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Sartsanga C, Phengchat R, Wako T, Fukui K, Ohmido N. Localization and quantitative distribution of a chromatin structural protein Topoisomerase II on plant chromosome using HVTEM and UHVTEM. Micron 2024; 179:103596. [PMID: 38359615 DOI: 10.1016/j.micron.2024.103596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
Topoisomerase II (TopoII) is an essential structural protein of the metaphase chromosome. It maintains the axial compaction of chromosomes during metaphase. It is localized at the axial region of chromosomes and accumulates at the centromeric region in metaphase chromosomes. However, little is known about TopoII localization and distribution in plant chromosomes, except for several publications. We used high voltage transmission electron microscopy (HVTEM) and ultra-high voltage transmission electron microscopy (UHVTEM) in conjunction with immunogold labeling and visualization techniques to detect TopoII and investigate its localization, alignment, and density on the barley chromosome at 1.4 nm scale. We found that HVTEM and UHVTEM combined with immunogold labeling is suitable for the detection of structural proteins, including a single molecule of TopoII. This is because the average size of the gold particles for TopoII visualization after silver enhancement is 8.9 ± 3.9 nm, which is well detected. We found that 31,005 TopoII molecules are distributed along the barley chromosomes in an unspecific pattern at the chromosome arms and accumulate specifically at the nucleolus organizer regions (NORs) and centromeric region. The TopoII density were 1.32-fold, 1.58-fold, and 1.36-fold at the terminal region, at the NORs, and the centromeric region, respectively. The findings of TopoII localization in this study support the multiple reported functions of TopoII in the barley metaphase chromosome.
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Affiliation(s)
- Channarong Sartsanga
- Graduate School of Human Development and Environment, Kobe University, Tsurukabuto 3-11, Nada-ku, 657-8501, Kobe, Japan
| | - Rinyaporn Phengchat
- Nanotechnology Research Centre, National Research of Council, 11421 Saskatchewan Drive, T6G 2M9 Edmonton, Alberta, Canada
| | - Toshiyuki Wako
- Institute of Crop Sciences, National Agriculture and Food Research Organization, 2-1-1 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kiichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Suita, Osaka 565-0871, Japan
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Tsurukabuto 3-11, Nada-ku, 657-8501, Kobe, Japan.
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Zhu X, Huang Q, Luo J, Kong D, Zhang Y. Mini-review: Gene regulatory network benefits from three-dimensional chromatin conformation and structural biology. Comput Struct Biotechnol J 2023; 21:1728-1737. [PMID: 36890880 PMCID: PMC9986247 DOI: 10.1016/j.csbj.2023.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Gene regulatory networks are now at the forefront of precision biology, which can help researchers better understand how genes and regulatory elements interact to control cellular gene expression, offering a more promising molecular mechanism in biological research. Interactions between the genes and regulatory elements involve different promoters, enhancers, transcription factors, silencers, insulators, and long-range regulatory elements, which occur at a ∼10 µm nucleus in a spatiotemporal manner. In this way, three-dimensional chromatin conformation and structural biology are critical for interpreting the biological effects and the gene regulatory networks. In the review, we have briefly summarized the latest processes in three-dimensional chromatin conformation, microscopic imaging, and bioinformatics, and we have presented the outlook and future directions for these three aspects.
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Affiliation(s)
- Xiusheng Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qitong Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Animal Breeding and Genomics, Wageningen University & Research, Wageningen 6708PB, the Netherlands
| | - Jing Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Dashuai Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,College of Life Science and Engineering, Foshan University, Foshan, China
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