{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/26a5e962f82c75788dfa615ef68ed419c/slegewie", "tags" : [ "Acid,","Alternative","Analysis,","Base","Binding","Cells,","Exons,","F-H,","Group","HEK293","Heterogeneous-Nuclear","Humans,","Introns,","Kinases,","Linear","MCF-7","Mas,","Models,","Mutagenesis,","Mutation,","Neoplasms,","Nucleic","Protein-Tyrosine","Proteins,","Proto-Oncogene","RNA","RNA-Binding","Receptor","Regulatory","Ribonucleoprotein","Sequence","Sequence,","Sequences,","Sites,","Splicing," ], "intraHash" : "6a5e962f82c75788dfa615ef68ed419c", "interHash" : "e8adf17ba8666d4a803d7d7d88a2433b", "label" : "Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis", "user" : "slegewie", "description" : "", "date" : "2025-03-05 15:52:38", "changeDate" : "2025-03-05 15:52:38", "count" : 1, "pub-type": "article", "journal": "Nature Communications", "year": "2018", "url": "", "author": [ "Simon Braun","Mihaela Enculescu","Samarth T. Setty","Mariela Cortés-López","Bernardo P. de Almeida","F. X. Reymond Sutandy","Laura Schulz","Anke Busch","Markus Seiler","Stefanie Ebersberger","Nuno L. Barbosa-Morais","Stefan Legewie","Julian König","Kathi Zarnack" ], "authors": [ {"first" : "Simon", "last" : "Braun"}, {"first" : "Mihaela", "last" : "Enculescu"}, {"first" : "Samarth T.", "last" : "Setty"}, {"first" : "Mariela", "last" : "Cortés-López"}, {"first" : "Bernardo P.", "last" : "de Almeida"}, {"first" : "F. X. Reymond", "last" : "Sutandy"}, {"first" : "Laura", "last" : "Schulz"}, {"first" : "Anke", "last" : "Busch"}, {"first" : "Markus", "last" : "Seiler"}, {"first" : "Stefanie", "last" : "Ebersberger"}, {"first" : "Nuno L.", "last" : "Barbosa-Morais"}, {"first" : "Stefan", "last" : "Legewie"}, {"first" : "Julian", "last" : "König"}, {"first" : "Kathi", "last" : "Zarnack"} ], "volume": "9","number": "1","pages": "3315","abstract": "Mutations causing aberrant splicing are frequently implicated in human diseases including cancer. Here, we establish a high-throughput screen of randomly mutated minigenes to decode the cis-regulatory landscape that determines alternative splicing of exon 11 in the proto-oncogene MST1R (RON). Mathematical modelling of splicing kinetics enables us to identify more than 1000 mutations affecting RON exon 11 skipping, which corresponds to the pathological isoform RON∆165. Importantly, the effects correlate with RON alternative splicing in cancer patients bearing the same mutations. Moreover, we highlight heterogeneous nuclear ribonucleoprotein H (HNRNPH) as a key regulator of RON splicing in healthy tissues and cancer. Using iCLIP and synergy analysis, we pinpoint the functionally most relevant HNRNPH binding sites and demonstrate how cooperative HNRNPH binding facilitates a splicing switch of RON exon 11. Our results thereby offer insights into splicing regulation and the impact of mutations on alternative splicing in cancer.", "language" : "eng", "pmid" : "30120239", "file" : "Volltext:C\\:\\\\Users\\\\SL\\\\Zotero\\\\storage\\\\29LKX6JF\\\\Braun et al. - 2018 - Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagen.pdf:application/pdf", "issn" : "2041-1723", "pmcid" : "PMC6098099", "doi" : "10.1038/s41467-018-05748-7", "bibtexKey": "braun_decoding_2018" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2a8704533a8dfa10f1d5f42ed6d4aef19/slegewie", "tags" : [ "Animals,","Base","Development,","Drosophila","Embryonic","Expression","Gene","Genetic,","Glucose,","Kinetics,","Messenger,","Proteins,","Proteome,","RNA,","Regulation,","Sequence,","Transcription,","Transcriptome","melanogaster," ], "intraHash" : "a8704533a8dfa10f1d5f42ed6d4aef19", "interHash" : "42325feb1689d483604c5222faf8ebb8", "label" : "Quantifying post-transcriptional regulation in the development of Drosophila melanogaster", "user" : "slegewie", "description" : "", "date" : "2025-03-05 15:52:38", "changeDate" : "2025-03-05 15:52:38", "count" : 1, "pub-type": "article", "journal": "Nature Communications", "year": "2018", "url": "", "author": [ "Kolja Becker","Alina Bluhm","Nuria Casas-Vila","Nadja Dinges","Mario Dejung","Sergi Sayols","Clemens Kreutz","Jean-Yves Roignant","Falk Butter","Stefan Legewie" ], "authors": [ {"first" : "Kolja", "last" : "Becker"}, {"first" : "Alina", "last" : "Bluhm"}, {"first" : "Nuria", "last" : "Casas-Vila"}, {"first" : "Nadja", "last" : "Dinges"}, {"first" : "Mario", "last" : "Dejung"}, {"first" : "Sergi", "last" : "Sayols"}, {"first" : "Clemens", "last" : "Kreutz"}, {"first" : "Jean-Yves", "last" : "Roignant"}, {"first" : "Falk", "last" : "Butter"}, {"first" : "Stefan", "last" : "Legewie"} ], "volume": "9","number": "1","pages": "4970","abstract": "Even though proteins are produced from mRNA, the correlation between mRNA levels and protein abundances is moderate in most studies, occasionally attributed to complex post-transcriptional regulation. To address this, we generate a paired transcriptome/proteome time course dataset with 14 time points during Drosophila embryogenesis. Despite a limited mRNA-protein correlation (ρ\u2009=\u20090.54), mathematical models describing protein translation and degradation explain 84\\% of protein time-courses based on the measured mRNA dynamics without assuming complex post transcriptional regulation, and allow for classification of most proteins into four distinct regulatory scenarios. By performing an in-depth characterization of the putatively post-transcriptionally regulated genes, we postulate that the RNA-binding protein Hrb98DE is involved in post-transcriptional control of sugar metabolism in early embryogenesis and partially validate this hypothesis using Hrb98DE knockdown. In summary, we present a systems biology framework for the identification of post-transcriptional gene regulation from large-scale, time-resolved transcriptome and proteome data.", "language" : "eng", "pmid" : "30478415", "file" : "Volltext:C\\:\\\\Users\\\\SL\\\\Zotero\\\\storage\\\\U4MU6BPV\\\\Becker et al. - 2018 - Quantifying post-transcriptional regulation in the development of Drosophila melanogaster.pdf:application/pdf", "issn" : "2041-1723", "pmcid" : "PMC6255845", "doi" : "10.1038/s41467-018-07455-9", "bibtexKey": "becker_quantifying_2018" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2930ecfe113b73f241ab0452b05337d89/bastian", "tags" : [ "Bacterial,","Base","Biotechnology","Complex,","Corynebacterium","DNA,","Dehydrogenase","Deletion,","Expression,","Fermentation,","Gene","Genes,","Kinetics,","Lysine,","Pyruvate","Sequence,","glutamicum,","myown" ], "intraHash" : "930ecfe113b73f241ab0452b05337d89", "interHash" : "97097cd65b8e231a2578efbc7586a5dc", "label" : "Effect of pyruvate dehydrogenase complex deficiency on L-lysine production with Corynebacterium glutamicum", "user" : "bastian", "description" : "", "date" : "2018-02-09 13:18:17", "changeDate" : "2018-02-09 12:18:56", "count" : 1, "pub-type": "article", "journal": "Appl. Microbiol. Biotechnol.", "year": "2007", "url": "", "author": [ "Bastian Blombach","Mark E. Schreiner","Matthias Moch","Marco