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The coding sequence mediates induction of 5-lipoxygenase expression by Smads3/4

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 2006年第4期348卷 1403-1410页

作者： Seuter, Sabine Sorg, Bernd L. Steinhilber, Dieter Goethe Univ Frankfurt Inst Pharmaceut Chem ZAFES D-60438 Frankfurt Germany

5-Lipoxygenase (5-LO) expression is strongly induced by transforming growth factor-beta (TGF beta) and 1 alpha,25-dihydroxyvitamin D-3 in Mono Mac 6 cells. Since Smads have been described as downstream effectors of TGF beta, we have investigated the role of the TGF beta/Smad signalling system in the regulation of 5-LO gene expression. The rapid induction of 5-LO mRNA, determined with real-time quantitative RT-PCR, suggests that 5-LO is a primary TGF beta target gene. In reporter gene assays with plasmids containing the 5-LO promoter plus different parts of the gene, Smads3/4 mediate a prominent upregulation of reporter activity that strongly depends on the coding sequence and to a lesser extent on the 3'-UTR and introns J-M. Deletion studies revealed the most profound decrease of inducibility by Smads3/4 when exons 10-14 are deleted. sequence analysis and deletion studies indicate the existence of up to four Smad binding elements and at least one TGFP responsive element far downstream of the transcriptional start site. (c) 2006 Elsevier Inc. All rights reserved.

关键词： 5-lipoxygenase coding sequence transforming growth factor-beta Smad3/4 gene expression response element reporter gene assay

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REDEFINITION OF THE coding sequence OF THE MXI1 GENE AND IDENTIFICATION OF A POLYMORPHIC REPEAT IN THE 3' NONcoding REGION THAT ALLOWS THE DETECTION OF LOSS OF HETEROZYGOSITY OF CHROMOSOME 10Q25 IN GLIOBLASTOMAS

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HUMAN GENETICS 1995年第6期95卷 709-711页

作者： ALBAROSA, R DIDONATO, S FINOCCHIARO, G IST NAZL NEUROL C BESTA DIV BIOCHIM & GENETI-20133 MILANITALY

The MXI1 gene encodes a protein interacting with Max, a regulatory factor of the Myc oncogene, and is located on chromosome 10q25, a region showing frequent loss of heterozygosity in malignant gliomas. We have reassessed the coding sequence of MXI1 and found that, at the 3' end, the open reading frame is 28 codons shorter than previously described. We have also found an AAAAC polymorphic repeat (two alleles, 45% heterozygosity) in the 3' non-coding region of the gene. Six anaplastic astrocytomas and nine glioblastomas, the most malignant form of glioma, were informative for this polymorphism. Loss of heterozygosity was demonstrated in all glioblastomas, but not in the remaining tumors.

关键词： Malignant Glioma Chromosomes Lipoblastoma redefinition coding sequence Loss of Heterozygosity oncogene myc 10q25 heterozygosity

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A GERM LINE MUTATION WITHIN THE coding sequence FOR THE PUTATIVE 5-PHOSPHORIBOSYL-1-PYROPHOSPHATE BINDING-SITE OF HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE (HPRT) IN A LESCH-NYHAN PATIENT - MISSENSE MUTATIONS WITHIN A FUNCTIONALLY IMPORTANT REGION PROBABLY CAUSE DISEASE

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HUMAN GENETICS 1992年第4期90卷 385-388页

作者： FUJIMORI, S TAGAYA, T KAMATANI, N AKAOKA, I TOKYO WOMENS MED COLL INST RHEUMATOLTOKYO 162JAPAN

Lesch-Nyhan syndrome caused by a complete deficiency of hypoxanthine guanine phosphoribosyltransferase (HPRT) is the result of a heterogeneous group of germ line mutations. Identification of each mutant gene provides valuable information as to the type of mutation that occurs spontaneously. We report here a newly identified HPRT mutation in a Japanese patient with Lesch-Nyhan syndrome. This gene, designated HPRT Tokyo, had a single nucleotide change from G to A, as identified by sequencing cDNA amplified by the polymerase chain reaction. Allele specific oligonucleotide hybridization analysis using amplified genomic DNA showed that the mutant gene was transmitted from the maternal germ line. This mutation would lead to an amino acid substitution of Asp for Gly at the amino acid position 140 located within the putative 5-phosphoribosyl-1-pyrophosphate (PRPP) binding region. Missense mutations in human HPRT deficient patients thus far reported tend to accumulate in this functionally active region. However, a comparison of the data suggested that both missense and synonymous mutations can occur at any coding sequence of the human germ line HPRT gene, but that a limited percentage of all the missense mutations cause disease. The probability that a mutation will cause disease tends to be higher when the missense mutation is within a functionally important sequence.

