Kramer, Katharina

[["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.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"]]