• Genomics & Informatics
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• 제2권4호
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• pp.163-166
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• 2004

• Genomics & Informatics
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• 제3권4호
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• pp.142-148
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• 2005

The immune response-related genes have been suggested to be the most favorable genes for positive selection during evolution. Comparing the entire DNA sequence of chimpanzee chromosome 22 (PTR22) with human chromosome 21 (HSA21), we have identified 15 orthologs having indel in their coding sequences. Among them, interferon-${\alpha}$ receptor-1 gene (IFNAR1), an immuneresponse-related gene, is subjected to comparative genomic analysis. Chimpanzee IFNAR1 showed the same genomic structure as human IFNAR1 (11 exons and 10 introns) except the 3 bp insertion in exon 4. The sequence alignment of IFNAR1 coding sequence indicated that 'ISPP' amino acid sequence motif is highly conserved in chimpanzee and other animals including mouse and chicken. However, the human IFNAR1 shows that one proline residue is missing in the sequence motif. The homology modeling of the IFNAR1 structures suggests that the proline deletion in human IFNAR1 leads to the formation of the following ${\alpha}$-helix, whereas two sequential prolines in chimpanzee IFNAR1 inhibit it. As a result, human IFNAR1 may adopt a characteristic structure distinct from chimpanzee IFNAR1. This human specific trait could contribute to specific immune response in the most optimized manner for humans. Further molecular biological studies on the IFNAR1 will help us to gain insights into the molecular implication of species-specific host-pathogen interaction in primate evolution.

• 한국유전체학회:학술대회논문집
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• 한국유전체학회 2006년도 The 15th Korean Genome Organization Conference KOGO 2006 Annual Meeting
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• pp.72-72
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• 2006

• BMB Reports
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• 제54권5호
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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.

• 대한예방의학회:학술대회논문집
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• 대한예방의학회 2003년도 하계워크샵 및 전공의 연수교육 강의집
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• pp.23-32
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• 2003

o Genome epidemiology can contribute to public health by disease prevention and health promotion o Genome epidemiology contributes most by identifying modifiable environmental factors that interact with the genome structure and function

• Fisheries and Aquatic Sciences
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• 제25권3호
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• pp.158-166
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• 2022

The complete mitochondrial genome of Tremoctopus violaceus was sequenced to analyze its organization and phylogenetic status within the order Octopoda. The mitochondrial genome of T. violaceus had a structure and organization similar to that of other Octopoda. The content of the nucleotides A, C, G, and T was 31.68 %, 7.71 %, 20.02 %, and 40.58 %, respectively. All protein-coding genes (PCG) began with the ATG codon, excluding ND4 and ATP6, which began with ATC and ATT, respectively, and terminated with TAG, TAA, TA, or T. Codons for isoleucine were the most used codons, whereas those for arginine were used the least. Two extra tRNAs, trnN and trnL, were found in the control region. These tRNAs have a D-armless structure. The control region had excess A + T content (83.16 %) and a stem-loop structure with two elements, which is reported for the first time in Octopoda by our study. Bayesian inference using 13 PCG revealed that Octopus and Octopodidae were polyphyletic, and that Tremoctopodidae diverged relatively earlier within Octopoda. The mitochondrial genome of T. violaceus and its characteristics may help to understand the evolutionary history of Octopoda and establish a marine biodiversity conservation strategy.

• 한국유전체학회:학술대회논문집
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• 한국유전체학회 2004년도 The 13th Korea Genome Conference
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• pp.50.2-50.2
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• 2004

• Genomics & Informatics
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• 제4권4호
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• pp.167-169
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• 2006

PABAP (Palindrome Analysis by BLAST Program) is an analysis system that identifies palindromic sequences from a large genome sequence up to several megabases long. It uses NCBI BLAST as a searching engine, and data processing such as alignment filtration and detection of inverted repeats which satisfy user-defined parameters is performed by manipulating data after populating into a MySQL database. PABAP outperforms publicly available palindrome search program in that it can detect large palindrome with internal spacer at a faster speed from bacterial genomes. It is a standalone application and is freely available for noncommercial users.

• Genomics & Informatics
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• 제10권1호
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• pp.65-67
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• 2012

We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study. To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information. This system helps researchers browsing these variants with gene and structure variant annotations. Users can easily find specific regions with search options and verify them from system-integrated genome browsers with annotations.

• BMB Reports
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• 제48권6호
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• pp.301-302
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• 2015

Hypoxia is associated with many pathological conditions as well as the normal physiology of metazoans. We identified a lactate-dependent signaling pathway in hypoxia, mediated by the oxygen- and lactate-regulated protein NDRG family member 3 (NDRG3). Oxygen negatively regulates NDRG3 expression at the protein level via the PHD2/VHL system, whereas lactate, produced in excess under prolonged hypoxia, blocks its proteasomal degradation by binding to NDRG3. We also found that the stabilized NDRG3 protein promotes angiogenesis and cell growth under hypoxia by activating the Raf-ERK pathway. Inhibiting cellular lactate production abolishes NDRG3-mediated hypoxia responses. The NDRG3-Raf-ERK axis therefore provides the genetic basis for lactate-induced hypoxia signaling, which can be exploited for the development of therapies targeting hypoxia-induced diseases in addition to advancing our understanding of the normal physiology of hypoxia responses. [BMB Reports 2015; 48(6): 301-302]