The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA.

Abstract

Upstream binding factor (UBF) is an important transactivator of RNA polymerase I and is a member of a family of proteins that contain nucleic acid binding domains named high-mobility-group (HMG) boxes because of their similarity to HMG chromosomal proteins. UBF is a highly sequence-tolerant DNA-binding protein for which no binding consensus sequence has been identified. Therefore, it has been suggested that UBF may recognize preformed structural features of DNA, a hypothesis supported by UBF's ability to bind synthetic DNA cruciforms, four-way junctions, and even tRNA. We show here that full-length UBF can also bend linear DNA to mediate circularization of probes as small as 102 bp in the presence of DNA ligase. Longer probes in the presence of UBF become positively supercoiled when ligated, suggesting that UBF wraps the DNA in a right-handed direction, opposite the direction of DNA wrapping around a nucleosome. The dimerization domain and HMG box 1 are necessary and sufficient to circularize short probes and supercoil longer probes in the presence of DNA ligase. UBF's sequence tolerance coupled with its ability to bend and wrap DNA makes UBF an unusual eukaryotic transcription factor. However, UBF's ability to bend DNA might explain how upstream and downstream rRNA gene promoter domains interact. UBF-induced DNA wrapping could also be a mechanism by which UBF counteracts histone-mediated gene repression.

Involvement of in situ conformation of ribosomal genes and selective distribution of upstream binding factor in rRNA transcription.

“…The binding of UBF on DNA induced DNA wrapping that has been proposed to play a role on the UBF counteracts histone-mediated gene repression (Bazett-Jones et al, 1994;Putnam et al, 1994;Moss and Stefanovsky, 1995). The model proposed for UBF binding to DNA is compatible with competition of UBF with histones (Moss and Stefanovsky, 1995).…”

“…UBF may also interact with a negatively acting factor to promote ribosomal gene transcription . The binding of dimers of UBF is due to several HMG-Box sequences (Bazett-Jones et al, 1994) that bend, wrap, and supercoil the enhancer DNA of the rDNA promoter (Putnam et al, 1994). It has been demonstrated that UBF plays a role in regulating the efficiency of RNA pol I transcription in vitro as well as in vivo (for a review, Moss and Stefanovsky, 1995).…”

Contribution of DNA Conformation and Topology in Right-handed DNA Wrapping by the Bacillus subtilis LrpC Protein

“…Eukaryotic dimers of (H 3 -H 4 ) (35) and HMf tetramers (40) are able, under certain conditions, to constrain positive supercoils, as observed for LrpC. Other proteins that activate transcription, such as the eukaryotic transcription factors UBF or SWI/SNF or the B. subtilis PurR regulator, are known to bind upstream of the promoters they regulate and to introduce one positive supercoil (41)(42)(43)(44). Therefore, it is likely that the capacity of LrpC to induce right-handed supercoiling is involved in its regulatory activity.…”

rRNA gene silencing and nucleolar dominance: Insights into a chromosome-scale epigenetic on/off switch

“…UBF persists at NORs throughout metaphase [21][22][23], which is when secondary constrictions are apparent, and is absent from those mammalian NORs that are not active and that do not form secondary constrictions. UBF binds cooperatively to naked DNA [24] and wraps the DNA [25] in a right-handed direction, thereby constraining positive supercoils [26,27], unlike histones which wrap DNA in a left-handed direction and constrain negative supercoils. However, UBF can also bind to nucleosomal DNA and displace linker histone H1, which plays a role in chromatin compaction [28].…”