PubMed Health⌕ Search

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 973 records · Page 54Linked to original sources
PubMed2003

c-Src protein tyrosine kinase activity is required for muscarinic receptor-mediated DNA synthesis and neurogenesis via ERK1/2 and c-AMP-responsive element-binding protein signaling in neural precursor cells.

The G protein-coupled muscarinic acetylcholine receptor (mAChR) isoforms have been identified in neural stem/progenitor (or precursor) cells. In previous studies, activation of these receptors induced elevations in intracellular Ca(2+) signals and mitogen-activated protein (MAP) kinase activity that led to enhanced DNA synthesis along with neurogenesis in neural precursor cells. Here we report that the nonreceptor protein tyrosine kinase c-src activity is required for the muscarinic receptor-activated MAP kinase and cAMP-responsive element-binding protein (CREB). Stimulation of neural precursor cells dissociated from embryonic day 13 rat cortical neuroepithelium with the muscarinic receptor agonist carbachol (CCh) induced phosphorylations of c-src that were detected by antibodies raised against phospho-Tyr416 (Ptyr416), phospho-Tyr527 (Ptyr527), and phospho-Tyr215 (Ptyr215) of the kinase. Although an increase in Ptyr416 suggested direct activation of c-src, Ptyr215 may serve as an alternative mechanism underlying activation of c-src without dephosphorylation of Ptyr-527. Both extracellular signal-regulated kinase (Erk1/2) and CREB were significantly activated after CCh treatment indicated by increases in phosphorylation of these two proteins. The c-Src inhibitor PP1 abolished the CCh-induced activation of Erk1/2 and CREB in a dose-dependent manner. Moreover, CCh stimulated expression of the neuronal specific marker MAP2, which was inhibited by PP1. Cell proliferation assays and immunocytochemistry revealed that PP1 inhibited the CCh-induced DNA synthesis and MAP2(+) production. These results suggest that c-src activity is essential for the muscarinic receptor-mediated proliferation and neurogenesis in neural precursor cells via Erk1/2 and CREB signaling pathways.

Animals↗
PubMed2000

Linkage group alignment of sorghum RFLP maps using a RIL mapping population.

Several molecular maps have been constructed in sorghum (Sorghum bicolor L. Moench) using a variety of probes from different grass species such as sorghum, maize, sugarcane, rice, oat, and barley. In order to enhance the utility of the existing mapping information by the sorghum research community, alignment and integration of all major molecular maps is necessary. To achieve this objective, a genetic map of 214 loci with a total map distance of 1200 cM was constructed using 98 F7 sorghum recombinant inbred lines (RILs) from a cross between two inbred lines, B35 and Tx7000. Few cDNA clones of sorghum and maize related to photosynthesis and drought stress were mapped on this map for the first time. Five major restriction fragment length polymorphism (RFLP) maps independently developed in this species were used for alignment purpose. The distributions of previously mapped markers were compared with their respective sorghum maps to align each of the linkage groups. In general, consistent linear order among markers was maintained in all the linkage maps. The successful alignment of these RFLP maps will now allow selection of a large number of markers for any region of the sorghum genome with many potential applications ranging from fine mapping and marker-assisted selection to map-based cloning for the improvement of sorghum and related species.

Chromosome Mapping↗
PubMed2002

Clean SEA-HSQC: a method to map solvent exposed amides in large non-deuterated proteins with gradient-enhanced HSQC.

The recent introduction of the SEA-TROSY experiment (Pellecchia et al. (2001) J. Am. Chem. Soc., 123, 4633-4634) can alleviate the problem of resonance overlap in 15N/2H labeled proteins. This method selectively observes solvent exposed amide protons with a SEA element. However, SEA-TROSY spectra may be contaminated with exchange-relayed NOE contributions from fast exchanging hydroxyl or amine protons and longitudinal relaxation contributions. Furthermore, for non-deuterated proteins or protein-ligand complexes, SEA-TROSY spectra may contain NOE contributions from aliphatic protons. In this communication, a modified version of the SEA element, a Clean SEA element, is introduced to eliminate these artifacts.

