Nucleolar protein upstream binding factor is sequestered into adenovirus DNA replication centres during infection without affecting RNA polymerase I location or ablating rRNA synthesis

Soon after infection, poliovirus (PV) shuts off host-cell transcription, which is catalysed by all three cellular RNA polymerases. rRNA constitutes more than 50 % of all cellular RNA and is transcribed from rDNA by RNA polymerase I (pol I). Here, evidence has been provided suggesting that both pol I transcription factors, SL-1 (selectivity factor) and UBF (upstream binding factor), are modified and inactivated in PV-infected cells. The viral protease 3Cpro appeared to cleave the TATA-binding protein-associated factor 110 (TAF110), a subunit of the SL-1 complex, into four fragments in vitro. In vitro protease-cleavage assays using various mutants of TAF110 and purified 3Cpro indicated that the Q265G266 and Q805G806 sites were cleaved by 3Cpro. Both SL-1 and UBF were depleted in PV-infected cells and their disappearance correlated with pol I transcription inhibition. rRNA synthesis from a template containing a human pol I promoter demonstrated that both SL-1 and UBF were necessary to restore pol I transcription fully in PV-infected cell extracts. These results suggested that both SL-1 and UBF are transcriptionally inactivated in PV-infected HeLa cells.

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Upstream binding factor stabilizes Rib 1, the TATA-binding-protein-containing Xenopus laevis RNA polymerase I transcription factor, by multiple protein interactions in a DNA-independent manner.

Molecular and Cellular Biology ◽

10.1128/mcb.16.10.5572 ◽

1996 ◽

Vol 16 (10) ◽

pp. 5572-5578 ◽

Cited By ~ 8

Author(s):

M Bodeker ◽

C Cairns ◽

B McStay

Keyword(s):

Xenopus Laevis ◽

Rna Polymerase ◽

Protein Interactions ◽

Tata Binding Protein ◽

Rna Polymerase I ◽

Independent Manner ◽

Multiple Protein ◽

Binding Factor ◽

Upstream Binding Factor ◽

Polymerase I

Initiation of RNA polymerase I transcription in Xenopus laevis requires Rib 1 and upstream binding factor (UBF). UBF and Rib 1 combine to form a stable transcription complex on the Xenopus ribosomal gene promoter. Here we show that Rib 1 comprises TATA-binding protein (TBP) and TBP-associated factor components. Thus, Rib 1 is the Xenopus equivalent of mammalian SL 1. In contrast to SL 1, Rib 1 is an unstable complex that readily dissociates into TBP and associated components. We identify a novel function for UBF in stabilizing Rib 1 by multiple protein interactions. This stabilization occurs in solution in a DNA-independent manner. These results may partially explain the difference in UBF requirement between Xenopus and mammalian systems.

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TBP-TAF Complex SL1 Directs RNA Polymerase I Pre-initiation Complex Formation and Stabilizes Upstream Binding Factor at the rDNA Promoter

Journal of Biological Chemistry ◽

10.1074/jbc.m501595200 ◽

2005 ◽

Vol 280 (33) ◽

pp. 29551-29558 ◽

Cited By ~ 44

Author(s):

J. Karsten Friedrich ◽

Kostya I. Panov ◽

Pavel Cabart ◽

Jackie Russell ◽

Joost C. B. M. Zomerdijk

Keyword(s):

Complex Formation ◽

Rna Polymerase ◽

Rna Polymerase I ◽

Initiation Complex ◽

Binding Factor ◽

Upstream Binding Factor ◽

Polymerase I

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The species-specific RNA polymerase I transcription factor SL-1 binds to upstream binding factor.

Molecular and Cellular Biology ◽

10.1128/mcb.16.2.557 ◽

1996 ◽

Vol 16 (2) ◽

pp. 557-563 ◽

Cited By ~ 27

Author(s):

W M Hempel ◽

A H Cavanaugh ◽

R D Hannan ◽

L Taylor ◽

L I Rothblum

Keyword(s):

Rna Polymerase ◽

Binding Protein ◽

Sodium Dodecyl ◽

Tata Binding Protein ◽

Rna Polymerase I ◽

Rrna Genes ◽

Cell Extracts ◽

Binding Factor ◽

Upstream Binding Factor ◽

Polymerase I

Transcription of the 45S rRNA genes is carried out by RNA polymerase I and at least two trans-acting factors, upstream binding factor (UBF) and SL-1. We have examined the hypothesis that SL-1 and UBF interact. Coimmunoprecipitation studies using an antibody to UBF demonstrated that TATA-binding protein, a subunit of SL-1, associates with UBF in the absence of DNA. Inclusion of the detergents sodium dodecyl sulfate and deoxycholate disrupted this interaction. In addition, partially purified UBF from rat cell nuclear extracts and partially purified SL-1 from human cells coimmunoprecipitated with the anti-UBF antibody after mixing, indicating that the UBF-SL-1 complex can re-form. Treatment of UBF-depleted extracts with the anti-UBF antibody depleted the extracts of SL-1 activity only if UBF was added to the extract prior to the immunodepletion reaction. Furthermore, SL-1 activity could be recovered in the immunoprecipitate. Interestingly, these immunoprecipitates did not contain RNA polymerase I, as a monospecific antibody to the 194-kDa subunit of RNA polymerase I failed to detect that subunit in the immunoprecipitates. Treatment of N1S1 cell extracts with the anti-UBF antibody depleted the extracts of SL-1 activity but not TFIIIB activity, suggesting that the binding of UBF to SL-1 is specific and not solely mediated by an interaction between UBF and TATA-binding protein, which is also a component of TFIIIB. These data provide evidence that UBF and SL-1 interact.

