Kramer, Katharina

[["dc.bibliographiccitation.firstpage","705"],["dc.bibliographiccitation.issue","8"],["dc.bibliographiccitation.journal","Nature Structural & Molecular Biology"],["dc.bibliographiccitation.lastpage","713"],["dc.bibliographiccitation.volume","23"],["dc.contributor.author","Lazzaretti, Daniela"],["dc.contributor.author","Veith, Katharina"],["dc.contributor.author","Kramer, Katharina"],["dc.contributor.author","Basquin, Claire"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Irion, Uwe"],["dc.contributor.author","Bono, Fulvia"],["dc.date.accessioned","2020-12-10T18:09:33Z"],["dc.date.available","2020-12-10T18:09:33Z"],["dc.date.issued","2016"],["dc.identifier.doi","10.1038/nsmb.3254"],["dc.identifier.eissn","1545-9985"],["dc.identifier.issn","1545-9993"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/73692"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.title","The bicoid mRNA localization factor Exuperantia is an RNA-binding pseudonuclease"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","11"],["dc.contributor.author","Stützer, Alexandra"],["dc.contributor.author","Welp, Luisa M."],["dc.contributor.author","Raabe, Monika"],["dc.contributor.author","Sachsenberg, Timo"],["dc.contributor.author","Kappert, Christin"],["dc.contributor.author","Wulf, Alexander"],["dc.contributor.author","Lau, Andy M."],["dc.contributor.author","David, Stefan-Sebastian"],["dc.contributor.author","Chernev, Aleksandar"],["dc.contributor.author","Kramer, Katharina"],["dc.contributor.author","Politis, Argyris"],["dc.contributor.author","Kohlbacher, Oliver"],["dc.contributor.author","Fischle, Wolfgang"],["dc.contributor.author","Urlaub, Henning"],["dc.date.accessioned","2021-04-14T08:31:49Z"],["dc.date.available","2021-04-14T08:31:49Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1038/s41467-020-19047-7"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/83722"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.eissn","2041-1723"],["dc.title","Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e1000611"],["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","PLoS Biology"],["dc.bibliographiccitation.lastpage","19"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Mueller, M."],["dc.contributor.author","Heym, R. G."],["dc.contributor.author","Mayer, A."],["dc.contributor.author","Kramer, K."],["dc.contributor.author","Schmid, M."],["dc.contributor.author","Cramer, P."],["dc.contributor.author","Urlaub, H."],["dc.contributor.author","Jansen, R.-P."],["dc.contributor.author","Niessing, D."],["dc.date.accessioned","2017-09-07T11:44:17Z"],["dc.date.available","2017-09-07T11:44:17Z"],["dc.date.issued","2011"],["dc.description.abstract","In eukaryotes, hundreds of mRNAs are localized by specialized transport complexes. For localization, transcripts are recognized by RNA-binding proteins and incorporated into motor-containing messenger ribonucleoprotein particles (mRNPs). To date, the molecular assembly of such mRNPs is not well understood and most details on cargo specificity remain unresolved. We used ASH1-mRNA transport in yeast to provide a first assessment of where and how localizing mRNAs are specifically recognized and incorporated into mRNPs. By using in vitro-interaction and reconstitution assays, we found that none of the implicated mRNA-binding proteins showed highly specific cargo binding. Instead, we identified the cytoplasmic myosin adapter She3p as additional RNA-binding protein. We further found that only the complex of the RNA-binding proteins She2p and She3p achieves synergistic cargo binding, with an at least 60-fold higher affinity for localizing mRNAs when compared to control RNA. Mutational studies identified a C-terminal RNA-binding fragment of She3p to be important for synergistic RNA binding with She2p. The observed cargo specificity of the ternary complex is considerably higher than previously reported for localizing mRNAs. It suggests that RNA binding for mRNP localization generally exhibits higher selectivity than inferred from previous in vitro data. This conclusion is fully consistent with a large body of in vivo evidence from different organisms. Since the ternary yeast complex only assembles in the cytoplasm, specific mRNA recognition might be limited to the very last steps of mRNP assembly. Remarkably, the mRNA itself triggers the assembly of mature, motor-containing complexes. Our reconstitution of a major portion of the mRNA-transport complex offers new and unexpected insights into the molecular assembly of specific, localization-competent mRNPs and provides an important step forward in our mechanistic understanding of mRNA localization in general."],["dc.identifier.doi","10.1371/journal.pbio.1000611"],["dc.identifier.gro","3142744"],["dc.identifier.isi","000289938900006"],["dc.identifier.pmid","21526221"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/182"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","1545-7885"],["dc.relation.orgunit","Abteilung