title: Nanopores suggest a negligible influence of CpG methylation on nucleosome packaging and stability.
abstract: Nucleosomes are the fundamental repeating units of chromatin, and dynamic regulation of their positioning along DNA governs gene accessibility in eukaryotes. Although epigenetic factors have been shown to influence nucleosome structure and dynamics, the impact of DNA methylation on nucleosome packaging remains controversial. Further, all measurements to date have been carried out under zero-force conditions. In this paper, we present the first automated force measurements that probe the impact of CpG DNA methylation on nucleosome stability. In solid-state nanopore force spectroscopy, a nucleosomal DNA tail is captured into a pore and pulled on with a time-varying electrophoretic force until unraveling is detected. This is automatically repeated for hundreds of nucleosomes, yielding statistics of nucleosome lifetime vs electrophoretic force. The force geometry, which is similar to displacement forces exerted by DNA polymerases and helicases, reveals that nucleosome stability is sensitive to DNA sequence yet insensitive to CpG methylation. Our label-free method provides high-throughput data that favorably compares with other force spectroscopy experiments and is suitable for studying a variety of DNA-protein complexes.
authors.affiliation: Lehrstuhl für Bioelektronik, Physics Department and ZNN/WSI, Technische Universität München , Am Coulombwall 4a, 85748 Garching, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Langecker
authors.forename: Andrey
authors.initials: A
authors.lastname: Ivankin
authors.forename: Spencer
authors.initials: S
authors.lastname: Carson
authors.forename: Shannon R M
authors.initials: SR
authors.lastname: Kinney
authors.forename: Friedrich C
authors.initials: FC
authors.lastname: Simmel
authors.forename: Meni
authors.initials: M
authors.lastname: Wanunu
mesh_terms: D018899:CpG Islands; D004247:DNA / Q000737:chemistry*; D019175:DNA Methylation; D058608:Nanopores; D009707:Nucleosomes / Q000737:chemistry*
chemical_list: D009707:Nucleosomes; D004247:DNA
keywords: force; methylation; nanopore; nucleosome; solid-state; spectroscopy