Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.1.27.1 (RNase)
16,360 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

We report the isolation and characterization of genomic and cDNA clones encoding zebrafish fibroblast growth factor 3 (FGF3). An initial cDNA clone was generated by PCR amplification using degenerate oligo primers corresponding to a conserved region of protein found in the mouse and human homologues. Screening a cDNA library made from 30-33-h-old zebrafish embryos with this PCR product led to the isolation of two cDNA clones. Sequence analysis of the longest cDNA insert (1810 bp) revealed a 256-amino-acid (aa) orf. The central region, composed of approx. 155 aa, shares 78% identity with the analogous region of Xenopus laevis FGF3 and 72% identity with the product of the more distantly related human gene. However, the N-and C-terminal domains of zebrafish FGF3 are very different from those of other known homologues. The cDNA was used as a probe on genomic DNA to create a physical map of the locus and to isolate a genomic clone encompassing the entire coding region and 5' sequences. DNA sequencing and RNase protection analyses indicate that zebrafish Fgf-3 (ZFgf-3) is structurally analogous to the mouse gene and regulated through two different promoters. The transcription start point of the proximal promoter aligns to that of mouse promoter P3 and lies within a conserved region of sequence.
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PMID:The zebrafish Fgf-3 gene: cDNA sequence, transcript structure and genomic organization. 865 46

We describe the cloning and sequence analysis of a nearly full-length cDNA as well as a corresponding 5.2-kilobase pair genomic fragment encoding FREAC-4, a member of the forkhead family of transcription factors. The cDNA is collinear with respect to the coding region of the intronless genomic clone. The conceptual translation product predicts a protein of 465 amino acids with a hyperacidic amino-terminal end, a DNA binding forkhead domain and a carboxyl-terminal part that is rich in homopolymeric runs of prolines and alanines. The transcription start is identified using an RNase protection assay. A 2.7-kilobase pair genomic DNA fragment, located immediately upstream of the translation start, was fused to a luciferase reporter gene. Significant levels of luciferase activity were detected when this construct was transfected into two kidney-derived cell lines, 293 and COS-7 cells, whereas only background reporter gene expression was observed in a cell line of nonkidney origin. Cotransfections with plasmids expressing WT-1, WTAR (a mutated form of WT-1), p53, and a mutated form of p53 revealed a complex pattern of regulation with a 3-fold induction with WT-1, a 7-fold induction with mutated p53, and a 4-fold repression with wild-type p53. A 5'-promoter deletion series delimits a DNA fragment necessary for WT-1 inducibility in cotransfection experiments. This fragment is shown to contain at least one cis-element that is capable of interacting with recombinant WT-1.
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PMID:Characterization of the human forkhead gene FREAC-4. Evidence for regulation by Wilms' tumor suppressor gene (WT-1) and p53. 870 77

A truncated cDNA clone encoding Tetrahymena thermophila histone H2A2 was isolated using synthetic degenerate oligonucleotide probes derived from H2A protein sequences of Tetrahymena pyriformis. The cDNA clone was used as a homologous probe to isolate a truncated genomic clone encoding H2A1. The remaining regions of the genes for H2A1 (HTA1) and H2A2 (HTA2) were then isolated using inverse PCR on circularized genomic DNA fragments. These partial clones were assembled into intact HTA1 and HTA2 clones. Nucleotide sequences of the two genes were highly homologous within the coding region but not in the noncoding regions. Comparison of the deduced amino acid sequences with protein sequences of T. pyriformis H2As showed only two and three differences respectively, in a total of 137 amino acids for H2A1, and 132 amino acids for H2A2, indicating the two genes arose before the divergence of these two species. The HTA2 gene contains a TAA triplet within the coding region, encoding a glutamine residue. In contrast with the T. thermophila HHO and HTA3 genes, no introns were identified within the two genes. The 5'- and 3'-ends of the histone H2A mRNAs; were determined by RNase protection and by PCR mapping using RACE and RLM-RACE methods. Both genes encode polyadenylated mRNAs and are highly expressed in vegetatively growing cells but only weakly expressed in starved cultures. With the inclusion of these two genes, T. thermophila is the first organism whose entire complement of known core and linker histones, including replication-dependent and basal variants, has been cloned and sequenced.
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PMID:Cloning and characterization of the major histone H2A genes completes the cloning and sequencing of known histone genes of Tetrahymena thermophila. 876 Aug 89

We have previously characterized a tobacco cDNA encoding a novel type RNA-binding protein (RZ-1), which contains a zinc finger motif in addition to a consensus sequence-type RNA-binding domain and is localized in the nucleus. Here we isolated its genomic clone from a Nicotiana sylvestris genomic library. Southern blot analysis suggested that RZ-1 is coded for by a single locus per haploid genome. Comparison of the cDNA and genomic sequences indicated that the RZ-1 gene contains two introns, one in the coding region and another in the 3'-untranslated region. RT-PCR and ribonuclease protection analyses showed that splicing of RZ-1 pre-mRNA occurs efficiently. The RZ-1 protein is actively synthesized in rapidly dividing tobacco cells, as demonstrated by immunoblot analysis.
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PMID:Structure and expression of the tobacco nuclear gene encoding RNA-binding protein RZ-1: the existence of an intron in the 3'-untranslated region. 880 57