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LYAR potentiates rRNA synthesis by recruiting BRD2/4 and the MYST-type acetyltransferase KAT7 to rDNA

Nucleic Acids Research ◽

10.1093/nar/gkz747 ◽

2019 ◽

Vol 47 (19) ◽

pp. 10357-10372 ◽

Cited By ~ 4

Author(s):

Keiichi Izumikawa ◽

Hideaki Ishikawa ◽

Harunori Yoshikawa ◽

Sally Fujiyama ◽

Akira Watanabe ◽

...

Keyword(s):

Ribosomal Rna ◽

Rna Polymerase I ◽

Rrna Synthesis ◽

Histone H4 ◽

Rdna Transcription ◽

Binding Factor ◽

Rdna Loci ◽

Upstream Binding Factor ◽

Polymerase I ◽

Cell Growth And Proliferation

Abstract Activation of ribosomal RNA (rRNA) synthesis is pivotal during cell growth and proliferation, but its aberrant upregulation may promote tumorigenesis. Here, we demonstrate that the candidate oncoprotein, LYAR, enhances ribosomal DNA (rDNA) transcription. Our data reveal that LYAR binds the histone-associated protein BRD2 without involvement of acetyl-lysine–binding bromodomains and recruits BRD2 to the rDNA promoter and transcribed regions via association with upstream binding factor. We show that BRD2 is required for the recruitment of the MYST-type acetyltransferase KAT7 to rDNA loci, resulting in enhanced local acetylation of histone H4. In addition, LYAR binds a complex of BRD4 and KAT7, which is then recruited to rDNA independently of the BRD2-KAT7 complex to accelerate the local acetylation of both H4 and H3. BRD2 also helps recruit BRD4 to rDNA. By contrast, LYAR has no effect on rDNA methylation or the binding of RNA polymerase I subunits to rDNA. These data suggest that LYAR promotes the association of the BRD2-KAT7 and BRD4-KAT7 complexes with transcription-competent rDNA loci but not to transcriptionally silent rDNA loci, thereby increasing rRNA synthesis by altering the local acetylation status of histone H3 and H4.

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Coilin participates in the suppression of RNA polymerase I in response to cisplatin-induced DNA damage

Molecular Biology of the Cell ◽

10.1091/mbc.e10-08-0731 ◽

2011 ◽

Vol 22 (7) ◽

pp. 1070-1079 ◽

Cited By ~ 33

Author(s):

Andrew S. Gilder ◽

Phi M. Do ◽

Zunamys I Carrero ◽

Angela M. Cosman ◽

Hanna J. Broome ◽

...

Keyword(s):

Dna Damage ◽

Rna Polymerase ◽

Rna Polymerase I ◽

Rrna Synthesis ◽

Γ Irradiation ◽

Small Nuclear Ribonucleoprotein ◽

Pol I ◽

Upstream Binding Factor ◽

Polymerase I ◽

Nuclear Ribonucleoprotein

Coilin is a nuclear phosphoprotein that concentrates within Cajal bodies (CBs) and impacts small nuclear ribonucleoprotein (snRNP) biogenesis. Cisplatin and γ-irradiation, which cause distinct types of DNA damage, both trigger the nucleolar accumulation of coilin, and this temporally coincides with the repression of RNA polymerase I (Pol I) activity. Knockdown of endogenous coilin partially overrides the Pol I transcriptional arrest caused by cisplatin, while both ectopically expressed and exogenous coilin accumulate in the nucleolus and suppress rRNA synthesis. In support of this mechanism, we demonstrate that both cisplatin and γ-irradiation induce the colocalization of coilin with RPA-194 (the largest subunit of Pol I), and we further show that coilin can specifically interact with RPA-194 and the key regulator of Pol I activity, upstream binding factor (UBF). Using chromatin immunoprecipitation analysis, we provide evidence that coilin modulates the association of Pol I with ribosomal DNA. Collectively, our data suggest that coilin acts to repress Pol I activity in response to cisplatin-induced DNA damage. Our findings identify a novel and unexpected function for coilin, independent of its role in snRNP biogenesis, establishing a new link between the DNA damage response and the inhibition of rRNA synthesis.

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The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA.

