Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Gene Components”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 415 records · Page 23Linked to original sources

Synergistic activation of the insulin gene promoter by the beta-cell enriched transcription factors MafA, Beta2, and Pdx1.

Specific expression of the insulin gene in pancreatic islet beta-cells requires multiple cis-regulatory elements in its promoter. Pdx1, MafA, and Beta2 have been identified as beta-cell enriched transcription factors that bind to these elements. Pdx1 has been shown to bind to A1, A3, A5, and GG2, and Beta2 binds to E1 by forming a heterodimer with the ubiquitous factor E47. MafA was recently identified as a C1-element binding factor. However, interactions between these factors and the promoter have not been characterized in detail. In this report, we show that these transactivators synergistically stimulate insulin promoter activity. Among multiple binding sites for Pdx1, MafA, and Beta2, at least GG2, C1, and E1 elements located in the promoter region between -150 and -100 base pairs are necessary for the synergism. We also found that neither MafB nor c-Maf, close relatives of MafA, showed synergistic activation. These results suggest that co-expression and functional synergism of these beta-cell enriched transactivators, MafA, Pdx1, and Beta2, are critical for establishing the beta-cell-specific and efficient expression of the insulin gene.

Basic Helix-Loop-Helix Proteins↗

Gene structure of pig sterol 12alpha-hydroxylase (CYP8B1) and expression in fetal liver: comparison with expression of taurochenodeoxycholic acid 6alpha-hydroxylase (CYP4A21).

Cholic acid is the major trihydroxy bile acid formed in most mammals. The domestic pig (Sus scrofa) is an exception. The bile of adult pig is devoid of cholic acid whereas hyocholic acid is found in amounts equal to that of cholic acid in humans. The pathway leading to formation of hyocholic acid is believed to be species-specific and to have evolved in the pig to compensate for a nonexistent or deficient cholic acid biosynthesis. However, a high level of cholic acid has recently been found in the bile of fetal pig. Here we describe that a gene encoding the key enzyme in cholic acid biosynthesis, the sterol 12alpha-hydroxylase (CYP8B1), is in fact present in the pig genome. The deduced amino acid sequence shows 81% identity to the human and rabbit orthologues. CYP8B1 mRNA is expressed at significant levels in fetal pig liver. Both CYP8B1 and the key enzyme in hyocholic acid formation, taurochenodeoxycholic acid 6alpha-hydroxylase (CYP4A21), were found to be expressed in pig liver in a developmental-dependent but opposite fashion.

Adult↗

Genomic organization, alternative splicing, and promoter analysis of human dynamin-like protein gene.

The human dynamin-like protein, HdynIV, has recently been cloned and shown to be involved in the formation and trafficking of coated vesicles. In particular, one of the HdynIV variant overexpressions has been suggested to contribute to the pathogenesis of brain tumors. In this paper, we report on the genomic organization of the human HdynIV gene. The gene was found to correspond to 20 exons of genomic sequence on human chromosome 12, distributed over 64kb of genomic DNA. The two exons, numbers 15 and 16, are subjected to differential splicing, generating four different transcripts of a perfect match to our recent report on the four different spliced HdynIV variants [DNA Cell Biol. 19 (2000) 189]. We have also characterized the 5(') regulatory region of the HdynIV gene in order to understand the molecular mechanisms regulating its expression. The transcriptional initiation site was identified by 5(')-RACE. The 5(')-flanking sequence of the HdynIV gene contains three GC boxes that concatenate Ap2- and Sp1-binding motifs, but that does not contain either the TATA or CAAT consensus sequence. A region between -140 and +92 contributed to high promoter activity. Deletion analysis demonstrated that the minimal promoter activity required the region of -110 to -100. Electrophoretic mobility shift assay demonstrated that a putative transcriptional factor bound to the region of -119 to -90. Site-directed mutagenesis analysis of this region revealed that nucleotides at -108 to -100 were essential for transactivation mediated by this transcriptional factor. In conclusion, we have characterized the minimal HdynIV promoter and shown that CTCCCAGCA (-108 to -100) sequence may act as a novel transcriptional element for regulating HdynIV gene expression.

Alternative Splicing↗

Sea urchin neural alpha2 tubulin gene: isolation and promoter analysis.

