3' Untranslated Regions ; genetics ; 5' Untranslated Regions ; genetics ; Enterovirus B, Human ; genetics ; Genome, Viral ; genetics ; Humans ; Poly A ; genetics

SINE-VNTR-Alu (SVA) elements are present in hominoid primates and are divided into 6 subfamilies (SVA-A to SVA-F) and active in the human population. Using a bioinformatic tool, 22 SVA element-associated genes are identified in the human genome. In an analysis of genomic structure, SVA elements are detected in the 5' untranslated region (UTR) of HGSNAT (SVA-B), MRGPRX3 (SVA-D), HYAL1 (SVA-F), TCHH (SVA-F), and ATXN2L (SVA-F) genes, while some elements are observed in the 3'UTR of SPICE1 (SVA-B), TDRKH (SVA-C), GOSR1 (SVA-D), BBS5 (SVA-D), NEK5 (SVA-D), ABHD2 (SVA-F), C1QTNF7 (SVA-F), ORC6L (SVA-F), TMEM69 (SVA-F), and CCDC137 (SVA-F) genes. They could contribute to exon extension or supplying poly A signals. LEPR (SVA-C), ALOX5 (SVA-D), PDS5B (SVA-D), and ABCA10 (SVA-F) genes also showed alternative transcripts by SVA exonization events. Dominant expression of HYAL1_SVA appeared in lung tissues, while HYAL1_noSVA showed ubiquitous expression in various human tissues. Expression of both transcripts (TDRKH_SVA and TDRKH_noSVA) of the TDRKH gene appeared to be ubiquitous. Taken together, these data suggest that SVA elements cause transcript isoforms that contribute to modulation of gene regulation in various human tissues.
3' Untranslated Regions ; 5' Untranslated Regions ; Exons ; Gene Expression Profiling ; Genome, Human ; Genomics ; Humans ; Lung ; Organ Specificity ; Poly A ; Primates ; Protein Isoforms

BACKGROUND: TT virus (TTV) infection is highly prevalent in the general population and in the patients infected with hepatitis B virus (HBV) or hepatitis C vius (HCV). The aim of the present study was to assess the positive rates of TTV DNA using different PCR primer sets in healthy and HBV or HCV-infected individuals in Korea. METHODS: TTV DNA was investigated in serum samples of 69 healthy individuals and 59 HBV-infected and 34 HCV-infected individuals by nested PCR assays using primers from N22 region, 5'-untranslated region (UTR), and 3' UTR of viral genome. RESULTS: TTV DNA was detected in 43% of total study populations using N22 primers, in 69% using 5' UTR primers and, in 64% using 3' UTR primers. No significant difference was observed in the positive rates of TTV DNA between healthy and HBV or HCV- infected individuals. CONCLUSION: The PCR assays for TTV DNA using 5' UTR primers and 3' UTR primers exhibited higher positive rates than that of the assay using N22 primers without any significant difference between healthy and HBV or HCV-infected individuals.
3' Untranslated Regions ; 5' Untranslated Regions ; DNA ; Genome, Viral ; Hepatitis B virus ; Hepatitis B* ; Hepatitis C ; Hepatitis* ; Humans ; Korea ; Polymerase Chain Reaction* ; Torque teno virus*

OBJECTIVEClone of sucrose synthase of Dendribium officinale and expression analysis, to provide the theory basis for research the relationship between polysaccharide synthesis of D. officinale and sucrose synthase activity.

METHODAccording to homologous sequence of sucrose synthase gene on GenBank, application the technology of RT-PCR and RACE, clone the full length of D. officinale. Target gene amplified with T vector was transformed into competent E. coli. BL21, IPTG induced expression, SDS-PAGE analysis.

RESULTA full length cDNA encoding sucrose synthase was isolated from the D. officinale, named DOSS1, the GenBank accession number is HQ856835, the cDNA is 2781 bp in length containing an open reading frame of 2424 bp encoding 807 amino acids with a predicted molecular mass of 92.3 x 10(3), the deduced amino acid sequence of D. officinale sucrose synthase shares 95% identity with Mokara yellow (AF530568); shares 90% identity with Oncidium goldiana (AF530567); shares more than 80% with other monocotyledonous plants.

CONCLUSIONCloned the sucrose synthase gene and induced an obvious band successfully.

