Structural biology of mammalian transcription regulation

Project Information

TRANSREGULON

Grant agreement ID: 693023

DOI 10.3030/693023

Project closed

EC signature date 24 May 2016

Start date 1 July 2016

End date 30 June 2020

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 2 496 250,00

EU contribution € 2 496 250,00

Coordinated by

MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV
Germany

Publications

Peer reviewed articles (38)

CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response

Author(s): Grégoire Stik, Enrique Vidal, Mercedes Barrero, Sergi Cuartero, Maria Vila-Casadesús, Julen Mendieta-Esteban, Tian V. Tian, Jinmi Choi, Clara Berenguer, Amaya Abad, Beatrice Borsari, François le Dily, Patrick Cramer, Marc A. Marti-Renom, Ralph Stadhouders, Thomas Graf
Published in: Nature Genetics, Issue 52/7, 2020, Page(s) 655-661, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-020-0643-0

TT‐seq captures enhancer landscapes immediately after T‐cell stimulation

Author(s): Margaux Michel, Carina Demel, Benedikt Zacher, Björn Schwalb, Stefan Krebs, Helmut Blum, Julien Gagneur, Patrick Cramer
Published in: Molecular Systems Biology, Issue 13/3, 2017, Page(s) 920, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20167507

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN

Author(s): Benedikt Zacher, Margaux Michel, Björn Schwalb, Patrick Cramer, Achim Tresch, Julien Gagneur
Published in: PLOS ONE, Issue 12/1, 2017, Page(s) e0169249, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0169249

CDK9-dependent RNA polymerase II pausing controls transcription initiation

Author(s): Saskia Gressel, Björn Schwalb, Tim Michael Decker, Weihua Qin, Heinrich Leonhardt, Dirk Eick, Patrick Cramer
Published in: eLife, Issue 6, 2017, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/eLife.29736

Mechanism of RNA polymerase II stalling by DNA alkylation

Author(s): Stefano Malvezzi, Lucas Farnung, Claudia M. N. Aloisi, Todor Angelov, Patrick Cramer, Shana J. Sturla
Published in: Proceedings of the National Academy of Sciences, Issue 114/46, 2017, Page(s) 12172-12177, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.1706592114

RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases

Author(s): Sofia Battaglia, Michael Lidschreiber, Carlo Baejen, Phillipp Torkler, Seychelle M Vos, Patrick Cramer
Published in: eLife, Issue 6, 2017, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/eLife.25637

Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex

Author(s): Youwei Xu, Carrie Bernecky, Chung-Tien Lee, Kerstin C. Maier, Björn Schwalb, Dimitry Tegunov, Jürgen M. Plitzko, Henning Urlaub, Patrick Cramer
Published in: Nature Communications, Issue 8, 2017, Page(s) 15741, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/ncomms15741

Structure of transcribing RNA polymerase II-nucleosome complex

Author(s): Lucas Farnung, Seychelle M. Vos, Patrick Cramer
Published in: Nature Communications, Issue 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-07870-y

Structures of transcription pre-initiation complex with TFIIH and Mediator

Author(s): S. Schilbach, M. Hantsche, D. Tegunov, C. Dienemann, C. Wigge, H. Urlaub, P. Cramer
Published in: Nature, 2017, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature24282

Genome-wide Analysis of RNA Polymerase II Termination at Protein-Coding Genes

Author(s): Carlo Baejen, Jessica Andreani, Phillipp Torkler, Sofia Battaglia, Bjoern Schwalb, Michael Lidschreiber, Kerstin C. Maier, Andrea Boltendahl, Petra Rus, Stephanie Esslinger, Johannes Söding, Patrick Cramer
Published in: Molecular Cell, Issue 66/1, 2017, Page(s) 38-49.e6, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2017.02.009