Amides↗
PubMed1999

Mapping the functional anatomy of BgK on Kv1.1, Kv1.2, and Kv1.3. Clues to design analogs with enhanced selectivity.

BgK is a peptide from the sea anemone Bunodosoma granulifera, which blocks Kv1.1, Kv1.2, and Kv1.3 potassium channels. Using 25 analogs substituted at a single position by an alanine residue, we performed the complete mapping of the BgK binding sites for the three Kv1 channels. These binding sites included three common residues (Ser-23, Lys-25, and Tyr-26) and a variable set of additional residues depending on the particular channel. Shortening the side chain of Lys-25 by taking out the four methylene groups dramatically decreased the BgK affinity to all Kv1 channels tested. However, the analog K25Orn displayed increased potency on Kv1.2, which makes this peptide a selective blocker for Kv1.2 (K(D) 50- and 300-fold lower than for Kv1.1 and Kv1.3, respectively). BgK analogs with enhanced selectivity could also be made by substituting residues that are differentially involved in the binding to some of the three Kv1 channels. For example, the analog F6A was found to be >500-fold more potent for Kv1.1 than for Kv1.2 and Kv1.3. These results provide new information about the mechanisms by which a channel blocker distinguishes individual channels among closely related isoforms and give clues for designing analogs with enhanced selectivity.

Amino Acid Substitution↗
PubMed1985

A human hepatitis B viral enhancer element.

Fragments of the cloned hepatitis B virus (HBV) genome were assayed in vivo for the presence of a transcriptional enhancer element. We demonstrate that sequences positioned approximately 450 bp upstream from the HBcAg gene promoter are required for its efficient activity. These HBV stimulatory sequences activate transcription when inserted upstream to a heterologous SV40 early promoter. Like other known enhancer elements, this HBV sequence acts in an orientation-independent manner. Furthermore, the HBV enhancer element exhibits a preferred activity in a human hepatoma cell line.

Animals↗
PubMed1998

Cloning and mapping of ZNF231, a novel brain-specific gene encoding neuronal double zinc finger protein whose expression is enhanced in a neurodegenerative disorder, multiple system atrophy (MSA).

A novel brain-specific gene, neuronal double zinc finger protein (ZNF231), was cloned and mapped. We used the high-density cDNA filter method to analyze the gene-expression profile in brains with multiple system atrophy (MSA). MSA is a sporadic progressive neurodegenerative disease characterized clinically by cerebellar symptoms, parkinsonism, autonomic dysfunction, or their various combinations, but its pathogenesis has yet to be clarified. In total, 8300 cDNA clones were screened, and a novel gene, ZNF231, was identified, whose expression was elevated in cerebella of patients with MSA. Its transcript is approximately 16 kb long and encodes an open reading frame of 3926 amino acid residues that has several interesting motifs; two glycine-proline dipeptide repeats (aa 22-32 and aa 61-74), a pair of homologous C8 double zinc finger motifs (aa 169-226 and aa 465-521), a leucine zipper motif (aa 561-582), a SH3 domain-binding motif (aa 825-831), two nuclear targeting signals (aa 1011-1028 and aa 1071-1091), two glutamine-rich domains (aa 2428-2473 and aa 3775-3804), and a histidine-rich domain (aa 3597-3682). These features suggest that the new gene encodes a nuclear protein or transcription regulator. Northern blot and RT-PCR analyses showed that its expression is specific to the brain and apparently restricted to the neurons. Elevation of ZNF231 expression may be involved in the pathogenesis of multiple system atrophy. The gene for ZNF231 is located on chromosome 3p21.

Amino Acid Sequence↗
PubMed1988

Functional analysis of the long terminal repeats of intracisternal A-particle genes: sequences within the U3 region determine both the efficiency and direction of promoter activity.

