Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Poster Abstracts

6-POS Board 6 Sequence-dependent Nucleosome Dynamics: Implications for Transcription Factor Binding Jan Huertas 1 , Caitlin M. MacCarthy 1 , Hans R. Schöler 1,2 , Vlad Cojocaru 1,3 . 1 Max Planck Institute for Molecular Biomedicine, Münster, Germany, 2 University of Münster, Münster, Germany, 3 University of Münster, Münster, Germany. Transcription factors are proteins that bind to DNA to regulate gene expression. In most cases, accessibility to DNA is a prerequisite for their function. However, in the nucleus the DNA is packed into chromatin, which is often inaccessible. The fundamental unit of chromatin is the nucleosome, in which 147 DNA basepairs are wrapped around a core of eight histone proteins. Interestingly, a series of transcription factors, known as pioneers, are able to bind to closed chromatin states, recognizing their binding sites even in the presence of nucleosomes. They can help open chromatin, increase DNA accessibility, and support binding of other transcription factors. For example, Oct4, a master regulator of stem cell pluripotency, is able to bind native nucleosomes in a sequence specific manner. We confirmed this experimentally and showed that Oct4 does not bind to nucleosomes with DNA sequences engineered to optimize the positioning of the histone core. Binding to such sequences was not observed even when canonical Oct4 binding sites were introduced using a systematic structural modeling approach. To understand the nucleosome properties that facilitate Oct4 binding, we performed 3µs of all- atom simulations of three nucleosomes with different DNA sequences, each with a characteristic Oct4 binding profile. Remarkably, we found that the nucleosome mobility correlates with the number of Oct4 factor binding sites available. We identified differences in dynamics and structural properties of the three nucleosomes, most of which are located in the regions known to be important for nucleosome unwrapping. Interestingly, the regions containing the Oct4 binding sites were characterized by higher mobility. We validated our findings by probing the stability of the nucleosomes in thermal unwrapping experiments. These findings suggest that nucleosome dynamics are determinant for the ability of pioneer transcription factors to recognize their binding sites in closed chromatin.

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