3' Untranslated Regions ; genetics ; 5' Untranslated Regions ; genetics ; Cloning, Molecular ; Dendrobium ; enzymology ; genetics ; metabolism ; Escherichia coli ; genetics ; Gene Expression Regulation, Plant ; Glucosyltransferases ; genetics ; metabolism ; Phylogeny ; Polysaccharides ; biosynthesis

Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most important animal pathogens in swine industry worldwide. In this study, we isolated the large-plaque forming variant virus designated PL97-1/LP1 from the parental strain PL97-1, the first Korean strain of PRRSV, isolated from the serum of an infected pig in 1997. We found that the 15411-nucleotide genome of PL97-1/LP1 consisted of a 189-nucleotide 5' untranslated region (UTR), a 15071-nucleotide protein-coding region, and a 151-nucleotide 3'UTR, followed by a poly (A) tail of about 50~60 nucleotides in size. The 5'-end of PL97-1/LP1 began with ATGACGTAT. Comparison of the PL97-1/LP1 genome with the 11 fully sequenced PRRSV genomes currently available revealed sequence similarity from 99.6~99.7% (the North American VR-2332 and two VR-2332-derived vaccine strains MLV RespPRRS/Repro and RespPRRS MLV) to 62.0% (the Dutch Lelystad strain). Phylogenetc analysis revealed that PL97-1/LP1 is most closely related to the North American genotype VR-2332, two VR-2332-derived vaccine strains, and Chinese BJ-4. It is distantly related to the European genotype Lelystad. The entire nucleotide sequence of PL97-1/LP1 was identical to that of the parental virus PL97-1 except for three silent nucleotide substitutions, one in ORF1a (U4230C), one in ORF1b (C10977U), and one in ORF5 (U13976A). This nucleotide sequence has been submitted to the GenBank database under the accession number AY612613.
3' Untranslated Regions ; 5' Untranslated Regions ; Animals ; Arterivirus ; Asian Continental Ancestry Group ; Base Sequence* ; Databases, Nucleic Acid ; Genome ; Genotype ; Humans ; Nucleotides ; Parents ; Porcine Reproductive and Respiratory Syndrome* ; Porcine respiratory and reproductive syndrome virus* ; RNA* ; Swine

MicroRNAs (miRNAs) play an important role in infection and replication of virus in host cells. To identify cellular miRNAs involved in the host response to enterovirus 71 (EV71) infection, we examined miRNAs effects on the replication of EV71 in rhabdomyosarcoma cells. We constructed target gene of miRNAs screening system. 3'untranslated region (UTR) dual luciferase reporter analysis was used to identify putative miRNA targets in the EV71 virus genome. First, 13 segments of EV71 virus genomes were inserted to the pMIR vector and the luciferase expression were assayed to identify the target gene of putative miRNA. The reporter gene expression of the cells transfected with the vector containing 5'-UTR was significantly downregulated. Then we screened the miRNAs that may target to 5'-UTR using online analysis programs. Furthermore, Western blotting and real-time PCR test were performed to investigate the effect of miRNAs on viral replication. The study showed that miR373 and miR542-5p could suppress the replication of EV71 virus through binding to the 5'-UTR gene. Cellular miRNAs could regulate the replication of EV71 virus in host cells, and our paper should report the role of miR373 and miR542-5p in this regulation for the first time. Our findings supported the notion that the cellular miRNAs might be essential in the host-pathogen interactions.
3' Untranslated Regions ; 5' Untranslated Regions ; Down-Regulation ; Enterovirus A, Human ; physiology ; Enterovirus Infections ; virology ; Gene Expression ; Host-Pathogen Interactions ; Humans ; MicroRNAs ; genetics ; Rhabdomyosarcoma ; virology ; Tumor Cells, Cultured ; Virus Replication

BACKGROUNDSeveral studies have evaluated the association between polymorphisms of thymidylate synthase (TS) and cancer risk in diverse populations but with conflicting results. By pooling the relatively small samples in each study, it is possible to evaluate the association using a meta-analysis.

METHODSA comprehensive search was conducted to identify all case-control studies on TS on a 28-bp tandem repeats in 5'untranslated region (5'UTR) and a 6-bp insertion (ins) and deletion (del) mutation in 3'UTR of the gene and cancer risk. Meta-analysis was conducted using a fixed and random effect model.

RESULTSOur meta-analysis on a total of 13 307 cancer cases and 18 226 control subjects from 37 published case-control studies showed no significant association between the risk of cancer and the 5'UTR 28-bp tandem repeats polymorphism (3R/3R vs. 2R/2R: OR = 1.06, 95%CI, 0.93 - 1.20) or the 3'UTR 6-bp ins/del polymorphism (del6/del6 vs. ins6/ins6: OR = 0.93, 95%CI, 0.81 - 1.08) with significant between-study heterogeneity. In the cancer type- and ethnic subgroup-stratification analyses, we did not find any association between TS polymorphisms and cancer risk either.

CONCLUSIONTS 5'UTR 28-bp tandem repeats and 3'UTR 6-bp ins/del polymorphisms may not be associated with cancer risk.

