• Journal of Animal Science and Technology
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• 제51권4호
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• pp.283-288
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• 2009

본 연구는 비육돈 268두를 대상으로 13번 염색체 중 POU1F1 intron 3영역의 유전자 Single Nucleotide Polymorphism(SNP)은 Msp I 제한효소에 의해서 구분된다. 직접 제작한 Primer로 POU1F1 유전자 중 intron 3영역을 증폭할 수 있도록 제작하였고, 823bp의 증폭산물을 기대할 수 있었다. 그 SNP 유전자형을 3개 군으로 분류하여 빈도 추정과 함께 육질관련 형질과의 연관성을 분석한 결과는 다음과 같다. POU1F1 SNP의 DD 유전자형은 84.33%로 가장 높은 출현율을 보인 반면에 CC 유전자형은 0.75%로 매우 낮게 나타났다. 대립유전자 D 빈도는 0.918로 매우 높게 출현하였으나, C 빈도는 0.082로 매우 낮게 출현하였다. Hardy-Weinberg 법칙에 따른 적합도 검정에서는 유의성 없이(p>0.05) 유전적 평형을 이루고 있는 집단임을 알 수 있었다. CD와 DD 유전자형 집단에서 등지방두께, 도체중, Hunter a 및 b값, 그리고 pH에서는 모두 유의한 차이를 보이지 않았으나, Hunter $L^*$값은 CD(37.26) 보다 DD(40.15) 유전자형 개체군에서 짙게 나타났고(p<0.05), 육색도판에 의한 육색은 DD(3.91) 보다 CD(5.09) 유전자형 개체에서 짙게 나타났다((p<0.001). 따라서 이러한 POU1F1 유전자의 SNP 유전자형은 돼지의 성장이나 도체관련 형질과의 연관성을 더욱 깊이 있게 탐색하여 명확한 구명으로 우량 돈육 생산을 위한 DNA marker로 활용되어야 할 것으로 사료된다.

• 식물조직배양학회지
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• 제26권1호
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• pp.41-47
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• 1999

토마토의 genomic DNA library로부터 분리한 tPALl, tPAL4유전자의 염기서열을 분석하여 tPAL5 유전자와 비교 분석한 결과는 다음과 같다. tPAL5 유전자는 722개의 아미노산과 710 bp의 intron을 가지고 있으나 tPALl은 intron을 가지고 있지 않으며 또한 tPAL5 유전자와 비교하여 249개의 짧은 polypeptide를 가지고 있었다. tPAL4유전자인 경우 357개의 아미노산과 305bp의 intron을 가지고 있었다. tPAL 효소간의 아미노산 homology는 tPAL1유전자와 tPAL4 유전자간은 87.2%, tPALl과 tPAL5는 85.3%, tPAL4 와 tPAL5 는 91.4%의 homology를 보였다. 또한, tPALl, tPAL4 유전자는 정상적인 polypeptide를 가지는 tPAL5유전자와 비교하여 비정상적인 stop codon을 가진 짧은 polypeptide로 구성되어 있었다. 다양한 식물 종으로부터 분리된 PAL유전자의 염기서열을 비교한 결과 토마토 (Lycopersicon esculentum), 감자 (Solanum tuberosum), 고구마 (Ipomoea batatas)간의 유연관계과 높았으며, parsley (Petroselinum crispum), bean (Phaseolus vulgaris), pea (Pisum sativum), alfalfa (Medicago sativa) 등이 각각 서로간에 유연관계가 높았다. 또한, 토마토에서 분리한 family내에서 tPAL4와 tPAL5 유전자는 homology가 매우 높았고 (93.0%), tPAL1와 tPAL4유전자 사이는 다소 낮았으며 (84.4%), 특히 tPAL4는 감자의 PAL 유전자와 매우 높았다 (90.6%).

• Asian Pacific Journal of Cancer Prevention
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• 제15권6호
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• pp.2631-2634
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• 2014

Background: p53 gene is a well-known tumor suppressor gene that has several polymorphisms in both its exons and introns. It has been suggested that intron 3 16 bp duplication polymorphism may affect the gene function resulting in reduction or suppression of p53 anti tumor activity. In most case control studies a duplicated allele has been noticeably more frequent in cases rather than controls but there are also conflicting results. The aim of this study was to assess the association of intron 3 16 bp duplication polymorphism of p53 with breast cancer risk among Iranian-Azeri population. We also analyzed the clinicopathological information of patients as an epidemiological description of breast cancer in the north-west of Iran. Materials and Methods: This case-control study was performed on 221 breast cancer patients and 170 controls. Genomic DNA was extracted from peripheral blood samples and tumor tissues. p53 PIN3 genotype was determined using electrophoresis of PCR products on 8% non-denaturing polyacrylamide gels and silver staining. Results: In the control and case groups, respectively, 62.9% and 61.1% had no 16 bp insertion (A1A1 genotype), 7.1% and 7.7% had insertion in both p53 alleles (A2A2) and 30% and 31.2% were heterozygous (A1A2). There was no significant difference between genotype frequencies as well as allelic frequencies in two case and control groups. Conclusions: According to the result of the present study, the intron 3 16 bp duplication polymorphism of p53 could not be assessed as a marker of risk factor for predisposition to breast cancer in Azeri population. However, a high frequency of A2 allele (22.1%) in our population suggested that intron 3 16 bp duplication polymorphism may be a valuable marker for study in other cancers with well designed large groups.

