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PubMed2006

Krox20 hindbrain cis-regulatory landscape: interplay between multiple long-range initiation and autoregulatory elements.

The vertebrate hindbrain is subject to a transient segmentation process leading to the formation of seven or eight metameric territories termed rhombomeres (r). This segmentation provides the basis for the subsequent establishment of hindbrain neuronal organization and participates in the patterning of the neural crest involved in craniofacial development. The zinc-finger gene Krox20 is expressed in r3 and r5, and encodes a transcription factor that plays a key role in hindbrain segmentation, coordinating segment formation, specification of odd- and even-numbered rhombomeres, and cell segregation between adjacent segments, through the regulation of numerous downstream genes. In order to further elucidate the genetic network underlying hindbrain segmentation, we have undertaken the analysis of the cis-regulatory sequences governing Krox20 expression. We have found that the control of Krox20 transcription relies on three very long-range (200 kb) enhancer elements (A, B and C) that are conserved between chick, mouse and human genomes. Elements B and C are activated at the earliest stage of Krox20 expression in r5 and r3-r5, respectively, and do not require the Krox20 protein. These elements are likely to function as initiators of Krox20 expression. Element B contains a binding site for the transcription factor vHNF1, the mutation of which abolishes its activity, suggesting that vHNF1 is a direct initiator of Krox20 expression in r5. Element A contains Krox20-binding sites, which are required, together with the Krox20 protein, for its activity. This element therefore allows the establishment of a direct positive autoregulatory loop, which takes the relay of the initiator elements and maintains Krox20 expression. Together, our studies provide a basis for a model of the molecular mechanisms controlling Krox20 expression in the developing hindbrain and neural crest.

Animals↗

PubMed1999

A sequence motif distinct from Hox binding sites controls the specificity of a Hox response element.

Hox transcription factors, in combination with cofactors such as PBC proteins, provide diverse developmental fates to cells on the anteroposterior body axis of animal embryos. However, the mechanisms by which the different Hox proteins and their cofactors generate those diverse fates remain unclear. Recent findings have provided support for a model where the DNA binding sites that directly interact with Hox-PBC heterodimers determine which member of the Hox protein family occupies and thereby regulates a given target element. In the experiments reported here, we test the function of chimeric Hox response elements and, surprisingly, find evidence that runs counter to this view. A 21 bp cofactor binding sequence from an embryonic Deformed Hox response element, containing no Hox or Hox-PBC binding sites, was combined with single or multimeric sites that bind heterodimers of Labial-type Hox and PBC proteins. Normally, multimerized Labial-PBC binding sites are sufficient to trigger a Labial-specific activation response in either Drosophila or mouse embryos. Here we find that the 21 bp sequence element plays an important role in Deformed specificity, as it is capable of switching a Labial-PBC binding site/response element to a Deformed response element. Thus, cofactor binding sites that are separate and distinct from homeodomain binding sites can dictate the regulatory specificity of a Hox response element.

Animals↗

PubMed2000

P element homing to the Drosophila bithorax complex.

P elements containing a 7 kb DNA fragment from the middle of the Drosophila bithorax complex insert preferentially into the bithorax complex or into the adjacent chromosome regions. This 'homing' property is similar to that reported for the engrailed promoter (Hama, C., Ali, Z. and Kornberg, T. B. (1990) Genes Dev. 4, 1079-1093). The 7 kb fragment does not contain any known promoter, but it acts as a boundary element separating adjacent segmental domains. An enhancer-trap P element was constructed with the homing fragment and the selectable marker flanked by FRT sites. P insertions can be trimmed down by Flp-mediated recombination to just the lacZ reporter, so that the (beta)-galactosidase pattern is not influenced by sequences inside the P element. Twenty insertions into the bithorax complex express (beta)-galactosidase in segmentally limited patterns, reflecting the segmental domains of the bithorax complex where the elements reside. The mapping of segmental domains has now been revised, with enlargement of the abx/bx, bxd/pbx, and the iab-3 domains. The FRT sites in the P elements permit recombination between pairs of elements on opposite chromosomes, to generate duplications or deletions of the DNA between the two insertion sites. Using this technique, the length of the Ultrabithorax transcription unit was varied from 37 to 138 kb, but there was surprisingly little effect on Ultrabithorax function.