Expression of Talpha2 gene, during sea urchin Paracentrotus lividus development, is spatially and temporally regulated. In order to characterize this gene, we isolated the relevant genomic sequences and scanned the isolated 5'-flanking region in searching for cis-regulatory elements required for proper expression. Gel mobility shift and footprinting assays, as well as reporter gene (CAT and beta-gal) expression assays, were used to address cis-regulatory elements involved in regulation. Here we report that an upstream 5'-flanking fragment of PlTalpha2 gene drives temporal expression of reporter genes congruent with that of endogenous Talpha2 gene. The fragment contains cis-elements able to bind nuclear proteins from the gastrula stage (at which the Talpha2 gene is expressed) whose sequences could be consistent with the consensus sequences for transcription factors present in data bank.

Animals↗

Functional mapping of tissue-specific elements of the human alpha-fetoprotein gene enhancer.

Serum alpha-fetoprotein (AFP) levels in hepatocellular carcinoma (HCC) patients and expression of the protein in cultured HCC cell lines are highly variable. These observations may arise from features correlated with tissue-specific expression of the gene. Extremely strong and potent liver-specific enhancer activity is confined from -4.1 to -3.3 kb upstream to the human AFP gene in contrast with that of the rodent which exists in three widely separated regions. To understand the tissue-specific expression of AFP, we examined cis-acting elements in the enhancer. Results revealed binding sites for selected liver-enriched transcription factors (LETFs) in both domains A (-4120 to -3756 bp) and B (-3492 to -3300 bp) of the gene. These sites included: one hepatocyte nuclear factor (HNF)-1 and HNF-4, two HNF-3, and two C/EBP binding sites in domain A. An adjacent domain B contained one HNF-3 site and three C/EBP sites plus a previously identified HNF-1 site. Each of these elements alone has the ability to stimulate heterogeneous promoter activity in a dose-dependent manner when transfected into AFP producing cells. A comparative study showed that the presence of two HNF-1 and one HNF-4 site is a characteristic feature of human but not rodent AFP enhancer. The mRNA levels of the liver-enriched transcription factors (LETFs) were variable in individual HCC cell lines and together with silencer activities may underlie differential expression of the AFP gene.

Albumins↗

Osteoporosis in MCHR1-deficient mice.

It is well recognized that the hypothalamus is of central importance in the regulation of food intake and fat mass. Recent studies indicate that it also plays an important role in the regulation of bone mass. Melanin concentrating hormone (MCH) is highly expressed in the hypothalamus and has been implicated in regulation of energy homeostasis. We developed MCHR1 inactivated mice to evaluate the physiological role of this receptor. Interestingly, the MCHR1(-/-) mice have osteoporosis, caused by a reduction in the cortical bone mass, while the amount of trabecular bone is unaffected. The reduction in cortical bone mass is due to decreased cortical thickness. Serum levels of c-telopeptide, a marker of bone resorption, are increased in MCHR1(-/-) mice, indicating that the MCHR1(-/-) mice have a high bone turnover osteoporosis. In conclusion, the MCHR1(-/-) mice have osteoporosis, indicating that MCHR1-signalling is involved in a tonic stimulation of bone mass.

Absorptiometry, Photon↗

Molecular cloning and characterization of a human gene involved in transcriptional regulation of hTERT.

Human telomerase reverse transcriptase (hTERT), the catalytic subunit of telomerase in human, has been identified as the rate-limiting factor in telomerase activity, but its detailed mechanism of transcription regulation remains unclear. In this investigation, a novel human gene telomerase transcriptional elements-interacting factor (TEIF) was isolated from HeLa cell based on hTERT promoter yeast one-hybrid assay. TEIF has a 2358-bp open reading frame encoding a predicted protein of 786 amino acids, which is functionally conserved in general eukaryotic species. The transcription of TEIF was detected in cells and expressed an 86-kDa native protein, distributing mainly in cellular nuclei. Its interaction with hTERT promoter was identified and the DNA binding potential was credited to C-terminus of TEIF. Transfection of TEIF into HeLa cells presented marked transactivation of hTERT promoter and stimulated both endogenous hTERT transcription and telomerase activities. These results suggest that TEIF protein might be a transcription regulator and take part in the activation of hTERT.

Adaptor Proteins, Vesicular Transport↗

Discovery of a novel superfamily of type III polyketide synthases in Aspergillus oryzae.

