UBF levels determine the number of active ribosomal RNA genes in mammals

Abstract

In mammals, the mechanisms regulating the number of active copies of the ∼200 ribosomal RNA (rRNA) genes transcribed by RNA polymerase I are unclear. We demonstrate that depletion of the transcription factor upstream binding factor (UBF) leads to the stable and reversible methylation-independent silencing of rRNA genes by promoting histone H1–induced assembly of transcriptionally inactive chromatin. Chromatin remodeling is abrogated by the mutation of an extracellular signal-regulated kinase site within the high mobility group box 1 domain of UBF1, which is required for its ability to bend and loop DNA in vitro. Surprisingly, rRNA gene silencing does not reduce net rRNA synthesis as transcription from remaining active genes is increased. We also show that the active rRNA gene pool is not static but decreases during differentiation, correlating with diminished UBF expression. Thus, UBF1 levels regulate active rRNA gene chromatin during growth and differentiation.

Heterozygous De Novo UBTF Gain-of-Function Variant Is Associated with Neurodegeneration in Childhood

“…Depletion of UBF was shown to silence rDNA and its total ablation is likely incompatible with life. 17,18 In agreement, UBTF is highly intolerant to both deleterious and missense variants; in the ExAC cohort, the number of UBTF variants markedly deviate from the expected by its length (Z ¼ 5.61) with expected/observed number of missense variants 295/98 and of loss-of-function (LOF) variants 36/0.…”

“…26 Finally, UBF is an important regulator of chromatin structure at the rDNA locus; it was shown to outcompete linker Histone H1 resulting in decondensation of rDNA chromatin. 17 Changes in chromatin status at the rDNA locus, coupled with nucleolar alterations, have been previously reported in Huntington disease [MIM 143100] 16 and were regulated by UBF post-translational modification by acetylation at Lys-352 and methylation at Lys-232. 16,27 The abnormally increased nucleolar size and reduced number of nucleoli per cell which was observed in the cells of the affected individual, suggest that the mutant hyperactive UBF causes an alteration in rDNA chromatin structure.…”

“…Such a dysregulation would have a profound impact, since rDNA heterochromatin status is tightly regulated during differentiation and has a broader effect on heterochromatin formation throughout the nucleus. 17,28 Obviously, the data and the consequent assumptions should be regarded as preliminary, because all derived from a single cell line of an affected individual and one healthy control.…”

Ribosomal RNA Gene Transcription Mediated by the Master Genome Regulator Protein CCCTC-binding Factor (CTCF) Is Negatively Regulated by the Condensin Complex

“…It has been reported that UBF interacts with CTCF and that CTCF binding enhances the recruitment of UBF to the rDNA locus (47). Nucleolar UBF, in turn, ensures that rDNA repeats remain accessible to RNA polymerase I (47).…”

“…It has been reported that UBF interacts with CTCF and that CTCF binding enhances the recruitment of UBF to the rDNA locus (47). Nucleolar UBF, in turn, ensures that rDNA repeats remain accessible to RNA polymerase I (47). Our experiments showed that the binding of UBF onto the rDNA repeat increases significantly after CTCF overexpression and that down-regulation of SMC2 further enhances this effect, which suggests that CTCF, as a mediator, regulates RNA polymerase I-mediated rRNA gene transcription.…”