The transcriptional activity of five intracisternal A-particle (IAP) long terminal repeats (LTRs) in mouse embryonal carcinoma PCC3-A/1 cells and in Ltk- cells was determined. We tested the promoter activity of the LTRs by coupling them to the reporter gene chloramphenicol acetyltransferase (CAT) or guanosine-xanthine phosphoribosyltransferase (gpt). Each LTR was tested for promoter function in both the sense (5' to 3') and antisense (3' to 5') orientation preceding the reporter gene. The transcriptional activity of individual IAP gene LTRs varied considerably, and the LTR from IAP81 possessed promoter activity in both directions. The bidirectional activity of the IAP81 LTR confirmed by monitoring Ecogpt expression in stably transfected Ltk- cells, with the initiation sites for sense and antisense transcription being localized to within the IAP81 LTR by S1 nuclease mapping. Deletions of LTR81 show that for normal 5'-to-3' gene transcription (sense direction), the 3'U3/R region determines the basal level of transcription, whereas sequences within the 5'U3 region enhance transcription four- to fivefold. Deletion mapping for antisense transcription indicates that a 64-base-pair region (nucleotides 47 to 110) within the U3 region is essential for activity. These data indicate that the U3 region contains all the regulatory elements for bidirectional transcription in IAP LTRs.

Acetyltransferases↗
PubMed1992

Phosphorylation of transcription factor p62TCF by MAP kinase stimulates ternary complex formation at c-fos promoter.

Transcription of the proto-oncogene c-fos is stimulated rapidly and transiently by serum growth factors and mitogens. Critical for this response is the serum-response element which is bound in vivo in a ternary complex containing the transcription factors p67SRF and p62TCF (ref. 2). Disruption of the ternary complex correlates with impaired induction by serum and phorbol ester. Mitogen-activated protein (MAP) kinase is a serine/threonine kinase which is activated 1-5 minutes after treatment of cells with mitogens and growth factors that induce re-entry into the cell cycle, making MAP kinase a candidate for the transmission of proliferative signals. Here we show that p62TCF is phosphorylated by MAP kinase in vitro and that phosphorylation results in enhanced ternary complex formation. Serum-starved Swiss 3T3 cells treated with epidermal growth factor, which induces MAP kinase in these cells, are induced to express c-fos and yield p62TCF active in ternary complex formation. In contrast, treatment of Swiss 3T3 cells with insulin, which does not activate MAP kinase under these conditions, does not lead to enhanced ternary complex formation nor does it induce c-fos transcription. Our results link the expression of the human c-fos proto-oncogene to signal transduction pathways known to be activated before its own induction.

3T3 Cells↗
PubMed1996

Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo.

Previous studies on the regulation of the segmentation gene even-skipped (eve) have centered on the transcription of stripe 2. Here, we characterize another enhancer module contained within the complex eve promoter that directs expression of stripes 3 and 7. This enhancer is approximately 500 bp in length and maps approximately 3.3 kb upstream of the transcription start site. The stripe 3 + 7 enhancer appears to be regulated by one or more ubiquitously distributed activators, including components of a JAK-Stat pathway. The two-stripe pattern results via multiple tiers of repressors which delimit this ubiquitous activation. The zinc finger repressor hunchback appears to be responsible for establishing the anterior border of stripe 3 and the posterior border of stripe 7. knirps, a member of the nuclear receptor family of transcription factors, appears to establish the posterior border of stripe 3 and the anterior border of stripe 7. Activator and repressor proteins bind in vitro to several sites within the enhancer. These findings suggest a general model for the regulation of segmentation stripes, whereby enhancers integrate positional information provided by broadly distributed activators and spatially restricted repressors.

Alleles↗
PubMed1997

Tumor necrosis factor alpha and interleukin-1beta regulate the murine manganese superoxide dismutase gene through a complex intronic enhancer involving C/EBP-beta and NF-kappaB.

