Cramer, Patrick

[["dc.bibliographiccitation.firstpage","8"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Structural & Molecular Biology"],["dc.bibliographiccitation.lastpage","13"],["dc.bibliographiccitation.volume","27"],["dc.contributor.author","Wang, Haibo"],["dc.contributor.author","Farnung, Lucas"],["dc.contributor.author","Dienemann, Christian"],["dc.contributor.author","Cramer, Patrick"],["dc.date.accessioned","2022-02-21T12:35:13Z"],["dc.date.available","2022-02-21T12:35:13Z"],["dc.date.issued","2020"],["dc.description.abstract","Recognition of histone-modified nucleosomes by specific reader domains underlies the regulation of chromatin-associated processes. Whereas structural studies revealed how reader domains bind modified histone peptides, it is unclear how reader domains interact with modified nucleosomes. Here, we report the cryo-electron microscopy structure of the PWWP reader domain of human transcriptional coactivator LEDGF in complex with an H3K36-methylated nucleosome at 3.2-Å resolution. The structure reveals multivalent binding of the reader domain to the methylated histone tail and to both gyres of nucleosomal DNA, explaining the known cooperative interactions. The observed cross-gyre binding may contribute to nucleosome integrity during transcription. The structure also explains how human PWWP domain-containing proteins are recruited to H3K36-methylated regions of the genome for transcription, histone acetylation and methylation, and for DNA methylation and repair."],["dc.identifier.doi","10.1038/s41594-019-0345-4"],["dc.identifier.pmid","31819277"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/100140"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/196"],["dc.language.iso","en"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","1545-9985"],["dc.relation.issn","1545-9993"],["dc.relation.workinggroup","RG Cramer"],["dc.title","Structure of H3K36-methylated nucleosome-PWWP complex reveals multivalent cross-gyre binding"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.contributor.author","Farnung, Lucas"],["dc.contributor.author","Ochmann, Moritz"],["dc.contributor.author","Engeholm, Maik"],["dc.contributor.author","Cramer, Patrick"],["dc.date.accessioned","2022-02-23T11:49:10Z"],["dc.date.available","2022-02-23T11:49:10Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1101/2020.11.30.403857"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/100351"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/136"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.workinggroup","RG Cramer"],["dc.title","Structural basis of nucleosome transcription mediated by Chd1 and FACT"],["dc.type","preprint"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","382"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Nature Structural & Molecular Biology"],["dc.bibliographiccitation.lastpage","387"],["dc.bibliographiccitation.volume","28"],["dc.contributor.author","Farnung, Lucas"],["dc.contributor.author","Ochmann, Moritz"],["dc.contributor.author","Engeholm, Maik"],["dc.contributor.author","Cramer, Patrick"],["dc.date.accessioned","2022-02-22T12:16:36Z"],["dc.date.available","2022-02-22T12:16:36Z"],["dc.date.issued","2021"],["dc.description.abstract","Efficient transcription of RNA polymerase II (Pol II) through nucleosomes requires the help of various factors. Here we show biochemically that Pol II transcription through a nucleosome is facilitated by the chromatin remodeler Chd1 and the histone chaperone FACT when the elongation factors Spt4/5 and TFIIS are present. We report cryo-EM structures of transcribing Saccharomyces cerevisiae Pol II-Spt4/5-nucleosome complexes with bound Chd1 or FACT. In the first structure, Pol II transcription exposes the proximal histone H2A-H2B dimer that is bound by Spt5. Pol II has also released the inhibitory DNA-binding region of Chd1 that is poised to pump DNA toward Pol II. In the second structure, Pol II has generated a partially unraveled nucleosome that binds FACT, which excludes Chd1 and Spt5. These results suggest that Pol II progression through a nucleosome activates Chd1, enables FACT binding and eventually triggers transfer of FACT together with histones to upstream DNA."],["dc.identifier.doi","10.1038/s41594-021-00578-6"],["dc.identifier.pmid","33846633"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/100171"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/267"],["dc.language.iso","en"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","1545-9985"],["dc.relation.issn","1545-9993"],["dc.relation.workinggroup","RG