Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription
The spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To tackle this problem, we analyzed all stereochemically possible configurations of two-start chromatin fibers with DNA linkers L = 10-70 bp (nucleosome repeat length NRL = 157-217 bp). In our model, the energy of a f...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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AIMS Press
2015-11-01
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| Series: | AIMS Biophysics |
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| Online Access: | http://www.aimspress.com/biophysics/article/494/fulltext.html |
| _version_ | 1818011181784236032 |
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| author | Davood Norouzi Ataur Katebi Feng Cui Victor B. Zhurkin |
| author_facet | Davood Norouzi Ataur Katebi Feng Cui Victor B. Zhurkin |
| author_sort | Davood Norouzi |
| collection | DOAJ |
| description | The spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To tackle this problem, we analyzed all stereochemically possible configurations of two-start chromatin fibers with DNA linkers L = 10-70 bp (nucleosome repeat length NRL = 157-217 bp). In our model, the energy of a fiber is a sum of the elastic energy of the linker DNA, steric repulsion, electrostatics, and the H4 tail-acidic patch interaction between two stacked nucleosomes. We found two families of energetically feasible conformations of the fibers—one observed earlier, and the other novel. The fibers from the two families are characterized by different DNA linking numbers—that is, they are topologically different. Remarkably, the optimal geometry of a fiber and its topology depend on the linker length: the fibers with linkers L = 10<i>n</i> and 10<i>n</i> + 5 bp have DNA linking numbers per nucleosome D<i>Lk</i> >>-1.5 and -1.0, respectively. In other words, the level of DNA supercoiling is directly related to the length of the inter-nucleosome linker in the chromatin fiber (and therefore, to NRL). We hypothesize that this topological polymorphism of chromatin fibers may play a role in the process of transcription, which is known to generate different levels of DNA supercoiling upstream and downstream from RNA polymerase. A genome-wide analysis of the NRL distribution in active and silent yeast genes yielded results consistent with this assumption. |
| first_indexed | 2024-04-14T06:04:51Z |
| format | Article |
| id | doaj.art-941d297233974e86bc82d4b93f774993 |
| institution | Directory Open Access Journal |
| issn | 2377-9098 |
| language | English |
| last_indexed | 2024-04-14T06:04:51Z |
| publishDate | 2015-11-01 |
| publisher | AIMS Press |
| record_format | Article |
| series | AIMS Biophysics |
| spelling | doaj.art-941d297233974e86bc82d4b93f7749932022-12-22T02:08:37ZengAIMS PressAIMS Biophysics2377-90982015-11-012461362910.3934/biophy.2015.4.613201504613Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcriptionDavood Norouzi0Ataur Katebi1Feng Cui2Victor B. Zhurkin3Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USALaboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USAThomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623, USLaboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USAThe spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To tackle this problem, we analyzed all stereochemically possible configurations of two-start chromatin fibers with DNA linkers L = 10-70 bp (nucleosome repeat length NRL = 157-217 bp). In our model, the energy of a fiber is a sum of the elastic energy of the linker DNA, steric repulsion, electrostatics, and the H4 tail-acidic patch interaction between two stacked nucleosomes. We found two families of energetically feasible conformations of the fibers—one observed earlier, and the other novel. The fibers from the two families are characterized by different DNA linking numbers—that is, they are topologically different. Remarkably, the optimal geometry of a fiber and its topology depend on the linker length: the fibers with linkers L = 10<i>n</i> and 10<i>n</i> + 5 bp have DNA linking numbers per nucleosome D<i>Lk</i> >>-1.5 and -1.0, respectively. In other words, the level of DNA supercoiling is directly related to the length of the inter-nucleosome linker in the chromatin fiber (and therefore, to NRL). We hypothesize that this topological polymorphism of chromatin fibers may play a role in the process of transcription, which is known to generate different levels of DNA supercoiling upstream and downstream from RNA polymerase. A genome-wide analysis of the NRL distribution in active and silent yeast genes yielded results consistent with this assumption.http://www.aimspress.com/biophysics/article/494/fulltext.htmlchromatin fibernucleosome repeat lengthDNA linking numberDNA topologyregulation of transcription |
| spellingShingle | Davood Norouzi Ataur Katebi Feng Cui Victor B. Zhurkin Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription AIMS Biophysics chromatin fiber nucleosome repeat length DNA linking number DNA topology regulation of transcription |
| title | Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription |
| title_full | Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription |
| title_fullStr | Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription |
| title_full_unstemmed | Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription |
| title_short | Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription |
| title_sort | topological diversity of chromatin fibers interplay between nucleosome repeat length dna linking number and the level of transcription |
| topic | chromatin fiber nucleosome repeat length DNA linking number DNA topology regulation of transcription |
| url | http://www.aimspress.com/biophysics/article/494/fulltext.html |
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