• BMB Reports
• /
• v.57 no.5
• /
• pp.216-231
• /
• 2024

Mammalian genomes are intricately compacted to form sophisticated 3-dimensional structures within the tiny nucleus, so called 3D genome folding. Despite their shapes reminiscent of an entangled yarn, the rapid development of molecular and next-generation sequencing technologies (NGS) has revealed that mammalian genomes are highly organized in a hierarchical order that delicately affects transcription activities. An increasing amount of evidence suggests that 3D genome folding is implicated in diseases, giving us a clue on how to identify novel therapeutic approaches. In this review, we will study what 3D genome folding means in epigenetics, what types of 3D genome structures there are, how they are formed, and how the technologies have developed to explore them. We will also discuss the pathological implications of 3D genome folding. Finally, we will discuss how to leverage 3D genome folding and engineering for future studies.

• Genomics & Informatics
• /
• v.2 no.4
• /
• pp.184-190
• /
• 2004

An approach for genome analysis based on assembly of fragments of DNA from the whole genome can be applied to obtain the complete nucleotide sequence of the genome of Zymomonas mobilis. However, the problem of fragment assembly raise thorny computational issues. Computer simulation studies of sequence assembly usually show some abnormal assemblage of artificial sequences containing repetitive or duplicated regions, and suggest methods to correct those abnormalities. In this paper, we describe five simulation studies which had been performed previous to the actual genome assembly process of Zymomonas mobilis ZM4.

• BMB Reports
• /
• v.48 no.1
• /
• pp.6-12
• /
• 2015

Various biological molecules naturally existing in diversified species including fungi, bacteria, and bacteriophage have functionalities for DNA binding and processing. The biological molecules have been recently actively engineered for use in customized genome editing of mammalian cells as the molecule-encoding DNA sequence information and the underlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newly constructed artificial molecular tools have enabled modifications of specific endogenous genetic elements in the genome context at efficiencies that are much higher than that of the conventional homologous recombination based methods. This minireview introduces the most recently spotlighted molecular genome engineering tools with their key features and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal of the inherent DNA sequence recognition rigidity from the original molecular platforms, the addition of newly tailored targeting functions into the engineered molecules, and the enhancement of their targeting specificity. Effective targeted genome engineering of mammalian cells will enable not only sophisticated genetic studies in the context of the genome, but also widely-applicable universal therapeutics based on the pinpointing and correction of the disease-causing genetic elements within the genome in the near future.

• Journal of Microbiology and Biotechnology
• /
• v.14 no.5
• /
• pp.1081-1085
• /
• 2004

Genome research has become very popular in most nations. In order to enhance the efficiency of collaboration among genome research groups, ways to store and share data, communicate with each other, be guided through right research strategies, and to easily use well-established databases. In addition, since techniques and softwares for genome research groups are well established, a similar research road map could commonly be applied. In this study, we developed a web-based work place for effective genome research, named 'BioPlace.' From the beginning of writing a proposal, research members can work on the same environment with convenient aid to share files or data. BioPlace provides various ways of collaboration methods among genome researchers. The BioPlace system supports two types of workplaces, namely 'Personal Workspace' and 'Team Workspace.' For each BioPlace user, a Persona] Workspace is provided, while a Team Workspace is provided for each group with the same purpose. In addition, BioPlace provides a 'General Research Road Map' for genome research, and several Korean user interfaces for BLAST, PDB, and Primer3. We expect that BioPlace may facilitate collaboration of genome research among the experienced scientists and help beginners in many different ways as well.

• Proceedings of the Zoological Society Korea Conference
• /
• 1998.10b
• /
• pp.343.2-343
• /
• 1998

No Abstract, See Full Text

• Proceedings of the PSK Conference
• /
• 2002.04a
• /
• pp.94-95
• /
• 2002

• Genomics & Informatics
• /
• v.11 no.1
• /
• pp.2-6
• /
• 2013

Until recently, since the Human Genome Project, the general view has been that the majority of the human genome is composed of junk DNA and has little or no selective advantage to the organism. Now we know that this conclusion is an oversimplification. In April 2003, the National Human Genome Research Institute (NHGRI) launched an international research consortium called Encyclopedia of DNA Elements (ENCODE) to uncover non-coding functional elements in the human genome. The result of this project has identified a set of new DNA regulatory elements, based on novel relationships among chromatin accessibility, histone modifications, nucleosome positioning, DNA methylation, transcription, and the occupancy of sequence-specific factors. The project gives us new insights into the organization and regulation of the human genome and epigenome. Here, we sought to summarize particular aspects of the ENCODE project and highlight the features and data that have recently been released. At the end of this review, we have summarized a case study we conducted using the ENCODE epigenome data.

• BMB Reports
• /
• v.51 no.7
• /
• pp.315-316
• /
• 2018

Genome engineering with clustered regularly interspaced short palindromic repeats (CRISPR) system can be used as a tool to correct pathological mutations or modulate gene expression levels associated with pathogenesis of human diseases. Owing to well-established local administration methods including intravitreal and subretinal injection, it is relatively easy to administer therapeutic genome engineering machinery to ocular tissues for treating retinal diseases. In this context, we have investigated the potential of in vivo genome engineering as a therapeutic approach in the form of ribonucleoprotein or CRISPR packaged in viral vectors. Major issues in therapeutic application of genome engineering include specificity and efficacy according to types of CRISPR system. In addition to previous platforms based on ribonucleoprotein and CRISPR-associated protein 9 derived from Campylobacter jejuni, we evaluated the therapeutic effects of a CRISPR RNA-guided endonuclease derived from Lachnospiraceae bacterium ND2006 (LbCpf1) in regulating pathological angiogenesis in an animal model of wet-type age-related macular degeneration. LbCpf1 targeting Vegfa or Hif1a effectively disrupted the expression of genes in ocular tissues, resulting in suppression of choroidal neovascularization. It was also notable that there were no significant off-target effects in vivo.

• The Korea Genome Conference
• /
• 2002.08a
• /
• pp.31-31
• /
• 2002

• KSBB Journal
• /
• v.31 no.4
• /
• pp.193-199
• /
• 2016

Global warming caused from the heavy consumption of fossil fuel is one of the biggest problems to be solved. Biofuel has been gained more attention as an alternative to reduce the consumption of fossil fuel. Recently, butanol produced from the genus Clostridium has been considered as one of the promising alternatives for gasoline, fossil based fuel. Nevertheless, the lack of the genome-engineering tools for the genus Clostridium is the major hurdle for the economic production of butanol. More recently, genome engineering tools have been developed for metabolic engineering of butanol-producing Clostridium species, which includes genome scale network model and genome editing tools on the basis of mobile group II introns and CRISPR/Cas system. In this study, the genome engineering tools for butanol-producing Clostridium species have been reviewed with a brief future perspective.