• 한국가축번식학회지
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• 제22권2호
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• pp.195-202
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• 1998

본 연구에서는 돼지 난자 내에 돼지, 사람, 소 및 생쥐의 정자를 미세 주입한 후 전핵형성과ㅏ 전핵의 이동을 관찰하였다. 핵과 미세소관은 정자 주입 후 간접면역 형광염색을 실시한 후 공초점주사현미경으로 관찰하였다. 돼지 난자 내에 돼지정자를 직접 주입하였을 경우 일반적인 수정과정과 동일하게 정자중편부에서 성상체가 형성되었고, 이 성상체에 의해서 웅성 및 자성 전핵의 이동(44%), 유사분열(3%) 및 2-세포기(13%)까지 정상적인 수정이 이루어지는 것을 관찰할 수가 있었다. 반면에 이종(사람, 소 및 생쥐)의 정자를 돼지난자에 직접 주입하였을 경우 단위발생시 난 활성이 유도된 난자와 같이 난자자체에서 형성된 미세소관에 의해 전핵이 이동(47, 30 및 17%)하는 것을 볼 수가 있었다. 하지만, 접합체 형성 및 2-세포기로의 분리되는 과정은 관찰할 수 없었다. 이러한 결과로 돼지 난자 내에 이종의 정자가 주입되었을 때 정자의 핵은 비록이적으로 전핵으로 발달되고 난자 중심부로 이동된다는 것을 보여주는 것인데, 이때 전핵을 움직이는 것은 정자에서 유래된 중심체에 의한 것이 아니라 난자세포질 자체의 미세소관에 의한 것으로 관찰되었다.

• Clinical and Experimental Reproductive Medicine
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• 제24권3호
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• pp.301-309
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• 1997

본 연구에서는 체외수정, 난자내 정자 직접주입, 난자내 정자 두부 미두 주입 후의 핵과 미세소관의 변화를 관찰하였다. 핵과 미세소관의 움직임은 형광염색을 실시한 후 공초점주사현미경을 이용하여 관찰하였다. 체외수정에서 관찰된 바와 동일하게 정자를 난자에 직접주입 한 직후 정자 중편부에서 성상체가 형성되었고, 이 성상체에 의해 자성 웅성 전핵이 융합되는 것으로 관찰되었다. 그러나 난자내 정자를 직접주입하였을 경우 웅성전핵으로 발달하는 비율이 낮았다. 이는 주입된 정자가 원형질막과 perinuclear theca에 싸인 체 난자내로 들어가 난자내의 sperm nucleus decondensing factor와 정자 핵과의 반응이 억제되기 때문으로 생각된다. 정자 두부 만을 주입하였을 경우 성상체가 형성되지 않았지만 자성 웅성 전핵 사이 또는 그 주위에서 두터운 미세소관층이 관찰이 되었다. 따라서 소에 있어서는 정자의 중편부에 위치하여 microtubule organizing center (MTOC)의 역할을 하는 중심립 또는 중심체 없이도 모계에서 유래된 미세소관이 형성되어 이것이 전핵의 융합과 세포분열에 관여하는 것으로 생각된다. 정자의 미부 만을 주입하였을 경우 성상체가 형성이 되지 않았으며, 자성핵 사이에 형성된 미세소관과 떨어져서 관찰되었다. 따라서 주입된 정자의 꼬리는 미세소관형성과 관련이 없는 것으로 생각된다. 이러한 결과는 소에 있어서, 수정 시 정자로부터 유래되는 중심립 또는 중심체가 없이도 미세소관을 형성하여 미세소관에 의해 이후의 배발달이 정상적으로 일어남을 보여주고 있다.

• Genomics & Informatics
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• 제4권1호
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• pp.11-15
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• 2006

The aim of this study is to identify hRad21-binding sites in human chromosome, the core component of cohesin complex that held sister chromatids together. After chromatin immunoprecipitation with an hRad21 antibody, it was cloned the recovered DNA and sequenced 30 independent clones. Among them, 20 clones (67%) contained repetitive elements including short interspersed transposable elements (SINE or Alu elements), long terminal repeat (LTR) and long interspersed transposable elements (LINE), fourteen of these twenty (70%) repeats clones had Alu elements, which could be categorized as the old and the young Alu Subfamily, eleven of the fourteen (73%) Alu elements belonged to the old Alu Subfamily, and only three Alu elements were categorized as young Alu subfamily. There is no CpG island within these selected clones. Association of hRad21 with Alu was confirmed by chromatin immunoprecipitation-PCR using conserved Alu primers. The primers were designed in the flanking region of Alu, and the specific Alu element was shown in the selected clone. From these experiments, it was demonstrated that hRad21 could bind to SINE, LTRs, and LINE as well as Alu.

• Genomics & Informatics
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• 제15권1호
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• pp.11-18
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• 2017

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, 'ChIPseeker' performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.

