DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study.
In eukaryotes, DNA achieves a highly compact structure primarily due to its winding around the histone cores. The nature wrapping of DNA around histone core form a 1.7 left-handed superhelical turns, contributing to negative supercoiling in chromatin. During transcription, negative supercoils genera...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2025-01-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://doi.org/10.1371/journal.pcbi.1012362 |
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| author | Chunhong Long Hongqiong Liang Biao Wan |
| author_facet | Chunhong Long Hongqiong Liang Biao Wan |
| author_sort | Chunhong Long |
| collection | DOAJ |
| description | In eukaryotes, DNA achieves a highly compact structure primarily due to its winding around the histone cores. The nature wrapping of DNA around histone core form a 1.7 left-handed superhelical turns, contributing to negative supercoiling in chromatin. During transcription, negative supercoils generated behind the polymerase during transcription may play a role in triggering nucleosome reassembly. To elucidate how supercoils influence the dynamics of wrapping of DNA around the histone cores, we developed a novel model to simulate the intricate interplay between DNA and histone. Our simulations reveal that both positively and negatively supercoiled DNAs are capable of wrapping around histone cores to adopt the nucleosome conformation. Notably, our findings confirm a strong preference for negative supercoiled DNA during nucleosome wrapping, and reveal that the both of the negative writhe and twist are beneficial to the formation of the DNA wrapping around histone. Additionally, the simulations of the multiple nucleosomes on the same DNA template indicate that the nucleosome tends to assemble in proximity to the original nucleosome. This advancement in understanding the spontaneous formation of nucleosomes may offer insights into the complex dynamics of chromatin assembly and the fundamental mechanisms governing the structure and function of chromatin. |
| format | Article |
| id | doaj-art-d692bbf118974dc9bfb304f7194ef25e |
| institution | Kabale University |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-d692bbf118974dc9bfb304f7194ef25e2025-02-09T05:30:27ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582025-01-01211e101236210.1371/journal.pcbi.1012362DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study.Chunhong LongHongqiong LiangBiao WanIn eukaryotes, DNA achieves a highly compact structure primarily due to its winding around the histone cores. The nature wrapping of DNA around histone core form a 1.7 left-handed superhelical turns, contributing to negative supercoiling in chromatin. During transcription, negative supercoils generated behind the polymerase during transcription may play a role in triggering nucleosome reassembly. To elucidate how supercoils influence the dynamics of wrapping of DNA around the histone cores, we developed a novel model to simulate the intricate interplay between DNA and histone. Our simulations reveal that both positively and negatively supercoiled DNAs are capable of wrapping around histone cores to adopt the nucleosome conformation. Notably, our findings confirm a strong preference for negative supercoiled DNA during nucleosome wrapping, and reveal that the both of the negative writhe and twist are beneficial to the formation of the DNA wrapping around histone. Additionally, the simulations of the multiple nucleosomes on the same DNA template indicate that the nucleosome tends to assemble in proximity to the original nucleosome. This advancement in understanding the spontaneous formation of nucleosomes may offer insights into the complex dynamics of chromatin assembly and the fundamental mechanisms governing the structure and function of chromatin.https://doi.org/10.1371/journal.pcbi.1012362 |
| spellingShingle | Chunhong Long Hongqiong Liang Biao Wan DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. PLoS Computational Biology |
| title | DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. |
| title_full | DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. |
| title_fullStr | DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. |
| title_full_unstemmed | DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. |
| title_short | DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study. |
| title_sort | dna spontaneously wrapping around a histone core prefers negative supercoiling a brownian dynamics study |
| url | https://doi.org/10.1371/journal.pcbi.1012362 |
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