A novel role for the Pol I transcription factor UBTF in maintaining genome stability through the regulation of highly transcribed Pol II genes

Abstract

Mechanisms to coordinate programs of highly transcribed genes required for cellular homeostasis and growth are unclear. 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. Here, we report that the two isoforms of UBTF (UBTF1/2) are also enriched at highly expressed Pol II-transcribed genes throughout the mouse genome. Further analysis of UBTF1/2 DNA binding in immortalized human epithelial cells and their isogenically matched transformed counterparts reveals an additional repertoire of UBTF1/2-bound genes involved in the regulation of cell cycle checkpoints and DNA damage response. As proof of a functional role for UBTF1/2 in regulating Pol II transcription, we demonstrate that UBTF1/2 is required for recruiting Pol II to the highly transcribed histone gene clusters and for their optimal expression. Intriguingly, lack of UBTF1/2 does not affect chromatin marks or nucleosome density at histone genes. Instead, it results in increased accessibility of the histone promoters and transcribed regions to micrococcal nuclease, implicating UBTF1/2 in mediating DNA accessibility. Unexpectedly, UBTF2, which does not function in Pol I transcription, is sufficient to regulate histone gene expression in the absence of UBTF1. Moreover, depletion of UBTF1/2 and subsequent reduction in histone gene expression is associated with DNA damage and genomic instability independent of Pol I transcription. Thus, we have uncovered a novel role for UBTF1 and UBTF2 in maintaining genome stability through coordinating the expression of highly transcribed Pol I (UBTF1 activity) and Pol II genes (UBTF2 activity).

Inhibition of RNA polymerase I transcription initiation by CX-5461 activates non-canonical ATM/ATR signaling

“…Active rDNA chromatin is open/accessible and bound by UBF, which is essential in determining and maintaining the active rDNA state [9, 57–59]. While, silenced rDNA is devoid of UBF and Pol I and can be distinguished from the active rDNA pool by differential accessibility to psoralen followed by Southern blotting [58].…”

“…Reverse transcription qPCR, Western blot analysis, ChIP, Immunofluorescence-fluorescent in situ hybridisation (IF-FISH), psoralen crosslinking and chromatin accessibility by real time-PCR (CHART-PCR) assays were carried out as described previously [58, 59]. A brief summary of these assays and lists of antibodies and primer sequences are provided in the Supplementary Data.…”

Detection of Potential Metastatic Prostate Cancer Circulating Biomarkers by Comparison of miRNA Profiles in DU145 Cells and Culture Medium

“…This protein is directly involved in the signal pathways that are activated by DNA damage and is involved in the maintenance of genome stability [8]. In turn, hsa-miR-6782-5p is located in UBTF gene, coding for protein promoting transcription of ribosomal RNA and presumably playing an important role in chromatin remodeling and in response to DNA injury [11]. Hence, the above host genes can be overexpressed in the tumor cell within the mechanism maintaining genome stability.…”

The linker histone H1.2 is a novel component of the nucleolar organizer regions

“…UBF has indeed been reported to associate with selected genes in the nucleoplasm (31)(32)(33)(34)(35). As a chromatin-binding protein, the broad distribution of H1.2 in the nucleoplasm is natural.…”

“…Nuclei rather than nucleoli were used because UBF also binds to selected genes outside the nucleoli and regulates RNA polymerase II (Pol II)-mediated gene expression (33)(34)(35). The nuclei were first extracted with Triton X-100 to deplete the nuclear envelope and these nuclei, known as TxN, mostly remained intact and oval and retained the nuclear protein profile (data not shown, Figure 1A).…”