Downloads

Movies, animations, podcast

• Podcast: Familie Hansen Award 2009 6.19 MB
• Video Portrait of the Philip Morris Award 2007 20.89 MB
• Video: Familie Hansen Award 2009 46.43 MB
• Animation: Assembly of the pre-initiation complex and promoter opening (Plaschka C, Hantsche M et al.: Transcription initiation complex structures elucidate DNA opening. Nature, 533, 353-358(2016)) 8.21 MB
• Animation: Nucleotide assembly by the RNA polymerase II elongation complex
  (Brueckner F et al.: A movie of the RNA polymerase nucleotide addition cycle. Curr Opin Struct Biol 19, 294-299 (2009).) 10.87 MB
• Animation: The RNA polymerase II elongation complex
  (Brueckner F et al.: A movie of the RNA polymerase nucleotide addition cycle. Curr Opin Struct Biol 19, 294-299 (2009).) 7.56 MB
• Animation: A movie of RNA polymerase II transcription
  (Cheung ACM, Cramer P: A movie of RNA polymerase II transcription. Cell 149, 1431-1437 (2009).) 28.4 MB

Models

• Model archeal RNAP-Spt4/5
  (Martinez-Rucobo FW et al.: Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J 30, 1302-1310 (2011).) 574.55 kB
• Model bacterial RNAP-NusG
  (Martinez-Rucobo FW et al.: Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J 30, 1302-1310 (2011).) 498.54 kB
• Models of closed and open pre-initiation complexes (Plaschka C, Hantsche M et al.: Transcription initiation complex structure elucidate DNA opening. Nature 533, 353-358(2016)) 193.15 MB
• Pol II-TFIIB model1 (BUSTER electron density map for PDB 3KF1 available upon request)
  (Kostrewa D et al.: RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462, 323-330 (2009).) 632.49 kB
• Expressome model with DNA, mRNA, and tRNA 1.72 MB
• Pol II initially transcribing complex model
  (Mühlbacher, W. et al. Conserved architecture of the core RNA polymerase II initiation complex. Nat. Commun. 5, 4310, doi:10.1038/ncomms5310 (2014).) 1.44 MB
• Pol II-TFIIB model2
  (Kostrewa D et al.: RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462, 323-330 (2009).) 627.75 kB
• Pol I-RRN3 model
  (Blattner C et al.: Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes Dev 25, 2093-2105 (2009).) 705.64 kB
• Model yeast Pol II-Spt4/5 elongation complex
  (Martinez-Rucobo FW et al.: Architecture of the RNA polymerase-Spt4/5 complex and basis of universal transcription processivity. EMBO J 30, 1302-1310 (2011).) 695.08 kB

Data

• List of 32 transcripts under attenuation control
  (Schulz D, Schwalb B, Kiesel A, Baejen C, Torkler P, Gagneur J, Soeding J, Cramer P: Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell 155 (5),1075-1087 (2013).) 347.0 B
• Annotation file of Nrd1 unterminated transcripts (NUTs)
  (Schulz D, Schwalb B, Kiesel A, Baejen C, Torkler P, Gagneur J, Soeding J, Cramer P: Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell 155 (5), (2013).) 121.18 kB
• List of cITC-cMed protein crosslinks (Plaschka et al.: Architecture of the RNA polymerase II-Mediator core initiation complex. Nature (2015) doi:10.1038/nature14229) 61.25 kB
• List of cMed protein crosslinks (Plaschka et al.: Architecture of the RNA polymerase II-Mediator core initiation complex. Nature (2015) doi:10.1038/nature14229) 21.34 kB
• Turnover measurements in S. cerevisiae: mRNA levels, synthesis- and decay rates
  (Sun M et al.: Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation. Genome Res 22, 1350-1359 (2012).) 633.2 kB
• Turnover measurements in S. pombe: mRNA levels, synthesis- and decay rates
  (Sun M et al.: Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation. Genome Res 22, 1350-1359 (2012).) 561.63 kB
• HMM based genome-wide transcription unit (TU) annotation. (Schwalb, B; Michel, M; Zacher, B; Frühauf, K; Demel, C; Tresch, A; Gagneur, J; Cramer, P: TT-seq maps the human transient transcriptome. Science (6290), 1225 - 1228 (2016)) 1.27 MB

Software

• Software: R script containing details of the model for the 3'-transition. (Beaten C, Andreani J et al: Genome-wide analysis of RNA polymerase II termination at protein-coding genes, (2017).) 673.0 B
• Software: R package to calculate gene-specific synthesis and degradation rates from TT-seq/4sU-seq and RNA-seq data. (Michel M, Schwalb B et al.: TT-seq maps the human transient transcriptome. Science 352, 1225-1228, (2016).) 401.29 kB

Miscellaneous

• Thoughts of the day 2020 1.43 MB