Upstream Binding Factor, an Evolutionarily Conserved Protein that Organises Ribosomal Gene Chromatin
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The nucleolus, the site of ribosome biogenesis, forms around arrays of ribosomal gene (rDNA) repeats termed nucleolar organiser regions (NORs). Transcriptionally active NORs appear as regions of under-condensed chromatin on metaphase chromosomes termed secondary constrictions. Silent NORs lose these chromosomal features and during interphase appear as foci of condensed chromatin dissociated from nucleoli. The architectural RNA polymerase I transcription factor, Upstream Binding Factor (UBF), has been shown to bind extensively over active rDNA repeats and we hypothesise that UBF is implicated in maintaining their open active chromatin state. Depletion of UBF in a variety of human cell lines, and in cells from the rat kangaroo Potorous, demonstrates that UBF is required for the maintenance of secondary constrictions on metaphase NORs. I also demonstrate that during interphase, UBF depletion induces rDNA condensation, with a proportion of NORs initially moving to the periphery and eventually dissociating from nucleoli. Thus I conclude that UBF levels set the proportion of NORs that are active. Phylogenetic analyses reveal that UBF is not restricted to vertebrates as previously thought, but present across animal phyla even in the most primitive metazoans. Surprisingly, UBF from divergent species, including Ciona intestinalis can specifically recognise and bind to human NORs. UBF has low DNA sequence specificity, and rDNA regulatory sequences have diverged rapidly throughout evolution. Thus we speculated that UBF binding to rDNA involves recognition of a specific chromatin state and is not solely reliant on the underlying DNA sequence. The SANT domain is a motif found in number of chromatin remodelling/binding complexes. A related domain present in the proto-oncogene myb functions as a histone tail interaction motif. SANT domains are characterised by the presence of three spatially conserved tryptophan residues. I have identified a SANT-like domain within the N-terminal dimerisation domain of UBF, that includes these conserved tryptophan residues. Mutational analysis reveals their critical nature for UBFs localisation. Future analysis of this novel SANT-like domain will provide insights into how UBF, a critical regulator of ribosome biogenesis, functions.
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