping for the visualization of high-dimensional patterns and their relative relationships. The mapping preserves exactly the original distances between points with respect to any two reference patterns in a special two-dimensional coordinate system, the relative distance plane (RDP). As only a single calculation of a distance matrix is required, this method is computationally efficient, an essential requirement for any exploratory data analysis. The data visualization afforded by this representation permits a rapid assessment of class pattern distributions. In particular, we can determine with a simple statistical test whether both training and validation sets of a 2-class, high-dimensional dataset derive from the same class distributions. We can explore any dataset in detail by identifying the subset of reference pairs whose members belong to different classes, cycling through this subset, and for each pair, mapping the remaining patterns. These multiple viewpoints facilitate the identification and confirmation of outliers. We demonstrate the effectiveness of this method on several complex biomedical datasets. Because of its efficiency, effectiveness, and versatility, one may use the RDP representation as an initial, data mining exploration that precedes classification by some classifier. Once final enhancements to the RDP mapping software are completed, we plan to make it freely available to researchers.

Algorithms↗

PubMed2003

A model of the effects of node-link mapping on drug abuse counseling.

This paper examines the effectiveness of a promising cognitive enhancement technique called node-link mapping. Maps provide a concrete, visual, and computationally efficient means for exploring personal issues, and have received substantial empirical support. We introduce two models to provide a framework for understanding how node-link mapping improves substance abuse counseling. The TCU Process Model reviews the general process of substance abuse treatment. The second model reflects an effective treatment session. Implications of the models and node-link mapping findings are discussed, as well as future research directions.

Algorithms↗

PubMed1996

Cloning and mapping of a novel human cDNA homologous to DROER, the enhancer of the Drosophila melanogaster rudimentary gene.

We have isolated a novel human cDNA clone that encodes a protein with 80% identity in amino acid sequence to DROER, the enhancer of the rudimentary gene in Drosophila melanogaster. The rudimentary gene product is thought to have significant enzymatic functions in the pyrimidine metabolic pathway, as well as a critical role in development of the wings. The human cDNA, termed ERH, consists of 797 nucleotides, which include an open reading frame of 312 nucleotides encoding 104 amino acids. The ERH gene was expressed in all normal human tissues examined. We assigned the ERH gene locus to chromosomal band 7q34 by fluorescence in situ hybridization.

Amino Acid Sequence↗

PubMed1990

Mechanism of specific expression of glutathione transferase P gene during hepatocarcinogenesis.

The mechanism of specific expression of glutathione transferase P gene during hepatocarcinogenesis of the rat has been investigated by cloning the gene and determining the upstream regulatory sequences. Two enhancers and a silencer are located within 3 kb upstream of the promoter. The stronger enhancer designated GPEI has two TPA (12-O-tetradecanoyl phorbol 13-acetate)-response element (TRE)-like sequences arranged in a palindrome at a 3 base pairs spacing. This special combination was found to form a very strong enhancer which could act efficiently even in F9 cells where the collagenase enhancer with a singlet TRE cannot work due to the low c-jun content. Whether this structure is operating with a very low concentration of c-jun/c-fos heterodimer or with any other proteins remains to be determined. These findings suggest that new and more efficient enhancers evolve by a combination of basic enhancer elements. The silencer region consists of several sequences that can bind specific protein(s) and works cooperatively.

Animals↗

PubMed1997

LTR retrotransposons and the evolution of eukaryotic enhancers.

Since LTR retrotransposons and retroviruses are especially prone to regional duplications and recombination events, these viral-like systems may be especially conducive to the evolution of closely spaced combinatorial regulatory motifs. Using the Drosophila copia LTR retrotransposon as a model, we show that a regulatory region contained within the element's untranslated leader region (ULR) consists of multiple copies of an 8 bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation in the number of these motifs is correlated with the enhancer strength of the ULR. Our results indicate that inter-element selection may favor the evolution of more active enhancers within permissive genetic backgrounds. We propose that LTR retroelements and perhaps other retrotransposons constitute drive mechanisms for the evolution of eukaryotic enhancers which can be subsequently distributed throughout host genomes to play a role in regulatory evolution.