• The Korean Journal of Physiology and Pharmacology
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• 제12권4호
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• pp.205-209
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• 2008

Recently, Sun et al (2008) reported that the IL6R polymorphism is associated with schizophrenia. Therefore, to detect the association between polymorphisms of interleukin 31 receptor A (IL31RA) and schizophrenia, we genotyped 9 SNPs [rs9292101 (intron 1), rs1009639 (exon 2, Pr043Pro), rs2161582 (intron 2), rs68761890 (intron 5), rs16884629 (intron 6), rs11956465 (intron 12), rs12153724 (intron 12), and rs16884641 (intron 14)] using the Golden Gate assay on Illumina BeadStation 500 GX. Two hundred eighteen patients with schizophrenia and 379 normal subjects were recruited. Patients with schizophrenia were diagnosed according to DSM-IV, and control subjects without history of psychiatric disorders were selected. We used SNPStats, Haploview, HapAnalyzer, SNPAnalyzer, and Helixtree programs for the evaluation of genetic data. Of nine polymorphisms, three SNPs (rs9292101, rs1009639, and rs11956465) were associated with schizophrenia. The rs9292101 and rs11956465 showed significant associations with the risk of schizophrenia in the codominant [rs9292101, odds ratio (OR)=0.74, 95% confidence interval (CI)=0.58${\sim}$0.95, p=0.017] and recessive (rs11956465, OR=0.64, 95% CI=0.42${\sim}$0.96, p=0.034) models, respectively. The rs1009639 also was statistically related to schizophrenia in both codominant (OR=0.76, 95% CI=0.60${\sim}$0.97, p=0.025) and dominant (OR=0.66, 95% CI=0.44${\sim}$0.98, p=0.035) models. Two linkage disequilibrium (LD) blocks were made. In the analysis of haplotypes, a haplotype (GCT) in block 1 and a haplotype (CCACAG) in block 2 showed significant associations between schizophrenia and control groups (haplotype GCT, frequency=0.509, chi square=4.199, p=0.040; haplotype CCACAG, frequency=0.289, chi square=5.691, p=0.017). The results suggest that IL31RA may be associated with risk of schizophrenia in Korean population.

• Molecules and Cells
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• 제26권5호
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• pp.474-480
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• 2008

OsMADS1 is a rice MADS box gene necessary for floral development. To identify the key cis-regulatory regions for its expression, we utilized transgenic rice plants expressing GUS fusion constructs. Histochemical analysis revealed that the 5.7-kb OsMADS1 intragenic sequences, encompassing exon 1, intron 1, and a part of exon 2, together with the 1.9-kb 5' upstream promoter region, are required for the GUS expression pattern that coincides with flower-preferential expression of OsMADS1. In contrast, the 5' upstream promoter sequence lacking this intragenic region caused ectopic expression of the reporter gene in both vegetative and reproductive tissues. Notably, incorporation of the intragenic region into the CaMV35S promoter directed the GUS expression pattern similar to that of the endogenous spatial expression of OsMADS1 in flowers. In addition, our transient gene expression assay revealed that the large first intron following the CaMV35S minimal promoter enhances flower-preferential expression of GUS. These results suggest that the OsMADS1 intragenic sequence, largely intron 1, contains a key regulatory region(s) essential for expression.

• Animal cells and systems
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• 제9권3호
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• pp.107-111
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• 2005

C. elegans DLK-1 has been reported to play an important role in synaptogenesis by shaping the structure of presynaptic terminal. In this study, we investigated the expression pattern and regulation of the dlk-1 gene in C. elegans. To determine the expression pattern, we made a dlk-1::gfp fusion construct, named pPDdg1, which consisted of -2.2 kb 5' upstream region, the first exon, the first intron, and a part of the second exon of the dlk-1 gene. By microinjecting this construct into the worm, we observed that the DLK-1::GFP was expressed mainly in neurons. We next examined the regulatory elements of gene expression by deletion analysis of pPDdg1. Removal of a large portion of the 5' upstream region (${\Delta}-361$ to -2246) of the gene had little effect on the expression pattern, whereas deletion of the first intron led to elimination of the DLK-1::GFP expression in most of the neurons. Our results suggest that the first intron of the C. elegans dlk-1 gene contains the regulatory element critical for gene expression.

