• BMB Reports
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• v.54 no.5
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• pp.233-245
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• 2021

In eukaryotes, the genome is hierarchically packed inside the nucleus, which facilitates physical contact between cis-regulatory elements (CREs), such as enhancers and promoters. Accumulating evidence highlights the critical role of higher-order chromatin structure in precise regulation of spatiotemporal gene expression under diverse biological contexts including lineage commitment and cell activation by external stimulus. Genomics and imaging-based technologies, such as Hi-C and DNA fluorescence in situ hybridization (FISH), have revealed the key principles of genome folding, while newly developed tools focus on improvement in resolution, throughput and modality at single-cell and population levels, and challenge the knowledge obtained through conventional approaches. In this review, we discuss recent advances in our understanding of principles of higher-order chromosome conformation and technologies to investigate 4D chromatin interactions.

• Genomics & Informatics
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• v.4 no.1
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• pp.45-47
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• 2006

D2GSNP is a web-based server for the selection of single nucleotide polymorph isms (SNPs) within genes related to human diseases. The D2GSNP is based on a relational database created by downloading and parsing OMIM, GAD, and dbSNP, and merging it with positional information of UCSC Golden Path. Totally our server provides 5,142 and 1,932 non-redundant disease genes from OMIM and GAD, respectively. With the D2GSNP web interface, users can select SNPs within genes responding to certain diseases and get their flanking sequences for further genotyping experiments such as association studies.

• Genomics & Informatics
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• v.20 no.4
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• pp.49.1-49.7
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• 2022

Many packages for a meta-analysis of genome-wide association studies (GWAS) have been developed to discover genetic variants. Although variations across studies must be considered, there are not many currently-accessible packages that estimate between-study heterogeneity. Thus, we propose a python based application called Beta-Meta which can easily process a meta-analysis by automatically selecting between a fixed effects and a random effects model based on heterogeneity. Beta-Meta implements flexible input data manipulation to allow multiple meta-analyses of different genotype-phenotype associations in a single process. It provides a step-by-step meta-analysis of GWAS for each association in the following order: heterogeneity test, two different calculations of an effect size and a p-value based on heterogeneity, and the Benjamini-Hochberg p-value adjustment. These methods enable users to validate the results of individual studies with greater statistical power and better estimation precision. We elaborate on these and illustrate them with examples from several studies of infertility-related disorders.

• Journal of Species Research
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• v.10 no.2
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• pp.154-158
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• 2021

An endemic endangered species, Aster altaicus var. uchiyamae (Danyang aster) B2015-0044, is cultivated at the Shingu Botanical Garden, which serves as the ex situ conservation institution for this species. In this work, we sequenced the chloroplast genome of A. altaicus var. uchiyamae B2015-0044. We found that the chloroplast (cp) genome of B2015-0044 was 152,457 base pairs(bps) in size: 84,247 bps of large single copy regions(LSC), 25,007 bps of inverted repeats(IRs), and 18,196 bps of small single copy regions. The B2015-0044 cp genome contains 79 protein-coding genes (PCGs), 4 RNA genes, 29 tRNA genes, and 3 pseudogenes. These results were identical to a previously reported cp genome (Park et al., 2017), except for two sites in introns and three in intergenic spacer (IGS) regions. For the intronic differences, we found that clpP.i1 had a 1-bp small simple repeat (SSR) (T) and petD.i had a 3-bp SSR (ATT). We found 1-bp SSRs in the IGSs of trnT_ggu~psbD and psbZ~trnG_gcc, C and A, respectively. The IGS of(ndhF)~rpl32 had a SNP. Based on our results, the cp genome of the A. altaicus var. uchiyamae can be classified into two genotypes, [C]¹-[A]¹²-[T]¹²-[ATT]⁴-C and [C]²-[A]¹¹-[T]¹¹-[ATT]²-A.

• Korean Journal of Plant Taxonomy
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• v.52 no.4
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• pp.269-274
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• 2022

Dracocephalum rupestre Hance is a perennial herb distributed across China, Mongolia, and Korea. This study reports the first complete chloroplast genome sequence of D. rupestre. The plastome is 151,230 bp long and exhibits a typical quadripartite structure comprising a large single-copy region of 82,536 bp, a small single-copy region of 17,408 bp, and a pair of identical inverted repeat regions of 25,643 bp each. It contains 130 genes, comprising 85 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis of D. rupestre and related species of Lamiaceae showed that the genus Dracocephalum is a monophyletic group, and D. rupestre is most closely related to D. psammophilum.