Animals↗

PubMed1995

The PiGMaP consortium linkage map of the pig (Sus scrofa).

A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (approximately 16.5 Morgans) than the genetic map of the homogametic sex (female) (approximately 21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be approximately 18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.

Animals↗

PubMed2023

Genome-wide identification of transcriptional enhancers during human placental development and association with function, differentiation, and disease†.

The placenta is a dynamic organ that must perform a remarkable variety of functions during its relatively short existence in order to support a developing fetus. These functions include nutrient delivery, gas exchange, waste removal, hormone production, and immune barrier protection. Proper placenta development and function are critical for healthy pregnancy outcomes, but the underlying genomic regulatory events that control this process remain largely unknown. We hypothesized that mapping sites of transcriptional enhancer activity and associated changes in gene expression across gestation in human placenta tissue would identify genomic loci and predicted transcription factor activity related to critical placenta functions. We used a suite of genomic assays [i.e., RNA-sequencing (RNA-seq), Precision run-on-sequencing (PRO-seq), and Chromatin immunoprecipitation-sequencing (ChIP-seq)] and computational pipelines to identify a set of >20 000 enhancers that are active at various time points in gestation. Changes in the activity of these enhancers correlate with changes in gene expression. In addition, some of these enhancers encode risk for adverse pregnancy outcomes. We further show that integrating enhancer activity, transcription factor motif analysis, and transcription factor expression can identify distinct sets of transcription factors predicted to be more active either in early pregnancy or at term. Knockdown of selected identified transcription factors in a trophoblast stem cell culture model altered the expression of key placental marker genes. These observations provide a framework for future mechanistic studies of individual enhancer-transcription factor-target gene interactions and have the potential to inform genetic risk prediction for adverse pregnancy outcomes.

Humans↗

PubMed1989

Mapping of functional regions of murine retrovirus long terminal repeat enhancers: enhancer domains interact and are not independent in their contributions to enhancer activity.

We have used deletion and recombinant long terminal repeat (LTR) mutants to examine enhancer activity differences between LTRs of the nonpathogenic Akv and the thymus lymphomagenic MCF13 murine retroviruses. Deletion mutant analysis revealed that major control regions for MCF13 and Akv LTR enhancer activity were similar but not identical. For both LTRs, major control regions were distinctly different in a murine T-cell and a fibroblast cell line. Recombinant enhancer analysis showed that LTRs could be divided into three regions capable of altering the level of enhancer activity through cooperative or antagonistic interaction. The contribution of each region to enhancer activity was dependent on its context with respect to the other regions. LTR enhancer function in different cell types appears to be the result of the interaction of enhancer modular elements.

AKR murine leukemia virus↗

PubMed2003

Differential regulation of CXCR4-mediated T-cell chemotaxis and mitogen-activated protein kinase activation by the membrane tyrosine phosphatase, CD45.

The chemokine receptor CXCR4 and its cognate ligand, stromal cell-derived factor-1alpha (CXCL12), regulate lymphocyte trafficking and play an important role in host immune surveillance. However, the molecular mechanisms involved in CXCL12-induced and CXCR4-mediated chemotaxis of T-lymphocytes are not completely elucidated. In the present study, we examined the role of the membrane tyrosine phosphatase CD45, which regulates antigen receptor signaling in CXCR4-mediated chemotaxis and mitogen-activated protein kinase (MAPK) activation in T-cells. We observed a significant reduction in CXCL12-induced chemotaxis in the CD45-negative Jurkat cell line (J45.01) as compared with the CD45-positive control (JE6.1) cells. Expression of a chimeric protein containing the intracellular phosphatase domain of CD45 was able to partially restore CXCL12-induced chemotaxis in the J45.01 cells. However, reconstitution of CD45 into the J45.01 cells restored the CXCL12-induced chemotaxis to about 90%. CD45 had no significant effect on CXCL12 or human immunodeficiency virus gp120-induced internalization of the CXCR4 receptor. Furthermore, J45.01 cells showed a slight enhancement in CXCL12-induced MAP kinase activity as compared with the JE6.1 cells. We also observed that CXCL12 treatment enhanced the tyrosine phosphorylation of CD45 and induced its association with the CXCR4 receptor. Pretreatment of T-cells with the lipid raft inhibitor, methyl-beta-cyclodextrin, blocked the association between CXCR4 and CD45 and markedly abolished CXCL12-induced chemotaxis. Comparisons of signaling pathways induced by CXCL12 in JE6.1 and J45.01 cells revealed that CD45 might moderately regulate the tyrosine phosphorylation of the focal adhesion components the related adhesion focal tyrosine kinase/Pyk2, focal adhesion kinase, p130Cas, and paxillin. CD45 has also been shown to regulate CXCR4-mediated activation and phosphorylation of T-cell receptor downstream effectors Lck, ZAP-70, and SLP-76. Our results show that CD45 differentially regulates CXCR4-mediated chemotactic activity and MAPK activation by modulating the activities of focal adhesion components and the downstream effectors of the T-cell receptor.