Animals↗

PubMed1990

[Pharmacokinetics of trace elements by noncompartmental analysis in rats (Part 1): Significance of the pharmacokinetic parameters].

Six-week-old male Wistar rats were administrated the radioisotopes of five trace elements (iron, zinc, copper, manganese and iodine) intravenously in order to elucidate the significance of their pharmacokinetics by noncompartmental analysis. The mean residence time (MRT) and variance of residence time (VRT) increased in the order Mn, Cu, I, Fe and Zn. Neither MRT nor VRT indicated any statistical significance between I and Fe. These results suggested that Mn and Cu were voided rapidly from the plasma, whereas Zn persisted in the plasma for the longest time among these elements. Though I and Fe showed quite different plasma disappearance curves, both were considered to diminish at almost the same speed. The volume of distribution at steady state (Vdss) increased in the order Cu (32 ml), Fe (62 ml), I (149 ml), Mn (185 ml) and Zn (1012 ml). The distribution coefficient (Kd) of these elements increased in the same order as Vdss did. For Cu and Fe, Vdss was intermediate between the plasma volume and total body fluid volume of the rat, while, for the others, Vdss was greater than the total body fluid volume. In particular, Vdss of Zn was the greatest among these elements. Hence, the present study suggested that the plasma concentrations of Cu and Fe may reflect their body contents fairy well, though those of I, Fe and Zn can hardly do so. Vdss and Kd are, therefore, considered to be useful as supplementary diagnostic indices to understand the plasma concentrations of trace elements. Systemic clearance (CLs) increased in the order Fe (0.02 ml/min), Zn (0.07 ml/min), I (0.21 ml/min), Cu (0.37 ml/min) and Mn (4.61 ml/min). The CLs of Mn was similar to the hepatic plasma flow rate of the rat in size, indicating that the Cls of Mn may be one of the greatest among trace elements. It appeared, therefore, that when administered intravenously, Mn may be transferred from the plasma to the tissues more easily than the other elements.

Animals↗

PubMed2002

Full-size P and KP elements predominate in wild Drosophila melanogaster.

We analyzed the genomic P elements of 57 wild-derived Drosophila melanogaster isofemale lines from Africa, Australia and Asia. All carried many P sequences per genome, and the full-size P and the internally deleted KP elements were very common or predominant in the populations. The genomic content of full-size P and KP elements does not correlate well with the P transposition-inducing and -repressing abilities of a line. Our results show that a large majority of type I repressor elements are full-size P elements, and almost all type II repressor elements are KP elements in the natural populations of D. melanogaster from these parts of the world.

Animals↗

PubMed2002

Characterization of the repetitive sequences in a 200-kb region around the rice waxy locus: diversity of transposable elements and presence of veiled repetitive sequences.

Repetitive genomic sequences might have various structural features and properties distinct from those of the known transposable elements (TE). Here, the content and properties of the repetitive sequences present in a 200-kb region around the rice waxy locus were analyzed using the available rice genomic database. In our previous Southern blotting analysis, 70% of the segments in this region showed smeared patterns, but according to the present database analysis, the proportion of repetitive sequences in this region was only 15%. The repetitive segments in this 200-kb region comprised 75 repetitive sequences that we classified into 46 subfamilies: 21 subfamilies were known TEs or repetitive sequences and 25 subfamilies consisted of newly identified TEs or novel types of repetitive sequences. The region contains no long terminal repeat (LTR) retrotransposable elements, but miniature inverted repeat transposable elements (MITEs) constituted a major class among the elements identified. These MITEs showed remarkable structural divergence: 12 elements were found to be new members of known MITE superfamilies, while five elements had novel terminal structures, and did not belong to any known TE families. Interestingly, about 10% of the repetitive sequences, including virus-like sequences did not have any of the usual characteristics of TEs, suggesting that a certain proportion of repetitive sequences that might not share the transpositional mechanisms of known elements are dispersed in the compact rice genome.

Base Sequence↗

PubMed2005

Comparison of sample preservation methods for clinical trace element analysis by inductively coupled plasma mass spectrometry.