Manganese superoxide dismutase (MnSOD), a tumor necrosis factor (TNF)-inducible reactive oxygen-scavenging enzyme, protects cells from TNF-mediated apoptosis. To understand how MnSOD is regulated, transient transfections of promoter-reporter gene constructions, in vitro DNA binding assays, and in vivo genomic footprint (IVGF) analysis were carried out on the murine MnSOD gene. The results of this analysis identified a 238-bp region of intron 2 that was responsive to TNF and interleukin-1beta (IL-1). This TNF response element (TNFRE) had the properties of a traditional enhancer element that functioned in an orientation- and position-independent manner. IVGF of the TNFRE revealed TNF- and IL-1-induced factor occupancy of sites that could bind NF-kappaB and C/EBP. The 5' portion of the TNFRE bound C/EBP-beta in vitro and was both necessary and sufficient for TNF responsiveness with the MnSOD promoter or with a heterologous promoter when in an upstream position. The 3' end of the TNFRE bound both NF-kappaB and C/EBP but was not necessary for TNF responsiveness with the MnSOD promoter. However, this 3' portion of the TNFRE was required for the TNFRE to function as a downstream enhancer with a heterologous promoter. These data functionally separate the MnSOD TNFRE into a region responsible for TNF activation and one that mediates induction when it is downstream of a promoter.

3T3 Cells↗
PubMed2005

[Self-organizing neural networks for automatic detection and classification of contrast (media) enhancement of lesions in dynamic MR-mammography].

PURPOSE: Investigation and statistical evaluation of "Self-Organizing Maps," a special type of neural networks in the field of artificial intelligence, classifying contrast enhancing lesions in dynamic MR-mammography. MATERIAL AND METHODS: 176 investigations with proven histology after core biopsy or operation were randomly divided into two groups. Several Self-Organizing Maps were trained by investigations of the first group to detect and classify contrast enhancing lesions in dynamic MR-mammography. Each single pixel's signal/time curve of all patients within the second group was analyzed by the Self-Organizing Maps. The likelihood of malignancy was visualized by color overlays on the MR-images. At last assessment of contrast-enhancing lesions by each different network was rated visually and evaluated statistically. RESULTS: A well balanced neural network achieved a sensitivity of 90.5 % and a specificity of 72.2 % in predicting malignancy of 88 enhancing lesions. Detailed analysis of false-positive results revealed that every second fibroadenoma showed a "typical malignant" signal/time curve without any chance to differentiate between fibroadenomas and malignant tissue regarding contrast enhancement alone; but this special group of lesions was represented by a well-defined area of the Self-Organizing Map. DISCUSSION: Self-Organizing Maps are capable of classifying a dynamic signal/time curve as "typical benign" or "typical malignant." Therefore, they can be used as second opinion. In view of the now known localization of fibroadenomas enhancing like malignant tumors at the Self-Organizing Map, these lesions could be passed to further analysis by additional post-processing elements (e.g., based on T2-weighted series or morphology analysis) in the future.

Algorithms↗
PubMed2000

Decreased extracellular-signal-regulated kinase and increased stress-activated MAP kinase activities in aged human skin in vivo.