• Interdisciplinary Bio Central
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• 제4권4호
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• pp.14.1-14.6
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• 2012

Splice site prediction in DNA sequence is a basic search problem for finding exon/intron and intron/exon boundaries. Removing introns and then joining the exons together forms the mRNA sequence. These sequences are the input of the translation process. It is a necessary step in the central dogma of molecular biology. The main task of splice site prediction is to find out the exact GT and AG ended sequences. Then it identifies the true and false GT and AG ended sequences among those candidate sequences. In this paper, we survey research works on splice site prediction based on support vector machine (SVM). The basic difference between these research works is nucleotide encoding technique and SVM kernel selection. Some methods encode the DNA sequence in a sparse way whereas others encode in a probabilistic manner. The encoded sequences serve as input of SVM. The task of SVM is to classify them using its learning model. The accuracy of classification largely depends on the proper kernel selection for sequence data as well as a selection of kernel parameter. We observe each encoding technique and classify them according to their similarity. Then we discuss about kernel and their parameter selection. Our survey paper provides a basic understanding of encoding approaches and proper kernel selection of SVM for splice site prediction.

• 원예과학기술지
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• 제35권3호
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• pp.323-332
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• 2017

Homology-specific transcriptional and post-transcriptional silencing, an intrinsic mechanism of gene regulation in most eukaryotes, can be induced by anti-sense, co-suppression, or hairpin-based double-stranded RNA. Hairpin-based RNA interference (RNAi) has been applied to analyze gene function and genetically modify crops. However, RNAi vector construction usually requires high-cost cloning steps and large amounts of time, or involves methods that are protected by intellectual property rights. We describe a more effective method for generating intron-spliced RNAi constructs. To produce intron-spliced hairpin RNA, an RNAi cassette was ligated with the first intron and splicing sequences of the Brassica rapa ssp. pekinensis histone deacetylase 1 gene. This method requires a single ligation of the PCR-amplified target gene to SpeI-NcoI and SacI-BglII enzyme sites to create a gene-specific silencing construct. We named the resulting binary vector system pKHi and verified its functionality by constructing a vector to silence DIHYDROFLAVONOL 4-REDUCTASE (DFR), transforming it into tobacco plants, and confirming DFR gene-silencing via PCR, RT-qPCR, and analysis of the accumulation of small interfering RNAs. Reduction of anthocyanin biosynthesis was also confirmed by analyzing flower color of the transgenic tobacco plants. This study demonstrates that small interfering RNAs generated through the pKHi vector system can efficiently silence target genes and could be used in developing genetically modified crops.

• 생명과학회지
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• 제19권5호
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• pp.664-670
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• 2009

지방분해와 열생산에 관여한다고 알려진 ADRB3 유전자의 염기서열 분석을 통하여 한국인에서 호발하는 유전자 다형성 부위를 먼저 확인한 후 이 유전자 다형성들과 HDL-C와의 연관성에 대하여 조사하고자 2006년 5월에서 12월 사이에 부산지역의 일개 대학병원에서 건강진단을 받은 991명을 대상으로 신장, 체중, 체질량지수, 허리둘레, 고밀도 지단백 콜레스테롤, 중성지방, 공복 혈당을 측정하였으며, 대상자들의 혈액에서 DNA를 분리하여 ADRB3 유전자에서 흔히 발생하는 유전자다형성 부위를 확인하였다. 연구결과 한국인에서 ADRB3 유전자의 intron2 +3893T>C의 변이를 처음으로 발견하였으며 열성 대립형질의 발현빈도는 0.164이었다. Exon1의 +188T>C와 intron2의 +3893T>C의 열성 대립형질인 C형이 있을 경우 HDL-C의 농도가 낮았다. 따라서 ADRB 유전자 다형성은 HDL-C과 관련이 있을 것으로 생각된다.

• Journal of Microbiology and Biotechnology
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• 제18권1호
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• pp.23-27
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• 2008

Self-splicing group I introns in tRNA anticodon loops have been found in diverse groups of bacteria. In this work, we identified $tRNA^{fMet}$ group I introns in six strains of marine Synechococcus elongatus. Introns with sizes around 280 bp were consistently obtained in all the strains tested. In a phylogenetic analysis using the nucleotide sequence determined in this study with other cyanobacterial $tRNA^{fMet}$ and $tRNA^{Leu}$ intron sequences, the Synechococcus sequence was grouped together with the sequences from other unicellular cyanobacterial strains. Interestingly, the phylogenetic tree inferred from the intronic sequences clearly separates the different tRNA introns, suggesting that each family has its own evolutionary history.