Molecular Basis of RNA Polymerase III Transcription Repression by Maf1

Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
Cell (Impact Factor: 32.24). 10/2010; 143(1):59-70. DOI: 10.1016/j.cell.2010.09.002
Source: PubMed


RNA polymerase III (Pol III) transcribes short RNAs required for cell growth. Under stress conditions, the conserved protein Maf1 rapidly represses Pol III transcription. We report the crystal structure of Maf1 and cryo-electron microscopic structures of Pol III, an active Pol III-DNA-RNA complex, and a repressive Pol III-Maf1 complex. Binding of DNA and RNA causes ordering of the Pol III-specific subcomplex C82/34/31 that is required for transcription initiation. Maf1 binds the Pol III clamp and rearranges C82/34/31 at the rim of the active center cleft. This impairs recruitment of Pol III to a complex of promoter DNA with the initiation factors Brf1 and TBP and thus prevents closed complex formation. Maf1 does however not impair binding of a DNA-RNA scaffold and RNA synthesis. These results explain how Maf1 specifically represses transcription initiation from Pol III promoters and indicate that Maf1 also prevents reinitiation by binding Pol III during transcription elongation.

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Available from: Alessandro Vannini, Oct 13, 2015
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    • "This interaction also inhibits Pol III from binding to BRF1, which in turn prevents recruitment of Pol III to Pol III promoters. Furthermore, MAF1 also inhibits Pol III transcription through direct binding with Pol III, which interferes with the recruitment of Pol III to the assembled TFIIIB/DNA complexes (Desai et al., 2005; Vannini et al., 2010). In addition, association of MAF1 with Pol III-transcribed genes has been detected genome-wide concomitant with an increase in occupation during repression; this indicates that direct interaction of MAF1 with Pol III genes is also an important attribute of repression (Roberts et al., 2006). "
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    ABSTRACT: MAF1 represses Pol III-mediated transcription by interfering with TFIIIB and Pol III. Herein, we found that MAF1 knockdown induced CDKN1A transcription and chromatin looping concurrently with Pol III recruitment. Simultaneous knockdown of MAF1 with Pol III or BRF1 (subunit of TFIIIB) diminished the activation and looping effect, which indicates that recruiting Pol III was required for activation of Pol II-mediated transcription and chromatin looping. ChIP analysis after MAF1 knockdown indicated enhanced binding of Pol III and BRF1, as well as of CFP1, p300, and PCAF, which are factors that mediate active histone marks, along with the binding of TBP and POLR2E to the CDKN1A promoter. Simultaneous knockdown with Pol III abolished these regulatory events. Similar results were obtained for GDF15. Our results reveal a novel mechanism by which MAF1 and Pol III regulate the activity of a protein-coding gene transcribed by Pol II.
    eLife Sciences 06/2015; 4. DOI:10.7554/eLife.06283 · 9.32 Impact Factor
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    • "For efficient termination on 6T tracts, C53/C37 & C11 augment the core mechanism via an auxiliary mechanism (Arimbasseri and Maraia, 2013). The C53/37 subcomplex appears to associate with the same surface of the C2 lobe domain identified as important for termination in Hall's laboratory; moreover, this general region appears juxtaposed to the docking site for the N-terminal domain of C11 (Fernandez-Tornero et al., 2007; Fernandez-Tornero et al., 2010; Vannini et al., 2010; Wu et al., 2011). This is consistent with mutation of a segment of the analogous C2 lobe of zebra fish pol III as well as S. pombe pol III that causes loss of C11 (Yee et al., 2007b). "
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    ABSTRACT: Suppressor tRNAs bear anticodon mutations that allow them to decode premature stop codons in metabolic marker gene mRNAs, that can be used as in vivo reporters of functional tRNA biogenesis. Here, we review key components of a suppressor tRNA system specific to Schizosaccharomyces pombe and its adaptations for use to study specific steps in tRNA biogenesis. Eukaryotic tRNA biogenesis begins with transcription initiation by RNA polymerase (pol) III. The nascent pre-tRNAs must undergo folding, 5' and 3' processing to remove the leader and trailer, nuclear export, and splicing if applicable, while multiple complex chemical modifications occur throughout the process. We review evidence that precursor-tRNA processing begins with transcription termination at the oligo(T) terminator element, which forms a 3' oligo(U) tract on the nascent RNA, a sequence-specific binding site for the RNA chaperone, La protein. The processing pathway bifurcates depending on a poorly understood property of pol III termination that determines the 3' oligo(U) length and therefore the affinity for La. We thus review the pol III termination process and the factors involved including advances using gene-specific random mutagenesis by dNTP analogs that identify key residues important for transcription termination in certain pol III subunits. The review ends with a 'technical approaches' section that includes a parts lists of suppressor-tRNA alleles, strains and plasmids, and graphic examples of its diverse uses. Published by Elsevier B.V.
    Gene 11/2014; 556(1). DOI:10.1016/j.gene.2014.11.034 · 2.14 Impact Factor
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    • "The stabilization of the inherently flexible subcomplex C82/34/31 upon nucleic acid binding represented one of the key findings. In particular, the subunits C82 and C31, together with the C-terminus of the subunit C34 constitute a globular assembly engulfed between the jaw, the clamp and the stalk domain, while the two adjacent N-terminal WH domains of the subunit C34 form a molecular bridge between the clamp coiled-coil domain and the protrusion [19] [34] (Fig. 1). The arrangement of the two adjacent C34 WH domains resembled the Pol I-specific A49 tWH domain, which has been proposed to occupy a similar location in Pol I [28] [30]. "
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    ABSTRACT: RNA polymerase I and III are responsible for the bulk of nuclear transcription in actively growing cells and their activity impacts the cellular biosynthetic capacity. As a consequence, RNA polymerase I and III deregulation has been directly linked to cancer development. The complexity of RNA polymerase I and III transcription apparatuses has hampered their structural characterization. However, in the last decade tremendous progresses have been made, providing insights into the molecular and functional architecture of these multi-subunit transcriptional machineries. Here we summarize the available structural data on RNA polymerase I and III, including specific transcription factors and global regulators. Despite the overall scarcity of detailed structural data, the recent advances in the structural biology of RNA polymerase I and III represent the first step towards a comprehensive understanding of the molecular mechanism underlying RNA polymerase I and III transcription. This article is part of a Special Issue entitled: Transcription by Odd Pols.
    Biochimica et Biophysica Acta 09/2012; 2013(3-4). DOI:10.1016/j.bbagrm.2012.09.009 · 4.66 Impact Factor
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