Adaptor Proteins, Signal Transducing↗

PubMed1992

Synthetic peptides of human CD4 enhance binding of Ig to monocyte/macrophage cells. I. Characterization and mapping studies.

Human T cell glycoprotein CD4 binds to class II MHC molecules and to HIV envelope protein gp120. We have shown that CD4 and synthetic peptides corresponding to amino acid residues 21-49 of the first extracellular domain of CD4, also bind Ig and, with greater avidity, antibody:Ag complex. We investigated the effect of CD4 synthetic peptides on the binding and uptake of human Ig by monocyte/macrophage U937 cells. We found that a synthetic peptide corresponding to amino acid residues 21-49 enhanced binding to U937 cells of both aggregated and nonaggregated Ig. The enhancement was concentration dependent, occurred both in normal and low ionic strength conditions, and varied with the time and the temperature of the preincubation step. The enhancement was maximal after preincubation for 3 h at 37 degrees C. A peptide concentration of 20 micrograms/ml was sufficient for optimal binding of both nonaggregated and aggregated Ig. CD4 peptide 21-49 also enhanced binding of Ig to Staphylococcus aureus protein A. These studies open a new perspective in the way monocyte/macrophage cells handle Ig, antibody:Ag or Id:anti-Id complex, in particular when present at threshold amounts in a nonprecipitating form.

Amino Acid Sequence↗

PubMed2006

Temperature modulates P2X receptor-mediated cardiovascular responses to muscle afferent activation.

Static muscle contraction increases ATP release into the muscle interstitial space. Elevated ATP in muscle stimulates thin fiber muscle afferents and increases blood pressure via engagement of purinergic P2X receptors. In addition, ATP activates P2X receptors and enhances cardiovascular responses induced by stimulation of muscle mechanoreceptors. In this study, we examined whether elevated muscle temperature would attenuate and whether reduced temperature would potentiate P2X effects on reflex muscle responses. alpha,beta-Methylene ATP (alpha,beta-MeATP) was injected into the arterial blood supply of hindlimb muscle to stimulate P2X receptors, and muscle stretch was induced to activate mechanically sensitive muscle afferents as alpha,beta-MeATP was injected in 10 anesthetized cats. Femoral arterial injection of alpha,beta-MeATP (1.0 mM) increased mean arterial pressure (MAP) by 35+/-5 (35 degrees C), 26+/-3 (37 degrees C), and 19+/-3 mmHg (39 degrees C; P<0.05 vs. 35 degrees C), respectively. Muscle stretch (2 kg) elevated MAP. The MAP response was significantly enhanced 34% and 36% when alpha,beta-MeATP (0.2 mM) was arterially infused 5 min before muscle stretch at 35 degrees and 37 degrees C, respectively. However, as muscle temperature reached 39 degrees C, the stretch-evoked response was augmented only 6% by alpha,beta-MeATP injection, and the response was significantly attenuated compared with the response with muscle temperature of 35 degrees and 37 degrees C. In addition, we also examined effects of muscle temperature on alpha,beta-MeATP enhancement of the cardiovascular responses to static muscle contraction while the muscles were freely perfused and the circulation to the muscles was occluded. Because muscle temperature was 37 degrees C, arterial injections of alpha,beta-MeATP significantly augmented contraction-evoked MAP response by 49% (freely perfused) and 53% (ischemic condition), respectively. It is noted that this effect was significantly attenuated at a muscle temperature of 39 degrees C. These data indicate that the effect of P2X receptor on reflex muscle response is sensitive to alternations of muscle temperature and that elevated temperature attenuates the response.