Molecular and Cellular Biology ◽

10.1128/mcb.14.10.6476 ◽

1994 ◽

Vol 14 (10) ◽

pp. 6476-6488 ◽

Cited By ~ 38

Author(s):

C D Putnam ◽

G P Copenhaver ◽

M L Denton ◽

C S Pikaard

Keyword(s):

Rna Polymerase ◽

High Mobility ◽

Rna Polymerase I ◽

High Mobility Group ◽

Dna Ligase ◽

Dimerization Domain ◽

Hmg Box ◽

Binding Factor ◽

Upstream Binding Factor ◽

Polymerase I

Upstream binding factor (UBF) is an important transactivator of RNA polymerase I and is a member of a family of proteins that contain nucleic acid binding domains named high-mobility-group (HMG) boxes because of their similarity to HMG chromosomal proteins. UBF is a highly sequence-tolerant DNA-binding protein for which no binding consensus sequence has been identified. Therefore, it has been suggested that UBF may recognize preformed structural features of DNA, a hypothesis supported by UBF's ability to bind synthetic DNA cruciforms, four-way junctions, and even tRNA. We show here that full-length UBF can also bend linear DNA to mediate circularization of probes as small as 102 bp in the presence of DNA ligase. Longer probes in the presence of UBF become positively supercoiled when ligated, suggesting that UBF wraps the DNA in a right-handed direction, opposite the direction of DNA wrapping around a nucleosome. The dimerization domain and HMG box 1 are necessary and sufficient to circularize short probes and supercoil longer probes in the presence of DNA ligase. UBF's sequence tolerance coupled with its ability to bend and wrap DNA makes UBF an unusual eukaryotic transcription factor. However, UBF's ability to bend DNA might explain how upstream and downstream rRNA gene promoter domains interact. UBF-induced DNA wrapping could also be a mechanism by which UBF counteracts histone-mediated gene repression.

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Mutations in nucleolar proteins lead to nucleolar accumulation of polyA+ RNA in Saccharomyces cerevisiae.

Molecular Biology of the Cell ◽

10.1091/mbc.6.9.1103 ◽

1995 ◽

Vol 6 (9) ◽

pp. 1103-1110 ◽

Cited By ~ 30

Author(s):

T Kadowaki ◽

R Schneiter ◽

M Hitomi ◽

A M Tartakoff

Keyword(s):

Saccharomyces Cerevisiae ◽

Rna Polymerase ◽

Rna Polymerase I ◽

Nucleolar Protein ◽

Rrna Synthesis ◽

Ribosomal Subunits ◽

Nucleolar Proteins ◽

Synthesis And Processing ◽

Polymerase I ◽

Nucleolar Components

Synthesis of mRNA and rRNA occur in the chromatin-rich nucleoplasm and the nucleolus, respectively. Nevertheless, we here report that a Saccharomyces cerevisiae gene, MTR3, previously implicated in mRNA transport, codes for a novel essential 28-kDa nucleolar protein. Moreover, in mtr3-1 the accumulated polyA+ RNA actually colocalizes with nucleolar antigens, the nucleolus becomes somewhat disorganized, and rRNA synthesis and processing are inhibited. A strain with a ts conditional mutation in RNA polymerase I also shows nucleolar accumulation of polyA+ RNA, whereas strains with mutations in the nucleolar protein Nop1p do not. Thus, in several mutant backgrounds, when mRNA cannot be exported i concentrates in the nucleolus. mRNA may normally encounter nucleolar components before export and proteins such as Mtr3p may be critical for export of both mRNA and ribosomal subunits.

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The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA

Molecular and Cellular Biology ◽

10.1128/mcb.14.10.6476-6488.1994 ◽

1994 ◽

Vol 14 (10) ◽

pp. 6476-6488

Author(s):

C D Putnam ◽

G P Copenhaver ◽

M L Denton ◽

C S Pikaard

Keyword(s):

Rna Polymerase ◽

High Mobility ◽

Rna Polymerase I ◽

High Mobility Group ◽

Dna Ligase ◽

Dimerization Domain ◽

Hmg Box ◽

Binding Factor ◽

Upstream Binding Factor ◽

Polymerase I

Upstream binding factor (UBF) is an important transactivator of RNA polymerase I and is a member of a family of proteins that contain nucleic acid binding domains named high-mobility-group (HMG) boxes because of their similarity to HMG chromosomal proteins. UBF is a highly sequence-tolerant DNA-binding protein for which no binding consensus sequence has been identified. Therefore, it has been suggested that UBF may recognize preformed structural features of DNA, a hypothesis supported by UBF's ability to bind synthetic DNA cruciforms, four-way junctions, and even tRNA. We show here that full-length UBF can also bend linear DNA to mediate circularization of probes as small as 102 bp in the presence of DNA ligase. Longer probes in the presence of UBF become positively supercoiled when ligated, suggesting that UBF wraps the DNA in a right-handed direction, opposite the direction of DNA wrapping around a nucleosome. The dimerization domain and HMG box 1 are necessary and sufficient to circularize short probes and supercoil longer probes in the presence of DNA ligase. UBF's sequence tolerance coupled with its ability to bend and wrap DNA makes UBF an unusual eukaryotic transcription factor. However, UBF's ability to bend DNA might explain how upstream and downstream rRNA gene promoter domains interact. UBF-induced DNA wrapping could also be a mechanism by which UBF counteracts histone-mediated gene repression.

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