• Title/Summary/Keyword: Intron

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Promyelocytic Leukemia (PML) Gene Mutations may not Contribute to Gastric Adenocarcinoma Development

  • Imani-Saber, Zeinab;Yousefi-Razin, Ehsan;Javaheri, Mona;Mirfakhraie, Reza;Motalleb, Gholamreza;Ghafouri-Fard, Soudeh
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.8
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    • pp.3523-3525
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    • 2015
  • Gastric cancer is the second most common cause of cancer death worldwide. Environmental as well as genetic factors have been shown to be involved in its genesis. Among genetic factors, loss of function of a tumor suppressive gene named promyelocytic leukemia (PML) has been demonstrated in gastric cancer. In order to cast light in the mechanism by which PML protein is under-expressed in gastric cancer cells, we analyzed all exons and intron-exon boundaries of PML gene in 50 formalin-fixed paraffin-embedded tissue blocks from gastric carcinoma tumors by means of PCR-SSCP and CSGE, with direct sequencing of abnormally shifted bands. We found a novel sequence variant of unknown significance localized in intron 5 in 3 samples (c.1398+84delA). We did not detect any deleterious mutations of the PML gene. This study shows that PML mutations may not contribute to gastric adenocarcinoma development. Post-translational modifications or protein degradation might be mechanisms by which PML is not expressed in gastric tumors.

Tail-to-Head Tandem Duplication and Simple Repetitive Sequences of the Cytoplasmic Actin Genes in Greenling Hexagrammos otakii (Teleostei; Scorpaeniformes)

  • Lee, Sang-Yoon;Kim, Dong-Soo;Nam, Yoon-Kwon
    • Fisheries and Aquatic Sciences
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    • v.14 no.4
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    • pp.303-310
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    • 2011
  • We characterized a cytoplasmic actin gene locus in greenling Hexagrammos otakii (Scorpaeniformes). Genomic clones isolated from the greenling DNA library contained two homologous cytoplasmic actin gene copies (HObact2.1 and HObact2.2) in a tail-to-head orientation. Their gene structure is characterized by six translated exons and one non-translated exon. Exon-intron organization and the nucleotide sequences of the two actin gene isoforms are very similar. However, only the HObact2.1 isoform contains microsatellite-like, dinucleotide repeats in the 5'-flanking region (named HOms2002) and intron 1 following the non-translated exon 1 (named HOms769). One microsatellite locus (HOms769) was highly polymorphic while the other (HOms2002) was not. Based on bioinformatic analysis, different transcription factor binding motifs are related to stress and immune responses in the two actin isoforms. Semiquantitative and real-time reverse transcription-PCR assays showed that both isoform transcripts were detectable ubiquitously in all the tissues examined. However, the basal expression levels of each isoform varied across tissues. Overall, the two isoforms showed a similar, but not identical, expression pattern. Our data suggest that the cytoplasmic actin genes may be the result of a recent duplication event in the greenling genome, which has not experienced significant subfunctionalization in their housekeeping roles.

Association of genotype of POU1F1 intron 1 with carcass characteristics in crossbred pigs

  • Kim, Gye-Woong;Yoo, Jae-Young;Kim, Hack-Youn
    • Journal of Animal Science and Technology
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    • v.56 no.7
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    • pp.25.1-25.6
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    • 2014
  • This study was carried out to investigate the association of POU1F1 (POU domain, class 1, transcription factor 1, Pit1, renamed as POU1F1) gene with backfat thickness (mm), carcass weight (kg), pH, and color values ($L^*$, $a^*$, $b^*$) in crossbred pigs (Landrace ${\times}$ Yorkshire ${\times}$ Duroc). Frequency of the AA genotype indel was at the highest level (66.67%). Frequency of A allele (0.81) was higher than that of b allele (0.19). This population followed Hardy-Weinberg equilibrium. Carcass weights and $a^*$ values of the three genotypes were all significantly different (p < 0.05), respectively. However, backfat thickness, $L^*$, $b^*$, visual color, and pH of the three genotypes were not significantly different (p > 0.05). Visual color was negatively correlated with $L^*$ (r = -0.521) and $b^*$ (r = -0.390) values, $L^*$ value was correlated with $b^*$ (r = 0.419) value, and $a^*$ value was positively correlated with $b^*$ (r = 0.612) value. These results indicate that the POU1F1 gene affected carcass weight and meat redness.

