Molecular Mechanism of Spontaneous Nucleosome Unraveling

David Winogradoff, and Aleksei Aksimentiev
Journal of Molecular Biology 431(2) 323-335 (2019)
DOI:10.1016/j.jmb.2018.11.013  BibTex

Highlight

Meters of DNA wrap around histone proteins to form nucleosomes and fit inside the micron-diameter nucleus. For the genetic information encoded in the DNA to become available for transcription, replication and repair, the DNA--histone assembly must be disrupted. Experiment has indicated that the outer stretches of nucleosomal DNA "breathe" by spontaneously detaching from and reattaching to the histone core. Here, we report direct observation of spontaneous DNA breathing in atomistic molecular dynamics simulations, detailing a microscopic mechanism of the DNA breathing process. According to our simulations, the outer stretches of nucleosomal DNA detach in discrete steps involving five or ten base pairs, with the detachment process being orchestrated by the motion of several conserved histone residues. The inner stretches of nucleosomal DNA are found to be more stably associated with the histone core by more abundant nonspecific DNA--protein contacts, providing a microscopic interpretation of nucleosome unraveling experiments. The CG content of nucleosomal DNA is found to anticorrelate with the extent of unwrapping, supporting the possibility that AT-rich segments may signal the start of transcription by forming less stable nucleosomes.

Abstract

Meters of DNA wrap around histone proteins to form nucleosomes and fit inside the micron-diameter nucleus. For the genetic information encoded in the DNA to become available for transcription, replication and repair, the DNA--histone assembly must be disrupted. Experiment has indicated that the outer stretches of nucleosomal DNA "breathe" by spontaneously detaching from and reattaching to the histone core. Here, we report direct observation of spontaneous DNA breathing in atomistic molecular dynamics simulations, detailing a microscopic mechanism of the DNA breathing process. According to our simulations, the outer stretches of nucleosomal DNA detach in discrete steps involving five or ten base pairs, with the detachment process being orchestrated by the motion of several conserved histone residues. The inner stretches of nucleosomal DNA are found to be more stably associated with the histone core by more abundant nonspecific DNA--protein contacts, providing a microscopic interpretation of nucleosome unraveling experiments. The CG content of nucleosomal DNA is found to anticorrelate with the extent of unwrapping, supporting the possibility that AT-rich segments may signal the start of transcription by forming less stable nucleosomes.

Movie 1. Widom 601L nucleosome in 0.150 M NaCl. Animation illustrating the 2-μs MD trajectory of a nucleosome featuring the Widom 601L DNA sequence in 0.150 M NaCl. Colors highlight the histone core (white), surrounding DNA (dark gray), and histone residues H3 His39 and H2A Arg77 (red).

Movie 2. Widom 601L nucleosome in 1.0 M MgCl2. Animation illustrating the 2-μs MD trajectory of a nucleosome featuring the Widom 601L DNA sequence in 1.0 M MgCl2. Colors highlight the histone core (white), surrounding DNA (green), and histone residues H3 His39 and H2A Arg77 (red).

Movie 3. Widom 601L nucleosome in 3.0 M NaCl. Animation illustrating the 2-μs MD trajectory of a nucleosome featuring the Widom 601L DNA sequence in 3.0 M NaCl. Colors highlight the histone core (white), surrounding DNA (cyan), and histone residues H3 His39 and H2A Arg77 (red).

Movie 4. Widom 601L DNA only in 1.0 M MgCl2. Animation illustrating the 0.30-μs MD trajectory of the Widom 601L DNA sequence in 1.0 M MgCl2, starting in a super-helically wound state, excluding the histone core. DNA shown in green.

Movie 5. Poly-AT nucleosome in 1.0 M MgCl2. Animation illustrating the 2-μs MD trajectory of a nucleosome featuring the poly-AT DNA sequence (i.e., ATAT…) in 1.0 M MgCl2. Colors highlight the histone core (white) and surrounding DNA (red).

Movie 6. 5S RNA gene nucleosome in 1.0 M MgCl2. Animation illustrating the 2-μs MD trajectory of a nucleosome featuring the 5S RNA gene DNA sequence in 1.0 M MgCl2. Colors highlight the histone core (white) and surrounding DNA (orange).

Movie 7. Poly-GC nucleosome in 1.0 M MgCl2. Animation illustrating the 2-μs MD trajectory of a nucleosome featuring the poly-GC DNA sequence (i.e., GCGC…) in 1.0 M MgCl2. Colors highlight the histone core (white) and surrounding DNA (blue).