In silico evidence for sequence-dependent nucleosome sliding

Journal Article · 17 October 2017 · Proceedings of the National Academy of Sciences of the United States of America

DOI: https://doi.org/10.1073/pnas.1705685114 · OSTI ID:1400015

Lequieu, Joshua  ^[1]; Schwartz, David C. ^[2]; de Pablo, Juan J. ^[3]

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1. Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637,
2. Laboratory for Molecular and Computational Genomics, Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706,, Laboratory of Genetics, University of Wisconsin–Madison, Madison, WI 53706,, UW-Biotechnology Center, University of Wisconsin–Madison, Madison, WI 53706,
3. Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637,, Materials Science Division, Argonne National Laboratory, Argonne, IL 60439

Significance The dynamic compaction of DNA into chromatin is essential for gene expression. Errors during compaction are associated with numerous diseases. Several molecular factors are known to affect chromatin dynamics, but their relative importance and the interplay between them are poorly understood. A detailed molecular model is used here to examine chromatin dynamics at the level of its most fundamental building block, namely the nucleosome. Nucleosome dynamics are demonstrated to be encoded in the DNA sequence itself, and key fundamental factors are uncovered that can significantly alter these dynamics at the molecular level. The results serve to complete a hitherto unavailable description of nucleosome dynamics by introducing previously unappreciated molecular processes, with the potential to influence macroscopic chromatin structure and genetics.

• Research Organization: Argonne National Lab. (ANL), Argonne, IL (United States)
• Sponsoring Organization: Midwest Integrated Center for Computational Materials (MICCoM); National Institute of Standards and Technology (NIST), Center for Hierarchical Materials Design (CHiMaD); National Institutes of Health (NIH), National Human Genome Research Institute (NHGRI); U.S. Department of Commerce; USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division
• Grant/Contract Number: AC02-06CH11357
• OSTI ID: 1400015
• Journal Information: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 44 Vol. 114; ISSN 0027-8424
• Publisher: Proceedings of the National Academy of SciencesCopyright Statement
• Country of Publication: United States
• Language: English