The ability of human skin to rejuvenate itself diminishes with the passage of time, resulting in increased fragility. This increased fragility reflects both reduced growth of skin cells and loss of collagenous connective tissue. Oxidative damage plays a central role in cellular aging. Cellular responses to growth signals and oxidative stress are mediated, in part, by growth-factor-activated and stress-activated MAP kinases. We report here that the extracellular-signal-regulated MAP kinase pathway is reduced and the stress-activated MAP kinase pathway is increased in old, compared with young, human skin in vivo. Extracellular-signal-regulated kinase activity was 45% lower in old skin (mean age 84.3 y) relative to young skin (mean age 23.8 y). This lower extracellular- signal-regulated kinase activity resulted from reduced activation, since total extracellular-signal-regulated kinase protein levels did not differ between young and old skin, whereas phosphorylated (i.e., activated) extracellular-signal-regulated kinase protein was reduced 60% in old skin. Cyclin D2, which is regulated by extracellular-signal-regulated kinase and functions to promote cell cycle progression, was reduced 50% in old skin compared with young skin. In contrast, stress-activated MAP kinase activity was elevated 3.4-fold in old skin compared with young skin. This increased activity resulted from enhanced activation, since total stress-activated MAP kinase protein levels were similar in old and young skin. Transcription factor c-Jun, which is activated by stress-activated MAP kinases and promotes expression of connective-tissue-degrading matrix metalloproteinases, was elevated 2-fold in old skin compared with young skin. Treatment of old skin with vitamin A (retinol) for 7 d stimulated extracellular-signal-regulated kinase activity, consistent with its demonstrated ability to stimulate cell growth in old human skin. Taken together, these data indicate that alterations in MAP kinase activities play a key role in the pathophysiology of human skin aging.

Adolescent↗
PubMed2006

High resolution pH(e) imaging of rat glioma using pH-dependent relaxivity.

Previous studies using MR spectroscopy have shown that the extracellular pH (pH(e)) of tumors is acidic compared to normal tissues. This has a number of important sequelae that favor the emergence of more aggressive and therapy-resistant tumors. New MRI methods based on pH-sensitive T1 relaxivity are an attractive alternative to previous spectroscopic methods, as they allow improvements in spatial and temporal resolution. Recently, pH-dependent GdDOTA-4AmP5- and a pH-independent analog, GdDOTP5-, were used to image renal pH in mice. The current study has used a similar approach to image pH(e) in rat gliomas. Significant differences were observed compared to the renal study. First, the relaxivity of GdDOTP5- was found to be affected by the higher extracellular protein content of tumors. Second, the pixel-by-pixel analysis of the GdDOTP5- and GdDOTA-4AmP5- pharmacokinetics showed significant dispersion, likely due to the temporal fluctuations in tumor perfusion. However, there was a robust correlation between the maximal enhancements produced by the two boluses. Therefore, to account for the local time-courses differences, pH(e) maps were calculated at the time of maximal enhancement in each pixel. Finally, the comparison of the pH(e) and the time to maximal intensity maps revealed an inverse relationship between pH(e) and tumor perfusion.

Analysis of Variance↗
PubMed1998

Integrin-mediated tyrosine phosphorylation of SHPS-1 and its association with SHP-2. Roles of Fak and Src family kinases.

SHPS-1 is a receptor-like glycoprotein that undergoes tyrosine phosphorylation and binds SHP-2, an Src homology 2 domain containing protein tyrosine phosphatase, in response to various mitogens. Cell adhesion to extracellular matrix proteins such as fibronectin and laminin also induced the tyrosine phosphorylation of SHPS-1 and its association with SHP-2. These responses were markedly reduced in cells overexpressing the Csk kinase or in cells that lack focal adhesion kinase or the Src family kinases Src or Fyn. However, unlike Src, focal adhesion kinase did not catalyze phosphorylation of the cytoplasmic domain of SHPS-1 in vitro. Overexpression of a catalytically inactive SHP-2 markedly inhibited activation of mitogen-activated protein (MAP) kinase in response to fibronectin stimulation without affecting the extent of tyrosine phosphorylation of focal adhesion kinase or its interaction with the docking protein Grb2. Overexpression of wild-type SHPS-1 did not enhance fibronectin-induced activation of MAP kinase. These results indicate that the binding of integrins to the extracellular matrix induces tyrosine phosphorylation of SHPS-1 and its association with SHP-2, and that such phosphorylation of SHPS-1 requires both focal adhesion kinase and an Src family kinase. In addition to its role in receptor tyrosine kinase-mediated MAP kinase activation, SHP-2 may play an important role, partly through its interaction with SHPS-1, in the activation of MAP kinase in response to the engagement of integrins by the extracellular matrix.