The effects of chemical additives and storage temperatures on measurement of 16 trace elements in urine by inductively coupled plasma mass spectrometry (ICP-MS) were evaluated. A 24-hour urine specimen was supplemented with concentrations of the elements. Aliquots containing 1 of 4 chemical additives were stored at 3 different temperatures in sealed polypropylene containers. Elemental concentrations were determined by ICP-MS for the resulting samples after 1, 2, 8, and 65 days of storage. Initial element concentrations measured within 8 hours of specimen preparation were consistent with expected concentrations (except for aluminum). For most elements, preservation and storage conditions yielded consistent measured concentrations throughout the experiment. Notable exceptions were for aluminum (general rise over time) and mercury (general decrease over time). Adding boric acid and potassium pyrosulfate resulted in sample contamination; elemental contamination was concentration-dependent for both. Although little microbial contamination was observed during the experiment, refrigeration of samples is recommended to curtail bacterial growth in nonsterile specimens. In light of these results, refrigerated urine storage without the use of chemical additives is an effective preservation method for ICP-MS analysis of many trace elements.

Humans↗

PubMed2006

The structural basis for promoter -35 element recognition by the group IV sigma factors.

The control of bacterial transcription initiation depends on a primary sigma factor for housekeeping functions, as well as alternative sigma factors that control regulons in response to environmental stresses. The largest and most diverse subgroup of alternative sigma factors, the group IV extracytoplasmic function sigma factors, directs the transcription of genes that regulate a wide variety of responses, including envelope stress and pathogenesis. We determined the 2.3-A resolution crystal structure of the -35 element recognition domain of a group IV sigma factor, Escherichia coli sigma(E)4, bound to its consensus -35 element, GGAACTT. Despite similar function and secondary structure, the primary and group IV sigma factors recognize their -35 elements using distinct mechanisms. Conserved sequence elements of the sigma(E) -35 element induce a DNA geometry characteristic of AA/TT-tract DNA, including a rigid, straight double-helical axis and a narrow minor groove. For this reason, the highly conserved AA in the middle of the GGAACTT motif is essential for -35 element recognition by sigma(E)4, despite the absence of direct protein-DNA interactions with these DNA bases. These principles of sigma(E)4/-35 element recognition can be applied to a wide range of other group IV sigma factors.

Amino Acid Sequence↗

PubMed2000

Concentrations of trace elements in osteoarthritic knee-joint effusions.

Concentrations of the 18 elements, barium (Ba), beryllium (Be), bismuth (Bi), calcium (Ca), cadmium (Cd), cesium (Cs), copper (Cu), lanthanum (La), lithium (Li), magnesium (Mg), molybdenum (Mo), lead (Pb), rubidium (Rb), antimony (Sb), tin (Sn), strontium (Sr), thallium (Tl), and zinc (Zn), were determined in the synovial fluids of osteoarthritic knee joints and in the corresponding sera of 16 patients by inductively coupled plasma-mass spectrometry. Knee-joint effusions have lower elemental concentrations than their corresponding sera. For the essential elements Ca, Cu, Mg, and Zn and for the nonessential and toxic elements Ba, Be, Bi, La, and Sb, this difference was highly significant. Strong positive correlations between concentrations in effusions and sera for the essential elements Cu and Mg and for the nonessential elements Cs, Li, Rb, and Sr could be established. The grade of localized hyperperfusion of the knee region in the blood pool phase of 99mTc HDP bone scan indicating inflammation did not correlate with any elemental concentration determined.

Adult↗

PubMed2002

Effects of elements in human blood pressure control.

This review enumerates and discusses the elements involved in the control of human blood pressure via a historical evolutionary form. The older and most recent element literature presentations were researched using MEDLINE and a manual review of documents cited. Independent data extraction and cross-referencing was performed. Of the 28 known elements that can influence blood pressure, 15 were found to be involved in human blood pressure regulation. The elements were divided into four groups: electrolyte, composed of sodium, potassium, calcium, and magnesium; metal, which included zinc, copper, and iron; toxic, made up of lead, mercury, cadmium, barium, thallium, arsenic; miscellaneous (lithium and selenium). Evolutionary historical data, possible mechanisms of actions, and interactions between elements that have been shown to influence blood pressure are discussed. Controversy exists over the therapeutic use of elements to alter blood pressure but is absent in the case of the toxic group where preventive control is a proven public health matter. The significance of these 15 elements in the regulation of human blood pressure has been established and ongoing studies will continue to reinforce their influence and importance.