Cramer"],["dc.rights","CC BY 4.0"],["dc.title","Structural basis of nucleosome transcription mediated by Chd1 and FACT"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","607"],["dc.bibliographiccitation.issue","7720"],["dc.bibliographiccitation.journal","Nature"],["dc.bibliographiccitation.lastpage","612"],["dc.bibliographiccitation.volume","560"],["dc.contributor.author","Vos, Seychelle M."],["dc.contributor.author","Farnung, Lucas"],["dc.contributor.author","Boehning, Marc"],["dc.contributor.author","Wigge, Christoph"],["dc.contributor.author","Linden, Andreas"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Cramer, Patrick"],["dc.date.accessioned","2020-12-10T18:09:59Z"],["dc.date.available","2020-12-10T18:09:59Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1038/s41586-018-0440-4"],["dc.identifier.eissn","1476-4687"],["dc.identifier.issn","0028-0836"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/73819"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.title","Structure of activated transcription complex Pol II–DSIF–PAF–SPT6"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","12172"],["dc.bibliographiccitation.issue","46"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences of the United States of America"],["dc.bibliographiccitation.lastpage","12177"],["dc.bibliographiccitation.volume","114"],["dc.contributor.author","Malvezzi, Stefano"],["dc.contributor.author","Farnung, Lucas"],["dc.contributor.author","Aloisi, Claudia M. N."],["dc.contributor.author","Angelov, Todor"],["dc.contributor.author","Cramer, Patrick"],["dc.contributor.author","Sturla, Shana J."],["dc.date.accessioned","2018-01-09T12:11:12Z"],["dc.date.available","2018-01-09T12:11:12Z"],["dc.date.issued","2017"],["dc.description.abstract","Several anticancer agents that form DNA adducts in the minor groove interfere with DNA replication and transcription to induce apoptosis. Therapeutic resistance can occur, however, when cells are proficient in the removal of drug-induced damage. Acylfulvenes are a class of experimental anticancer agents with a unique repair profile suggesting their capacity to stall RNA polymerase (Pol) II and trigger transcription-coupled nucleotide excision repair. Here we show how different forms of DNA alkylation impair transcription by RNA Pol II in cells and with the isolated enzyme and unravel a mode of RNA Pol II stalling that is due to alkylation of DNA in the minor groove. We incorporated a model for acylfulvene adducts, the stable 3-deaza-3-methoxynaphtylethyl-adenosine analog (3d-Napht-A), and smaller 3-deaza-adenosine analogs, into DNA oligonucleotides to assess RNA Pol II transcription elongation in vitro. RNA Pol II was strongly blocked by a 3d-Napht-A analog but bypassed smaller analogs. Crystal structure analysis revealed that a DNA base containing 3d-Napht-A can occupy the +1 templating position and impair closing of the trigger loop in the Pol II active center and polymerase translocation into the next template position. These results show how RNA Pol II copes with minor-groove DNA alkylation and establishes a mechanism for drug resistance."],["dc.identifier.doi","10.1073/pnas.1706592114"],["dc.identifier.pmid","29087308"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/11584"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1091-6490"],["dc.title","Mechanism of RNA polymerase II stalling by DNA alkylation"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","601"],["dc.bibliographiccitation.issue","7720"],["dc.bibliographiccitation.journal","Nature"],["dc.bibliographiccitation.lastpage","606"],["dc.bibliographiccitation.volume","560"],["dc.contributor.author","Vos, Seychelle M."],["dc.contributor.author","Farnung, Lucas"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Cramer, Patrick"],["dc.date.accessioned","2020-12-10T18:09:59Z"],["dc.date.available","2020-12-10T18:09:59Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1038/s41586-018-0442-2"],["dc.identifier.eissn","1476-4687"],["dc.identifier.issn","0028-0836"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/73820"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.title","Structure of paused transcription complex Pol II–DSIF–NELF"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","668"],["dc.bibliographiccitation.issue","7"],["dc.bibliographiccitation.journal","Nature Structural & Molecular Biology"],["dc.bibliographiccitation.lastpage","677"],["dc.bibliographiccitation.volume","27"],["dc.contributor.author","Vos, Seychelle