Animals↗
PubMed2005

Does Schumann resonance affect our blood pressure?

OBJECTIVES: To investigate whether Schumann resonance (SR) affects blood pressure (BP), heart rate (HR), and depression and, if so, whether the putative BP reactivity to SR (BPR-SR) is associated with health-related lifestyle (HLS), disease-related illnesses (DRI), and depression. METHODS: A sample of 56 adults in Urausu, Hokkaido, Japan, wore an ambulatory BP monitor, except for the time in the shower, for seven consecutive days. They completed the Geriatric Depression Scale-Short Form and a health survey questionnaire on HLS and DRI. Group mean differences and within-individual differences in systolic (S) and diastolic (D) BP, mean arterial pressure (MAP), double product (DP), and HR were, respectively, compared between normal and enhanced SR days, using Student's t-test. Correlations between BPR-SR and other characteristics (i.e. age, gender, HLS, DRI, subjective health, and depression) were analyzed, using Pearson's product moment correlation. RESULTS AND DISCUSSION: Group mean SBP, DBP, MAP, and DP for enhanced SR days were lower than those for normal days (P=0.005-0.036). DRI was negatively associated with BPR-SR in SBP, DBP, MAP, and DP (P=0.003-0.024), suggesting a better health status for those who showed lower BP on enhanced SR days. HLS was negatively associated with BPR-SR in DBP and MAP (P=0.016-0.029). Males showed higher BPR-SR in DBP and MAP than females (P=0.004-0.016). Neither subjective health nor depression was significantly associated with BPR-SR. Future studies based on larger sample sizes are planned to see whether possible health effects can be generalized.

Adult↗
PubMed1987

Structure and evolution of human apolipoprotein genes: identification of regulatory elements of the human apolipoprotein E gene.

The structures of the major human apolipoprotein genes have been determined. The genes for apoE, apoC-I, apoC-II, apoC-III, apoA-I, apoA-II and apoA-IV have similar structures, consisting of four exons and three introns, which suggests that they evolved from a common ancestral gene. The third and fourth exons of the ancestral gene appear to have evolved from the duplication of a 66-nucleotide repeat unit that encodes a 22-residue alpha-helical peptide element of amphipathic character. The apoA-I, apoC-III and apoA-IV genes are linked closely within a 20-kilobase (kb) span of chromosome 11. The apoE and apoC-I genes, together with an apoC-I' pseudogene, are linked closely within a 25-kb span of chromosome 19. To characterize potential functional relationships among the apolipoprotein genes, initial studies have been done to identify the molecular elements involved in the regulation of the human apoE gene. Fragments of the 5'-flanking portion of this gene were inserted into appropriate plasmid vectors, which contained the bacterial chloramphenicol acetyl transferase gene, and were examined for promoter activity and potential enhancer activity after transfection into cultured mammalian cells. Deletion mapping of the promoter region has identified multiple functional elements, including an enhancer, two G-C boxes (Sp 1 transcription factor binding sites) and an upstream control element. In addition, there is an enhancer located in the first intron. Interactions among these various control elements are likely to determine the ways in which the expression of the apoE gene is regulated.

Apolipoproteins E↗
PubMed1985

Mutational analyses of the Moloney murine sarcoma virus enhancer.

Retroviral enhancers seem to play an integral role in determining tissue tropism. In an attempt to define the sequences essential for Moloney murine sarcoma virus (Mo-MSV) enhancer activity, we have undertaken deletion and insertion mutational analyses of the 72-bp repeats. We demonstrate that, in contrast to simian virus 40 (SV40), the proximal 19 bp of the 72-bp unit of Mo-MSV are not essential for enhancer function in mouse fibroblasts. Our analysis further localizes the 5' boundary of the Mo-MSV enhancer to a 5'-CAGGAT-3' region.

Acetyltransferases↗