Blood Pressure↗

PubMed2002

Trace element changes in sclerotic heart valves from patients undergoing aortic valve surgery.

Several trace elements are essential nutrients for an optimal functioning of organs and tissues, including the immune system and the heart. The pathogenesis of some heart diseases has been associated with changes in the balance of certain trace elements. The etiology of nonrheumatic aortic valve sclerosis is unknown, however. A prospective study was performed on trace element changes in the sclerotic valves of 46 patients undergoing surgical aortic valve replacement because of aortic stenosis. Valves from 15 individual forensic cases without known cardiac disease served as controls. The contents of 15 trace elements (Al, As, Cd, Ca, Co, Cu, Fe, Pb, Mg, Mn, Hg, Se, Ag, V, and Zn) were measured by inductively coupled plasma - mass spectrometry (ICP-MS) of aortic valve tissue from both patients and forensic autopsy controls. Some trace elements showed similar concentrations in sclerotic and control valves (Al, Ag, Hg, Mn), whereas a few were moderately changed in the sclerotic as compared with the control valves, including an increase in Cd by 52% (p < 0.05) and decreases in Se by 14% (p < 0.05), in V by 42% (p < 0,001), and in Cu by 45% (p < 0.001). However, there were pronounced increases (p < 0.001) in the concentrations of As (5-fold), Ca (70-fold), Co(10-fold), Fe (20-fold), Pb (8-fold), Mg (20-fold), and Zn (10-fold) in the sclerotic valves. Thus, sclerotic aortic valve disease is associated with a pronounced imbalance in several trace elements of well-known importance for cardiovascular and immune function as well as in trace elements with hitherto unknown significance.

Adolescent↗

PubMed2003

Accumulation of elements in the arteries and cardiac valves of Thai with aging.

To elucidate whether the extent of element accumulation in the arteries and cardiac valves with aging was different between different races, the authors investigated the accumulation of elements in the arteries and cardiac valves of the Thai with aging and the relationships among elements in the cardiac valves. After ordinary dissection at Chiang Mai University was finished, 16 arteries and 4 cardiac valves were resected and element contents were determined by inductively coupled plasma-atomic emission spectrometry. In the 16 arteries, the average content of calcium was the highest in the site of the abdominal aorta ramifying into the common iliac arteries, and it decreased in the order internal iliac, coronary, abdominal aorta, common iliac, external iliac, superior mesenteric, inferior mesenteric, thoracic aorta, brachial, radial, common carotid, subclavian, ulnar, axillary, renal, and internal thoracic arteries. The average contents of phosphorus and magnesium in respective arteries were parallel with the average contents of calcium, except for the coronary artery. In comparison with the arteries of the Japanese, the trend of calcium accumulation in the arteries of the Thai was almost similar to that in the arteries of the Japanese, except for the coronary artery and thoracic aorta. The calcium accumulation in the coronary artery was much higher in the Thai than in the Japanese, whereas that in the thoracic aorta was lower in the Thai than in the Japanese. Regarding elements in the cardiac valves, the calcium content increased remarkably in the seventies in the aortic valve and in the nineties in the pulmonary valve, but it hardly increased in both the mitral and tricuspid valves with aging. The average content of calcium was the highest in the aortic valve, and it decreased in the order pulmonary, tricuspid, and mitral valves. Regarding the relationship among elements in the aortic valves, it was found that there were extremely significant direct correlations among the contents of calcium, phosphorus, and magnesium, whereas there were significant direct correlations between zinc and either calcium or phosphorus contents. Although significant correlations were found between sulfur and the other element contents in the aortic valves fo the Japanese, no significant correlations were found between them in the aortic valves of the Thai. In the mitral valves, extremely or very significant direct correlations were found among the contents of calcium, phosphorus, magnesium, and sulfur, with some exceptions that there were no significant correlations between phosphorus and either magnesium or sulfur contents. in addition, no significant correlation was found in the calcium content between the aortic valve and coronary artery in the same individuals.

