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PubMed1986

Complete nucleotide sequence of the gene for human interleukin 1 alpha.

The chromosomal gene for human interleukin 1 alpha (IL-1 alpha) was isolated from a human genomic DNA library by using as a probe cloned human IL-1 alpha cDNA. Complete nucleotide sequence of about 12 kilobase pairs (kbp) long was determined and the structure and organization of this gene were elucidated. This gene contains seven exons and six introns. The first exon encodes the 5'-untranslated region. Most of the prepeptide portion of the precursor polypeptide is encoded by the next three exons, and the mature form of IL-1 alpha is encoded by the remaining three exons. The last exon also encodes the intronless 3'-untranslated region. The fourth intron as well as both 5'- and 3'-flanking regions contains the sequence of an Alu family member. In the middle part of the last intron, a 46-bp sequence with a unique structure is repeated five times in a head to tail manner. These repeats are flanked by the regions containing alternative purine and pyrimidine tracts. In the 5'-flanking region, immediately upstream of the putative TATA box, the 16-bp sequence highly homologous to the binding site of the adenovirus 2 major late promoter transcription factor is identified. The nucleotide sequence reported here showed only one nucleotide substitution in the 3'-untranslated exon in comparison with the nucleotide sequence of the cDNA from HL-60, a promyelocytic leukemia cell line, previously cloned and sequenced in our laboratories.

Base Composition↗
PubMed1986

Insertion and/or deletion of many repeated DNA sequences in human and higher ape evolution.

The total numbers of copies of two repeat families, L1 (Kpn I) and Alu, have been measured in the DNA of four higher apes by an accurate titration method. The number of members of the Alu family repeats in the four genomes are as follows: human, 910,000; chimpanzee, 330,000; gorilla, 410,000; orangutan, 580,000. For the Kpn I family (3'-ward higher frequency region) the number of copies in these genomes are as follows: human, 107,000; chimpanzee, 51,000; gorilla, 64,000; orangutan, 84,000. Thermal stability measurements show that, although the families of repeats are moderately divergent in sequence, little net sequence change has occurred during the evolution of the higher apes. Most or all of the members of these families of repeats are interspersed throughout the genome. Therefore, a large number of events of insertion and/or deletion of these DNA sequences has occurred during higher primate evolution.

Animals↗
PubMed1990

Assembly of the Alu domain of the signal recognition particle (SRP): dimerization of the two protein components is required for efficient binding to SRP RNA.

The signal recognition particle (SRP), a cytoplasmic ribonucleoprotein, plays an essential role in targeting secretory proteins to the rough endoplasmic reticulum membrane. In addition to the targeting function, SRP contains an elongation arrest or pausing function. This function is carried out by the Alu domain, which consists of two proteins, SRP9 and SRP14, and the portion of SRP (7SL) RNA which is homologous to the Alu family of repetitive sequences. To study the assembly pathway of the components in the Alu domain, we have isolated a cDNA clone of SRP9, in addition to a previously obtained cDNA clone of SRP14. We show that neither SRP9 nor SRP14 alone interacts specifically with SRP RNA. Rather, the presence of both proteins is required for the formation of a stable RNA-protein complex. Furthermore, heterodimerization of SRP9 and SRP14 occurs in the absence of SRP RNA. Since a partially reconstituted SRP lacking SRP9 and SRP14 [SRP(-9/14)] is deficient in the elongation arrest function, it follows from our results that both proteins are required to assemble a functional domain. In addition, SRP9 and SRP14 synthesized in vitro from synthetic mRNAs derived from their cDNA clones restore elongation arrest activity to SRP(-9/14).

Amino Acid Sequence↗
PubMed2001

Angiotensin-converting enzyme activity and the ACE Alu polymorphism in autosomal dominant polycystic kidney disease.