Forstgenetik und Forstpflanzenzüchtung"],["dc.title","A Cytoplasmic Complex Mediates Specific mRNA Recognition and Localization in Yeast"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3478"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Journal of Proteomics"],["dc.bibliographiccitation.lastpage","3494"],["dc.bibliographiccitation.volume","75"],["dc.contributor.author","Schmidt, Carla"],["dc.contributor.author","Kramer, Katharina"],["dc.contributor.author","Urlaub, Henning"],["dc.date.accessioned","2018-11-07T09:09:10Z"],["dc.date.available","2018-11-07T09:09:10Z"],["dc.date.issued","2012"],["dc.description.abstract","Protein-RNA complexes play many important roles in diverse cellular functions. They are involved in a wide variety of different processes in growth and differentiation at the various stages of the cell cycle. As their function and catalytic activity are directly coupled to the structural arrangement of their components-proteins and ribonucleic acids-the investigation of protein-RNA interactions is of great functional and structural importance. Here we discuss the most prominent examples of protein-RNA complexes and describe some frequently used purification strategies. We present various techniques and applications of mass spectrometry to study protein-RNA complexes. We discuss the analysis of intact complexes as well as proteomics-based and crosslinking-based approaches in which proteins are cleaved into smaller peptides. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry. (c) 2012 Elsevier B.V. All rights reserved."],["dc.identifier.doi","10.1016/j.jprot.2012.04.030"],["dc.identifier.isi","000307086500009"],["dc.identifier.pmid","22575267"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/26194"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Elsevier Science Bv"],["dc.relation.issn","1874-3919"],["dc.title","Investigation of protein-RNA interactions by mass spectrometry-Techniques and applications"],["dc.type","review"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2222"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","The EMBO Journal"],["dc.bibliographiccitation.lastpage","2234"],["dc.bibliographiccitation.volume","31"],["dc.contributor.author","Schmitzova, Jana"],["dc.contributor.author","Rasche, Nicolas"],["dc.contributor.author","Dybkov, Olexander"],["dc.contributor.author","Kramer, Katharina"],["dc.contributor.author","Fabrizio, Patrizia"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Luehrmann, Reinhard"],["dc.contributor.author","Pena, Vladimir"],["dc.date.accessioned","2018-11-07T09:10:31Z"],["dc.date.available","2018-11-07T09:10:31Z"],["dc.date.issued","2012"],["dc.description.abstract","The yeast splicing factor Cwc2 contacts several catalytically important RNA elements in the active spliceosome, suggesting that Cwc2 is involved in determining their spatial arrangement at the spliceosome's catalytic centre. We have determined the crystal structure of the Cwc2 functional core, revealing how a previously uncharacterized Torus domain, an RNA recognition motif (RRM) and a zinc finger (ZnF) are tightly integrated in a compact folding unit. The ZnF plays a pivotal role in the architecture of the whole assembly. UV-induced crosslinking of Cwc2-U6 snRNA allowed the identification by mass spectrometry of six RNA-contacting sites: four in or close to the RRM domain, one in the ZnF and one on a protruding element connecting the Torus and RRM domains. The three distinct regions contacting RNA are connected by a contiguous and conserved positively charged surface, suggesting an expanded interface for RNA accommodation. Cwc2 mutations confirmed that the connector element plays a crucial role in splicing. We conclude that Cwc2 acts as a multipartite RNA-binding platform to bring RNA elements of the spliceosome's catalytic centre into an active conformation. The EMBO Journal (2012) 31, 2222-2234. doi:10.1038/emboj.2012.58; Published online 9 March 2012"],["dc.description.sponsorship","Max Planck Society"],["dc.identifier.doi","10.1038/emboj.2012.58"],["dc.identifier.isi","000303596900015"],["dc.identifier.pmid","22407296"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/26508"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Nature Publishing Group"],["dc.relation.issn","0261-4189"],["dc.title","Crystal structure of Cwc2 reveals a novel architecture of a multipartite RNA-binding protein"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","749"],["dc.bibliographiccitation.issue","7"],["dc.bibliographiccitation.journal","Genes & Development"],["dc.bibliographiccitation.lastpage","764"],["dc.bibliographiccitation.volume","28"],["dc.contributor.author","Loedige, Inga"],["dc.contributor.author","Stotz, Mathias"],["dc.contributor.author","Qamar, Saadia"],["dc.contributor.author","Kramer, Katharina"],["dc.contributor.author","Hennig, Janosch"],["dc.contributor.author","Schubert, Thomas"],["dc.contributor.author","Loeffler, Patrick"],["dc.contributor.author","Laengst, Gernot"],["dc.contributor.author","Merkl, Rainer"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Meister, Gunter"],["dc.date.accessioned","2018-11-07T09:41:52Z"],["dc.date.available","2018-11-07T09:41:52Z"],["dc.date.issued","2014"],["dc.description.abstract","The