Identification of Novel Single Nucleotide Polymorphisms on ADSL Gene Using Economic Traits in Korean Native Chicken (한국재래닭의 ADSL 유전자 내 단일염기변이를 이용한 경제형질과의 연관성 분석)

  • Lee, J.A.;Jeon, S.A.;Oh, J.D.;Park, K.D.;Choi, K.D.;Jeon, G.J.;Lee, H.K.;Kong, H.S.
    • Korean Journal of Poultry Science
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    • v.36 no.3
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    • pp.207-213
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    • 2009
  • Adenylosuccinate lyase (ADSL) deficiency is a disease of purine metabolism which affects patients both biochemicall and behaviorally. An obstacle of this purine nucleotide cycle(PNC) can be caused brain functional disorder and growth disorder. So ADSL deficiency, which is associated with sever mental retardation, autistic features and energy metabolism. This study was performed to identify SNP on ADSL gene in chicken. The nucleotides were observed as T to C ($7724^{th}$ nucleotide), C to T ($7732^{nd}$ nucleotide), G to T ($10108^{th}$ nucleotide), A to T ($10356^{th}$ nucleotide), G to A($10375^{th}$ nucleotide), A to C ($10402^{nd}$ nucleotide), A to T ($12716^{th}$ nucleotide), T to A ($12717^{th}$ nucleotide), C to T ($15491^{st}$ nucleotide), C to T ($15542^{nd}$ nucleotide) and C to T ($15550^{th}$ nucleotide). The nucleotide substitutions at $15542^{nd}$ and $15550^{th}$ (GeneBank accession no. AY665559) were found as missense mutation (alanine$\rightarrow$valine, proline$\rightarrow$serine, respectively). This study will be useful for farther researches for identifying association between these SNPs and energy metabolism in chicken. The C15550T SNP showed three genotypes, CC, CT, TT by digestion with the genotype TT had significantly faster the first lay day (150.0) than CT (162.0, P<0.05) and genotype TT (150.0, P<0.05) had significantly higher the egg production rate than CT (172.4, P<0.05). According to result of this study, a C15550T was found to have a significantly effect first lay day and mean egg production. It will be possible to use SNP marker on selecting chicken to improve important economic traits, which is the first lay day and mean egg production.

Role of MYH Polymorphisms in Sporadic Colorectal Cancer in China: A Case-control, Population-based Study

  • Yang, Liu;Huang, Xin-En;Xu, Lin;Zhou, Jian-Nong;Yu, Dong-Sheng;Zhou, Xin;Li, Dong-Zheng;Guan, Xin
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.11
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    • pp.6403-6409
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    • 2013
  • Purpose: Biallelic germline variants of the 8-hydroxyguanine (8-OG) repair gene MYH have been associated with colorectal neoplasms that display somatic $G:C{\rightarrow}T:A$ transversions. However, the effect of single germline variants has not been widely studied, prompting the present investigation of monoallelic MYH variants and susceptibility to sporadic colorectal cancer (CRC) in a Chinese population. Patients and Methods: Between January 2006 and December 2012, 400 cases of sporadic CRC and 600 age- and sex-matched normal blood donors were screened randomly for 7 potentially pathogenic germline MYH exons using genetic testing technology. Variants of heterozygosity at the MYH locus were assessed in both sporadic cancer patients and healthy controls. Univariate and multivariate analyses were performed to determine risk factors for cancer onset. Results: Five monoallelic single nucleotide polymorphisms (SNPs) were identified in the 7 exon regions of MYH, which were detected in 75 (18.75%) of 400 CRC patients as well as 42 (7%) of 600 normal controls. The region of exon 1 proved to be a linked polymorphic region for the first time, a triple linked variant including exon 1-316 $G{\rightarrow}A$, exon 1-292 $G{\rightarrow}A$ and intron 1+11 $C{\rightarrow}T$, being identified in 13 CRC patients and 2 normal blood donors. A variant of base replacement, intron 10-2 $A{\rightarrow}G$, was identified in the exon 10 region in 21 cases and 7 controls, while a similar type of variant in the exon 13 region, intron 13+12 $C{\rightarrow}T$, was identified in 8 cases and 6 controls. Not the only but a newly missense variant in the present study, p. V463E (Exon 14+74 $T{\rightarrow}A$), was identified in exon 14 in 6 patients and 1 normal control. In exon 16, nt. 1678-80 del GTT with loss of heterozygosity (LOH) was identified in 27 CRC cases and 26 controls. There was no Y165C in exon 7 or G382D in exon 14, the hot-spot variants which have been reported most frequently in Caucasian studies. After univariate analysis and multivariate analysis, the linked variant in exon 1 region (p=0.002), intron 10-2 $A{\rightarrow}G$ (p=0.004) and p. V463E (p=0.036) in the MYH gene were selected as 3 independent risk factors for CRC. Conclusions: According to these results, the linked variant in Exon 1 region, Intron 10-2 $A{\rightarrow}G$ of base replacement and p. V463E of missense variant, the 3 heterozygosity variants of MYH gene in a Chinese population, may relate to the susceptibility to sporadic CRC. Lack of the hot-spot variants of Caucasians in the present study may due to the ethnic difference in MYH gene.