BACKGROUND: Previous studies concerning Alu I/D polymorphism in the ACE gene and ADPKD severity have used the Alu genotypes as a representative of the true biological variable, namely ACE activity. However, wide individual and ethnic differences in the proportion of variance in ACE activity explained by the I/D genotype may have confounded these studies. This investigation examines the association between ADPKD severity and ACE in terms of plasma enzyme activity and I/D genotypes in individuals from three different countries. METHODS: Blood samples were collected from 307 ADPKD patients (116 Australian, 124 Bulgarian and 67 Polish) for determination of ACE activity levels and I/D genotypes. Chronic renal failure (CRF) was present in 117 patients and end-stage renal failure (ESRF) in 68 patients. RESULTS: ACE activity was related to the I/D genotype, showing a dosage effect of the D allele (P=0.006). The proportion of variance due to the Alu polymorphism was 14%. No difference in ACE activity and I/D genotype distribution was found between patients with CRF versus normal renal function (P=0.494; P=0.576) or between those with ESRF versus those without ESRF (P=0.872; P=0.825). No effect of the I/D genotype on age at development and progression to renal failure (CRF; ESRF) was detected in the overall group, and in subgroups based on ethnic origin, linkage status and sex. CONCLUSION: ACE is not likely to play a role as a determinant of ADPKD phenotype severity.

Adolescent↗
PubMed1993

Transport of 5-aminolevulinic acid by the dipeptide permease in Salmonella typhimurium.

In a previous search for mutants of Salmonella typhimurium that are defective in heme synthesis, one class that is apparently defective in 5-aminolevulinic acid (ALA) uptake (alu) was found. Here, I describe the characterization of these mutations. The mutations all map to a single locus near 77.5 min on the genetic map, which is transcribed counterclockwise. Nutritional tests, genetic and physical mapping, and partial DNA sequence analysis revealed that alu mutants are defective in a periplasmic binding protein-dependent permease that also transports dipeptides, encoded by the dpp operon. The uptake of labeled ALA is defective in dpp mutants and is markedly increased in a strain that has elevated transcription of the dpp locus. Unlabeled L-leucyl-glycine competes with labeled ALA for uptake. In a strain carrying both a dpp-lac operon fusion and a functional copy of the dpp locus, the expression of beta-galactosidase is not induced by ALA, nor, in a hemL mutant, does expression of dpp change substantially during starvation for ALA. The dipeptide permease displays a relaxed substrate specificity that allows transport of the important nonpeptide nutrient ALA, whose structure is closely related to that of glycyl-glycine.

Aminolevulinic Acid↗
PubMed1986

Analysis of six distinct integrated hepatitis B virus sequences cloned from the cellular DNA of a human hepatocellular carcinoma.

Six distinct hepatitis B virus (HBV) integrations and the flanking cellular sequences were cloned from a hepatoma DNA preparation. None of the cloned fragments retains the entire HBV sequences but the surface antigen (HBsAg) gene and the HBV enhancer are retained in three of the six clones. The other three clones carry only short and possibly highly rearranged HBV genomic sequences and seem to contain some GC-rich clusters. Members of the repetitive Alu family are also found in the vicinity of five of the six integration regions which may have contributed to genome instability. In these six clones, the preferred integration sites are shown to lie within the single-strand region of the HBV genome. None of the clones carries in the flanking cellular sequences any of the 17 oncogenes tested, although the possibility still exists that an oncogene may be found on the side of the genome which has not been cloned. This work thus paves the way for detailed sequence analysis of virus-host junctions, for transfection studies of the HBV integration events, and for a search of genes in the flanking cellular sequences which may have been activated by the retained HBV enhancer using the clones described.

Base Sequence↗
PubMed1999

Quantitative analysis of survival motor neuron copies: identification of subtle SMN1 mutations in patients with spinal muscular atrophy, genotype-phenotype correlation, and implications for genetic counseling.

Problems with diagnosis and genetic counseling occur for patients with autosomal recessive proximal spinal muscular atrophy (SMA) who do not show the most common mutation: homozygous absence of at least exon 7 of the telomeric survival motor neuron gene (SMN1). Here we present molecular genetic data for 42 independent nondeleted SMA patients. A nonradioactive quantitative PCR test showed one SMN1 copy in 19 patients (45%). By sequencing cloned reverse-transcription (RT) PCR products or genomic fragments of SMN1, we identified nine different mutations in 18 of the 19 patients, six described for the first time: three missense mutations (Y272C, T274I, S262I), three frameshift mutations in exons 2a, 2b, and 4 (124insT, 241-242ins4, 591delA), one nonsense mutation in exon 1 (Q15X), one Alu-mediated deletion from intron 4 to intron 6, and one donor splice site mutation in intron 7 (c.922+6T-->G). The most frequent mutation, Y272C, was found in 6 (33%) of 18 patients. Each intragenic mutation found in at least two patients occurred on the same haplotype background, indicating founder mutations. Genotype-phenotype correlation allowed inference of the effect of each mutation on the function of the SMN1 protein and the role of the SMN2 copy number in modulating the SMA phenotype. In 14 of 23 SMA patients with two SMN1 copies, at least one intact SMN1 copy was sequenced, which excludes a 5q-SMA and suggests the existence of further gene(s) responsible for approximately 4%-5% of phenotypes indistinguishable from SMA. We determined the validity of the test, and we discuss its practical implications and limitations.

