A novel TBP-associated factor of SL1 functions in RNA polymerase I transcription

Gorski, Julia J.; Pathak, Shalini; Panov, Kostya I.; Kasciukovic, Taciana; Panova, Tanya; Russell, Jackie; Zomerdijk, Joost C.B.M.

doi:10.1038/sj.emboj.7601601

Cited by 81 publications

(72 citation statements)

References 42 publications

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“…The sample was separated on a 1D gel, digested in gel with trypsin, and analyzed by mass spectrometry (Raw data, available as a Scaffold file, are available upon request.). Among the identified TBP-interacting proteins were all subunits of known TBP complexes, including the newly reported TAF I 41 subunit of SL1 (14) (Fig. 1A).…”

Section: Resultsmentioning

confidence: 99%

“…First TBP is incorporated with 13-14 TBP-associated factors (TAFs) into the TFIID complex involved in pol II transcription (13). Next in pol I transcription, TBP is part of the SL1 complex consisting of four other subunits: TAF I 110, TAF I 63, TAF I 48, and TAF I 41 (14). The pol III system uses the TFIIIB complex consisting of TBP, Brf1, and Bdp1 proteins (15).…”

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confidence: 99%

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Quantitative Proteomics Reveals Regulation of Dynamic Components within TATA-binding Protein (TBP) Transcription Complexes

Mousson

Kolkman

Pijnappel

et al. 2008

Molecular & Cellular Proteomics

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Affinity purification in combination with isotope labeling of proteins has proven to be a powerful method to discriminate specific from nonspecific interactors. However, in the standard SILAC (stable isotope labeling by amino acids in cell culture) approach dynamic components may easily be assigned as nonspecific. We compared two affinity purification protocols, which in combination revealed information on the dynamics of protein complexes. We focused on the central component in eukaryotic transcription, the human TATA-binding protein, which is involved in different complexes. All known TATA-binding protein-associated factors (TAFs) were detected as specific interactors. Interestingly one of them, BTAF1, exchanged significantly in cell extracts during the affinity purification. The development of quantitative mass spectrometry has had a major impact in proteomics allowing quantification of protein expression levels under different conditions (1-3). Among the applications of quantitative mass spectrometry the accurate determination of specificity of protein-protein interactions is crucial to the understanding of multisubunit protein assemblies. To discriminate between specific and nonspecific interacting proteins within complexes, most widely used methods in quantitative proteomics are stable isotope labeling approaches such as SILAC, 1 ICAT, and isotopic differentiation of interactions as random or targeted (I-DIRT) (3-9). In the most common approach stable isotopelabeled amino acids are used in cell cultures (SILAC) in combination with affinity purification (3). In such experiments, two cell populations differing by the presence of a tagged protein are grown in identical culture media with the exception that the first medium contains a "light," e.g. naturally abundant isotope of a selected amino acid, whereas the second medium contains a "heavy," e.g. stable isotope version of this amino acid. The labeled amino acid is efficiently incorporated during protein synthesis in the cell. This leads to a difference in mass for chemically identical peptides that can be detected by mass spectrometry. Two populations of cells can be combined directly after harvesting, and subsequent purification will have the same effect on the heavy and light forms of the proteins. The relative abundance of proteins ("SILAC ratio") is derived by comparison of the integrated mass spectrometry peak areas of the labeled and unlabeled forms of a peptide. Incorporation of heavy forms of arginine and lysine offers the advantage that most tryptic peptides can be used for quantification. The relevance of multisubunit protein assemblies in cellular regulation pathways is well recognized (10), but progress in determining pathways of assembly and disassembly of complexes and regulation of (individual) subunit exchange has been hampered by a lack of generic methods. The importance of developing such methods is stressed by observations that a single protein can reside simultaneously in multiple protein complexes of distinct functions. The TATA-bindin...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Quantitative Proteomics Reveals Regulation of Dynamic Components within TATA-binding Protein (TBP) Transcription Complexes

Mousson

Kolkman

Pijnappel

et al. 2008

Molecular & Cellular Proteomics

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“…In contrast, three mouse recombinant TAF I s and the TBP complex did not reconstitute the TIF-IB activity in an in vitro transcription system (Heix et al, 1997). Later, a further TAF I , TAF I D (also known as TAF I 41 and TAF1D), was identified from the TBP-antibody affinity-purified SL1 fraction (Gorski et al, 2007). TAF I D co-migrates with TBP on SDS-PAGE, so it remained unidentified for more than 10 years following the initial identification of the SL1 complex (Comai et al, 1992).…”