• Korean Journal of Plant Taxonomy
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• v.49 no.4
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• pp.334-344
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• 2019

The genome size is defined as the amount of DNA in an unreplicated gametic chromosome complement and is expressed as the 1C value. It is a fundamental parameter of organisms that is useful for studies of the genome, as well as biodiversity and conservation. The genome sizes of Korean plants, including Carex (Cyperaceae), have been poorly reported. In this study, we report the genome sizes of 43 species and infraspecific taxa of Korean Carex using flow cytometry, and these results represent about 24.4% of the Carex species and infraspecific taxa distributed on the Korean peninsula. The Plant DNA C-Value Database (release 7.1) updated with and now including our data (a total of 372 Carex accessions) shows that the average genome size of members of the Carex species is 0.47 pg (1C), and the largest genome (C. cuspidate Bertol.; 1C = 1.64 pg) is 8.2 times larger than the smallest (C. brownii Tuck., C. kobomugi Ohwi, C. nubigena D. Don ex Tilloch & Taylor, and C. paxii Kuk.; 1C = 0.20 pg). The large genomes are frequently found in the subgen. Carex, especially in sect. Aulocystis, sect. Digitatae, sect. Glaucae, sect. Paniceae, and sect. Siderostictae. Our data updates the current understanding of genome sizes in Carex. This will serve as the basis for understanding the phylogeny and evolution of Carex and will be especially useful for future genome studies.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.42 no.6
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• pp.790-799
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• 1997

Aegilops genus is known to include the donor species of the Band D genome of the bread wheat(ABD). An effort to establish a better strategy for phylogenetic relationships about Aegilops polyploids by AFLPs(Amplified Fragment Length Polymorphisms) was conducted using the 19 Aegilops sPP. and T. aestivum. The 207 polymorphic bands from the amplified products on the 6% acrylamide denaturing sequencing gels were obtained with the 7 AFLP primer combinations, and used to account for the genetic similarities and cluster analysis using NTSYS program. According to the genome analysis, the $M^h$-genome of Ae. heldreichii was estimated as an intermediate genome between the M-genome of Ae. comosa and N-genome of Ae. uniaristata and supposed to be incorporated in the establishing process of UM-genome as a possible diploid donor. And Ae. ventricosa(DN) was more close to Ae. umbellulata(U) than Ae. squarrosa(D). The close relationship between Ae. squarrosa and T. aestivum was perceived as a diploid donor of D-genome. As for the polyploid species, hexaploid Ae. triaristata was more closely related to Ae. columnaris rather than tetraploid Ae. triaristata. The clustered groups were, basically same to the previous Gihara's sections based on phenotypes and pairing analysis of interspecific hybrids. AFLP was evaluated as an efficient and powerful method in the genome evaluation of closely related species.

• Journal of Life Science
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• v.17 no.6 s.86
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• pp.772-777
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• 2007

A rice OsLeuD gene for small subunit of 3-isopropylmalate isomerase (IPMI) (EC 4.2.1.33) has been isolated. OsLeuD gene is located on 109.3 cM of chromosome 2. OsLeuD gene was expressed abundantly in metabolically active organs including leaves and developing seeds, indicating that OsLeuD gene expression is developmentally regulated. The cDNA of OsLeuD gene was coded for 257 amino acids which showed 58% and 48% homology to small subunits of IPMI in OsLeuD genes of cyanobacteria and green sulfur bacteria, respectively. The molecular character of OsLeuD is closely related to those of photosynthetic bacteria rather than those of eukaryotes including fungi and yeast. This suggests that OsLeuD gene in chromosomal genome of plants may possibly be originated from chloroplast genome.

• BMB Reports
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• v.35 no.4
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• pp.403-408
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• 2002

A hypothetical 21.0 kDa protein (ORF O197) from Escherichia coli K-12 was cloned, purified, and characterized. The protein sequence of ORF O197(termed EcO197) shares a 33.5% identity with that of a novel NTPase from Methanococcus jannaschii. The EcO197 protein was purified using Ni-NTA affinity chromatography, protease digestion, and gel filtration column. It hydrolyzed nucleoside triphosphates with an O6 atom-containing purine base to nucleoside monophosphate and pyrophosphate. The EcO197 protein had a strong preference for deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP), while it had little activity in the standard nucleoside triphosphates (dATP, dCTP, dGTP, and dTTP). These aberrant nucleotides can be produced by oxidative deamination from purine nucleotides in cells; they are potentially mutagenic. The mutation protection mechanisms are caused by the incorporation into DNA of unwelcome nucleotides that are formed spontaneously. The EcO197 protein may function to eliminate specifically damaged purine nucleotide that contains the 6-keto group. This protein appears to be the first eubacterial dITP-and XTP-hydrolyzing enzyme that has been identified.

• Genomics & Informatics
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• v.14 no.4
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• pp.160-165
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• 2016

Over the past decade, the detection of gene-gene interactions has become more and more popular in the field of genome-wide association studies (GWASs). The goal of the GWAS is to identify genetic susceptibility to complex diseases by assaying and analyzing hundreds of thousands of single-nucleotide polymorphisms. However, such tests are computationally demanding and methodologically challenging. Recently, a simple but powerful method, named "BOolean Operation-based Screening and Testing" (BOOST), was proposed for genome-wide gene-gene interaction analyses. BOOST was designed with a Boolean representation of genotype data and is approximately equivalent to the log-linear model. It is extremely fast, and genome-wide gene-gene interaction analyses can be completed within a few hours. However, BOOST can not adjust for covariate effects, and its type-1 error control is not correct. Thus, we considered two-step approaches for gene-gene interaction analyses. First, we selected gene-gene interactions with BOOST and applied logistic regression with covariate adjustments to select gene-gene interactions. We applied the two-step approach to type 2 diabetes (T2D) in the Korea Association Resource (KARE) cohort and identified some promising pairs of single-nucleotide polymorphisms associated with T2D.