Genetic Polymorphisms of MYL2 and ADCYAP1R1 Genes and Their Association with Carcass Traits in Finished Pigs (비육돈의 도체형질과 MYL2, ADCYAP1R1 유전자 다형성의 상관관계)

  • Han, ang-Hyun;Shin, Kwang-Yun;Lee, Sung-Soo;Ko, Moon-Suck;Seong, Pil-Nam;Kwon, Ki-Baek;Cho, In-Cheol
    • Journal of Animal Science and Technology
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    • v.50 no.3
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    • pp.301-308
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    • 2008
  • DNA variation of MYL2 intron 5 A345G and ADCYAP1R1 intron 2 A337G were investigated for carcass trait association in finished pigs. Three genotypes(two homozygotes and their heterozygote) were found at 10.6% AA, 45.6% AG and 43.8% GG in MYL2 and 60.5% AA, 34.6% AG, and 22.2% GG for ADCYAP1R1. In finished pig population, individuals containing genotype G- of MYL2 had significantly heavier carcass weight by more than 2.4 kg and thicker backfat thickness by more than 1.3 mm than those of AA homozygous pigs(p<0.05). No significant difference was found in other traits tested in this study such as marbling score, meat color, texture, moisture and separation score(p>0.05). The ADCYAP1R1 intron 2 377GG homozygotes showed coarse texture, i.e., meat quality was inferior than those of AG and AA genotypes, and the moisture level of homozygote AA was higher than those of AG and GG genotypes(p<0.05). The other carcass traits were not significantly associated with ADCYAP1R1 genotypes(p>0.05). The genetic polymorphism of MYL2 and ADCYAP1R1 genes affected the carcass traits in finished pig population. Further studies to explain the association between genetic variations and their phenotypic effects including economic traits in pigs are required including critical mutation in both genes through molecular approaches.

Analysis of the ADSF/resistin Gene Polymorphism Associated with Carcass Traits in Hanwoo (한우 ADSF/resistin 유전자의 단일 염기 다형과 육질관련형질 상관 분석)

  • Park, J.A.;Kang, H.K.;Chae, E.J.;Seo, K.S.;Kim, S.H.;Yun, C.H.;Moon, Y.S.
    • Journal of Animal Science and Technology
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    • v.49 no.5
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    • pp.577-584
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    • 2007
  • Adipocyte-specific secretory factor(ADSF)/resistin, an hormone, is a small cysteine-rich protein secreted from adipose tissue and ADSF/resistin has been implicated in modulating adipogenesis in human and rodents. Although the exact role of ADSF/resistin in bovine has not been identified, it may have directly or indirectly involved in adipocyte differentiation. The objective of this study was to investigate its DNA polymorphism associated with carcass traits in Korean Native Cattle(Hanwoo). To investigate DNA polymorphism in Hanwoo ADSF/resistin gene, blood samples were taken from 295 Hanwoo steers belonging to progeny testing at Hanwoo Improvement Center in Korea. Seven single nucleotide polymorphisms(SNPs) were found in intron regions but not in any other regions including promoter (1.7kb) and 4 exons. The highest frequency among SNPs was C186A(0.16/0.84) following G964A (0.156/0.884). The significant correlation(P<0.05) between the SNPs and economic traits was found on 764Ains associated with marbling but not from any other SNPs determined.  A computer simulation was also conducted to assess the efficiency of marker assisted selection(MAS) versus the conventional breeding scheme.  Results revealed that MAS was more efficient as a breeding tool compared to the conventional. In conclusion, ADSF/Resistin gene is one of candidate genes to evaluate the quality, especially marbling score, in Hanwoo.