Cyclic AMP Response Element-Binding Protein↗
PubMed1994

The association between salt sensitivity of blood pressure and some polymorphic factors.

OBJECTIVE: To examine the association in Japanese subjects between the salt sensitivity of blood pressure and polymorphic factors. DESIGN AND METHODS: One hundred and four patients with essential hypertension were classified as salt-sensitive or non-salt-sensitive depending on their blood pressure response to salt restriction. An insertion/deletion polymorphism of the angiotensin converting enzyme (ACE) gene was examined by detecting an alu sequence in intron 16. The ACE genotype was classified as II, ID or DD depending on whether each allele had this sequence. The haptoglobin phenotype was determined by the starch-gel electrophoresis method, and was classified as three phenotypes, 1-1, 2-1 or 2-2 form. RESULTS: The response of plasma renin activity to salt restriction was greater in patients with the DD form than in those with other forms, although there were no significant differences in the ratio salt-sensitive: non-salt-sensitive patients among the three ACE genotype groups. However, the ratio was significantly larger in the haptoglobin 2-1 phenotype group than in the 2-2 group. CONCLUSIONS: The salt sensitivity of blood pressure was associated with the haptoglobin phenotype, but was not associated with the ACE genotype. However, the response of plasma renin activity to salt restriction was different according to the ACE genotype.

Adult↗
PubMed1995

Human CC10 gene expression in airway epithelium and subchromosomal locus suggest linkage to airway disease.

The CC10 gene encodes the Clara cell 10-kDa protein, which is expressed in airway epithelial cells. Quantification of CC10 gene expression in freshly isolated human proximal airway epithelial cells demonstrated very high mRNA levels, approximately fivefold greater than gamma-actin mRNA, and in situ hybridization localized CC10 mRNA to nonciliated airway epithelial cells. Sequence analysis demonstrated that the human CC10 gene is comprised of three short exons separated by a long first and short second intron, and with a 5' flanking region typical of a regulated gene. Three Alu repeats were observed in intron 1 and one in intron 2. Two polymorphic regions within the introns were identified. First, a microsatellite was localized 5' to the third Alu repeat in intron 1 with a variable number of 4- and 5-base pair (bp) repeats and a heterozygosity of 0.71. Second, in 3% of the 168 chromosomes examined, there was the insertion of a human-specific Alu repeat in intron 2, 45 bp 3' to the exon 2-intron junction. In three Centre d'Etude du Polymorphisme Humain families, meiotic breakpoint analysis using these two polymorphic loci localized the CC10 gene to 11 p12-q13 between markers D11S16 and D11S97, a region recently linked to atopy and to the beta-subunit of the high-affinity immunoglobulin E receptor. The observations in the present study of high-level expression of the CC10 gene in the epithelium of conducting airways and a subchromosomal localization of the gene to a region potentially linked to inflammatory airway disease, together with the reported anti-inflammatory and immune-modulating properties of the protein, suggest the CC10 gene product may be important in modulating inflammation within the airways. If so, the highly heterozygous microsatellite described in the present study should facilitate analysis of a possible linkage of the CC10 gene with an inherited susceptibility to asthma.

Asthma↗
PubMed2004

Rhesus macaque class I duplicon structures, organization, and evolution within the alpha block of the major histocompatibility complex.

