1
|
Lukauskas S, Tvardovskiy A, Nguyen NV, Stadler M, Faull P, Ravnsborg T, Özdemir Aygenli B, Dornauer S, Flynn H, Lindeboom RGH, Barth TK, Brockers K, Hauck SM, Vermeulen M, Snijders AP, Müller CL, DiMaggio PA, Jensen ON, Schneider R, Bartke T. Publisher Correction: Decoding chromatin states by proteomic profiling of nucleosome readers. Nature 2024; 628:E6. [PMID: 38594341 DOI: 10.1038/s41586-024-07392-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Affiliation(s)
- Saulius Lukauskas
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Nhuong V Nguyen
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Mara Stadler
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig Maximilian University Munich, Munich, Germany
| | - Peter Faull
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Proteomic Sciences Technology Platform, The Francis Crick Institute, London, UK
- Northwestern Proteomics Core Facility, Northwestern University, Chicago, IL, USA
| | - Tina Ravnsborg
- VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Scarlett Dornauer
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Helen Flynn
- Proteomic Sciences Technology Platform, The Francis Crick Institute, London, UK
| | - Rik G H Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Teresa K Barth
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Munich, Germany
- Clinical Protein Analysis Unit (ClinZfP), Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Kevin Brockers
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Munich, Germany
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Christian L Müller
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig Maximilian University Munich, Munich, Germany
- Center for Computational Mathematics, Flatiron Institute, New York, NY, USA
| | - Peter A DiMaggio
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Ole N Jensen
- VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
- MRC Laboratory of Medical Sciences (LMS), London, UK.
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.
| |
Collapse
|
2
|
Lukauskas S, Tvardovskiy A, Nguyen NV, Stadler M, Faull P, Ravnsborg T, Özdemir Aygenli B, Dornauer S, Flynn H, Lindeboom RGH, Barth TK, Brockers K, Hauck SM, Vermeulen M, Snijders AP, Müller CL, DiMaggio PA, Jensen ON, Schneider R, Bartke T. Decoding chromatin states by proteomic profiling of nucleosome readers. Nature 2024; 627:671-679. [PMID: 38448585 PMCID: PMC10954555 DOI: 10.1038/s41586-024-07141-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
DNA and histone modifications combine into characteristic patterns that demarcate functional regions of the genome1,2. While many 'readers' of individual modifications have been described3-5, how chromatin states comprising composite modification signatures, histone variants and internucleosomal linker DNA are interpreted is a major open question. Here we use a multidimensional proteomics strategy to systematically examine the interaction of around 2,000 nuclear proteins with over 80 modified dinucleosomes representing promoter, enhancer and heterochromatin states. By deconvoluting complex nucleosome-binding profiles into networks of co-regulated proteins and distinct nucleosomal features driving protein recruitment or exclusion, we show comprehensively how chromatin states are decoded by chromatin readers. We find highly distinctive binding responses to different features, many factors that recognize multiple features, and that nucleosomal modifications and linker DNA operate largely independently in regulating protein binding to chromatin. Our online resource, the Modification Atlas of Regulation by Chromatin States (MARCS), provides in-depth analysis tools to engage with our results and advance the discovery of fundamental principles of genome regulation by chromatin states.
Collapse
Affiliation(s)
- Saulius Lukauskas
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Andrey Tvardovskiy
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Nhuong V Nguyen
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Mara Stadler
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig Maximilian University Munich, Munich, Germany
| | - Peter Faull
- MRC Laboratory of Medical Sciences (LMS), London, UK
- Proteomic Sciences Technology Platform, The Francis Crick Institute, London, UK
- Northwestern Proteomics Core Facility, Northwestern University, Chicago, IL, USA
| | - Tina Ravnsborg
- VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | | | - Scarlett Dornauer
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Helen Flynn
- Proteomic Sciences Technology Platform, The Francis Crick Institute, London, UK
| | - Rik G H Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Teresa K Barth
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Munich, Germany
- Clinical Protein Analysis Unit (ClinZfP), Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Kevin Brockers
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Munich, Germany
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Christian L Müller
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Statistics, Ludwig Maximilian University Munich, Munich, Germany
- Center for Computational Mathematics, Flatiron Institute, New York, NY, USA
| | - Peter A DiMaggio
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Ole N Jensen
- VILLUM Center for Bioanalytical Sciences and Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Till Bartke
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany.
- MRC Laboratory of Medical Sciences (LMS), London, UK.
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK.
| |
Collapse
|
3
|
Affiliation(s)
- Kevin Brockers
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Faculty of Biology, LMU, 82152 Martinsried, Germany
| |
Collapse
|
4
|
Bräuer KE, Brockers K, Moneer J, Feuchtinger A, Wollscheid-Lengeling E, Lengeling A, Wolf A. Phylogenetic and genomic analyses of the ribosomal oxygenases Riox1 (No66) and Riox2 (Mina53) provide new insights into their evolution. BMC Evol Biol 2018; 18:96. [PMID: 29914368 PMCID: PMC6006756 DOI: 10.1186/s12862-018-1215-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 06/07/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Translation of specific mRNAs can be highly regulated in different cells, tissues or under pathological conditions. Ribosome heterogeneity can originate from variable expression or post-translational modifications of ribosomal proteins. The ribosomal oxygenases RIOX1 (NO66) and RIOX2 (MINA53) modify ribosomal proteins by histidine hydroxylation. A similar mechanism is present in prokaryotes. Thus, ribosome hydroxylation may be a well-conserved regulatory mechanism with implications in disease and development. However, little is known about the evolutionary history of Riox1 and Riox2 genes and their encoded proteins across eukaryotic taxa. RESULTS In this study, we have analysed Riox1 and Riox2 orthologous genes from 49 metazoen species and have constructed phylogenomic trees for both genes. Our genomic and phylogenetic analyses revealed that Arthropoda, Annelida, Nematoda and Mollusca lack the Riox2 gene, although in the early phylum Cnidaria both genes, Riox1 and Riox2, are present and expressed. Riox1 is an intronless single-exon-gene in several species, including humans. In contrast to Riox2, Riox1 is ubiquitously present throughout the animal kingdom suggesting that Riox1 is the phylogenetically older gene from which Riox2 has evolved. Both proteins have maintained a unique protein architecture with conservation of active sites within the JmjC domains, a dimerization domain, and a winged-helix domain. In addition, Riox1 proteins possess a unique N-terminal extension domain. Immunofluorescence analyses in Hela cells and in Hydra vulgaris identified a nucleolar localisation signal within the extended N-terminal domain of human RIOX1 and an altered subnuclear localisation for the Hydra Riox2. CONCLUSIONS Conserved active site residues and uniform protein domain architecture suggest a consistent enzymatic activity within the Riox orthologs throughout evolution. However, differences in genomic architecture, like single exon genes and alterations in subnuclear localisation, as described for Hydra, point towards adaption mechanisms that may correlate with taxa- or species-specific requirements. The diversification of Riox1/Riox2 gene structures throughout evolution suggest that functional requirements in expression of protein isoforms and/or subcellular localisation of proteins may have evolved by adaptation to lifestyle.
Collapse
Affiliation(s)
- Katharina E Bräuer
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Kevin Brockers
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Jasmin Moneer
- Department of Biology II, Ludwig Maximillians University, Munich, Großhaderner Strasse 2, 82152 Planegg-, Martinsried, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Evi Wollscheid-Lengeling
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Andreas Lengeling
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.,Present address: Max-Planck-Society, Administrative Headquarters, Hofgartenstr. 8, 80539, Munich, Germany
| | - Alexander Wolf
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany.
| |
Collapse
|