Adult↗

PubMed2004

Evolution of P elements in natural populations of Drosophila willistoni and D. sturtevanti.

To determine how population structure of the host species affects the spread of transposable elements and to assess the strength of selection acting on different structural regions, we sequenced P elements from strains of Drosophila willistoni and Drosophila sturtevanti sampled from across the distributions of these species. Elements from D. sturtevanti exhibited considerable sequence variation, and similarity among them was correlated to geographic distance between collection sites. By contrast, all D. willistoni elements sampled were essentially identical (pi < 0.2%) and exhibited patterns typical of a recent population expansion. While the canonical P elements sampled from D. sturtevanti appear to be long-time residents in that species, a rapid expansion of a very young canonical P-element lineage is suggested in D. willistoni, overcoming barriers such as large geographical distances and moderate levels of population subdivision. Between-species comparisons reveal selective constraints on P-element evolution, as indicated by significantly different substitution rates in noncoding, silent, and replacement sites. Most remarkably, in addition to replacement sites, selection pressure appears to be strong in the first and third introns and in the 3' and 5' flanking regions.

Animals↗

PubMed2004

An active transposable element, Herves, from the African malaria mosquito Anopheles gambiae.

Transposable elements have proven to be invaluable tools for genetically manipulating a wide variety of plants, animals, and microbes. Some have suggested that they could be used to spread desirable genes, such as refractoriness to Plasmodium infection, through target populations of Anopheles gambiae, thereby disabling the mosquito's ability to transmit malaria. To achieve this, a transposon must remain mobile and intact after the initial introduction into the genome. Endogenous, active class II transposable elements from An. gambiae have not been exploited as gene vectors/drivers because none have been isolated. We report the discovery of an active class II transposable element, Herves, from the mosquito An. gambiae. Herves is a member of a distinct subfamily of hAT elements that includes the hopper-we element from Bactrocera dorsalis and B. cucurbitae. Herves was transpositionally active in mobility assays performed in Drosophila melanogaster S2 cells and developing embryos and was used as a germ-line transformation vector in D. melanogaster. Herves displays an altered target-site preference from the distantly related hAT elements, Hermes and hobo. Herves is also present in An. arabiensis and An. merus with copy numbers similar to that found in An. gambiae. Preliminary data from an East African population are consistent with the element being transpositionally active in mosquitoes.

Africa↗

PubMed1990

The gene for the beta subunit of porcine LH: clusters of GC boxes and CACCC elements.

The gene for the beta subunit of porcine LH (LH-beta) was cloned from a genomic library constructed in EMBL3. The nucleotide sequence was determined for the entire gene transcriptional unit of porcine LH-beta in addition to 1277 and 372 bp of the 5'- and 3'-flanking regions respectively. Southern blot analysis of the porcine genomic DNA indicated that the LH-beta gene is present as a single copy. The transcriptional unit of porcine LH-beta spanned 1107 bp and contained three exons interrupted by two introns of 326 and 289 bp. The short untranslated sequence in the first exon and the location of the exon/intron junctions at amino acid residues -16/-15 and +41/+42 were highly conserved in the rat, human and bovine LH-beta genes. In the 5'-flanking region, one TATA box and two CCAAT boxes were present. The steroid-responsive element was not found up to 1277 bases upstream of the transcription start site. The potential AP-2 factor-responsive elements appeared nine times within the sequence that was determined, and four of them were located in the 5'-flanking region. Two distal AP-2 elements were arranged in an inverted repeat forming a 16 bp palindromic sequence. This feature suggested that hypothalamic gonadotrophin-releasing hormone stimulates expression of the LH-beta gene, predominantly by a signal-transduction system with the protein kinase C cascade and a mediator, the AP-2 factor. A further characteristic feature of the porcine LH-beta gene was the presence of clusters of GC boxes and CACCC elements in the 5'-flanking region and the downstream sequence. Co-existence of these regulatory elements with other elements, such as the AP-2 element or CCAAT box, was also found. The porcine LH-beta gene shows a structure distinct from the porcine FSH-beta and common alpha genes, which are counterparts of the LH-beta gene, reflecting differential control of their synthesis during gametogenesis.

