NUCLEOSOME BINDING BY THE POLYMERASE-I TRANSACTIVATOR UPSTREAM BINDING-FACTOR DISPLACES LINKER HISTONE H1

Upstream binding factor (UBF) is a vertebrate RNA polymerase I transcr iption factor that can bend and wrap DNA, To investigate UBF's likely role as an architectural protein of rRNA genes organized in chromatin, we tested UBF's ability to bind rRNA gene enhancers assembled into nu cleosome cores (DNA plus core histones) and nucleosomes (DNA plus core histones plus histone H1). UBF bound with low affinity to nucleosome cores formed with enhancer DNA probes of 162 bp. However, on nucleosom e cores which contained similar to 60 bp of additional linker DNA, UBF bound with high affinity similar to its binding to naked DNA, forming a ternary DNA-core histone-UBF complex. UBF could be stripped from te rnary complexes with competitor DNA to liberate nucleosome cores, rath er than free DNA, suggesting that UBF binding to nucleosome cores does not displace the core histones H2A, H2B, H3, and H4. DNase I, microco ccal nuclease, and exonuclease III footprinting suggests that UBF and histone H1 interact with DNA on both sides flanking the histone octame r. Footprinting shows that UBF outcompetes histone H1 for binding to a nucleosome core and will displace, if not dissociate, H1 from its bin ding site on a preassembled nucleosome. These data suggest that UBF ma y act to prevent or reverse the assembly of transcriptionally inactive chromatin structures catalyzed by linker histone binding.