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

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

Journal of Cell Science ◽

10.1242/jcs.02982 ◽

2006 ◽

Vol 119 (12) ◽

pp. 2621-2631 ◽

Cited By ~ 31

Author(s):

F. J. Lawrence

Keyword(s):

Dna Replication ◽

Rna Polymerase ◽

Rna Polymerase I ◽

Nucleolar Protein ◽

Rrna Synthesis ◽

Binding Factor ◽

Upstream Binding Factor ◽

Polymerase I

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Modifications of both selectivity factor and upstream binding factor contribute to poliovirus-mediated inhibition of RNA polymerase I transcription

Journal of General Virology ◽

10.1099/vir.0.80817-0 ◽

2005 ◽

Vol 86 (8) ◽

pp. 2315-2322 ◽

Cited By ~ 28

Author(s):

Rajeev Banerjee ◽

Mary K. Weidman ◽

Sonia Navarro ◽

Lucio Comai ◽

Asim Dasgupta

Keyword(s):

Rna Polymerase ◽

Rna Polymerase I ◽

Rrna Synthesis ◽

Selectivity Factor ◽

Pol I ◽

Binding Factor ◽

Infected Cells ◽

Upstream Binding Factor ◽

Polymerase I

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

The Journal of Cell Biology ◽

10.1083/jcb.200805146 ◽

2008 ◽

Vol 183 (7) ◽

pp. 1259-1274 ◽

Cited By ~ 122

Author(s):

Elaine Sanij ◽

Gretchen Poortinga ◽

Kerith Sharkey ◽

Sandy Hung ◽

Timothy P. Holloway ◽

...

Keyword(s):

Ribosomal Rna ◽

High Mobility ◽

Rrna Genes ◽

Rrna Synthesis ◽

Rrna Gene ◽

Extracellular Signal ◽

Binding Factor ◽

Upstream Binding Factor ◽

Polymerase I

In mammals, the mechanisms regulating the number of active copies of the ∼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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Nucleolar protein upstream binding factor is sequestered into adenovirus DNA replication centres during infection without affecting RNA polymerase I location or ablating rRNA synthesis

Journal of Cell Science ◽

10.1242/jcs.119.14.3020 ◽

2006 ◽

Vol 119 (14) ◽

pp. 3020-3020

Keyword(s):

Dna Replication ◽

Rna Polymerase ◽

Rna Polymerase I ◽

Nucleolar Protein ◽

Rrna Synthesis ◽

Binding Factor ◽

Upstream Binding Factor ◽

Polymerase I

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A role for upstream binding factor in organizing ribosomal gene chromatin

Biochemical Society Symposium ◽

10.1042/bss0730077 ◽

2006 ◽

Vol 73 ◽

pp. 77-84 ◽

Cited By ~ 14

Author(s):

Jane E. Wright ◽

Christine Mais ◽

José-Luis Prieto ◽

Brian McStay

Keyword(s):

Nucleolar Organizer ◽

Ribosomal Gene ◽

Rna Polymerase I ◽

Nucleolar Organizer Regions ◽

Binding Factor ◽

Upstream Binding Factor ◽

Acrocentric Chromosomes ◽

Polymerase I ◽

Secondary Constrictions ◽

Active Nors

Human ribosomal genes are located in NORs (nucleolar organizer regions) on the short arms of acrocentric chromosomes. During metaphase, previously active NORs appear as prominent chromosomal features termed secondary constrictions, which are achromatic in chromosome banding and positive in silver staining. The architectural RNA polymerase I transcription factor UBF (upstream binding factor) binds extensively across the ribosomal gene repeat throughout the cell cycle. Evidence that UBF underpins NOR structure is provided by an examination of cell lines in which large arrays of a heterologous UBF binding sequences are integrated at ectopic sites on human chromosomes. These arrays efficiently recruit UBF even to sites outside the nucleolus, and during metaphase form novel silver-stainable secondary constrictions, termed pseudo-NORs, that are morphologically similar to NORs.