Amino Acid Sequence↗

PubMed1998

Differences in co-variation of inorganic elements in the bulk and surface of human deciduous enamel: an induction analysis study.

This paper demonstrates a method for determination of co-variation between some inorganic elements in the bulk and surface areas of human tooth enamel. The technique is based on a computerised induction analysis of data obtained by secondary ion mass spectrometry (SIMS). When comparing the present data with an earlier study from our laboratory, it became evident that with only a moderate increase in the amount of data for the induction analysis, the results increased very considerably in reliability and precision. The patterns of co-variation between different elements differed between the bulk- and surface enamel. Only Mg expressed a similar pattern. In the bulk enamel the elements Na and P expressed a high degree of co-variation. Similarly, Mg and C expressed a high degree of co-variation. Mg was an element often found to co-vary with bulk enamel elements. In the enamel surface, F and Cl co-varied. In addition, Cl was an element often found to co-vary with other enamel surface elements.

Carbon↗

PubMed2000

Regulation of human CYP11B2 and CYP11B1: comparing the role of the common CRE/Ad1 element.

In humans, the final steps in corticosteroid production results from the activity of aldosterone synthase in the glomerulosa and 11beta-hydroxylase in the fasciculata. The regional expression of these isozymes is believed to result from transcriptional regulation of the aldosterone synthase (CYP11B2) and 11beta-hydroxylase (CYP11B1) genes. Previous studies suggest that the primary cis-element needed for agonist enhanced transcription of the CYP11B genes shares high sequence similarity to a consensus cAMP Response Element (CRE). Here the role of the CRE/Adl was studied. Reporter constructs prepared with the 5'flanking DNA of hCYP11B2 and hCYP11B1 were transfected into NCI-H295R (H295R) adrenocortical tumor cells. Both hCYP11B2 and hCYP11B1 driven reporter constructs responded in a similar manner to treatment with angiotensin II, potassium, dbcAMP, or forskolin. Mutation of the hCYP11B1 CRE/Adl element decreased basal reporter expression and decreased response to agonist. Mutation of the hCYP11B2 CRE/Adl element caused a loss of basal expression but retained response to agonist suggesting a role for other cis-elements in hormonal regulation of hCYP11B2. In addition, both cis-elements were able to form complexes with in vitro prepared CRE binding (CREB) protein, activating transcription factor (ATF)-1 and ATF-2 in mobility shift assays. However, only the ATF-2 complex migrated similarly to a complex seen using H295R nuclear extract. Taken together these data suggest that the CRE/Adl element plays an important role in the transcriptional regulation of both hCYP11B genes but does not play an important role in the regional distribution of the two isozymes within the adrenal.

Adrenal Glands↗

PubMed2005

Distal enhancer elements transcribe intergenic RNA in the IL-10 family gene cluster.

The IL-10 gene and homologs IL-19, IL-20, and IL-24 are expressed within a highly conserved 145-kb cytokine gene cluster. Like the Th2 IL-4 cytokine gene cluster, it is feasible that there is coordinate regulation of these cytokines by distal regulatory elements spanning the locus. We initiated a search to characterize regulatory elements within the IL-10 family locus and present data herein on a conserved 40-kb region between the IL-19 and IL-10 genes. We map the location of 17 DNase I-hypersensitive sites in different murine T cell populations and identify three enhancer elements, which function in T cells in vitro. Two of these enhancer elements, located 9 kb upstream and 6.45 kb downstream of IL-10, display cell-specific function in the Th1-Th2 cell clones AE7 and D10 and also exhibit basic promoter activity. The downstream element, IL-10CNS+6.45, binds AP-1 in the absence of NFAT and expresses intergenic RNA in a Th2-specific manner, further validating its role as a Th2-specific enhancer/promoter element. We show that the five most highly conserved noncoding sequences in the 40-kb region transcribe intergenic RNA; four of these regions possess promoter activity in vitro that could account for the expression of these transcripts. Hence, we speculate that these novel regulatory elements in the IL-10 family gene locus function via an intermediate regulatory RNA.

Animals↗