Drosophila protein brain tumor (Brat) forms a complex with Pumilio (Pum) and Nanos (Nos) to repress hunchback (hb) mRNA translation at the posterior pole during early embryonic development. It is currently thought that complex formation is initiated by Pum, which directly binds the hb mRNA and subsequently recruits Nos and Brat. Here we report that, in addition to Pum, Brat also directly interacts with the hb mRNA. We identify Brat-binding sites distinct from the Pum consensus motif and show that RNA binding and translational repression by Brat do not require Pum, suggesting so far unrecognized Pum-independent Brat functions. Using various biochemical and biophysical methods, we also demonstrate that the NHL (NCL-1, HT2A, and LIN-41) domain of Brat, a domain previously believed to mediate protein-protein interactions, is a novel, sequence-specific ssRNA-binding domain. The Brat-NHL domain folds into a six-bladed beta propeller, and we identify its positively charged top surface as the RNA-binding site. Brat belongs to the functional diverse TRIM (tripartite motif)-NHL protein family. Using structural homology modeling, we predict that the NHL domains of all TRIM-NHL proteins have the potential to bind RNA, indicating that Brat is part of a conserved family of RNA-binding proteins."],["dc.identifier.doi","10.1101/gad.236513.113"],["dc.identifier.isi","000334354700008"],["dc.identifier.pmid","24696456"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/10956"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/33826"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Cold Spring Harbor Lab Press, Publications Dept"],["dc.relation.issn","1549-5477"],["dc.relation.issn","0890-9369"],["dc.rights","CC BY-NC 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc/4.0"],["dc.title","The NHL domain of BRAT is an RNA-binding domain that directly contacts the hunchback mRNA for regulation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1064"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Nature Methods"],["dc.bibliographiccitation.lastpage","1070"],["dc.bibliographiccitation.volume","11"],["dc.contributor.author","Kramer, Katharina"],["dc.contributor.author","Sachsenberg, Timo"],["dc.contributor.author","Beckmann, Benedikt M."],["dc.contributor.author","Qamar, Saadia"],["dc.contributor.author","Boon, Kum-Loong"],["dc.contributor.author","Hentze, Matthias W."],["dc.contributor.author","Kohlbacher, Oliver"],["dc.contributor.author","Urlaub, Henning"],["dc.date.accessioned","2018-11-07T09:34:34Z"],["dc.date.available","2018-11-07T09:34:34Z"],["dc.date.issued","2014"],["dc.description.abstract","RNA-protein complexes play pivotal roles in many central biological processes. Although methods based on high-throughput sequencing have advanced our ability to identify the specific RNAs bound by a particular protein, there is a need for precise and systematic ways to identify RNA interaction sites on proteins. We have developed an experimental and computational workflow combining photo-induced cross-linking, high-resolution mass spectrometry and automated analysis of the resulting mass spectra for the identification of cross-linked peptides, cross-linking sites and the cross-linked RNA oligonucleotide moieties of such RNA-binding proteins. The workflow can be applied to any RNA-protein complex of interest or to whole proteomes. We applied the approach to human and yeast mRNA-protein complexes in vitro and in vivo, demonstrating its powerful utility by identifying 257 cross-linking sites on 124 distinct RNA-binding proteins. The open-source software pipeline developed for this purpose, RNPxl, is available as part of the OpenMS project."],["dc.identifier.doi","10.1038/NMETH.3092"],["dc.identifier.isi","000342719100027"],["dc.identifier.pmid","25173706"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/32197"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Nature Publishing Group"],["dc.relation.issn","1548-7105"],["dc.relation.issn","1548-7091"],["dc.title","Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3196"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Molecular & Cellular Proteomics"],["dc.bibliographiccitation.lastpage","3210"],["dc.bibliographiccitation.volume","14"],["dc.contributor.author","Zaman, Uzma"],["dc.contributor.author","Richter, Florian M."],["dc.contributor.author","Hofele, Romina V."],["dc.contributor.author","Kramer, Katharina"],["dc.contributor.author","Sachsenberg, Timo"],["dc.contributor.author","Kohlbacher, Oliver"],["dc.contributor.author","Lenz, Christof"],["dc.contributor.author","Urlaub, Henning"],["dc.date.accessioned","2018-11-07T09:48:31Z"],["dc.date.available","2018-11-07T09:48:31Z"],["dc.date.issued","2015"],["dc.description.abstract","Protein-RNA