Adenosine Triphosphate↗

PubMed1995

Fentanyl pretreatment attenuates the haemodynamic response to sudden inhalation of 5% isoflurane.

High concentrations of inhaled isoflurane can increase heart rate and/or arterial pressure. The purpose of this study was to determine whether fentanyl has a prophylactic effect on the isoflurane-induced circulatory response in adult patients. Thirty patients due to undergo elective surgery were randomly allocated to one of three groups of ten patients. Prior to surgery, one group inhaled 2.5% isoflurane, another inhaled 5.0% isoflurane, and the third group inhaled 5.0% isoflurane and were given fentanyl 2 micrograms.kg-1 i.v. two minutes before induction of anaesthesia. Anaesthesia was induced with thiamylal followed by vecuronium. The lungs were ventilated with 100% oxygen and either 2.5% or 5.0% isoflurane via face mask. Ventilation was continued for five minutes. Heart rate (HR) and mean arterial pressure (MAP) were recorded at two minutes before induction of anaesthesia (baseline), immediately before the induction of anaesthesia, and at three and five minutes after induction, respectively. It was found that 5.0% isoflurane caused an increase in HR compared with baseline (P < 0.01) and with the 2.5% isoflurane (P < 0.05): 2.5% isoflurane did not elicit this response. An increase was also noted in MAP, compared with the 2.5% isoflurane (P < 0.01): 2.5% isoflurane did not elicit this increase. Fentanyl pretreatment attenuated the increases in HR and in MAP that occurred with 5.0% isoflurane (P < 0.01). These results suggest that fentanyl attenuates the enhancement of both HR and MAP from face mask inhalation of a high concentration of isoflurane.

Adult↗

PubMed2004

Superior mediastinal and neck lymphatic mapping in mid- and lower-thoracic esophageal cancer as defined by ferumoxides-enhanced magnetic resonance imaging.

OBJECTIVE: The purpose of this study was to detect lymphatic drainage into the superior mediastinum and neck in thoracic esophageal cancer patients using ferumoxides-enhanced magnetic resonance imaging (MRI), and to have this information assist in determining the appropriate extent of lymphadenectomy. METHODS: Nine male patients with T2-T3 mid- and lower-thoracic esophageal cancer with lymph node metastasis were examined. The day before surgery, ferumoxides was endoscopically injected into the submucosal layer of the peritumoral lesion. Thereafter, lymph nodes in the superior mediastinum and neck, which were shown to be ferumoxides-enhanced on MRI, were harvested and evaluated; magnetic force from all harvested lymph nodes was measured ex vivo. RESULTS: MRI of the superior mediastinum and neck revealed 1(median) ferumoxides-enhanced lymph nodes in eight (89%) patients, and there was laterality in the lymphatic mapping in both areas. Of the 15 lymph nodes into which drainage was detected by enhanced MRI, 12 (80%) were magnetite-positive. In six patients (67%), magnetic resonance enhanced lymph nodes corresponded completely with the ex vivo magnetite examination, and in 3 patients (33%) there was partial agreement. In 3 (60%) of the 5 patients that showed paratracheal and/or supraclavicular lymph node metastases, all of the affected nodes were detected by MRI; in one patient some of the affected nodes were detected. CONCLUSION: Ferumoxides-enhanced MRI is useful for visualizing lymphatic drainage to the superior mediastinum and neck in thoracic esophageal cancer. It is an adequate procedure to form an estimate on the appropriate extent of lymphadenectomy.

Adult↗

PubMed1996

The reduction of preprotachykinin mRNA in the methamphetamine-induced behavioral sensitization.