Structural Basis of Mitochondrial Transcription Initiation

Author(s): Hauke S. Hillen, Yaroslav I. Morozov, Azadeh Sarfallah, Dmitry Temiakov, Patrick Cramer
Published in: Cell, Issue 171/5, 2017, Page(s) 1072-1081.e10, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2017.10.036

Architecture of a transcribing-translating expressome

Author(s): R. Kohler, R. A. Mooney, D. J. Mills, R. Landick, P. Cramer
Published in: Science, Issue 356/6334, 2017, Page(s) 194-197, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.aal3059

The APT complex is involved in non-coding RNA transcription and is distinct from CPF

Author(s): Michael Lidschreiber, Ashley D Easter, Sofia Battaglia, Juan B Rodríguez-Molina, Ana Casañal, Manuel Carminati, Carlo Baejen, Pawel Grzechnik, Kerstin C Maier, Patrick Cramer, Lori A Passmore
Published in: Nucleic Acids Research, 2018, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky845

Structure of paused transcription complex Pol II–DSIF–NELF

Author(s): Seychelle M. Vos, Lucas Farnung, Henning Urlaub, Patrick Cramer
Published in: Nature, Issue 560/7720, 2018, Page(s) 601-606, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-018-0442-2

Structural Molecular Biology—A Personal Reflection on the Occasion of John Kendrew's 100th Birthday

Author(s): Patrick Cramer
Published in: Journal of Molecular Biology, Issue 429/17, 2017, Page(s) 2603-2610, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2017.05.007

Nucleosome–Chd1 structure and implications for chromatin remodelling

Author(s): Lucas Farnung, Seychelle M. Vos, Christoph Wigge, Patrick Cramer
Published in: Nature, Issue 550/7677, 2017, Page(s) 539-542, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature24046

Structural Basis of RNA Polymerase I Transcription Initiation

Author(s): Christoph Engel, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane Oberthuer, Carlo Baejen, Carrie Bernecky, Patrick Cramer
Published in: Cell, Issue 169/1, 2017, Page(s) 120-131.e22, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2017.03.003

Spt5 Plays Vital Roles in the Control of Sense and Antisense Transcription Elongation

Author(s): Ameet Shetty, Scott P. Kallgren, Carina Demel, Kerstin C. Maier, Dan Spatt, Burak H. Alver, Patrick Cramer, Peter J. Park, Fred Winston
Published in: Molecular Cell, Issue 66/1, 2017, Page(s) 77-88.e5, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2017.02.023

Mechanism of Transcription Anti-termination in Human Mitochondria

Author(s): Hauke S. Hillen, Andrey V. Parshin, Karen Agaronyan, Yaroslav I. Morozov, James J. Graber, Aleksandar Chernev, Kathrin Schwinghammer, Henning Urlaub, Michael Anikin, Patrick Cramer, Dmitry Temiakov
Published in: Cell, Issue 171/5, 2017, Page(s) 1082-1093.e13, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2017.09.035

The Implication of Early Chromatin Changes in X Chromosome Inactivation

Author(s): Jan Jakub Żylicz, Aurélie Bousard, Kristina Žumer, Francois Dossin, Eusra Mohammad, Simão Teixeira da Rocha, Björn Schwalb, Laurène Syx, Florent Dingli, Damarys Loew, Patrick Cramer, Edith Heard
Published in: Cell, Issue 176/1-2, 2019, Page(s) 182-197.e23, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2018.11.041

Conserved RNA polymerase II initiation complex structure

Author(s): Merle Hantsche, Patrick Cramer
Published in: Current Opinion in Structural Biology, Issue 47, 2017, Page(s) 17-22, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2017.03.013

Structural basis of TFIIH activation for nucleotide excision repair

Author(s): Goran Kokic, Aleksandar Chernev, Dimitry Tegunov, Christian Dienemann, Henning Urlaub, Patrick Cramer
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-10745-5

Transcriptome maps of general eukaryotic RNA degradation factors

Author(s): Salma Sohrabi-Jahromi, Katharina B Hofmann, Andrea Boltendahl, Christian Roth, Saskia Gressel, Carlo Baejen, Johannes Soeding, Patrick Cramer
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.47040