cross-linking by UV irradiation at 254 nm wavelength has been established as an unbiased method to identify proteins in direct contact with RNA, and has been successfully applied to investigate the spatial arrangement of protein and RNA in large macromolecular assemblies, e.g. ribonucleoprotein-complex particles (RNPs). The mass spectrometric analysis of such peptide-RNA cross-links provides high resolution structural data to the point of mapping protein-RNA interactions to specific peptides or even amino acids. However, the approach suffers from the low yield of cross-linking products, which can be addressed by improving enrichment and analysis methods. In the present article, we introduce dithiothreitol (DTT) as a potent protein-RNA cross-linker. In order to evaluate the efficiency and specificity of DTT, we used two systems, a small synthetic peptide from smB protein incubated with U1 snRNA oligonucleotide and native ribonucleoprotein complexes from S. cerevisiae. Our results unambiguously show that DTT covalently participates in cysteine-uracil crosslinks, which is observable as a mass increment of 151.9966 Da (C4H8S2O2) upon mass spectrometric analysis. DTT presents advantages for cross-linking of cysteine containing regions of proteins. This is evidenced by comparison to experiments where (tris(2-carboxyethyl)phosphine) is used as reducing agent, and significantly less cross-links encompassing cysteine residues are found. We further propose insertion of DTT between the cysteine and uracil reactive sites as the most probable structure of the cross-linking products."],["dc.description.sponsorship","DFG grant [SFB860]"],["dc.identifier.doi","10.1074/mcp.M115.052795"],["dc.identifier.isi","000365638100008"],["dc.identifier.pmid","26450613"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/35327"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Amer Soc Biochemistry Molecular Biology Inc"],["dc.relation.issn","1535-9484"],["dc.relation.issn","1535-9476"],["dc.title","Dithiothreitol (DTT) Acts as a Specific, UV-inducible Cross-linker in Elucidation of Protein-RNA Interactions"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","138"],["dc.bibliographiccitation.journal","Methods"],["dc.bibliographiccitation.lastpage","148"],["dc.bibliographiccitation.volume","89"],["dc.contributor.author","Sharma, Kundan"],["dc.contributor.author","Hrle, Ajla"],["dc.contributor.author","Kramer, Katharina"],["dc.contributor.author","Sachsenberg, Timo"],["dc.contributor.author","Staals, Raymond H. J."],["dc.contributor.author","Randau, Lennart"],["dc.contributor.author","Marchfelder, Anita"],["dc.contributor.author","van der Oost, John"],["dc.contributor.author","Kohlbacher, Oliver"],["dc.contributor.author","Conti, Elena"],["dc.contributor.author","Urlaub, Henning"],["dc.date.accessioned","2018-11-07T09:49:28Z"],["dc.date.available","2018-11-07T09:49:28Z"],["dc.date.issued","2015"],["dc.description.abstract","Ribonucleoprotein (RNP) complexes play important roles in the cell by mediating basic cellular processes, including gene expression and its regulation. Understanding the molecular details of these processes requires the identification and characterization of protein-RNA interactions. Over the years various approaches have been used to investigate these interactions, including computational analyses to look for RNA binding domains, gel-shift mobility assays on recombinant and mutant proteins as well as co-crystallization and NMR studies for structure elucidation. Here we report a more specialized and direct approach using UV-induced cross-linking coupled with mass spectrometry. This approach permits the identification of cross-linked peptides and RNA moieties and can also pin-point exact RNA contact sites within the protein. The power of this method is illustrated by the application to different single- and multi-subunit RNP complexes belonging to the prokaryotic adaptive immune system, CRISPR-Cas (CRISPR: clustered regularly interspaced short palindromic repeats; Gas: CRISPR associated). In particular, we identified the RNA-binding sites within three Cas7 protein homologs and mapped the cross-linking results to reveal structurally conserved Cas7 - RNA binding interfaces. These results demonstrate the strong potential of UV-induced cross-linking coupled with mass spectrometry analysis to identify RNA interaction sites on the RNA binding proteins. (C) 2015 Elsevier Inc. All rights reserved."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft [DFG] [FOR 1680]"],["dc.identifier.doi","10.1016/j.ymeth.2015.06.005"],["dc.identifier.isi","000365062800017"],["dc.identifier.pmid","26071038"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/35514"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Academic Press Inc Elsevier Science"],["dc.relation.issn","1095-9130"],["dc.relation.issn","1046-2023"],["dc.title","Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]