A genomic clone containing sequence identical to the 5' region of the cDNA for rat Type I hexokinase was isolated from a lambda Charon 4A library. A 5.4-kb EcoRI fragment from this clone, containing the matching sequence, was sequenced in its entirety. Rapid amplification of 5' cDNA ends (5' RACE), reverse transcription polymerase chain reaction, and ribonuclease protection experiments were consistent with the existence of multiple transcriptional start sites clustered in three regions approximately 460, 300, and 100 nucleotides upstream from the translational start codon. Together with results of previous work, the 5' untranslated sequence defined in the present study accounts for the 4.3-kb mRNA for Type I hexokinase seen on Northern blots. Fragments from the 5' flanking region were cloned into a reporter vector containing the luciferase coding region. Based on transfection experiments with both PC12 and H9c2 cells, promoter activity was associated with a region lying between nucleotide positions -742 and -516 (with A of the ATG codon at the translational start site defined as +1). The promoter region lacks a TATA sequence and, together with the transcriptional start sites, is located within a GC rich segment (a "CpG island") approximately 1 kb in length. These characteristics have previously been associated with the promoter and transcriptional start sites of genes for "housekeeping enzymes."
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PMID:Isolation of the promoter for Type I hexokinase from rat. 891 47

Previous studies have demonstrated that three variant transcripts, AE1-3, AE1-4 and AE1-5, are derived from the AE1 gene in chicken kidney. These variant transcripts encode AE1 anion exchangers that possess alternative N-terminal cytoplasmic domains. To determine the mechanisms involved in generating these transcripts, a genomic clone, containing the unique sequences at the 5' ends of the AE1-4 and AE1-5 transcripts, was isolated. Characterization of this clone revealed that the sequences at the 5' ends of the AE1-3, AE1-4 and AE1-5 transcripts were each present with an approx. 1.2-kb BamHI fragment of the chicken AE1 gene. RNA blotting and RNase protection analyses using probes derived from this genomic clone have shown that the AE1-4 variant corresponds to the approx. 4.5-kb chicken kidney AE1 transcript, while the AE1-5 variant corresponds to the approx. 5.1-kb transcript. These studies have shown that the AE1-5 transcript extends further 5' than had been previously shown from cDNA cloning studies, and contains the sequence present at the 5' end of the AE1-4 transcript. In addition, primer extension analyses have shown that the variant kidney AE1 transcripts initiate transcription from a common site. This result indicates that the expression of the AE1-3, AE1-4, and AE1-5 transcripts is regulated by a single promoter, P3, that is distinct from the P1 and P2 erythroid-specific promoters of the chicken AE1 gene.
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PMID:Variant chicken kidney AE1 anion exchanger transcripts are derived from a single promoter by alternative splicing. 896 3

We isolated and sequenced genomic and cDNA clones of the guinea pig preprodynorphin (ppDyn) mRNA. The sequence of ppDyn mRNA was deduced from a combination of genomic and cDNA clones: The primary structure of two coding exons was derived from a genomic clone and 5' and 3' untranslated sequences were obtained using rapid amplification of cDNA ends (RACE). The predicted mRNA of 2,350 nucleotides coincides well with the size of transcripts in Northern blot analyses of RNA from different brain regions. The deduced amino acid sequence of guinea pig ppDyn shares 70%, 68%, and 61% identity to porcine, human, and rat ppDyn, respectively. The 5' untranslated sequences of guinea pig hippocampal and adrenal ppDyn mRNA are identical; both contain sequences of exon I and, like porcine mRNA, lack an exon (exon II) present in human and rat mRNA. Quantitative solution hybridization RNase protection analysis of total RNA from selected guinea pig brain regions was performed. The nucleus accumbens was found to have the greatest abundance of ppDyn mRNA, followed by caudate putamen, hippocampus, hypothalamus, amygdala, frontal cortex, olfactory bulb, and pons/medulla.
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PMID:Guinea pig preprodynorphin mRNA: primary structure and regional quantitation in the brain. 898 24

