title: Conditional inactivation of Upstream Binding Factor reveals its epigenetic functions and the existence of a somatic nucleolar precursor body.
abstract: Upstream Binding Factor (UBF) is a unique multi-HMGB-box protein first identified as a co-factor in RNA polymerase I (RPI/PolI) transcription. However, its poor DNA sequence selectivity and its ability to generate nucleosome-like nucleoprotein complexes suggest a more generalized role in chromatin structure. We previously showed that extensive depletion of UBF reduced the number of actively transcribed ribosomal RNA (rRNA) genes, but had little effect on rRNA synthesis rates or cell proliferation, leaving open the question of its requirement for RPI transcription. Using gene deletion in mouse, we now show that UBF is essential for embryo development beyond morula. Conditional deletion in cell cultures reveals that UBF is also essential for transcription of the rRNA genes and that it defines the active chromatin conformation of both gene and enhancer sequences. Loss of UBF prevents formation of the SL1/TIF1B pre-initiation complex and recruitment of the RPI-Rrn3/TIF1A complex. It is also accompanied by recruitment of H3K9me3, canonical histone H1 and HP1α, but not by de novo DNA methylation. Further, genes retain penta-acetyl H4 and H2A.Z, suggesting that even in the absence of UBF the rRNA genes can maintain a potentially active state. In contrast to canonical histone H1, binding of H1.4 is dependent on UBF, strongly suggesting that it plays a positive role in gene activity. Unexpectedly, arrest of rRNA synthesis does not suppress transcription of the 5S, tRNA or snRNA genes, nor expression of the several hundred mRNA genes implicated in ribosome biogenesis. Thus, rRNA gene activity does not coordinate global gene expression for ribosome biogenesis. Loss of UBF also unexpectedly induced the formation in cells of a large sub-nuclear structure resembling the nucleolar precursor body (NPB) of oocytes and early embryos. These somatic NPBs contain rRNA synthesis and processing factors but do not associate with the rRNA gene loci (NORs).
authors.affiliation: Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Edifice St Patrick, Québec, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Québec, Canada.
authors.forename: Nourdine
authors.initials: N
authors.lastname: Hamdane
authors.affiliation: Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Edifice St Patrick, Québec, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Québec, Canada.
authors.forename: Victor Y
authors.initials: VY
authors.lastname: Stefanovsky
authors.affiliation: Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Edifice St Patrick, Québec, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Québec, Canada.
authors.forename: Michel G
authors.initials: MG
authors.lastname: Tremblay
authors.affiliation: Department of Biochemistry III, Biochemistry Center Regensburg, University of Regensburg, Regensburg, Germany.
authors.forename: Attila
authors.initials: A
authors.lastname: Németh
authors.affiliation: Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Edifice St Patrick, Québec, Québec, Canada.
authors.forename: Eric
authors.initials: E
authors.lastname: Paquet
authors.affiliation: Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Edifice St Patrick, Québec, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Québec, Canada.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Lessard
authors.affiliation: Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
authors.forename: Elaine
authors.initials: E
authors.lastname: Sanij
authors.affiliation: Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia.
authors.forename: Ross
authors.initials: R
authors.lastname: Hannan
authors.affiliation: Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Edifice St Patrick, Québec, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Québec, Québec, Canada.
authors.forename: Tom
authors.initials: T
authors.lastname: Moss
mesh_terms: D000818:Animals; D002466:Cell Nucleolus / Q000235:genetics; D002843:Chromatin / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D018507:Gene Expression Regulation, Developmental; D024002:HMGB Proteins / Q000235:genetics; D006657:Histones / Q000235:genetics / Q000378:metabolism; D051379:Mice; D009865:Oocytes / Q000254:growth & development / Q000378:metabolism; D035463:Pol1 Transcription Initiation Complex Proteins / Q000037:antagonists & inhibitors / Q000235:genetics*; D012318:RNA Polymerase I / Q000037:antagonists & inhibitors / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D012270:Ribosomes / Q000235:genetics*; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D024002:HMGB Proteins; D006657:Histones; D035463:Pol1 Transcription Initiation Complex Proteins; D012335:RNA, Ribosomal; C063844:transcription factor UBF; D012318:RNA Polymerase I