To study the role of the preprotachykinin A (PPT) mRNA in methamphetamine (MAP)-induced behavioral sensitization, rats were daily injected within MAP (3 or 6 mg/kg, i.p., once a day) or saline for 14 days. Progressive enhancement was observed in MAP-induced stereotyped behavior. After 7 or 14 days of discontinuation of MAP treatment, the rats were decapitated and the brains were prepared for Northern blot analysis using a 32P-labeled oligonucleotide probe. Northern blot analysis revealed that the level of PPT mRNA in the striatum of 3 or 6 mg/kg MAP-treated rats was significantly decreased, compared to that in the saline-treated controls. These findings indicate that PPT mRNA expression plays an important role in MAP-induced long-lasting behavioral sensitization and dopamine hyperactivity.

Actins↗

PubMed1991

Delineation of human papillomavirus type 18 enhancer binding proteins: the intracellular distribution of a novel octamer binding protein p92 is cell cycle regulated.

The enhancer of human papillomavirus type 18 consists of two functionally redundant domains, one is partially conserved between HPV18 and HPV16, both mediate strong transcriptional enhancement. In contrast, short fragments of the enhancer mediate low transcriptional enhancement, suggesting that there is functional cooperation between HPV enhancer binding factors. Previously interactions of the enhancer with NF-1, AP1 and steroid receptors were shown by EMSA. Here we show by binding site blotting, that four novel sequence specific proteins p110, p92, p42 and p40 bind to the enhancer. Nuclear proteins p110 and p92 bind at repeated sites in the enhancer, proteins p42 and p40 only at one site. Recognition sequences for p110 and p92 were identified in a TTGCTTGCATAA sequence motif and consist of an overlapping p110 and p92 recognition site. The specific interaction of p110 with G residues of this 12 nucleotide long sequence was demonstrated by a mutant recognition site. Single recognition sites for p42 and p40 were localized in the enhancer by the use of overlapping oligonucleotides. In addition, electrophoretic mobility shift analysis identified Oct-1 and AP2 interactions with the enhancer. The AP2 binding site was mapped to a AGGCACATATT motif. The p92 protein binds to enhancer oligonucleotides, containing at least one copy of Oct-1 like recognition sequences, these oligonucleotides also bind synthetic Oct-1 protein. During serum starvation or at high saturation density, p92 moves from the nucleus into the cytoplasm. Immunoblots of cytoplasmic extracts with anti-Oct-1 antisera showed, that p92 is a novel octamer binding factor, which is not immunologically related to the Oct-1 protein. The intracellular p92 distribution is regulated at the G0/G1 boundary of the cell cycle, by nucleo-cytoplasmic translocation.

Base Sequence↗

PubMed1997

Identification of a multihormone responsive enhancer far upstream from the human tissue-type plasminogen activator gene.

A 2.4-kilobase (kb) DNA fragment, located 7.1 kb upstream from the human tissue-type plasminogen activator (t-PA) gene (t-PA2.4), acts as an enhancer which is activated by glucocorticoids, progesterone, androgens, and mineralocorticoids. Transient expression of t-PA-chloramphenicol acetyltransferase reporter constructs in HT1080 human fibrosarcoma cells identified a glucocorticoid responsive unit with four functional binding sites for the glucocorticoid receptor, located between bp -7,501 and -7,974. The region from bp -7,145 to -9,578 (t-PA2.4) was found to confer a cooperative induction by dexamethasone and all-trans-retinoic acid (RA) to its homologous and a heterologous promoter, irrespective of its orientation. The minimal enhancer, defined by progressive deletion analysis, comprised the region from -7.1 to -8.0 kb (t-PA0.9) and encompassed the glucocorticoid responsive unit and the previously identified RA-responsive element located at -7.3 kb (Bulens, F., Ibañez-Tallon, I., Van Acker, P., De Vriese, A., Nelles, L., Belayew, A., and Collen, D. (1995) J. Biol. Chem. 270, 7167-7175). The amplitude of the synergistic response to dexamethasone and RA increased by reducing the distance between the enhancer and the proximal t-PA promoter. The synergistic interaction was also observed between the aldosterone and the RA receptors. It is postulated that the t-PA0.9 enhancer might play a role in the hormonal regulation of the expression of human t-PA in vivo.

Cell Line↗