Stanford Home
Ovarian Kaleidoscope Database (OKdb)



Transgenic Mouse Models



Hsueh lab


since 01/2001:

upstream binding transcription factor, RNA polymerase I OKDB#: 1160
 Symbols: UBTF Species: human
 Synonyms: UBF, UBF1, UBF2, UBF-1, CONDBA, NOR-90  Locus: 17q21.31 in Homo sapiens

For retrieval of Nucleotide and Amino Acid sequences please go to: OMIM Entrez Gene
Mammalian Reproductive Genetics   Endometrium Database Resource   Orthologous Genes   UCSC Genome Browser   GEO Profiles new!   Amazonia (transcriptome data) new!


DNA Microarrays
link to BioGPS
General Comment Upstream binding factor (UBF) is a transcription factor required for expression of the 18S, 5.8S, and 28S ribosomal RNAs, along with SL1 (a complex of TBP ) and multiple TBP-associated factors or 'TAFs'). Two UBF polypeptides, of 94 and 97 kD, exist in the human. UBF is a nucleolar phosphoprotein with both DNA binding and transactivation domains

NCBI Summary: This gene encodes a member of the HMG-box DNA-binding protein family. The encoded protein plays a critical role in ribosomal RNA transcription as a key component of the pre-initiation complex, mediating the recruitment of RNA polymerase I to rDNA promoter regions. The encoded protein may also play important roles in chromatin remodeling and pre-rRNA processing, and its activity is regulated by both phosphorylation and acetylation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Pseudogenes of this gene are located on the short arm of chromosomes 3, 11 and X and the long arm of chromosome 11. [provided by RefSeq, Aug 2011]
General function Nucleic acid binding, DNA binding, Transcription factor
Cellular localization Nuclear
Ovarian function Oogenesis
Comment Trudee Fair et al 2001 reported the immunolocalization of Nucleolar Proteins During Bovine Oocyte Growth, Meiotic Maturation, and Fertilization. During the growth phase of the bovine oocyte transcripts, polypeptides and ribosomes are accumulated in the oocyte to drive and sustain future meiotic maturation, fertilization, and early embryonic development. The oocyte also furnishes the early embryo with the components required to establish a functional transcriptionally active nucleolus at the time of maternal embryonic transition. The temporal localization of nucleolar proteins fibrillarin, nucleophosmin, nucleolin, RNA polymerase I (RNA pol I), upstream binding factor (UBF), and coilin 5P10 was investigated in growing and fully grown immature bovine oocytes during in vitro maturation and during the first postfertilization cell cycle using whole-mount immunocytochemistry and confocal microscopy. During the oocyte growth phase, fibrillarin, nucleophosmin, nucleolin, RNA pol I, and UBF were localized to the oocyte nucleolus. On completion of the growth phase, nucleolin and nucleophosmin appeared to migrate to the periphery of the nucleolus and into the nucleoplasm, and the proportion of oocytes displaying RNA pol I localization had decreased. Fibrillarin appeared to be localized to large foci within the nucleolus and/or nucleoplasm. Nucleophosmin and nucleolin labeling was characterized by a homogenous signal over the nucleolus. RNA pol I and UBF were characterized by the localization of the antibodies to individual or clustered foci in the nucleolus and/or nucleoplasm. Following oocyte nucleus breakdown (ONBD), the proteins appeared to disperse into the cytoplasm.
Expression regulated by
Comment xyz
Ovarian localization Oocyte
Comment Age-associated dysregulation of protein metabolism in the mammalian oocyte. Duncan FE et al. (2017) Reproductive aging is characterized by a marked decline in oocyte quality that contributes to infertility, miscarriages, and birth defects. This decline is multifactorial, and the underlying mechanisms are under active investigation. Here, we performed RNA-Seq on individual growing follicles from reproductively young and old mice to identify age-dependent functions in oocytes. This unbiased approach revealed genes involved in cellular processes known to change with age, including mitochondrial function and meiotic chromosome segregation, but also uncovered previously unappreciated categories of genes related to proteostasis and organelles required for protein metabolism. We further validated our RNA-Seq data by comparing nucleolar structure and function in oocytes from reproductively young and old mice, as