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Epigenetic Programming of the rRNA Promoter by MBD3

Molecular and Cellular Biology ◽

10.1128/mcb.01880-06 ◽

2007 ◽

Vol 27 (13) ◽

pp. 4938-4952 ◽

Cited By ~ 61

Author(s):

Shelley E. Brown ◽

Moshe Szyf

Keyword(s):

Small Interfering Rna ◽

Rna Polymerase I ◽

Rrna Genes ◽

Rrna Gene ◽

Rrna Transcription ◽

Epigenetic Programming ◽

Binding Factor ◽

Upstream Binding Factor ◽

Polymerase I ◽

Interfering Rna

ABSTRACT Within the human genome there are hundreds of copies of the rRNA gene, but only a fraction of these genes are active. Silencing through epigenetics has been extensively studied; however, it is essential to understand how active rRNA genes are maintained. Here, we propose a role for the methyl-CpG binding domain protein MBD3 in epigenetically maintaining active rRNA promoters. We show that MBD3 is localized to the nucleolus, colocalizes with upstream binding factor, and binds to unmethylated rRNA promoters. Knockdown of MBD3 by small interfering RNA results in increased methylation of the rRNA promoter coupled with a decrease in RNA polymerase I binding and pre-rRNA transcription. Conversely, overexpression of MBD3 results in decreased methylation of the rRNA promoter. Additionally, overexpression of MBD3 induces demethylation of nonreplicating plasmids containing the rRNA promoter. We demonstrate that this demethylation occurs following the overexpression of MBD3 and its increased interaction with the methylated rRNA promoter. This is the first demonstration that MBD3 is involved in inducing and maintaining the demethylated state of a specific promoter.

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Regulation of ribosomal DNA transcription by insulin

AJP Cell Physiology ◽

10.1152/ajpcell.1998.275.1.c130 ◽

1998 ◽

Vol 275 (1) ◽

pp. C130-C138 ◽

Cited By ~ 50

Author(s):

Katherine M. Hannan ◽

Lawrence I. Rothblum ◽

Leonard S. Jefferson

Keyword(s):

Rna Polymerase ◽

Cell Types ◽

Rna Polymerase I ◽

Model Systems ◽

Serum Starvation ◽

Swiss Albino Mouse ◽

Rdna Transcription ◽

Cellular Content ◽

Upstream Binding Factor ◽

Polymerase I

The experiments reported here used 3T6-Swiss albino mouse fibroblasts and H4-II-E-C3 rat hepatoma cells as model systems to examine the mechanism(s) through which insulin regulates rDNA transcription. Serum starvation of 3T6 cells for 72 h resulted in a marked reduction in rDNA transcription. Treatment of serum-deprived cells with insulin was sufficient to restore rDNA transcription to control values. In addition, treatment of exponentially growing H4-II-E-C3 with insulin stimulated rDNA transcription. However, for both cell types, the stimulation of rDNA transcription in response to insulin was not associated with a change in the cellular content of RNA polymerase I. Thus we conclude that insulin must cause alterations in formation of the active RNA polymerase I initiation complex and/or the activities of auxiliary rDNA transcription factors. In support of this conclusion, insulin treatment of both cell types was found to increase the nuclear content of upstream binding factor (UBF) and RNA polymerase I-associated factor 53. Both of these factors are thought to be involved in recruitment of RNA polymerase I to the rDNA promoter. Nuclear run-on experiments demonstrated that the increase in cellular content of UBF was due to elevated transcription of the UBF gene. In addition, overexpression of UBF was sufficient to directly stimulate rDNA transcription from a reporter construct. The results demonstrate that insulin is capable of stimulating rDNA transcription in both 3T6 and H4-II-E-C3 cells, at least in part by increasing the cellular content of components required for assembly of RNA polymerase I into an active complex.

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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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Structure and function of ribosomal RNA gene chromatin

Biochemical Society Transactions ◽

10.1042/bst0360619 ◽

2008 ◽

Vol 36 (4) ◽

pp. 619-624 ◽

Cited By ~ 40

Author(s):

Joanna L. Birch ◽

Joost C.B.M. Zomerdijk

Keyword(s):

Ribosomal Rna ◽

Ribosome Biogenesis ◽

Rna Polymerase I ◽

Rrna Genes ◽

Rrna Gene ◽

Pol I ◽

And Function ◽

Polymerase I ◽

Cell Growth And Proliferation ◽

Cellular Control

Transcription of the major ribosomal RNAs by Pol I (RNA polymerase I) is a key determinant of ribosome biogenesis, driving cell growth and proliferation in eukaryotes. Hundreds of copies of rRNA genes are present in each cell, and there is evidence that the cellular control of Pol I transcription involves adjustments to the number of rRNA genes actively engaged in transcription, as well as to the rate of transcription from each active gene. Chromatin structure is inextricably linked to rRNA gene activity, and the present review highlights recent advances in this area.

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