DNA sequence-dependent positioning of the linker histone in a nucleosome: a single-pair FRET study

Abstract

The linker histone (LH) associates with the nucleosome with its globular domain (gH) binding in an on or off-dyad binding mode. The positioning of the LH may play a role in the compaction of higher-order structures of chromatin. Preference for different binding modes has been attributed to the LH’s amino acid sequence. We here study the effect of the linker DNA (L-DNA) sequence on the positioning of a full-length LH, Xenopus laevis H1.0b, by employing single-molecule FRET spectroscopy. Chromatosomes were fluorescently labelled on one of the two 40bp long L-DNA arms, and on the gH. We varied 11bp of DNA flanking the core (non-palindromic Widom 601) of each chromatosome construct, making them either A-tract, purely GC, or mixed, with 64% AT. The gH consistently exhibited higher FRET efficiency with the L-DNA containing the A-tract, than that with the pure-GC stretch, even when the stretches were swapped. However, it did not exhibit higher FRET efficiency with the L-DNA containing 64% AT-rich mixed DNA, compared to the pure-GC stretch. We explain our observations with a FRET-distance restrained model that shows that the gH binds on-dyad and that two arginines mediate recognition of the A-tract via its characteristically narrow minor groove.