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

Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia.
The Journal of Cell Biology (Impact Factor: 9.69). 01/2009; 183(7):1259-74. DOI: 10.1083/jcb.200805146
Source: PubMed

ABSTRACT In mammals, the mechanisms regulating the number of active copies of the approximately 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.

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Available from: Richard B Pearson, Aug 18, 2015
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    • "Antihyperacetylated H4 (06-946) and anti H3K9ac (07-352) antibodies were from Upstate (Millipore). Antibodies targeting UBF1/2 and the largest subunit of the Pol I complex (POLR1A/RPA194) were raised inhouse and were used as reported in Sanij et al.[3]. "
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    ABSTRACT: The upstream binding transcription factor (UBTF, also called UBF) is thought to function exclusively in RNA polymerase I (Pol I)-specific transcription of the ribosomal genes. We recently reported in Sanij et al.(2014) [1] that the two isoforms of UBF (UBF1/2) are enriched at Pol II-transcribed genes throughout the mouse and human genomes. By using chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq) of UBF1/2, Pol I, Pol II, H3K9me3, H3K4me4, H3K9ac and H4 hyperacetylation, we reported a correlation of UBF1/2 binding with enrichments in Pol II and markers of active chromatin. In addition, we examined a functional role for UBF1/2 in mediating Pol II transcription by performing expression array analysis in control and UBF1/2 depleted NIH3T3 cells. Our data demonstrate that UBF1/2 bind highly active Pol II-transcribed genes and mediate their expression without recruiting Pol I. Furthermore, we reported ChIP-sequencing analysis of UBF1/2 in immortalized human epithelial cells and their isogenically matched transformed counterparts. Here we report the experimental design and the description of the ChIP-sequencing and microarray expression datasets uploaded to NCBI Sequence Research Archive (SRA) and Gene Expression Omnibus (GEO).
    01/2015; 15. DOI:10.1016/j.gdata.2014.12.005
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    • "There are ~ 200 copies of the rRNA gene located in tandem arrays at 5 locations in the genome, on the short arms of the acrocentric chromosomes; only a proportion of these (approximately half) are transcriptionally competent , with an 'open' structure associated with euchromatic histone modifications (H4Ac and H3K4Me), while the rest are transcriptionally silenced, with a heavily CpG methylated heterochromatic structure (H3K9Me, HK27Me and H3K20Me) (reviewed in [11] [12] [13] [14] [15]). Transcriptionally competent rDNA repeats are not necessarily active, but those that are characterized by association with the transcription factor UBF can achieve very high rates of transcription by Pol I [16], accounting for N 30% of transcriptional activity of an exponentially growing cell [17] and [12]. Although the nucleoli are not membrane bound organelles, they segregate into three distinct regions: the pale-staining fibrillar center (FC), surrounded by the compact dense fibrillar component (DFC), which in turn is encased by an outer granular compartment (GC) (reviewed in [3] and [4]). "
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    ABSTRACT: The contribution of the nucleolus to cancer is well established with respect to its traditional role in facilitating ribosome biogenesis and proliferative capacity. More contemporary studies however, infer that nucleoli contribute a much broader role in malignant transformation. Specifically, extra-ribosomal functions of the nucleolus position it as a central integrator of cellular proliferation and stress signaling, and are emerging as important mechanisms for modulating how oncogenes and tumour suppressors operate in normal and malignant cells. The dependence of certain tumour cells to co-opt nucleolar processes to maintain their cancer phenotypes has now clearly been demonstrated by the application of small molecule inhibitors of RNA Polymerase I to block ribosomal DNA transcription and disrupt nucleolar function (Bywater et al., 2012 [1]). These drugs, which selectively kill tumour cells in vivo while sparing normal cells, have now progressed to clinical trials. It is likely that we have only just begun scratch the surface of the potential of the nucleolus as a new target for cancer therapy, with "suppression of nucleolar stress" representing an emerging "hallmark" of cancer.
    Biochimica et Biophysica Acta 01/2014; 1842(6). DOI:10.1016/j.bbadis.2013.12.009 · 4.66 Impact Factor
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    • "The promoter of transcriptionally active genes is hypomethylated and loaded with UBF and Pol I [18], poised ones are hypomethylated and associated with UBF and SL1 but not with Pol I [1], and silent ones are CpG methylated, not associated with components of the Pol I transcription machinery and the nucleosome is in the 'off' position [18] (Fig. 6). It seems that there is a fourth state of unmethylated rRNA genes which are not loaded with UBF and are not transcribed [11]. 10. "
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    ABSTRACT: rRNA synthesis is regulated by genetic and epigenetic mechanisms. Epigenetic states are metastable, changing in response to appropriate signals, thereby modulating transcription in vivo. The establishment, maintenance and reversal of epigenetic features are fundamental for the cell's ability to 'remember' past events, to adapt to environmental changes or developmental cues and to propagate this information to the progeny. As packaging into chromatin is critical for the stability and integrity of repetitive DNA, keeping a fraction of rRNA genes in a metastable heterochromatic conformation prevents aberrant exchanges between repeats, thus safeguarding nucleolar structure and rDNA stability. In this review, we will focus on the nature of the molecular signatures that characterize a given epigenetic state of rDNA in mammalian cells, including noncoding RNA, DNA methylation and histone modifications, and the mechanisms by which they are established and maintained. This article is part of a Special Issue entitled: Transcription by Odd Pols.
    Biochimica et Biophysica Acta 10/2012; 1829(3). DOI:10.1016/j.bbagrm.2012.10.004 · 4.66 Impact Factor
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