关键词： Lesch-Nyhan Syndrome Germ-Line Mutation Mutation genomic DNA Missense Mutation maladjustment Hybridization analysis Amino Acid Substitution Hypoxanthine Phosphoribosyltransferase coding sequence germ line Mutant genes Data comparison Function

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Complete cDNA coding sequence of the HLA-DRB1*1405 allele

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DNA sequence 2002年第6期13卷 359-361页

作者： Kohsaka, H Nasu, K Matsushita, S Miyasaka, N Tokyo Med & Dent Univ Grad Sch Dept Bioregulatory Med & Rheumatol Bunkyo Ku Tokyo 1138519 Japan Saitama Med Sch Dept Allergy & Immunol Moroyama Saitama 3500495 Japan

Cloning report of complete coding region of HLA-DRB1*1405 has never appeared in the literature. We have isolated and sequenced it from a B cell line with a DRB1*1405/1502 genotype. The sequence information of this gene and previously published DRB1 genes for the other DR serotypes facilitated us to find that the cytoplasmic domain sequences of DRB1 genes fall into three groups. It is known that antigen presenting cells are differentially activated when products of different MHC class II genes are triggered. Functional analyses would discern if these allelic differences in the cytoplasmic domain are of functional significance.

关键词： cDNA coding sequence DRB1*1405 HLA nucleotide sequence

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Marfan syndrome caused by a mutation in FBN1 that gives rise to cryptic splicing and a 33 nucleotide insertion in the coding sequence

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HUMAN GENETICS 2001年第4期109卷 416-420页

作者： Hutchinson, S Wordsworth, BP Handford, PA Univ Oxford Dept Biochem Oxford OX1 3QU England Wellcome Trust Ctr Human Genet Headington OX3 7BN England

We have studied a patient with Marfan syndrome whose mutation was not detected by heteroduplex analysis. Primary cultured patient fibroblasts were metabolically labelled and found to secrete fibrillin-1 defectively when compared with an age-matched control. Sequencing of patient cDNA, isolated by reverse transcription-polymerase chain reaction of patient fibroblast RNA, detected a 33-bp insertion. The reading frame of the mutant allele was maintained and predicted the insertion of 11 amino acids at the beginning of calcium-binding epidermal growth factor-like domain 29. Direct sequencing of genomic DNA detected a heterozygous G(+1)--> A transversion in intron 46 of FBN1. The 11 amino acid insertion was the consequence of the usage of a cryptic splice site 33-bp downstream of the mutation. This is the first reported case of a splicing defect in FBN1 leading to the production of a full-length fibrillin-1 transcript containing a large amino acid insertion.

关键词： Alternative Splicing Exons Marfan Syndrome Microfilament Proteins Mutagenesis Insertional 交替剪接外显子马凡综合征微丝蛋白质类诱变插入 splicing defect Exons Marfan Syndrome coding sequence Mutation Microfilament Proteins Mutagenesis FBN1 gene Alternative Splicing Insertion Mutation

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Signatures of protein biophysics in coding sequence evolution

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CURRENT OPINION IN STRUCTURAL BIOLOGY 2010年第3期20卷 385-389页

作者： Wilke, Claus O. Drummond, D. Allan Univ Texas Austin Ctr Computat Biol & Bioinformat Inst Cell & Mol Biol Austin TX 78712 USA Univ Texas Austin Sect Integrat Biol Austin TX 78712 USA Harvard Univ FAS Ctr Syst Biol Boston MA 02115 USA

Since the early days of molecular evolution, the conventional wisdom has been that the evolution of protein-coding genes is primarily determined by functional constraints. Yet recent evidence indicates that the evolution of these genes is strongly shaped by the biophysical processes of protein synthesis, protein folding, and specific as well as nonspecific protein-protein interactions. Selection pressures related to these biophysical processes affect primarily the amino-acid sequence of genes, but they also leave their mark on synonymous sites at the nucleotide level. While evidence for specific selection pressures related to protein biophysics is strong, there is currently no unifying framework that integrates the various selection pressures on coding sequences and disentangles their relative importance.