The alpha block of the human and chimpanzee major histocompatibility complex (MHC) class I genomic region contains 10 to 11 duplicated MHC class I genes, including the HLA/Patr-A, -G, and -F genes. In comparison, the alpha block of the rhesus macaque (Macaca mulatta, Mamu) has an additional 20 MHC class I genes within this orthologous region. The present study describes the identification and analysis of the duplicated segmental genomic structures (duplicons) and genomic markers within the alpha block of the rhesus macaque and their use to reconstruct the duplication history of the genes within this region. A variety of MHC class I genes, pseudogenes, transposons, and retrotransposons, such as Alu and ERV16, were used to categorize the 28 duplicons into four distinct structural categories. The phylogenetic relationship of MHC class I genes, Alu, and LTR16B sequences within the duplicons was examined by use of the Neighbor-Joining (NJ) method. Two single-duplicon tandem duplications, two polyduplicon tandem duplications with an accompanying inversion product per duplication, eight polyduplicon tandem duplications steps, 12 deletions, and at least two recombinations were reconstructed to explain the highly complex organization and evolution of the 28 duplicons (nine inversions) within the Mamu alpha block. On the basis of the phylogenetic evidence and the reconstructed tandem duplication history of the 28 duplicons, the Mamu/Patr/HLA-F ortholog was the first MHC class I gene to have been fixed without further duplication within the alpha block of primates. Assuming that the rhesus macaque and the chimpanzee/human lineages had started with the same number of MHC class I duplicons at the time of their divergence approximately 24 to 31 MYA, then the number of genes within the alpha block have been duplicated at an approximately three times greater rate in the rhesus macaque than in either the human or chimpanzee.

Animals↗
PubMed2005

Large scaled analysis of hepatitis B virus (HBV) DNA integration in HBV related hepatocellular carcinomas.

BACKGROUND AND AIMS: Hepatitis B virus (HBV) DNA integration into or close to cellular genes is frequently detected in HBV positive hepatocellular carcinomas (HCC). We have previously shown that viral integration can lead to aberrant target gene transcription. In this study, we attempted to investigate common pathways to hepatocarcinogenesis. METHODS: By using a modified Alu-polymerase chain reaction approach, we analysed 50 HCCs along with 10 previously published cases. RESULTS: Sixty eight cellular flanking sequences (seven repetitive or unidentified sequences, 42 cellular genes, and 19 sequences potentially coding for unknown proteins) were obtained. Fifteen cancer related genes and 25 cellular genes were identified. HBV integration recurrently targeted the human telomerase reverse transcriptase gene (three cases) and genes belonging to distinct pathways: calcium signalling related genes, 60s ribosomal protein encoding genes, and platelet derived growth factor and mixed lineage leukaemia encoding genes. Two tumour suppressor genes and five genes involved in the control of apoptosis were also found at the integration site. The viral insertion site was distributed over all chromosomes except 13, X, and Y. CONCLUSIONS: In 61/68 (89.7%) cases, HBV DNA was integrated into cellular genes potentially providing cell growth advantage. Identification of recurrent viral integration sites into genes of the same family allows recognition of common cell signalling pathways activated in hepatocarcinogenesis.

Adolescent↗
PubMed1997

Sequencing of the cholesteryl ester transfer protein 5' regulatory region using artificial transposons.

We have isolated and sequenced genomic clones encompassing more than 5 kb of the 5' flanking region of the cholesteryl ester transfer protein gene. This region contains multiple Alu repeats, a Mermaid repeat, and an extensive GA repeat, which made sequencing exceedingly difficult. To circumvent the problems that these repeats posed to traditional sequencing methodologies, we employed a novel transposon-facilitated technique, which greatly simplified sequencing of regions that had been difficult to accomplish otherwise. We utilized the artificial transposon, AT-2, a Bluescript derivative containing the dhfr gene and unique primer sites at both ends of the insertion DNA. Integration of the transposon occurred efficiently and covered the entire region of interest. Analysis of the sequence indicates a number of potential regulatory factor binding sites upstream of the previously characterized minimal promoter. The 5.7-kb regulatory region confers significant transcriptional activation in a conditionally transformed mouse hepatocyte line as compared to a minimal 137-bp promoter fragment. In addition, a tetranucleotide repeat of variable length that may provide a useful genetic marker has been identified 2 kb upstream of the CETP transcriptional start site.