Identification of genes encoding type III polyketide synthase (PKS) superfamily members in the industrially useful filamentous fungus, Aspergillus oryzae, revealed that their distribution is not specific to plants or bacteria. Among other Aspergilli (Aspergillus nidulans and Aspergillus fumigatus), A. oryzae was unique in possessing four chalcone synthase (CHS)-like genes (csyA, csyB, csyC, and csyD). Expression of csyA, csyB, and csyD genes was confirmed by RT-PCR. Comparative genome analyses revealed single putative type III PKS in Neurospora crassa and Fusarium graminearum, two each in Magnaporthe grisea and Podospora anserina, and three in Phenarocheate chrysosporium, with a phylogenic distinction from bacteria and plants. Conservation of catalytic residues in the CHSs across species implicated enzymatically active nature of these newly discovered homologs.

Acyltransferases↗

The cell-type-specificity of inherited predispositions to tumours: review and hypothesis.

Most hereditary predispositions to tumours affect only one particular cell type of the body but the genes bearing the relevant germ-line mutation are not cell-type-specific. Some predisposition syndromes include increased risks of lesions (developmental or tumourous) of unrelated cell types, in any individual predisposed to the main lesion (e.g. osteosarcoma in patients predisposed to retinoblastoma). Other predispositions to additional lesions occur only in members of some families with the predisposition to the basic lesion (e.g. Gardner's syndrome in some families suffering familial adenomatous polyposis). In yet other predisposition syndromes, different mutations of the same gene are associated with markedly differing family-specific clinical syndromes. In particular, identical germline mutations (e.g. in APC, RET and PTEN genes), have been found associated with differing clinical syndromes in different families. This paper reviews previously suggested mechanisms of the cell-type specificity of inherited predispositions to tumour. Models of tumour formation in predisposition syndromes are discussed, especially those involving a germline mutation (the first 'hit') of a tumour suppressor gene (TSG) and a second (somatic) hit on the second allele of the same TSG. A modified model is suggested, such that the second hit is a co-mutation of the second allele of the TSG and a regulator which is specific for growth and/or differentiation of the cell type which is susceptible to the tumour predisposition. In some cases of tumour, the second hit may be large enough to be associated with a cytogenetically-demonstrable abnormality of the part of the chromosome carrying the TSG, but in other cases, the co-mutation may be of 'sub-cytogenetic' size (i.e. 10(2)-10(5) bases). For the latter, mutational mechanisms of frameshift and impaired fidelity of replication of DNA by DNA polyerases may sometimes be involved. Candidate cell-type-specific regulators may include microRNAs and perhaps transcription factors. It is suggested that searching the introns within 10(5)-10(6) bases either side of known of exonic mutations of TSGs associated with inherited tumour predisposition might reveal microRNA cell-type-specific regulators. Additional investigations may involve fluorescent in situ hybridisations on interphase tumour nuclei.

Animals↗

Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers.

We present an analysis of chromatin fiber structure across the human genome. Compact and open chromatin fiber structures were separated by sucrose sedimentation and their distributions analyzed by hybridization to metaphase chromosomes and genomic microarrays. We show that compact chromatin fibers originate from some sites of heterochromatin (C-bands), and G-bands (euchromatin). Open chromatin fibers correlate with regions of highest gene density, but not with gene expression since inactive genes can be in domains of open chromatin, and active genes in regions of low gene density can be embedded in compact chromatin fibers. Moreover, we show that chromatin fiber structure impacts on further levels of chromatin condensation. Regions of open chromatin fibers are cytologically decondensed and have a distinctive nuclear organization. We suggest that domains of open chromatin may create an environment that facilitates transcriptional activation and could provide an evolutionary constraint to maintain clusters of genes together along chromosomes.

Cell Line↗

Intraflagellar transport is required in Drosophila to differentiate sensory cilia but not sperm.

BACKGROUND: Intraflagellar transport (IFT) uses kinesin II to carry a multiprotein particle to the tips of eukaryotic cilia and flagella and a nonaxonemal dynein to return it to the cell body. IFT particle proteins and motors are conserved in ciliated eukaryotes, and IFT-deficient mutants in algae, nematodes, and mammals fail to extend or maintain cilia and flagella, including sensory cilia. In Drosophila, the only ciliated cells are sensory neurons and sperm. no mechanoreceptor potential (nomp) mutations have been isolated that affect the differentiation and function of ciliated sense organs. The nompB gene is here shown to encode an IFT protein. Its mutant phenotypes reveal the consequences of an IFT defect in an insect. RESULTS: Mechanosensory and olfactory neurons in nompB mutants have missing or defective cilia. nompB encodes the Drosophila homolog of the IFT complex B protein IFT88/Polaris/OSM-5. nompB is expressed in the ciliated sensory neurons, and a functional, tagged NOMPB protein is located in sensory cilia and around basal bodies. Surprisingly, nompB mutant males produce normally elongated, motile sperm. Neuronally restricted expression and male germline mosaic experiments show that nompB-deficient sperm are fully functional in transfer, competition, and fertilization. CONCLUSIONS: NOMPB, the Drosophila homolog of IFT88, is required for the assembly of sensory cilia but not for the extension or function of the sperm flagellum. Assembly of this extremely long axoneme is therefore independent of IFT.

