RNA polymerase structure and function!!Patrick Cramer!!Gene Center Munich!Department of Biochemistry!Ludwig-Maximilians-Universität München!

Pol I (rRNA) Pol II (mRNA) Pol III (tRNA)

mitoPol

Ringel, Nature 2011!

Armache, PNAS 2003!Kuhn, Cell 2007! Vannini, Cell 2010!

Pol II Pol I Pol III Rpb1 A190 C160 Rpb2 A135 C128 Rpb3 AC40 AC40 Rpb11 AC19 AC19!Rpb9 A12.2 C11 Rpb5 Rpb5 Rpb5 Rpb6 Rpb6 Rpb6 Rpb8 Rpb8 Rpb8 Rpb10 Rpb10 Rpb10 Rpb12 Rpb12 Rpb12 Rpb4 A14 C17 Rpb7 A43 C25

A49 C53 A34.5 C37

C82 C34 C31

Cramer et al., Science 2000, 2001!

Pol II Pol I Pol III Rpb1 A190 C160 Rpb2 A135 C128 Rpb3 AC40 AC40 Rpb11 AC19 AC19!Rpb9 A12.2 C11 Rpb5 Rpb5 Rpb5 Rpb6 Rpb6 Rpb6 Rpb8 Rpb8 Rpb8 Rpb10 Rpb10 Rpb10 Rpb12 Rpb12 Rpb12 Rpb4 A14 C17 Rpb7 A43 C25 TFIIFα A49 Dim C53 TFIIFβ A34.5 Dim C37

C82 TFIIEβ A49 tWH C34

C31

Jasiak, Mol Cell 2006; Kuhn Cell 2007; Vannini, Cell 2010; Geiger Mol. Cell 2010!

Closed complex Open complex Elongation complex

Kostrewa Nature 2009; Kettenberger Mol Cell 2004; Andrecka NAR 2009!

Initiation-elongation transition

Basis for universal transcription processivity

Hirtreiter et al., and Werner, NAR 2010; Martinez et al. EMBO J. 2011!

Cheung and Cramer, Nature 2011.!

ChIP-chip classifies Pol II-associated factors!

Mayer et al., NSMB 2010!

The initiation-elongation transition

Spt4/5!

TSS!

TFIIS!

P

P

P

P

P

P

CTD!

Spt4/5!

RNA!

TFIIS!

P

P

P

Spt4/5!

CTD!

Scp1!phosphatase!

Cdk8/cycC!kinase!

P

P

P

TFIIS!

P

P

P

Spt4/5!

Pcf11 3’-RNA!processing factor!

Set2 histone!methyltransferase!

Spt6 nucleosome!re-assembly factor!

!CTD!

Scp1!phosphatase!

Cdk8/cycC!kinase!

Y S P T S P S!1 2 3 4 5 6 7!

S2P: 3’-mRNA processing & termination T4P: histone mRNA synthesis S5P: 5’-mRNA capping S7P: snRNA synthesis

Kin28! Y S P T S P S!1 2 3 4 5 6 7!

S5P!S7P!

Kin28! Y S P T S P S!1 2 3 4 5 6 7!

Ctk1!Bur1!S5P!

S7P!

Kin28! Y S P T S P S!1 2 3 4 5 6 7!

S2P!Ctk1!Bur1!S5P!

S7P!

Kin28! Y S P T S P S!1 2 3 4 5 6 7!

!Beyond the CTD: coordination of nuclear events!

!

Mayer, Schreieck et al. MCB 2012!

Structural biology!

Functional genomics!

Molecular systems biology!of genomic regulation!

Pol I-specific initiation regulation!

Rrn3 ‘activator’!

Kuhn et al. Cell 2007; Geiger et al. Mol. Cell 2010; Blattner et al. Genes Dev 2011!

Pol III-specific initiation regulation!

Jasiak et al. Mol. Cell 2006; Vannini, Ringel, Kusser et al. Cell 2010!

Maf1 repressor!

Pol II initiation regulation requires Mediator!

Lariviere et al., Curr. Op. Cell Biol. 2012!

Lariviere et al. Curr Op Cell Biol 2012!

!Transcription regulation requires Mediator!

!

cDTA monitors changes in mRNA metabolism during osmotic stress response!

Present lab members ! ! ! ! !!S. Benkert!C. Baejen!C. Buchen!A. Cheung!S. Etzold!C. Engel!F. Hoeg!K. Kinkelin!D. Kostrewa!L. Lariviere!

E. Lehmann!K. Leike!M. Lidschreiber!D. Martin !K. Maier!F. Martinez-Rucobo!A. Mayer!M. Michel!W. Mühlbacher!J. Niesser!

N. Pirkl!D. Pöllmann!S. Sainsbury!A. Schreieck!D. Schulz!K. Schwinghammer!M. Seizl!M. Sun!L. Wentzeck!T. Wild!

Past lab members ! ! ! !K.-J. Armache!S. Baumli !C. Blattner!M. Bertero !F. Brückner!E. Czeko!G. Damsma!S. Dengl!S. Geiger!S. Höppner !A. Jasiak!A. Jawahri!S. Jennebach!T. Kamenski!

Funding !!Freistaat Bayern!DFG!SFB646, TR5!CIPSM, NIM!FOR1068!EU FP7!FdCI!BIF!AvH!EMBO!Jung-Stiftung!ERC!

Recent collaborations!R. Beckmann (Munich)!D. Eick (Munich)!L. Dölken (Munich)!F. Holstege (Utrecht)!E. Kremmer (Munich)!J. Michaelis (Munich)!J. Rappsilber (Edinb.)!M. Siebert & J. Soeding!D. Temiakov (Stratford)!M. Zeller & M. Thomm !(Regensburg)!B. Schwalb & A. Tresch!F. Werner (London)!!

H. Kettenberger!T. Koschubs!C.-D. Kuhn!A.  Kusser !E. Lehmann!A. Meinhart!C. Miller!R. Ringel!W. Ruan!J. Sydow!A. Vannini!E. Vojnic!