VNTR Polymorphism of Tyrosine Hydroxylase Gene Intron 1 in Schizophrenics (정신분열병 환자의 Tyrosine Hydroxylase 유전자 Intron 1의 VNTR 다형성)

  • Paik, In-Ho;Toh, Kyu-Young;Lee, Chang-Uk;Kim, Jung-Jin;Lee, Soo-Jung;Lee, Chul
    • Korean Journal of Biological Psychiatry
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    • v.6 no.2
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    • pp.170-175
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    • 1999
  • Until recently, the etiology of schizophrenia was generally attributed to abnormalities in dopaminergic neurotransmission. Specifically, an excess of dopaminergic activity in the mesolimbic system has been postulated to produce the positive symptoms, while decreased dopaminergic activity in the mesocortical system has been suggested to cause negative symptoms. Accordingly, we performed an association study of schizophrenia with TH gene. Three hundred and seventy four biologically unrelated schizophrenic patients meeting DSM-III-R criteria from Kangnam St. Mary's Hospital affiliated with Catholic university of Korea were recruited for our study. The 393 healthy controls were volunteers for DNA library of Kangnam St. Mary's Hospital without personal or family history of psychiatric and neurologic illness. DNA was extracted from peripheral mononuclear cells and polymorphic region was amplified by polymerase chain reaction. TH intron 1 VNTR polymorphism was typed by silver staining. The allele distributions of TH gene were not different between schizophrenics and controls. However, the frequency of allele A was significantly higher in positive group than that of negative group of schizophrenics. These findings suggest that poitive schizophrenia may be associated with allele A of TH gene.

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Isolation of a Leucoanthocyanidin Dioxygenase (LDOX) Gene from a Spray-type Chrysanthemum (Dendranthema × grandiflorum) and Its Colored Mutants (스프레이형 국화와 화색변이체로부터 Leucoanthocyanidin dioxygenase (LDOX) 유전자의 분리)

  • Chung, Sung-Jin;Lee, Geung-Joo;Lee, Hye-Jung;Kim, Jin-Baek;Kim, Dong-Sub;Kang, Si-Yong
    • Horticultural Science & Technology
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    • v.28 no.5
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    • pp.818-827
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    • 2010
  • A full-length cDNA and genomic DNA of a $leucoanthocyanidin$ $dioxygenase$ ($DgLDOX$) gene was isolated from the petals of chrysanthemum 'Argus', and comparative features of the gene among three flower color mutants derived from a gamma-ray mutagenesis were characterized. The cDNA coding region of the gene was 1068 bp and was translated into 356 amino acids accordingly. The genomic DNA size was 1346 bp for 'Argus', while three mutants revealed ranges of 1363 to 1374 bp. A single intron between two coding exons for the $DgLDOX$ gene was found, of which size was 112 bp for 'Argus', but 128 or 137 bp for three flower color mutants, indicating that a genomic insertion in the intron occurred during the gamma-ray mutagenesis. DNA blot analysis revealed the $DgLDOX$ gene presenting as a single copy in the chrysanthemum genome. The $DgLDOX$ gene was expressed in both 'Argus' of light-pink color and two purple color mutants (AM1 and AM3) but had very weak expression in only white color mutant (AM2). The results demonstrated that variations in the flower color of the mutants might be associated with changes in the amino acid moieties in the coding exons or fragment insertions in the intron of the $DgLDOX$ gene, which potentially resulted in less expression of the gene in the white colored mutant.

Development of a CAPS Marker Derived from the Pg-Actin Gene Sequences and RAPD Markers in Platycodon grandiflorum (도라지에서의 RAPD 마커 분석과 Actin 유전자 염기서열에서 유래한 CAPS 분자표지 개발)

  • Kim, Munhwi;Jeong, Eunah;Jeong, Jeongsu;Kwon, Soontae;Jeon, Ikjo;Jeong, Jeong Hag;Lee, Je Min;Yeam, Inhwa
    • Korean Journal of Plant Resources
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    • v.28 no.5
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    • pp.648-655
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    • 2015
  • Balloon flower (Platycodon grandiflorum A. DC.) is a perennial plant of mainly Campanulaceae family, which have been widely used as a food ingredient and herbal medicine in East Asia. Although demands on related products and yearly cultivation area for balloon flower are increasing, diverse fundamental technologies and molecular breeding studies are not very well supported in Platycodons. In this study, 30 random amplification of polymorphic DNA (RAPD) primers were test in an attempt to explore genetic diversities. In addition, sequences information of the actin gene, a well conserved gene encoding a globular protein that forms microfilaments, was retrieved and analyzed. Two actin homologs were recovered; 3.4 kb fragment is a Pg-actin and 1.4 kb fragment is a Pg-actin homolog with 28.6% similarity. We have confirmed that the Pg-actin gene is configured into 4 exons and 3 introns. A single nucleotide polymorphism (SNP), G↔A, was detected on the intron 3, which served as a target for the CAPS marker development. The marker Pg-Actin-Int3 was applied to 32 balloon flower accessions. Balloon flower DNA sequence information generated in this study is expected to contribute to the analysis and molecular breeding and genetic diversity analysis of balloon flowers.