3' Untranslated Regions ; genetics ; 5' Untranslated Regions ; genetics ; Case-Control Studies ; Genetic Predisposition to Disease ; genetics ; Humans ; Neoplasms ; epidemiology ; genetics ; Polymorphism, Genetic ; genetics ; Tandem Repeat Sequences ; genetics ; Thymidylate Synthase ; genetics

OBJECTIVE: To investigate the genetic polymorphism in the 5' and 3' region of TPH2 gene of Northern Chinese Han population and to explore its application value in forensic medicine. METHODS: The sequence variants and the genetic polymorphisms of 6 SNP loci (rs4570625, rs11178997, rs11178998, rs41317118, rs17110747 and rs41317114) within a 905 bp 5' flanking region and a 1,104bp 3' flanking region of TPH2 gene were analyzed by DNA sequencing in a total of 244 unrelated healthy individuals in Northern Chinese Han population. The statistical analysis was carried out by Haploview v4.2 software. RESULTS: The genotypic distributions of the 6 SNP loci in the TPH2 gene were in accordance with Hardy-Weinberg equilibrium. One C/T variant in 92922 site was found. There was a high linkage disequilibrium among the 3 SNP loci (rs4570625, rs11178997 and rs11178998) in the 5' region and the 3 SNP loci (rs41317118, rs17110747 and rs41317114) in the 3' region of TPH2 gene, respectively. The parameters of population genetics of 6 SNP loci were obtained. CONCLUSION There are great polymorphisms in the 5' and 3' region of TPH2 gene in Northern Chinese Han population, which could be used as genetic indexes for association analysis of the related diseases, as well as for forensic individual identification and paternity testing.
3' Untranslated Regions ; 5' Untranslated Regions ; Asian People/genetics* ; China/ethnology* ; Forensic Genetics ; Gene Frequency ; Genetics, Population ; Genotype ; Humans ; Linkage Disequilibrium/genetics* ; Microsatellite Repeats ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Tryptophan Hydroxylase/genetics*

OBJECTIVES: Urocanase domain containing 1 (UROC1) has never been studied in prior studies on autism spectrum disorders (ASDs). UROC1 causes urocanic aciduria, one of the symptoms of which is mental retardation. The aim of this study was to investigate the association between the UROC1 gene and ASDs in a Korean population. METHODS: A total of 258 control and 214 patients with ASD were used as subjects of this study. SNPs selected from UROC1 were genotyped using Illumina Golden-Gate Genotyping assay with VeraCode(R) technology. Statistical analysis was performed using SAS and Plink software. RESULTS: We found no association of the 12 SNPs in the UROC1 gene with ASDs in a Korean population. CONCLUSION: Our study suggests that the 12 SNPs (11 SNPs and 1 SNP in the intron and 3'UTR region, respectively) in the UROC1 were not associated with ASDs in a Korean population. Further study on the exon region of UROC1 is needed.
3' Untranslated Regions ; Autistic Disorder ; Child ; Autism Spectrum Disorder ; Exons ; Humans ; Intellectual Disability ; Introns ; Phenothiazines ; Polymorphism, Single Nucleotide ; Urocanate Hydratase

BACKGROUND: The phagolysosomal function of alveolar macrophage against M. tuberculosis infection is influenced by Nramp1, which is encoded by the NRAMP1 gene. There are several genetic polymorphisms in NRAMP1, and these polymorphisms affect the innate host resistance through the defect in production and function of Nramp1. To investigate this relationship, we determined the NRAMP1 genetic polymorphism in patients with primary tuberculous pleurisy was determined. METHODS : 56 Fifty-six primary tuberculous pleurisy patient (,) who were diagnosed by pleural biopsy(,) were designated to the pleurisy group and 45 healthy adults were designated to the healthy control group. 3 Three genetic polymorphisms of NRAMP1 (,) such as a single point mutation in intron 4(469+14G/C, INT4), a nonconservative single-base substitution at codon 543 that changes aspartic acid to asparagine(D543N) and a TGTG deletion in the 3' untranslated region(1729+55del4, 3'UTR)(,) were determined. Polymerase chain reaction(PCR) and polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) were used. RESULTS: The frequencies of mutanat mutant genotypes of INT4 and 3'UTR were significantly high in pleurisy group(p=0.001, p=0.023). But the frequencies of D543N were not significantly different between the both two groups(p=0.079). Odds The odds ratios(,) which are a comparison with wild genotype for determining mutant genotypes(,) were 8.022(95% confidence interval=2.422 ~26.572) for INT4 and 5.733(95% confidence interval=1.137 ~28.916) for 3'UTR which were ;these were statistically significant. But the odds ratio for D543N was not significant. In the combined analysis of the INT4 and 3'UTR polymorphisms, as compared with GG/++ homozygotes, (delete) the odds ratios were 6.000(95% confidence interval=1.461 ~ 24.640) for GC/++ genotype and 14.000(95% confidence interval=1.610 ~121.754) for GC/+del when compared with GG/++ homozygotes which ;these were statisticallysignificant. CONCLUSION: Among the NRAMP1 genetic polymorphisms, a single point mutation in intron 4(469+14G/C, INT4) and a TGTG deletion in the 3' untranslated region(1729+55del4, 3'UTR) were closely related to the primary tuberculous pleurisy.
3' Untranslated Regions ; Adult ; Aspartic Acid ; Codon ; Genotype ; Homozygote ; Humans ; Introns ; Macrophages, Alveolar ; Odds Ratio ; Pleurisy ; Point Mutation ; Polymorphism, Genetic* ; Tuberculosis ; Tuberculosis, Pleural*