Global donor and acceptor splicing site kinetics in human cells

Author(s): Leonhard Wachutka, Livia Caizzi, Julien Gagneur, Patrick Cramer
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.45056

NASC-seq monitors RNA synthesis in single cells

Author(s): Gert-Jan Hendriks, Lisa A. Jung, Anton J. M. Larsson, Michael Lidschreiber, Oscar Andersson Forsman, Katja Lidschreiber, Patrick Cramer, Rickard Sandberg
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-11028-9

Structure of activated transcription complex Pol II–DSIF–PAF–SPT6

Author(s): Seychelle M. Vos, Lucas Farnung, Marc Boehning, Christoph Wigge, Andreas Linden, Henning Urlaub, Patrick Cramer
Published in: Nature, Issue 560/7720, 2018, Page(s) 607-612, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-018-0440-4

Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp

Author(s): Carrie Bernecky, Jürgen M Plitzko, Patrick Cramer
Published in: Nature Structural & Molecular Biology, Issue 24/10, 2017, Page(s) 809-815, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/nsmb.3465

Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

Author(s): Felix R. Wagner, Christian Dienemann, Haibo Wang, Alexandra Stützer, Dimitry Tegunov, Henning Urlaub, Patrick Cramer
Published in: Nature, Issue 579/7799, 2020, Page(s) 448-451, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2088-0

Structure of H3K36-methylated nucleosome–PWWP complex reveals multivalent cross-gyre binding

Author(s): Haibo Wang, Lucas Farnung, Christian Dienemann, Patrick Cramer
Published in: Nature Structural & Molecular Biology, Issue 27/1, 2020, Page(s) 8-13, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-019-0345-4

Structure of replicating SARS-CoV-2 polymerase

Author(s): Hauke S. Hillen, Goran Kokic, Lucas Farnung, Christian Dienemann, Dimitry Tegunov, Patrick Cramer
Published in: Nature, 2020, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2368-8

The pause-initiation limit restricts transcription activation in human cells

Author(s): Saskia Gressel, Björn Schwalb, Patrick Cramer
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-11536-8

Real-time cryo-electron microscopy data preprocessing with Warp

Author(s): Dimitry Tegunov, Patrick Cramer
Published in: Nature Methods, Issue 16/11, 2019, Page(s) 1146-1152, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-019-0580-y

Structure of the super-elongation complex subunit AFF4 C-terminal homology domain reveals requirements for AFF homo- and heterodimerization

Author(s): Ying Chen, Patrick Cramer
Published in: Journal of Biological Chemistry, Issue 294/27, 2019, Page(s) 10663-10673, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.ra119.008577

Nucleosome-CHD4 chromatin remodeler structure maps human disease mutations

Author(s): Lucas Farnung, Moritz Ochmann, Patrick Cramer
Published in: eLife, Issue 9, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.56178

Organization and regulation of gene transcription

Author(s): Patrick Cramer
Published in: Nature, Issue 573/7772, 2019, Page(s) 45-54, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-019-1517-4

Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

Author(s): Svetlana O. Dodonova, Fangjie Zhu, Christian Dienemann, Jussi Taipale, Patrick Cramer
Published in: Nature, Issue 580/7805, 2020, Page(s) 669-672, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-2195-y

Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation

Author(s): Seychelle M. Vos, Lucas Farnung, Andreas Linden, Henning Urlaub, Patrick Cramer
Published in: Nature Structural & Molecular Biology, Issue 27/7, 2020, Page(s) 668-677, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-020-0437-1

Structure of the transcription coactivator SAGA

Author(s): Haibo Wang, Christian Dienemann, Alexandra Stützer, Henning Urlaub, Alan C. M. Cheung, Patrick Cramer
Published in: Nature, Issue 577/7792, 2020, Page(s) 717-720, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-020-1933-5