• Genomics & Informatics
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• 제20권1호
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• pp.2.1-2.11
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• 2022

The method of single-cell RNA sequencing has been rapidly developed, and numerous experiments have been conducted over the past decade. Their results allow us to recognize various subpopulations and rare cell states in tissues, tumors, and immune systems that are previously unidentified, and guide us to understand fundamental biological processes that determine cell identity based on single-cell gene expression profiles. However, it is still challenging to understand the principle of comprehensive gene regulation that determines the cell fate only with transcriptome, a consequential output of the gene expression program. To elucidate the mechanisms related to the origin and maintenance of comprehensive single-cell transcriptome, we require a corresponding single-cell epigenome, which is a differentiated information of each cell with an identical genome. This review deals with the current development of single-cell epigenomic library construction methods, including multi-omics tools with crucial factors and additional requirements in the future focusing on DNA methylation, chromatin accessibility, and histone post-translational modifications. The study of cellular differentiation and the disease occurrence at a single-cell level has taken the first step with single-cell transcriptome and is now taking the next step with single-cell epigenome.

• 한국동물번식학회:학술대회논문집
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• 한국동물번식학회 2002년도 춘계학술발표대회 발표논문초록집
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• pp.51-51
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• 2002

Despite of importance of integrated events of nucleus and microtubule remodeling in nuclear transferred embryos with somatic cells, little information is available on this subject. In this study we compared chromatin, r-tubulin and microtubule organization in porcine oocytes following somatic cell nuclear transfer and parthenogenetically activation in order to clarify nuclear remodeling process and to demonstrate centrosome inheritance during nuclear transfer. (omitted)

• Genomics & Informatics
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• 제13권4호
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• pp.152-155
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• 2015

Recently, the Encyclopedia of DNA Elements (ENCODE) Analysis Working Group converted data from ChIP-seq analyses from the Broad Histone track into 15 corresponding chromatic maps that label sequences with different kinds of histone modifications in promoter regions. Here, we publish a frequency profile of the three ChromHMM promoter states, at 200-bp intervals, with particular reference to the existence of sequence patterns of promoter elements, GC-richness, and transcription starting sites. Through detailed and diligent analysis of promoter regions, researchers will be able to uncover new and significant information about transcription initiation and gene function.

• 한국발생생물학회지:발생과생식
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• 제27권1호
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• pp.9-24
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• 2023

The advancement in high-throughput sequencing (HTS) technology has revolutionized the field of biology, including genomics, epigenomics, transcriptomics, and metagenomics. This technology has become a crucial tool in many areas of research, allowing scientists to generate vast amounts of genetic data at a much faster pace than traditional methods. With this increased speed and scale of data generation, researchers can now address critical questions and gain new insights into the inner workings of living organisms, as well as the underlying causes of various diseases. Although the first HTS technology have been introduced about two decades ago, it can still be challenging for those new to the field to understand and use effectively. This review aims to provide a comprehensive overview of commonly used HTS technologies these days and their applications in terms of genome sequencing, transcriptome, DNA methylation, DNA-protein interaction, chromatin accessibility, three-dimensional genome organization, and microbiome.

• 생명과학회지
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• 제12권2호
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• pp.219-225
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• 2002

진핵세포의 염색체는 전사, 복제, 회복 등의 과정에서 관여하는 단백질의 기능으로 구조가 변하게 된다. 이때 관여하는 단백질은 DNA-단백질의 상호작용에 의해서 이루어지게 되는데, 이때 단백질의 일부분은 일정한 상동성이 존재하게 된다. 이러한 부분은 motif나 domain으로 구성되는데, 예를 들면, SAP domain등을 들 수 있다. S. pombe genomic DNA 데이터베이스를 검색하여 Arabidopsis PARP 과 KU70과 상동성을 보이는 새로운 유전자를 찾았다. 이를 SAPuvs (SAP UV Sensitive)라 명명하였으며, Ura4를 선별표지로 이용하여 S. pombe SAPuvs 유전자 결실세포를 구성하였다. SAPuvs 유전자 결실세포는 자외선 조사 실험에서 정상의 세포에 비해 현저하게 죽었다. 그러나, MMS 또는 MMS와 3AB의 처리 실험에서는 저항성을 보였다. 이러한 결과로 SAPuvs는 DNA 상해회복에서 염색사구조 형성에 연관되어 있음을 확인하였다.

• Molecules and Cells
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• 제41권7호
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• pp.695-702
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• 2018

The inner ear is a complex sensory organ responsible for hearing and balance. Formation of the inner ear is dependent on tight regulation of spatial and temporal expression of genes that direct a series of developmental processes. Recently, epigenetic regulation has emerged as a crucial regulator of the development of various organs. However, what roles higher-order chromatin organization and its regulator molecules play in inner ear development are unclear. CCCTC-binding factor (CTCF) is a highly conserved 11-zinc finger protein that regulates the three-dimensional architecture of chromatin, and is involved in various gene regulation processes. To delineate the role of CTCF in inner ear development, the present study investigated inner ear-specific Ctcf knockout mouse embryos (Pax2-Cre; $Ctcf^{fl/fl}$). The loss of Ctcf resulted in multiple defects of inner ear development and severely compromised otic neurogenesis, which was partly due to a loss of Neurog1 expression. Furthermore, reduced Neurog1 gene expression by CTCF knockdown was found to be associated with changes in histone modification at the gene's promoter, as well as its upstream enhancer. The results of the present study demonstrate that CTCF plays an essential role in otic neurogenesis by modulating histone modification in the Neurog1 locus.