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Albany 2019: 20th Conversation - Abstracts

category image Albany 2019
Conversation 20
June 11-15 2019
Adenine Press (2019)

How do DNA binding proteins interpret and modulate nucleosome dynamics ?

I will present our recent efforts to explore how linker histones and pioneer transcription factors interpret and modulate nucleosome dynamics to bind DNA wrapped around histones. Linker histones (LH) bind to nucleosomes in a 1:1 stoichiometry to form chromatosomes and to compact chromatin fibers. The geometry of the chromatosome remains debated. Different structures of the LH-nucleosome complex solved experimentally or proposed from computer simulations revealed alternative binding modes for the linker histone to nucleosomes. From Brownian and molecular dynamics simulations, we proposed that there is an ensemble of chromatosome structures. The LH isoform, nucleosome dynamics and DNA sequence are all factors that influence the LH binding mode to nucleosomes. Whereas LH proteins recognize nucleosomes in a sequence independent manner, the pioneer transcription factors (TFs) are a subclass of TFs that are able to recognize sequence specific binding sites on DNA wrapped in nucleosomes to regulate gene expression. Pioneer TFs were proposed to contribute to chromatin opening. Many of these factors are involved in cell identity transitions, and therefore they are of special importance for regenerative therapies. For example, the master regulators of stem cell pluripotency, Oct4 and Sox2 were proposed to be pioneer TFs. The structural basis for the pionner factor- nucleosome binding remains unknown. Moreover, it is still not understood if the binding of TFs to nucleosomes has a direct impact on nucleosome dynamics. To characterize the structural basis for Oct4-nucleosome recognition, we first performed molecular dynamics simulations of 3 nucleosomes: one with an artificial DNA sequence optimized for nucleosome stability and 2 with native DNA sequences containing 1 or multiple Oct4 binding sites respectively. We found that the nucleosome with multiple Oct4 binding sites was the most mobile. Interestingly, the amplitude of breathing and twisting motions in the DNA which were observed in all nucleosomes, was increased in the nucleosome with multiple Oct4 binding sites. Using an approach that combines structural modeling, molecular dynamics simulations with experimental approaches, we built different models of Oct4-nucleosome complexes and show that alternative but not all possible configurations are stable and compatible with the DNA curvature and DNA-histone interactions.

References:

    Öztürk MA, Cojocaru V, Wade RC (2018). Towards an ensemble view of the linker histone - nucleosome complex structure: A paradigm shift from one to many. Structure, 28(8), 1050-1057

    Öztürk MA, Cojocaru V, Wade RC (2018). Dependence of chromatosome structure on linker histone sequence and post-translational modifications. Biophys J., 114(10), 2363-2375

    Öztürk M, Pachov G, Wade RC, and Cojocaru V (2016). Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome. Nucleic Acids Research, 44(14), 6599–6613, doi: 10.1093/nar/gkw514

    Huertas J., MacCarthy C., Schöler H. R. (2019). Do transcription factors interpret nucleosome dynamics ? In preparation

Vlad Cojocaru

In Silico Biolmolecular Structure and Dynamics Group
The Hubrecht Institute for Developmental Biology and Stem Cell Research
Uppsalalaan8, 3584 CT
Utrecht, the Netherlands

Email: vlad.cojocaru@mpi-muenster.mpg.de