Biochemical studies have implicated both nucleosome core assembly and/or the subsequent binding of the linker histone H1 in transcriptional repression (4 -9). Because the affinities of sequence-specific DNA-binding proteins for nucleosomal DNA are often dramatically reduced compared with free DNA (reviewed in Ref. 10), nucleosomes repress the transcriptional process, at least in part, by inhibiting access of activator proteins to their cognate binding sites in chromatin. Factor occupancy of binding sites in nucleosomal arrays is most likely achieved through multiple mechanisms involving nucleosome disruption, nucleosome displacement in trans, or histone octamer sliding in cis (reviewed in Ref. 11). The idea of mobile nucleosomes (i.e. nucleosome sliding) is attractive in that it has the potential to create transient accessibility of factors to their binding sites. Its potential importance is further implicated in studies that illustrate the differential affinity of factors for sites at different translational and rotational positions within nucleosomes (12-15). Using a model system consisting of chromatin assembled on tandemly repeated sea urchin 5 S rRNA nucleosome positioning sequences (16), Bradbury and colleagues (17, 18) have previously reported that nucleosomes adopt a dominant position surrounded by minor positions 10 base pairs apart (i.e. in the same rotational frame). These data indicate that the cluster of octamer positions is in dynamic equilibrium in low ionic strength conditions. In the presence of the linker histone H1, this mobility is inhibited (19). The same group found that this short range sliding behavior also applies to bulk mononucleosomes and nucleosomes reconstituted onto sequences of the Alu family of ubiquitous repeats. Thus, they proposed that nucleosome mobility is a general behavior (20). Moreover, H1-mediated reduction in nucleosome mobility has been implicated in repression of transcription of a dinucleosome reconstituted onto a dimerized Xenopus somatic 5 S rRNA gene (2).In our previous studies, we reported for the first time direct inhibition of factor binding by the association of H1 with nucleosome cores. The binding of H1 to form a chromatosome significantly repressed the subsequent binding of USF 1 but only slightly inhibited GAL4-AH binding (1). In this report, we extend these studies to explore the underlying mechanisms by which H1 repressed USF binding. The results illustrate H1-mediated repression of USF binding to a stably positioned nucleosome. Thus, H1 repression in this instance occurred in the absence of nucleosome mobility. In addition, H1 repressed USF binding to a site on the opposite side of the histone octamer from the entry and exit points of the linker DNA. These data are consistent with a mechanism by which H1 stabilizes histone octamer-DNA interactions, thus reducing transient exposure of factor binding sites.
MATERIALS AND METHODSPreparation of DNA Probes-The 183-bp probe DNAs, referred to as GU or UG probes, were either directly generated by BamHI digesti...