Animals↗

The Arabidopsis heterochronic gene ZIPPY is an ARGONAUTE family member.

Plants progress through a temporal sequence of juvenile, adult, and reproductive phases, each marked by the expression of phase-specific traits. Here we show that loss-of-function mutations in ZIPPY (ZIP) cause the premature expression of adult vegetative traits but do not accelerate the onset of reproductive competence or flowering time. ZIP encodes ARGONAUTE7 (AGO7), one of ten members of the ARGONAUTE family in Arabidopsis. In addition to playing developmental roles, some ARGONAUTE family members are required for RNAi-like phenomena, such as posttranscriptional gene silencing. In contrast to Arabidopsis ARGONAUTE1, ZIP has no significant role in transgene silencing; its primary function is in the regulation of developmental timing.

Arabidopsis↗

The CMK-1 CaMKI and the TAX-4 Cyclic nucleotide-gated channel regulate thermosensory neuron gene expression and function in C. elegans.

The cultivation temperature (T(c)) modulates the thermosensory responses exhibited by C. elegans on thermal gradients. The AFD sensory neurons are essential for thermosensory behaviors, but the molecular mechanisms by which temperature is sensed and the memory of the T(c) is encoded are unknown. Here, we show that the CMK-1 Ca2+/calmodulin-dependent protein kinase I (CaMKI) and the TAX-4 cyclic nucleotide-gated channel regulate gene expression, morphology, and functions of the AFD thermosensory neurons. Mutations in cmk-1 and tax-4 result in temperature-dependent defects in AFD-specific gene expression, and TAX-4 functions are required during larval stages to maintain gene expression in the adult. CMK-1 and TAX-4 act cell autonomously to regulate AFD-mediated thermosensory behaviors. The molecular requirements for CMK-1 activity in the AFD neurons appear to be distinct from those previously described. We propose that the activation of distinct programs of AFD-specific gene expression at different temperatures by CMK-1 and TAX-4 enables C. elegans to sense and/or encode a memory for the T(c).

Animals↗

The Drosophila MOS ortholog is not essential for meiosis.

In metazoan oocytes, a metaphase arrest coordinates the completion of meiosis with fertilization. Vertebrate mos maintains the metaphase II arrest of mature oocytes and prevents DNA replication between the meiotic divisions. We identified a Drosophila homolog of mos and showed it to be the mos ortholog by two additional criteria. The dmos transcripts are present in Drosophila oocytes but not embryos, and injection of dmos into Xenopus embryos blocks mitosis and elevates active MAPK levels. In Drosophila, MAPK is activated in oocytes, consistent with a role in meiosis. We generated deletions of dmos and found that, as in vertebrates, dmos is responsible for the majority of MAPK activation. Unexpectedly, the oocytes that do mature complete meiosis normally and produce fertilized embryos that develop, although there is a reduction in female fertility and loss of some oocytes by apoptosis. Therefore, Drosophila contains a mos ortholog that activates a MAPK cascade during oogenesis and is nonessential for meiosis. This could be because there are redundant pathways regulating meiosis, because residual, low levels of active MAPK are sufficient, or because active MAPK is dispensable for meiosis in Drosophila. These results highlight the complexity of meiotic regulation that evolved to ensure accurate control over the reproductive process.

Amino Acid Sequence↗

TBP2, a vertebrate-specific member of the TBP family, is required in embryonic development of zebrafish.

TATA binding protein (TBP) is a key regulator of RNA polymerase transcription. It binds to core promoters, often in large multiprotein complexes, and nucleates RNA polymerase II (Pol II) transcription initiation. In addition to the previously described TBP-like factor present in metazoans (TLF/TRF2/TRP/TLP), we describe a third, vertebrate-specific member of the TBP protein family from zebrafish, called TBP2. Evolutionary conserved TBP2 homologs were also found in human, mouse, frog, and pufferfish. The N-terminal domains of TBP2s are divergent amongst themselves and different from those of TBPs; however, the core domain of TBP2s and TBPs are almost identical. TBP2 binds the TATA box, interacts with TFIIA and TFIIB (similarly to TBP), and can mediate Pol II transcription initiation. However, TBP2 shows contrasting expression patterns in the gonads and during embryonic development in comparison to TBP, suggesting differential function. Knockdown of zebrafish TBP2 results in specific reduction of the protein level, leading to a phenotype, which indicates the requirement of TBP2 for embryonic patterning. The presence of three different TBP family members in vertebrates suggests the existence of developmental stage- and tissue-specific preinitiation complexes with specific requirements for different TBP family members.

