Revealing the conformational landscape of nucleosomes
22 Mar 2022
A team of scientists led by Professor Jan Lipfert have developed a high-throughput pipeline to image nucleosomes using atomic force microscope imaging to reveal the conformational ensemble of nucleosome structures.
In each of our cells, the 2 m-long DNA genome needs to be packed into a ~10 µm-sized nucleus, yet remain accessible for read out and replication. This feat is achieved through hierarchical interactions with proteins and organization into chromatin. The fundamental units of chromatin are nucleosomes, which consist of ~150 base pairs of DNA wrapped around a core of histone proteins.
A team of scientists led by Professor Jan Lipfert in the Department of Physics have developed a high-throughput pipeline to image nucleosomes using atomic force microscope imaging to reveal the conformational ensemble of nucleosome structures. Using a state-of-the-art AFM and optimized sample preparation and imaging protocols, PhD student Sebastian Konrand and Postdoc Willem Vanderlinden managed to obtain >1000 individual nucleosome images in a single field of view. Analyzing such enormous data sets by hand would be tedious and prone to user bias. Therefore, the team created an analysis pipeline using tools from machine learning and image processing to assign and analyse the molecular structures in a fully automated fashion. Their results reveal how nucleosomes can “breathe”, i.e. how the DNA can dynamically fluctuate and unwrap from the histone core.
They researchers were particular interested in how nucleosome conformations are altered by epigenetic modifications, i.e. by chemical marks or “annotations” on the histone proteins that are known to play a major role in regulating the read out of our genome and are critical in ageing. They find that DNA unwrapping occurs in steps of 5 base pairs and can indeed be strongly affected by epigenetic marks.
Konrad SF, Vanderlinden W, Lipfert J. Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging. Biophys J. 2022 Mar 1;121(5):841-851. doi: 10.1016/j.bpj.2022.01.014.
Konrad SF, Vanderlinden W, Lipfert J A High-throughput Pipeline to Determine DNA and Nucleosome Conformations by AFM Imaging. Bio Protoc, 2021 Oct 5;11(19):e4180, doi: 10.21769/BioProtoc.4180.
Konrad SF, Vanderlinden W, Frederickx W, Brouns T, Menze BH, De Feyter S, Lipfert J High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes. Nanoscale, 2021 Mar 18;13(10):5435-5447, doi: 10.1039/d0nr08564b.