关键词： Biophysical Processes Genes Biophysics coding sequence selection pressure signatures

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ASSIGNMENT OF THE RAT VARIABLE coding sequence (VCS) GENE FAMILY TO CHROMOSOME-14

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MAMMALIAN GENOME 1995年第2期6卷 153-154页

作者： ROSINSKICHUPIN, I KURAMOTO, T COURTY, Y ROUGEON, F SERIKAWA, T KYOTO UNIV FAC MEDINST LAB ANIMSAKYO KUKYOTO 60601JAPAN

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A transciption termination signal immediately precedes the coding sequence for the chloramphenicol-inducible plasmid gene cat-86

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MGG Molecular & General Genetics 1985年第1期199卷 70-75页

作者： Ambulos Jr., Nicholas P. Mongkolsuk, Skorn Lovett, Paul S. Department of Biological Sciences University of Maryland Baltimore County Catonsville 21228 MD United States

The plasmid gene cat-86 specifies chloramphenicol-inducible, chloramphenicol acetyltransferase in Bacillus subtilis. The inducible regulation is independent of the promoter that is used to activate cat-86 and is independent of the cat-86 coding sequence. We have proposed that the regulation of cat-86 results from the transcription of a pair of inverted-repeat sequences that immediately precede the coding sequence. These transcripts are predicted to sequester the cat-86 ribosome binding site in a stable RNA stemloop which, in theory, should block the ribosome binding site from pairing with 16S rRNA. Inducible expression of cat-86 may therefore result in part from regulation of the translation of cat-86 mRNA. However, chloramphenicol-induction correlates with increased levels of cat-86 mRNA and the RNA stem-loop preceding the cat-86 coding sequence structurally resembles a rho-independent transcription terminator. We have therefore tested the inverted-repeats as a potential site of transcription termination. Transcription studies performed in vitro using SP6 RNA polymerase and in vivo by S1 mapping demonstrate that a substantial fraction of the potential cat-86 transcripts terminate at a site immediately 3′ to the inverted-repeats. The results of the in vivo experiments suggest that the termination signal may be partially relieved by growth of cells in chloramphenicol. © 1985 Springer-Verlag.

关键词： RNA polymerase SP6 In vivo Binding Sites Pairing Inverted Repeat sequences stopping Standing Orders Genetic Transcription Plasmids Regulation (biology) Regulation Transcription coding sequence Independent signals

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Signatures of adaptive evolution within human non-coding sequence

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HUMAN MOLECULAR GENETICS 2006年第Sup2期15卷 R170-R175页

作者： Ponting, Chris P. Lunter, Gerton Univ Oxford MRC Dept Physiol Anat & Genet Funct Genet Unit Oxford OX1 3QX England

The human genome is often portrayed as consisting of three sequence types, each distinguished by their mode of evolution. Purifying selection is estimated to act on 2.5-5.0% of the genome, whereas virtually all remaining sequence is considered to have evolved neutrally and to be devoid of functionality. The third mode of evolution, positive selection of advantageous changes, is considered rare. Such instances have been inferred only for a handful of sites, and these lie almost exclusively within protein-coding genes. Nevertheless, the majority of positively selected sequence is expected to lie within the wealth of functional 'dark matter' present outside of the coding sequence. Here, we review the evolutionary evidence for the majority of human-conserved DNA lying outside of the protein-coding sequence. We argue that within this non-coding fraction lies at least 1 Mb of functional sequence that has accumulated many beneficial nucleotide replacements. Illuminating the functions of this adaptive dark matter will lead to a better understanding of the sequence changes that have shaped the innovative biology of our species.

关键词： .positive selection adaptive evolution neutrally purifying positively functional sequence Nevertheless coding sequence non-coding protein-coding Review Issue No

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NONSYNONYMOUS POLYMORPHISM IN THE coding sequence OF HUMAN 3-BETA HYDROXYSTEROID DEHYDROGENASE (HSD3B)

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NUCLEIC ACIDS RESEARCH 1991年第23期19卷 6667-6667页

作者： RUSSELL, AJ GAFFNEY, D EDWARDS, CRW SUTCLIFFE, RG GLASGOW ROYAL INFIRM INST BIOCHEMGLASGOW G4 0SFSCOTLAND WESTERN GEN HOSP DEPT MEDEDINBURGH EH4 5XUSCOTLAND

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