Structural rearrangement of the histone octamer translocates DNA

• Applicant: Professor Dr. Mario Halic
• Subject Area: Structural Biology
• Term: from 2018 to 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 391636399

The packaging of DNA into chromatin regulates access to genetic material. The basic building block of chromatin is the nucleosome, which contains 150 base pairs (bp) of DNA wrapped around an octamer composed of two copies of histones H2A, H2B, H3, and H4. Nucleosomes are highly dynamic and can move along the DNA in an uncatalyzed or chromatin remodeling enzyme-driven way. Uncatalyzed nucleosome sliding is an intrinsic property of nucleosomes and resembles sliding achieved by chromatin remodeling enzymes. In cells, nucleosomes are positioned on DNA with the help of various chromatin remodelers. Mutations in chromatin remodelers strongly associate with or even drive cancers showing the importance of nucleosome organization in genome stability. Despite the importance of nucleosome remodeling, relatively little is known about the structural mechanisms of histone octamer translocation on the DNA.Using cryo EM we solved structures of the nucleosome with different organization of the histone octamer and DNA at 4.3 Å and 5.0 Å. We found that the histone octamer goes through conformational changes that distort the overall nucleosome structure. Rearrangements in the histone core a-helices move DNA gyres and induce strain that distorts the DNA. Our data show that the histone octamer is plastic and that structural changes in the histone octamer move DNA. This intrinsic plasticity of the nucleosome is exploited by chromatin remodelers and might be used by other chromatin machineries as well. Our current resolution is, however, not sufficient to observe DNA translocation at the nucleotide level. In this project our goal is to improve the resolution of our current structures to be able to resolve bases in DNA (~3.5 Å). This will allow us to follow single nucleotides in the DNA and will explain the mechanism of DNA translocation by the histone octamer. In addition to current constructs, we will also assemble nucleosomes with different DNA sequences and with histone mutants that promote uncatalyzed nucleosome sliding. Using these constructs we aim to obtain additional conformations showing intermediates of DNA translocation by the histone octamer.

• DFG Programme: Research Grants