Animals↗
PubMed2001

4G/5G polymorphism of the plasminogen activator inhibitor-1 gene and insertion/deletion polymorphism of the tissue-type plasminogen activator gene in atherothrombotic stroke.

BACKGROUND AND PURPOSE: Decreased fibrinolytic capacity due to increased plasminogen activator inhibitor-1 (PAI-1) activity and decreased tissue-type plasminogen activator (t-PA) activity has been associated with hypertension or atherothrombotic disorders. The aims of this study were to observe associations of the genetic polymorphism for PAI-1 and t-PA with hypertension and atherothrombotic stroke, and to elucidate whether impaired fibrinolytic activity in atherothrombotic stroke was related to atherothrombosis per se or to other risk factors such as hypertension. METHODS: Patients with atherothrombotic stroke (n = 60), hypertension (n = 100), and control subjects (n = 100) were enrolled. We genotyped all subjects for 4G/5G polymorphism in the promoter region of the PAI-1 gene and the Alu-repeat insertion/deletion (I/D) polymorphism in intron h of the t-PA gene by polymerase chain reaction and endonuclease digestion. RESULTS: The frequency of the 4G/4G genotype of PAI-1 was significantly higher in the atherothrombotic stroke patients than the control subjects (41.7 versus 21%; p = 0.005), but not in the hypertensive subjects. There was a significant association between 4G/4G genotype of PAI-1 and atherothrombotic stroke (adjusted odds ratio = 3.11, 95% confidence interval 1.18-8.15), adjusting for age, sex, total cholesterol, low-density lipoprotein, triglyceride, and body mass index. However, the number of the I/I genotype of t-PA in the atherothrombotic stroke or hypertensive patients was virtually identical to the control subjects. CONCLUSION: Our results suggest that the 4G/4G genotype of the PAI-1 gene is significantly associated with an increased risk of atherothrombotic stroke. This finding also supports that impaired fibrinolytic activity in atherothrombotic stroke is related to atherothrombosis per se, but not to hypertension, one of the most important risk factors of atherothrombotic stroke.

Adult↗
PubMed1997

Tissue plasminogen activator and risk of myocardial infarction. The Rotterdam Study.

BACKGROUND: Impaired fibrinolytic capacity, as assessed by euglobulin clot lysis time or plasma concentration of fibrinolytic parameters, has been associated with an increased risk of myocardial infarction (MI). We studied the association of a polymorphism in the gene for TPA and of plasma concentrations of TPA (antigen and activity) with the prevalence of MI. METHODS AND RESULTS: A case-control study was performed. Subjects with a history of MI (n = 121) and controls (n = 250) were drawn from the Rotterdam Study, a population-based cohort study of 7983 subjects > or = 55 years old. We determined TPA antigen and activity in plasma and genotyped all subjects for the Alu repeat insertion/deletion polymorphism in intron h in the TPA gene. Homozygosity for the insertion was associated with twice as many cases of MI as was homozygosity for the deletion (odds ratio, 2.24; 95% CI, 1.11-4.50). TPA antigen was positively associated with the risk of MI; compared with that in the lowest quartile, the relative risks (odds ratio) in the second, third, and upper quartiles were 1.7 (CI, 0.9-3.3), 2.3 (1.2-4.4), and 2.0 (1.0-3.8), respectively. When adjusted for body mass index, HDL and total cholesterol, systolic and diastolic blood pressures, and current smoking, the risk associated with TPA antigen concentration was attenuated. Increased concentrations of TPA activity tended to be associated with an increased risk of MI. CONCLUSIONS: This study provides evidence for an independent association of the insertion allele of the insertion/deletion polymorphism in the TPA gene with nonfatal MI. Increased TPA antigen is associated with an increased risk of MI; however, this association was not independent of cardiovascular disease risk factors.

Aged↗
PubMed2006

Association of polymorphisms in the Angiotensin-converting enzyme gene with Alzheimer disease in an Israeli Arab community.