this organelle is central for protein production. We examined key nucleolar markers, including upstream binding transcription factor (UBTF), an RNA polymerase I cofactor, and fibrillarin, an rRNA methyltransferase. In oocytes from mice of advanced reproductive age, UBTF was primarily expressed in giant fibrillar centers (GFCs), structures associated with high levels of rDNA transcription, and fibrillarin expression was increased ~2-fold. At the ultrastructural level, oocyte nucleoli from reproductively old mice had correspondingly more prominent fibrillar centers and dense fibrillar centers relative to young controls and more ribosomes were found in the cytoplasm. Taken together, our findings are significant because the growing oocyte is one of the most translationally active cells in the body and must accumulate high-quality maternally derived proteins to support subsequent embryo development. Thus, perturbations in protein metabolism are likely to have a profound impact on gamete health.////////////////// Bjerregaard B, et al reported the Regulation of Ribosomal RNA Synthesis During the Final Phases of Porcine Oocyte Growth. In porcine oocytes acquisition of meiotic competence coincides with a decrease of general tran-scriptional activity at the end of the oocyte growth phase and, specifically, of ribosomal RNA (rRNA) synthesis in the nucleolus. The present study investigated the regulation of rRNA synthesis during porcine oocyte growth. Localization and expression of components involved in regulation of the rRNA synthesis, (the RNA polymerase I-associated factor PAF53, upstream binding factor (UBF), and the pocket proteins p130 and pRb) were assessed by immunocytochemistry and semi-quantitative RT-PCR, and correlated with ultrastructural analysis and autoradiography following (3)H-uridine incubation in growing and fully grown porcine oocytes. In addition, meiotic resumption, ultrastructure, and expression of p130, UBF and PAF53 were analyzed in growing and fully grown porcine oocytes cultured with 100 micro M butyrolactone I (BL-I), a potent inhibitor of cyclin dependent kinases (cdk), to gain insight into the regulation of rRNA transcription during meiotic arrest. Immunocytochemical analysis demonstrated that p130 became co-localized with UBF and PAF53, and that the intensity of the PAF53 labeling decreased towards the end of the oocyte growth phase. These data suggest that the decrease in rRNA synthesis is regulated by inhibition of UBF by p130 as well as by decreased availability of PAF53. Moreover, expression of mRNA encoding PAF53 was decreased at the end of the oocyte growth phase. At the morphological level these events coin-cided with inactivation of the nucleolus as visualized by the transformation of the fibrillo-granular nucleolus to an electron-dense fibrillar sphere with remnants of the fibrillar centers at the surface. Meiotic inhibition with 100 micro M BL-I had a detrimental effect on the ability of porcine oocytes to resume meiosis, and on nucleolus morphology resulting in lack of RNA synthetic capability as the fibrillar components, where rRNA transcription and initial processing occur, condensed or even disintegrated.
Follicle stages
Mutations 1 mutations

Species: mouse
Mutation name: None
type: null mutation
fertility: infertile - ovarian defect
Comment: Conditional inactivation of upstream binding factor reveals its epigenetic functions and the existence of a somatic nucleolar precursor body. Hamdane N 2014 et al. 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 HP1a, 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). /////////////////////////

Genomic Region show genomic region
Phenotypes and GWAS show phenotypes and GWAS
Reprogenomic viewer show phenotypes and GWAshow RNAseq data and genomic region in Reprogenomic viewer site
(After opening the Reprogenomics Viewer site, select your gene and click on Chromosome + Link)
OMIM (Online Mendelian Inheritance in Man: an excellent source of general gene description and genetic information.)
OMIM \ Animal Model
KEGG Pathways
Recent Publications
Search for Antibody
blog comments powered by Disqus
Related Genes
Show data ...

created: May 4, 2001, 1:53 p.m. by: hsueh   email:
home page:
last update: Oct. 12, 2017, 3:07 p.m. by: hsueh    email:

Use the back button of your browser to return to the Gene List.

Click here to return to gene search form