M."],["dc.contributor.author","Farnung, Lucas"],["dc.contributor.author","Linden, Andreas"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Cramer, Patrick"],["dc.date.accessioned","2021-04-14T08:25:46Z"],["dc.date.available","2021-04-14T08:25:46Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1038/s41594-020-0437-1"],["dc.identifier.pmid","32541898"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/81729"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/49"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","1545-9985"],["dc.relation.issn","1545-9993"],["dc.relation.workinggroup","RG Cramer"],["dc.title","Structure of complete Pol II–DSIF–PAF–SPT6 transcription complex reveals RTF1 allosteric activation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.contributor.author","Oberbeckmann, Elisa"],["dc.contributor.author","Niebauer, Vanessa"],["dc.contributor.author","Watanabe, Shinya"],["dc.contributor.author","Farnung, Lucas"],["dc.contributor.author","Moldt, Manuela"],["dc.contributor.author","Schmid, Andrea"],["dc.contributor.author","Cramer, Patrick"],["dc.contributor.author","Peterson, Craig L."],["dc.contributor.author","Eustermann, Sebastian"],["dc.contributor.author","Hopfner, Karl-Peter"],["dc.contributor.author","Korber, Philipp"],["dc.date.accessioned","2022-02-23T10:02:59Z"],["dc.date.available","2022-02-23T10:02:59Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1101/2020.02.28.969618"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/100238"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/35"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.workinggroup","RG Cramer"],["dc.title","Ruler elements in chromatin remodelers set nucleosome array spacing and phasing"],["dc.type","preprint"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3096.e8"],["dc.bibliographiccitation.issue","15"],["dc.bibliographiccitation.journal","Molecular Cell"],["dc.bibliographiccitation.lastpage","3109.e8"],["dc.bibliographiccitation.volume","81"],["dc.contributor.author","Žumer, Kristina"],["dc.contributor.author","Maier, Kerstin C."],["dc.contributor.author","Farnung, Lucas"],["dc.contributor.author","Jaeger, Martin G."],["dc.contributor.author","Rus, Petra"],["dc.contributor.author","Winter, Georg"],["dc.contributor.author","Cramer, Patrick"],["dc.date.accessioned","2022-02-22T15:57:48Z"],["dc.date.available","2022-02-22T15:57:48Z"],["dc.date.issued","2021"],["dc.description.abstract","Transcription by RNA polymerase II (RNA Pol II) relies on the elongation factors PAF1 complex (PAF), RTF1, and SPT6. Here, we use rapid factor depletion and multi-omics analysis to investigate how these elongation factors influence RNA Pol II elongation activity in human cells. Whereas depletion of PAF subunits PAF1 and CTR9 has little effect on cellular RNA synthesis, depletion of RTF1 or SPT6 strongly compromises RNA Pol II activity, albeit in fundamentally different ways. RTF1 depletion decreases RNA Pol II velocity, whereas SPT6 depletion impairs RNA Pol II progression through nucleosomes. These results show that distinct elongation factors stimulate either RNA Pol II velocity or RNA Pol II progression through chromatin in vivo. Further analysis provides evidence for two distinct barriers to early elongation: the promoter-proximal pause site and the +1 nucleosome. It emerges that the first barrier enables loading of elongation factors that are required to overcome the second and subsequent barriers to transcription."],["dc.identifier.doi","10.1016/j.molcel.2021.05.028"],["dc.identifier.pmid","34146481"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/100195"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/403"],["dc.language.iso","en"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","1097-4164"],["dc.relation.issn","1097-2765"],["dc.relation.workinggroup","RG Cramer"],["dc.title","Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","5432"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Farnung, Lucas"],["dc.contributor.author","Vos, Seychelle M."],["dc.contributor.author","Cramer, Patrick"],["dc.date.accessioned","2022-03-01T11:45:57Z"],["dc.date.available","2022-03-01T11:45:57Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1038/s41467-018-07870-y"],["dc.identifier.pii","7870"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103510"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.eissn","2041-1723"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Structure of transcribing RNA polymerase II-nucleosome complex"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]