Several lines of evidence support for a role of angiotensin converting enzyme (ACE) in Alzheimer disease (AD). Most genetic studies have focused on an Alu insertion/deletion (I/D) polymorphism in the ACE gene (DCP1) and have yielded conflicting results. We evaluated the association between 15 single-nucleotide polymorphisms (SNPs) in DCP1, including the I/D variant, and AD in a sample of 92 patients with AD and 166 nondemented controls from an inbred Israeli Arab community. Although there was no evidence for association between AD and I/D, we observed significant association with SNPs rs4343 (P = .00001) and rs4351 (P = .01). Haplotype analysis revealed remarkably significant evidence of association with the SNP combination rs4343 and rs4351 (global P = 7.5 x 10(-7)). Individuals possessing the haplotype "GA" (frequency 0.21 in cases and 0.01 in controls) derived from these SNPs had a 45-fold increased risk of developing AD (95% CI 6.0-343.2) compared with those possessing any of the other three haplotypes. Longer range haplotypes including I/D were even more significant (lowest global P = 1.1 x 10(-12)), but the only consistently associated alleles were in rs4343 and rs4351. These results suggest that a variant in close proximity to rs4343 and rs4351 modulates susceptibility to AD in this community.

Aged↗
PubMed1994

Retrotransposition of a plant SINE into the wx locus during evolution of rice.

A new type of plant retroposon, p-SINE1, has been found in the wx locus of rice (Oryza sativa). It has some structural characteristics similar to those of mammalian SINEs, such as members of the Alu or B1 family. In order to estimate the time at which the integration of p-SINE1 into a single locus occurred during rice evolution, we examined the distribution of two members of p-SINE1 in several species of the Oryza genus by the polymerase chain reaction (PCR). We found that one member of p-SINE1 (p-SINE1-r2) in the ninth intron of the wx+ gene was present only in two closely related species, O. sativa and O. rufipogon, and was not present in the other species carrying the AA genome within the Oryza genus. This result indicates that p-SINE1-r2 was integrated into the wx locus after O. sativa and O. rufipogon had diverged from other species with the AA genome. In contrast to p-SINE1-r2, another member (p-SINE1-r1) located in the untranslated 5'-region of the wx+ gene was present not only in all species with the AA genome but also in species with a different genome (CCDD). This result suggests that p-SINE1-r1 was integrated into that position prior to the genomic divergence. Thus, it appears that each member of p-SINE1 was retroposed at a specific site at a different time during rice evolution.

Base Sequence↗
PubMed1998

Existence of a bovine LINE repetitive insert that appears in the cDNA of bovine protein BCNT in ruminant, but not in human, genomes.

A novel protein, BCNT, originally isolated from bovine brain and named after Bucentaur, contains an internal portion that is translated from part of bovine LINE repetitive sequence (Bov-B LINE). Human cDNA highly homologous to the bovine bcnt (bbcnt) cDNA has been isolated but does not contain a sequence similar to the Bov-B LINE insert (Nobukuni, T., Kobayashi, M., Omori, A., Ichinose, S., Iwanaga, T., Takahashi, I., Hashimoto, K., Hattori, S., Kaibuchi, K., Miyata, Y., Masui, T., Iwashita, S., 1997. An Alu-linked repetitive sequence corresponding to 280 amino acids is expressed in a novel bovine protein, but not in its human homologue. J. Biol. Chem. 272, 2801-2807). In this study, we conducted a polymerase chain reaction analysis to investigate whether such a Bov-B LINE insert is present in bcnt orthologs in other animals and in the genomic sequence of the human BCNT (hBCNT) gene. The results indicate that the Bov-B LINE insert is present in the genomic sequences of bcnt orthologs from sheep, goats, axis deer, and mouse deer (chevrotain), that is in Ruminantia, but not in pigs or human. Analysis of the bbcnt genomic sequence around the Bov-B LINE insert revealed a large part of the inserted Bov-B LINE sequence to be included in an exon; this is followed by a 54-nucleotide sequence that is highly homologous to Bov-B LINE in the 3'-side intron. The hBCNT gene was isolated and found to consist of seven exons and six introns, among which the intron corresponding to the Bov-B LINE insertion site in the bbcnt genome is 16.5kb in length with no sequence similar to Bov-B LINE. Based on these results, it seems likely that the Bov-B LINE insert is derived from a long Bov-B LINE repetitive sequence transposed to an ancestral bcnt gene in Ruminantia and reformed as a new exon through new splicing sites in the transposed sequence.

Amino Acid Sequence↗