{"entity": "researcher", "timestamp": "2026-03-09T09:27:27.405Z", "family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S", "orcid": "0000-0003-1181-0415", "affiliations": ["Department of Medical Biochemistry and Biophysics, Ume\u00e5 University, Ume\u00e5, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/dae5cb7a54364e74b4f0261ab8d8e0ce.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/dae5cb7a54364e74b4f0261ab8d8e0ce"}}, "publications": [{"entity": "publication", "iuid": "036d938b353a4b6084fc027f2a6fc9d6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/036d938b353a4b6084fc027f2a6fc9d6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/036d938b353a4b6084fc027f2a6fc9d6"}}, "title": "Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes.", "authors": [{"family": "Abdel-Fattah", "given": "Wael R", "initials": "WR"}, {"family": "Carlsson", "given": "Mattias", "initials": "M"}, {"family": "Hu", "given": "Guo-Zhen", "initials": "G"}, {"family": "Singh", "given": "Ajeet", "initials": "A"}, {"family": "Vergara", "given": "Alexander", "initials": "A", "orcid": "0000-0001-6535-9282", "researcher": {"href": "https://publications.scilifelab.se/researcher/8003432c3c264e78a754fe595297453b.json"}}, {"family": "Aslam", "given": "Rameen", "initials": "R"}, {"family": "Ronne", "given": "Hans", "initials": "H", "orcid": "0000-0002-1645-6091", "researcher": {"href": "https://publications.scilifelab.se/researcher/d700b0be9ea04b588f539186fb92df5d.json"}}, {"family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S", "orcid": "0000-0003-1181-0415", "researcher": {"href": "https://publications.scilifelab.se/researcher/dae5cb7a54364e74b4f0261ab8d8e0ce.json"}}], "type": "journal article", "published": "2024-04-13", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "issn-l": "0305-1048", "volume": null, "issue": null, "pages": null}, "abstract": "Mediator is a well-known transcriptional co-regulator and serves as an adaptor between gene-specific regulatory proteins and RNA polymerase II. Studies on the chromatin-bound form of Mediator revealed interactions with additional protein complexes involved in various transcription-related processes, such as the Lsm2-8 complex that is part of the spliceosomal U6 small nuclear ribonucleoprotein complex. Here, we employ Chromatin Immunoprecipitation sequencing (ChIP-seq) of chromatin associated with the Lsm3 protein and the Med1 or Med15 Mediator subunits. We identify 86 genes co-occupied by both Lsm3 and Mediator, of which 73 were intron-containing ribosomal protein genes. In logarithmically growing cells, Mediator primarily binds to their promoter regions but also shows a second, less pronounced occupancy at their 3'-exons. During the late exponential phase, we observe a near-complete transition of Mediator from these promoters to a position in their 3'-ends, overlapping the Lsm3 binding sites \u223c250 bp downstream of their last intron-exon boundaries. Using an unbiased RNA sequencing approach, we show that transition of Mediator from promoters to the last exon of these genes correlates to reduction of both their messenger RNA levels and splicing ratios, indicating that the Mediator and Lsm complexes cooperate to control growth-regulated expression of intron-containing ribosomal protein genes at the levels of transcription and splicing.", "doi": "10.1093/nar/gkae266", "pmid": "38613396", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "7645241"}], "notes": [], "created": "2024-04-26T08:51:21.044Z", "modified": "2024-06-28T06:31:12.260Z"}, {"entity": "publication", "iuid": "42bb648065a04077b503ed68fe0d859d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/42bb648065a04077b503ed68fe0d859d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/42bb648065a04077b503ed68fe0d859d"}}, "title": "Functional metabolomics as a tool to analyze Mediator function and structure in plants.", "authors": [{"family": "Davoine", "given": "Celine", "initials": "C"}, {"family": "Abreu", "given": "Ilka N", "initials": "IN"}, {"family": "Khajeh", "given": "Khalil", "initials": "K"}, {"family": "Blomberg", "given": "Jeanette", "initials": "J"}, {"family": "Kidd", "given": "Brendan N", "initials": "BN"}, {"family": "Kazan", "given": "Kemal", "initials": "K"}, {"family": "Schenk", "given": "Peer M", "initials": "PM"}, {"family": "Gerber", "given": "Lorenz", "initials": "L"}, {"family": "Nilsson", "given": "Ove", "initials": "O"}, {"family": "Moritz", "given": "Thomas", "initials": "T"}, {"family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S", "orcid": "0000-0003-1181-0415", "researcher": {"href": "https://publications.scilifelab.se/researcher/dae5cb7a54364e74b4f0261ab8d8e0ce.json"}}], "type": "journal article", "published": "2017-06-22", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "12", "issue": "6", "pages": "e0179640", "issn-l": "1932-6203"}, "abstract": "Mediator is a multiprotein transcriptional co-regulator complex composed of four modules; Head, Middle, Tail, and Kinase. It conveys signals from promoter-bound transcriptional regulators to RNA polymerase II and thus plays an essential role in eukaryotic gene regulation. We describe subunit localization and activities of Mediator in Arabidopsis through metabolome and transcriptome analyses from a set of Mediator mutants. Functional metabolomic analysis based on the metabolite profiles of Mediator mutants using multivariate statistical analysis and heat-map visualization shows that different subunit mutants display distinct metabolite profiles, which cluster according to the reported localization of the corresponding subunits in yeast. Based on these results, we suggest localization of previously unassigned plant Mediator subunits to specific modules. We also describe novel roles for individual subunits in development, and demonstrate changes in gene expression patterns and specific metabolite levels in med18 and med25, which can explain their phenotypes. We find that med18 displays levels of phytoalexins normally found in wild type plants only after exposure to pathogens. Our results indicate that different Mediator subunits are involved in specific signaling pathways that control developmental processes and tolerance to pathogen infections.", "doi": "10.1371/journal.pone.0179640", "pmid": "28640868", "labels": {"Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC5480960"}, {"db": "pii", "key": "PONE-D-16-45854"}], "notes": [], "created": "2023-04-12T14:19:27.306Z", "modified": "2025-10-17T13:03:18.678Z"}]}