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
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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. Chromatin-immunoprecipitation 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 TATA binding protein (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.
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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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    • "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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