Oldiges","Bernhard J. Eikmanns" ], "authors": [ {"first" : "Bastian", "last" : "Blombach"}, {"first" : "Mark E.", "last" : "Schreiner"}, {"first" : "Matthias", "last" : "Moch"}, {"first" : "Marco", "last" : "Oldiges"}, {"first" : "Bernhard J.", "last" : "Eikmanns"} ], "volume": "76","number": "3","pages": "615--623","abstract": "Intracellular precursor supply is a critical factor for amino acid productivity of Corynebacterium glutamicum. To test for the effect of improved pyruvate availability on L-lysine production, we deleted the aceE gene encoding the E1p enzyme of the pyruvate dehydrogenase complex (PDHC) in the L-lysine-producer C. glutamicum DM1729 and characterised the resulting strain DM1729-BB1 for growth and L-lysine production. Compared to the host strain, C. glutamicum DM1729-BB1 showed no PDHC activity, was acetate auxotrophic and, after complete consumption of the available carbon sources glucose and acetate, showed a more than 50\\% lower substrate-specific biomass yield (0.14 vs 0.33 mol C/mol C), an about fourfold higher biomass-specific L-lysine yield (5.27 vs 1.23 mmol/g cell dry weight) and a more than 40\\% higher substrate-specific L-lysine yield (0.13 vs 0.09 mol C/mol C). Overexpression of the pyruvate carboxylase or diaminopimelate dehydrogenase genes in C. glutamicum DM1729-BB1 resulted in a further increase in the biomass-specific L-lysine yield by 6 and 56\\%, respectively. In addition to L-lysine, significant amounts of pyruvate, L-alanine and L-valine were produced by C. glutamicum DM1729-BB1 and its derivatives, suggesting a surplus of precursor availability and a further potential to improve L-lysine production by engineering the L-lysine biosynthetic pathway.", "pmid" : "17333167", "issn" : "0175-7598", "language" : "eng", "doi" : "10.1007/s00253-007-0904-1", "bibtexKey": "blombach_effect_2007" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2751d62556f83a4d54902c3b9fac85dfb/bastian", "tags" : [ "(Lipoamide)","Acetates,","Bacterial","Bacterial,","Base","Corynebacterium","Data,","Dehydrogenase","Expression","Gene","Molecular","Proteins,","Pyruvate","Regulation,","Sequence","Sequence,","glutamicum,","myown" ], "intraHash" : "751d62556f83a4d54902c3b9fac85dfb", "interHash" : "9f5f5ec2cc8c58eb2101574f015cd25b", "label" : "RamB is an activator of the pyruvate dehydrogenase complex subunit E1p gene in Corynebacterium glutamicum", "user" : "bastian", "description" : "", "date" : "2018-02-09 13:18:17", "changeDate" : "2018-02-09 12:18:56", "count" : 1, "pub-type": "article", "journal": "J. Mol. Microbiol. Biotechnol.", "year": "2009", "url": "", "author": [ "Bastian Blombach","Annette Cramer","Bernhard J. Eikmanns","Mark Schreiner" ], "authors": [ {"first" : "Bastian", "last" : "Blombach"}, {"first" : "Annette", "last" : "Cramer"}, {"first" : "Bernhard J.", "last" : "Eikmanns"}, {"first" : "Mark", "last" : "Schreiner"} ], "volume": "16","number": "3-4","pages": "236--239","abstract": "In Corynebacterium glutamicum, the transcriptional regulator RamB negatively controls the expression of genes involved in acetate metabolism. Here we show that during growth in media containing glucose and in complex medium without glucose RamB activates expression of the aceE gene, encoding the E1p subunit of the pyruvate dehydrogenase complex. Thus, RamB functions both as repressor and as activator in C. glutamicum.", "pmid" : "17890844", "issn" : "1660-2412", "language" : "eng", "doi" : "10.1159/000108782", "bibtexKey": "blombach_ramb_2009" } ] }