Linker Histone Interaction Shows Divalent Character with both Supercoiled and Linear DNA

Abstract

The interaction of linker histone H1 with both linear and superhelical double-stranded DNA has been investigated at low ionic strengths. Gel mobility retardation experiments demonstrate strikingly different behavior for the two forms of DNA. First, the experiments strongly suggest that linker histone binds to superhelical DNA in a negatively cooperative mode. In contrast, binding of linker histone to linear DNA under the conditions employed here shows no cooperativity. Second, binding of linker histone to linear DNA results in aggregation of histone-DNA complexes, even at very low levels of input histone H1. Because H1 has been shown to interact as a monomer, this aggregation is evidence of the divalent character of the linker histone, for without H1's ability to bind to two duplex strands of DNA, aggregation could not occur. Although aggregation can be made to occur with superhelical DNA, it can do so only at near-saturation levels of input histone H1. Finally, in direct competition, linker histone binds to superhelical DNA to the complete exclusion of linear DNA, indicating that the linker histone's function is related to the crossover structures that differentiate superhelical DNA from linear DNA. We develop a model that explains the observed behavior of binding of linker histone to superhelical DNA that is consistent with both the divalent character of the linker histone and the negative cooperativity by which linker histone and superhelical DNA interact.

DNA coiled coils

“…Under such conditions, local supercoiled structures may be formed. Some proteins also prefer binding to supercoiled DNA (25). In any case, the structures we have found add a previously unrecognized element to the numerous architectures that can be built from DNA oligonucleotides (26).…”

Functional characterization of domains in AtTRB1, a putative telomere-binding protein in Arabidopsis thaliana

“…ever, telomeric dsDNA did not compete for the interaction as efficiently, and the non-telomeric probe was not released from the complex. This shows that the H1/5 domain interacts non-specifically with any DNA without preference for either telomeric or non-telomeric sequence (Ellen and van Holde, 2004) which, together with the high pI of the AtTRB1 fragments, suggests that electrostatic interactions take part in the interaction of the fragments of AtTRB1 with telomeric dsDNA. This may interfere with determining the sequence specificity of AtTRB1 binding to telomeric DNA.…”

Relevance of Arginines in the Mode of Binding of H1 Histones to DNA

“…The interaction appears to be a complex phenomenon dependent upon the ionic conditions (Clark and Kimura, 1990), DNA topology (Ellen and van Holde, 2004), and protein to DNA ratio. Studies on the mode of binding of H1 histones to DNA have indicated the presence of two potential DNA-binding sites on the globular domain of this histone, in addition to the binding groups of the positively charged N-and C-terminal tails (Cerf et al, 1993;Ramakrishnan et al, 1993;Goytisolo et al, 1996).…”

“…We present here studies on the effect of the addition of sperm and somatic H1 histones on the electrophoretic mobility of linear and circular DNA molecule analyzed by electrophoretic mobility shift assay (EMSA) (Clark and Thomas, 1986;Ellen and van Holde, 2004). Analyses have been performed on native and on lysine-or arginine-modified histones.…”