Single-stranded nucleic acid binding and coacervation by linker histone H1 (Leicher et al., NSMB 2022)
H1 coalesces around nascent ssDNA. (A) Schematic of the combined single-molecule fluorescence and force microscopy. A biotinylated λ-DNA molecule (48.5 kbp) is tethered between two streptavidin-coated polystyrene beads. (B) A representative kymograph of Cy3-H1 binding to DNA over time as the inter-bead distance was increased. (C) Total H1 signal across the DNA as a function of time for the kymograph shown in b. (D) Distribution of the H1 signal along the DNA at two specific time points (T1 and T2) as indicated by the arrows in b. a.u., arbitrary units. (E) Cartoon illustrating the distinct binding configurations of H1 on DNA under different tensions. ssDNA is created by force-induced unpeeling.
The linker histones H1 are key components of eukaryotic chromosomes and have been known to mediate chromatin compaction. H1 is also implicated in other DNA-templated processes such as DNA damage response, but the mechanisms for these non-canonical functions are less understood. In collaboration with the David Lab, we use single-molecule correlative fluorescence and force microscopy (smCFFM) to visualize the behavior of H1 on DNA under different tensions, which leads to the unexpected discovery that H1 preferentially forms phase-separated condensates with ssDNA over dsDNA. Using a droplet fusion assay controlled by optical tweezers, we find that the material properties of H1 condensates differ markedly between those formed with ssDNA (gel-like) versus dsDNA (liquid-like). These findings are corroborated by MD simulations performed by the Zhang Lab and in vivo imaging of H1 puncta. This study reveals that single-stranded nucleic acids are underappreciated interacting partners of H1, providing a fresh perspective for elucidating the non-architectural roles that various subtypes of linker histones differentially play inside the nucleus.
