We developed a method to multiplex single-molecule studies of modified chromatin substrates, termed XSCAN (Makasheva et al., JACS 2021). This method now enables us to detect chromatin interaction dynamics of DNA damage factors to multiple differently modified chromatin fibers at the same time in one single-molecule measurement, which allows us to directly determine how such protein read-out the histone PTM code in real time. We could apply this methodology to reveal how the genome editor Cas9 can invade nucleosomes, and the methods is now applied in various project to decode chromatin regulation.
We have investigated chromatin ubiquitylation by two E3 ligases, involved in DNA repair and gene repression, RNF168 and variant PRC1 (vPRC1). Utilizing chemical methods to synthesize ubiquitylated H1, we could show that the activity of RNF168 is stimulated by distinct polyubiquitinated H1 molecules within chromatin. We further developed methods to observe vPRC1 interaction dynamics with chromatin, and even directly detected chromatin ubiquitination reactions on the single-molecule scale. These studies provide novel insights how chromatin ubiquitin ligases are regulated.
We have developed methodologies to directly observe chromatin structure and dynamics, producing the first landscape for chromatin dynamics. This involved the combination of different single-molecule methods (in collaboration with Prof. C. Seidel, U. Düsseldorf) with a novel data analysis pipeline and theoretical modeling (Kilic et al., Nat. Commun. 2018).
We developed methods to synthesize histone proteins containing DNA damage related histone PTMs, and revealed that one of those modifications – ubiquitylation on lysine 15 in histone H2A – unravels chromatin fibers to facilitate repair processes (Kilic, Boichenko et al., Chem. Sci. 2018).
Another H2A modification, ubiquitination on K119 (H2Aub1), is critical for gene silencing during development. In collaboration with Prof. J. Müller, MPI Biochemistry, we observed however that excess of H2Aub1 disrupted chromatin silencing. Single-molecule imaging revealed that chromatin containing high levels of H2Aub1 is no longer able to compact and thus genes are derepressed. These experiments reveal that the exact balance of H2A ubiquitination is critical for development (Bonnet et al. Genes Dev 2022).
DNA binding proteins exploit chromatin dynamics to invade chromatin structure. We have observed how pioneer transcription factors can invade and open chromatin structure (Mivelaz et al., Mol Cell 2020), and how histone variants, such as the centromeric histone CENP-A, alter chromatin structure to allow DNA access for DNA binding factors (Nagpal & Fierz, bioRxiv, 2022).
Together, these studies show that chromatin structure is highly dynamic and directly regulated by PTMs and histone variants, enabling chromatin invasion of regulatory factors.
The overall results of this project have disseminated in various conferences and scientific meetings, and have been published in peer-reviewed manuscripts, including:
1. Kilic, S., Boichenko, I., Lechner C. and Fierz B., A bi-terminal protein ligation strategy to probe chromatin structure during DNA damage, Chemical Science, 2018, 9, 3704-3709
2. Multiplexed Single-Molecule Experiments Reveal Nucleosome Invasion Dynamics of the Cas9 Genome Editor, Makasheva K., Bryan, L.C. Anders, C., Panikularm, S., Jinek, M., Fierz, B., J. Am. Chem. Soc., 2021, 143, 40, 16313–16319
3. Kilic, S., Felekyan S., Doroshenko O., Boichenko I., Dimura M., Vardanyan H, Bryan LC., Arya G, Seidel, CAM* & Fierz B.*, Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α, Nature Commun., 2018, 9(1):235.
4. Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor, Mivelaz, M., Cao, A.-M. Kubik, S., Zencir, S., Hovius, R., Boichenko, I., Stachowicz, A.M. Kurat, C.F. Shore, D., Fierz B., Mol. Cell, 2020, p488-500.e9
5. Bonnet J, Boichenko I, Kalb R, Le Jeune M, Maltseva S, Pieropan M, Finkl K, Fierz B*, Müller J*. PR-DUB preserves Polycomb repression by preventing excessive accumulation of H2Aub1, an antagonist of chromatin compaction. Genes Dev. 2022 Nov 10. doi: 10.1101/gad.350014.122.