The active forms of all of the matrix metalloproteinases (MMPs) are inhibited by a family of specific inhibitors, the tissue inhibitors of metalloproteinases (TIMPs). Inhibition represents a major level of control of MMP activity. A detailed knowledge of the mechanisms controlling TIMP gene expression is therefore important. We have isolated a genomic clone of the human TIMP-1 gene. A 3 kbp XbaI fragment has been sequenced; this fragment contains 1718 bp 5' flanking sequences, exon 1, a 929 bp intron 1 and part of exon 2. Computer analysis reveals 10 consensus sequences for Sp1, six for activating protein 1 (AP-1), six for polyoma enhancer A3 (PEA3), 12 for AP-2 and five CCAAT boxes. The region hybridizing with a murine TIMP-1 promoter fragment has been subcloned and analysed further. RNase protection identifies six transcription start points, making exon 1 up to 48 bp in length. Transient transfection of promoter-chloramphenicol O-acetyltransferase reporter constructs into primary human connective tissue fibroblasts shows that a 904 bp fragment that hybridizes to a murine TIMP-1 promoter fragment contains a functional promoter. Constructs of -738/+95 to -194/+21 are inducible with serum or phorbol ester to a similar extent to the endogenous TIMP-1 gene. These results and further mapping with 5' deletion mutants from the -738/+95 region have demonstrated that an AP-1 site at -92/-86 is essential for basal expression of the gene. Point mutations within this region have further confirmed the role of this site, along with a more minor role for a neighbouring PEA3 site, in basal expression. Deletions from the 3' end also implicate a region across the exon 1/intron 1 boundary and especially +21 to +58 in basal expression. The +21/+58 region contains a putative binding site for the transcription factor leader-binding protein 1 (LBP-1). Gel-shift analysis shows that protein binds specifically to this region, but competition studies suggest that it is unlikely to be LBP-1.
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PMID:Transcriptional activity of the human tissue inhibitor of metalloproteinases 1 (TIMP-1) gene in fibroblasts involves elements in the promoter, exon 1 and intron 1. 918 25

Onconase is a cytotoxic ribonuclease with antitumor properties. A semisynthetic gene encoding the entire protein sequence was constructed by fusing oligonucleotides coding for the first 15 and last six of the 104 amino acid residues to a genomic clone that encoded the remaining amino acid residues. Additionally, the 15 N-terminal amino acid residues of onconase were replaced with the first 21 amino acid residues of the homologous human RNase, eosinophil-derived neurotoxin, EDN. Two versions of the hybrid EDN-onconase protein were cloned, expressed and purified. The chimera that contained a glycine in lieu of the aspartic acid present in native onconase (position 26 in the chimera) exhibited enzymatic activity more characteristic of EDN than native onconase and was considerably more active with respect to both RNase activity and cellular cytotoxicity than recombinant onconase. In contrast to native or recombinant onconase, the EDN chimera was recognized by anti-EDN polyclonal antibodies, demonstrating that the chimera also shared structural antigenic determinants to the human enzyme. These results demonstrate that a chimeric ribonuclease has cytotoxicity comparable to onconase in two out of four cell lines tested. The implications with regard to cancer therapy are presented.
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PMID:Expression and characterization of a cytotoxic human-frog chimeric ribonuclease: potential for cancer therapy. 919 72

Stromelysin-1, matrix metalloproteinase-3 (MMP-3), is an important endopeptidase selectively expressed by somatic cells in organ tissues. The renal tubulointerstitium, for example, comprises tubular epithelium and interstitial fibroblasts forming the principal mass of the kidney. We observed that mRNA encoding stromelysin-1 is detectable in murine renal fibroblasts, but not in proximal tubular epithelium. Transcripts measured by RNase protection assay in renal fibroblasts increase following exposure to phorbol ester, and thereafter, activated stromelysin-1 protein can be detected in culture media by Western blotting. A 6.4 Kb genomic clone containing the putative stromelysin-1 promoter was isolated and a relevant 2.1 Kb PstI restriction fragment including 2.1 Kb of the immediate 5'-flanking region was sequenced on both strands. Two transcriptional start sites were identified by primer extension; the major start site corresponded to a previously established position in the rat promoter, and a second undescribed minor transcriptional start site was located 16 bp upstream of the primary site. A HiNF-A chromatin-activating element at -106 bp was found in the early promoter region of pR336 and an active AP-1 site at -72 bp with an Ets/PEA-3 motif at -203 bp was suggested by transient transfection of luciferase minigenes into renal fibroblasts responsive to phorbol ester. This Ets element was identical to a site in the early promoter of the fibroblast-specific gene FSP1. A baseline enhancement in activity of pR336 in fibroblasts was further observed with the addition of 5' flanking sequence out to -1980 bp. This additional region of flanking sequence contains two modular regions: one of multiple PEA-3 elements between -684 bp and -1955 bp and a second region between -1929 bp and -1980 bps containing a second AP-1 site at -1929 bp, a MBF-1/ MEP-1 metal binding site, and a PPAR peroxisome proliferator element at -1950 bp. Our findings implicate a gene structure with expected activity in a mesenchymal phenotype. The PKC-dependent regulation of the stromelysin-1 gene supports the notion that it may be modulated during inflammation or tissue remodeling.
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PMID:Identification of promoter activity and differential expression of transcripts encoding the murine stromelysin-1 gene in renal cells. 921 54


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