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

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

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