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Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA

Hisashi Ishida1*, Hidetoshi Kono1*

1 National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan

* Corresponding authors emails: ishida.hisashi@qst.go.jp, kono.hidetoshi@qst.go.jp
DOI10.24435/materialscloud:r9-xt [version v1]

Publication date: Jan 27, 2021

How to cite this record

Hisashi Ishida, Hidetoshi Kono, Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA, Materials Cloud Archive 2021.23 (2021), doi: 10.24435/materialscloud:r9-xt.

Description

Torsional stress has a significant impact on the structure and stability of the nucleosome. RNA polymerase imposes torsional stress on the DNA in chromatin and unwraps the DNA from the nucleosome to access the genetic information encoded in the DNA. To understand how the torsional stress affects the stability of the nucleosome, we examined the unwrapping of two half superhelical turns of nucleosomal DNA from either end of the DNA under torsional stress with all-atom molecular dynamics simulations. The free energies for unwrapping the DNA indicate that positive stress that overtwists DNA facilitates a large-scale asymmetric unwrapping of the DNA without a large extension of the DNA. During the unwrapping, one end of the DNA was dissociated from H3 and H2A-H2B while the other end of the DNA stably remained wrapped. The detailed analysis indicates that this asymmetric dissociation is facilitated by the geometry and bendability of the DNA under positive stress. The geometry stabilized the interaction between the major groove of the twisted DNA and the H3 αN-helix, and the straightened DNA destabilized the interaction with H2A-H2B. Under negative stress, the DNA became more bendable and flexible, which facilitated the binding of the unwrapped DNA to the octamer in a stable state. Consequently, we conclude that the torsional stress has a significant impact on the affinity of the DNA and the octamer through the inherent nature of the DNA, and can change the accessibility of regulatory proteins.

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Files

File name Size Description
README.txt
MD5md5:a82d6093544286fb7a58be1952a39a85
3.5 KiB README
prmtop
MD5md5:3f7ef8c39c52add2082cb9946ac95968
8.3 MiB parameter/topology file (amber-format) to visualize the nucleosome using VMD software
Figure1.tar.gz
MD5md5:767758115ff19a176efd6d3f8a735478
314.6 KiB coordinate of the nucleosome (pdb-format) for Figure 1
Figure3.tar.gz
MD5md5:eb94d768c893b9e0133fccdd001f8b9b
5.5 MiB coordinate of the nucleosoem (pdb-format) for Figure 3
Trajectory_posi.tar.gz
MD5md5:64e19ae355bf52cdc8b114898ecd6778
713.4 MiB trajectory of the nucleosome (mdcrd-format) under positive stress
Trajectory_nega.tar.gz
MD5md5:c3832a3b96c585b86b78893453b95d48
713.8 MiB trajectory of the nucleosome (mdcrd-format) under negative stress
Trajectory_none.tar.gz
MD5md5:75ee33fa7a67466a713c140a6aa5e417
713.6 MiB trajectory of the nucleosome (mdcrd-format) under no stress

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

Keywords

nucleosome unwrapping DNA bendability torsional stress

Version history:

2021.23 (version v1) [This version] Jan 27, 2021 DOI10.24435/materialscloud:r9-xt