Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast
During the repair of double-strand breaks (DSBs) in DNA, active mobilizations for conformational changes in chromosomes have been widely observed in eukaryotes, from yeast to animal and plant cells. DSB-damaged loci in the yeast genome showed increased mobility and relocation to the nuclear peripher...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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The Biophysical Society of Japan
2022-04-01
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| Series: | Biophysics and Physicobiology |
| Subjects: | |
| Online Access: | https://doi.org/10.2142/biophysico.bppb-v19.0012 |
| _version_ | 1818009959068073984 |
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| author | Shinjiro Nakahata Tetsushi Komoto Masashi Fujii Akinori Awazu |
| author_facet | Shinjiro Nakahata Tetsushi Komoto Masashi Fujii Akinori Awazu |
| author_sort | Shinjiro Nakahata |
| collection | DOAJ |
| description | During the repair of double-strand breaks (DSBs) in DNA, active mobilizations for conformational changes in chromosomes have been widely observed in eukaryotes, from yeast to animal and plant cells. DSB-damaged loci in the yeast genome showed increased mobility and relocation to the nuclear periphery. However, the driving forces behind DSB-induced chromatin dynamics remain unclear. In this study, mathematical models of normal and DSB-damaged yeast chromosomes were developed to simulate their structural dynamics. The effects of histone degradation in the whole nucleus and the change in the physical properties of damaged loci due to the binding of SUMOylated repair proteins were considered in the model of DSB-induced chromosomes based on recent experimental results. The simulation results reproduced DSB-induced changes to structural and dynamical features by which the combination of whole nuclear histone degradation and the rigid structure formation of repair protein accumulations on damaged loci were suggested to be primary contributors to the process by which damaged loci are relocated to the nuclear periphery. |
| first_indexed | 2024-04-14T05:49:24Z |
| format | Article |
| id | doaj.art-4cc366be19394df6bb79444c137dee93 |
| institution | Directory Open Access Journal |
| issn | 2189-4779 |
| language | English |
| last_indexed | 2024-04-14T05:49:24Z |
| publishDate | 2022-04-01 |
| publisher | The Biophysical Society of Japan |
| record_format | Article |
| series | Biophysics and Physicobiology |
| spelling | doaj.art-4cc366be19394df6bb79444c137dee932022-12-22T02:09:11ZengThe Biophysical Society of JapanBiophysics and Physicobiology2189-47792022-04-011910.2142/biophysico.bppb-v19.0012Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeastShinjiro Nakahata0Tetsushi Komoto1Masashi Fujii2Akinori Awazu3Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, JapanGraduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, JapanGraduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, JapanGraduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, JapanDuring the repair of double-strand breaks (DSBs) in DNA, active mobilizations for conformational changes in chromosomes have been widely observed in eukaryotes, from yeast to animal and plant cells. DSB-damaged loci in the yeast genome showed increased mobility and relocation to the nuclear periphery. However, the driving forces behind DSB-induced chromatin dynamics remain unclear. In this study, mathematical models of normal and DSB-damaged yeast chromosomes were developed to simulate their structural dynamics. The effects of histone degradation in the whole nucleus and the change in the physical properties of damaged loci due to the binding of SUMOylated repair proteins were considered in the model of DSB-induced chromosomes based on recent experimental results. The simulation results reproduced DSB-induced changes to structural and dynamical features by which the combination of whole nuclear histone degradation and the rigid structure formation of repair protein accumulations on damaged loci were suggested to be primary contributors to the process by which damaged loci are relocated to the nuclear periphery.https://doi.org/10.2142/biophysico.bppb-v19.0012chromatindna double-strand breakhistone degradationrepair protein accumulations |
| spellingShingle | Shinjiro Nakahata Tetsushi Komoto Masashi Fujii Akinori Awazu Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast Biophysics and Physicobiology chromatin dna double-strand break histone degradation repair protein accumulations |
| title | Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast |
| title_full | Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast |
| title_fullStr | Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast |
| title_full_unstemmed | Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast |
| title_short | Mathematical model of chromosomal dynamics during DNA double strand break repair in budding yeast |
| title_sort | mathematical model of chromosomal dynamics during dna double strand break repair in budding yeast |
| topic | chromatin dna double-strand break histone degradation repair protein accumulations |
| url | https://doi.org/10.2142/biophysico.bppb-v19.0012 |
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