Section: Introductionmentioning

confidence: 99%

“…TAF I D co-migrates with TBP on SDS-PAGE, so it remained unidentified for more than 10 years following the initial identification of the SL1 complex (Comai et al, 1992). TAF I D is involved in rDNA transcription in vivo (Gorski et al, 2007). Thus, we hypothesize that TAF I D is a final component in reconstituting the human SL1 activity in mouse cells and overcoming the rDNA transcription species barrier.…”

Section: Introductionmentioning

confidence: 99%

Reconstitution of human rRNA gene transcription in mouse cells by complete SL1 complex

Murano

Okuwaki

Momose

et al. 2014

Journal of Cell Science

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An important characteristic of the transcription of a ribosomal RNA gene (rDNA) mediated by DNA-dependent RNA polymerase (Pol) I is its stringent species specificity. SL1/TIF-IB is a key complex for species specificity, but its functional complex has not been reconstituted. Here, we established a novel and highly sensitive monitoring system for Pol I transcription to reconstitute the SL1 activity in which a transcript harboring a reporter gene synthesized by Pol I is amplified and converted into translatable mRNA by the influenza virus RNA-dependent RNA polymerase. Using this monitoring system, we reconstituted Pol I transcription from the human rDNA promoter in mouse cells by expressing four human TATA-binding protein (TBP)-associated factors (TAF I s) in the SL1 complex. The reconstituted SL1 also re-activated human rDNA transcription in mouse A9 cells carrying an inactive human chromosome 21 that contains the rDNA cluster. Chimeric SL1 complexes containing human and mouse TAF I s could be formed, but these complexes were inactive for human rDNA transcription. We conclude that four human TAF I s are necessary and sufficient to overcome the barrier of species specificity for human rDNA transcription in mouse cells.

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“…It then induces a loop structure that brings the upstream control element and the core promoter of the rRNA gene into close proximity and facilitates the recruitment of SL1 and Pol I (Bazett-Jones et al, 1994;Bell and Dutta, 2002;Jantzen et al, 1992). SL1 is a protein complex that contains the TATA-binding protein (TBP) and Pol-I-specific TBP-associated factors (Comai et al, 1992Gorski et al, 2007;Heix et al, 1997;Zomerdijk et al, 1994). SL1 therefore recognizes the Pol-I-specific promoter and confers the selectivity of the PIC for rDNA transcription.…”

Section: Introductionmentioning

confidence: 99%

DNA replication initiator Cdc6 also regulates ribosomal DNA transcription initiation

Huang

Wang

et al. 2016

Journal of Cell Science

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RNA-polymerase-I-dependent ribosomal DNA (rDNA) transcription is fundamental to rRNA processing, ribosome assembly and protein synthesis. However, how this process is initiated during the cell cycle is not fully understood. By performing a proteomic analysis of transcription factors that bind RNA polymerase I during rDNA transcription initiation, we identified that the DNA replication initiator Cdc6 interacts with RNA polymerase I and its co-factors, and promotes rDNA transcription in G1 phase in an ATPaseactivity-dependent manner. We further showed that Cdc6 is targeted to the nucleolus during late mitosis and G1 phase in a manner that is dependent on B23 (also known as nucleophosmin, NPM1), and preferentially binds to the rDNA promoter through its ATP-binding domain. Overexpression of Cdc6 increases rDNA transcription, whereas knockdown of Cdc6 results in a decreased association of both RNA polymerase I and the RNA polymerase I transcription factor RRN3 with rDNA, and a reduction of rDNA transcription. Furthermore, depletion of Cdc6 impairs the interaction between RRN3 and RNA polymerase I. Taken together, our data demonstrate that Cdc6 also serves as a regulator of rDNA transcription initiation, and indicate a mechanism by which initiation of rDNA transcription and DNA replication can be coordinated in cells.

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A novel TBP-associated factor of SL1 functions in RNA polymerase I transcription

Cited by 81 publications

References 42 publications

Quantitative Proteomics Reveals Regulation of Dynamic Components within TATA-binding Protein (TBP) Transcription Complexes

Quantitative Proteomics Reveals Regulation of Dynamic Components within TATA-binding Protein (TBP) Transcription Complexes

Reconstitution of human rRNA gene transcription in mouse cells by complete SL1 complex

DNA replication initiator Cdc6 also regulates ribosomal DNA transcription initiation

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