Animals↗

Mutual exclusion of sensory bristles and tendons on the notum of dipteran flies.

BACKGROUND: Genes of the achaete-scute complex encode transcription factors whose activity regulates the development of neural cells. The spatially restricted expression of achaete-scute on the mesonotum of higher flies governs the development and positioning of the large sensory bristles. On the scutum the bristles are arranged into conserved patterns, based on an ancestral arrangement of four longitudinal rows. This pattern appears to date back to the origin of cyclorraphous flies about 100-140 million years ago. The origin of the four-row bauplan, which is independent of body size, and the reasons for its conservation, are not known. RESULTS: We report that tendons for attachment of the indirect flight muscles are invariably located between the bristle rows of the scutum throughout the Diptera. Tendon development depends on the activity of a transcription factor encoded by the gene stripe. In Drosophila, stripe and achaete-scute have separate expression domains, leading to spatial segregation of tendon precursors and bristle precursors. Furthermore the products of these genes act antagonistically: ectopic sr expression prevents bristle development and ectopic sc expression prevents normal muscle attachment. The product of stripe acts downstream of Achaete-Scute and interferes with the development of bristle precursors. CONCLUSIONS: The pattern of flight muscles has changed little throughout the Diptera and we argue that the sites of muscle attachment may have constrained the positioning of bristles during the course of evolution. This could account for the pattern of four bristle rows on the scutum.

Animals↗

High coding density on the largest Paramecium tetraurelia somatic chromosome.

Paramecium, like other ciliates, remodels its entire germline genome at each sexual generation to produce a somatic genome stripped of transposons and other multicopy elements. The germline chromosomes are fragmented by a DNA elimination process that targets heterochromatin to give a reproducible set of some 200 linear molecules 50 kb to 1 Mb in size. These chromosomes are maintained at a ploidy of 800n in the somatic macronucleus and assure all gene expression. We isolated and sequenced the largest megabase somatic chromosome in order to explore its organization and gene content. The AT-rich (72%) chromosome is compact, with very small introns (average size 25 nt), short intergenic regions (median size 202 nt), and a coding density of at least 74%, higher than that reported for budding yeast (70%) or any other free-living eukaryote. Similarity to known proteins could be detected for 57% of the 460 potential protein coding genes. Thirty-two of the proteins are shared with vertebrates but absent from yeast, consistent with the morphogenetic complexity of Paramecium, a long-standing model for differentiated functions shared with metazoans but often absent from simpler eukaryotes. Extrapolation to the whole genome suggests that Paramecium has at least 30,000 genes.

Animals↗

Feo, the Drosophila homolog of PRC1, is required for central-spindle formation and cytokinesis.

We performed a functional analysis of fascetto (feo), a Drosophila gene that encodes a protein homologous to the Ase1p/PRC1/MAP65 conserved family of microtubule-associated proteins (MAPs). These MAPs are enriched at the spindle midzone in yeast and mammals and at the fragmoplast in plants, and are essential for the organization and function of these microtubule arrays. Here we show that the Feo protein is specifically enriched at the central-spindle midzone and that its depletion either by mutation or by RNAi results in aberrant central spindles. In Feo-depleted cells, late anaphases showed normal overlap of the antiparallel MTs at the cell equator, but telophases displayed thin MT bundles of uniform width instead of robust hourglass-shaped central spindles. These thin central spindles exhibited diffuse localizations of both the Pav and Asp proteins, suggesting that these spindles comprise improperly oriented MTs. Feo-depleted cells also displayed defects in the contractile apparatus that correlated with those in the central spindle; late anaphase cells formed regular contractile structures, but these structures did not constrict during telophase, leading to failures in cytokinesis. The phenotype of Feo-depleted telophases suggests that Feo interacts with the plus ends of central spindle MTs so as to maintain their precise interdigitation during anaphase-telophase MT elongation and antiparallel sliding.

Animals↗