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Liu L, Trendel J, Jiang G, Liu Y, Bruckmann A, Küster B, Sprunck S, Dresselhaus T, Bleckmann A. RBPome identification in egg-cell like callus of Arabidopsis. Biol Chem 2023; 404:1137-1149. [PMID: 37768858 DOI: 10.1515/hsz-2023-0195] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 09/11/2023] [Indexed: 09/30/2023]
Abstract
RNA binding proteins (RBPs) have multiple and essential roles in transcriptional and posttranscriptional regulation of gene expression in all living organisms. Their biochemical identification in the proteome of a given cell or tissue requires significant protein amounts, which limits studies in rare and highly specialized cells. As a consequence, we know almost nothing about the role(s) of RBPs in reproductive processes such as egg cell development, fertilization and early embryogenesis in flowering plants. To systematically identify the RBPome of egg cells in the model plant Arabidopsis, we performed RNA interactome capture (RIC) experiments using the egg cell-like RKD2-callus and were able to identify 728 proteins associated with poly(A+)-RNA. Transcripts for 97 % of identified proteins could be verified in the egg cell transcriptome. 46 % of identified proteins can be associated with the RNA life cycle. Proteins involved in mRNA binding, RNA processing and metabolism are highly enriched. Compared with the few available RBPome datasets of vegetative plant tissues, we identified 475 egg cell-enriched RBPs, which will now serve as a resource to study RBP function(s) during egg cell development, fertilization and early embryogenesis. First candidates were already identified showing an egg cell-specific expression pattern in ovules.
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Affiliation(s)
- Liping Liu
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Jakob Trendel
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Guojing Jiang
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Yanhui Liu
- College of Life Science, Longyan University, Longyan 364012, China
| | - Astrid Bruckmann
- Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Bernhard Küster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
| | - Andrea Bleckmann
- Cell Biology and Plant Biochemistry, University of Regensburg, D-93053 Regensburg, Germany
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Trendel J, Boileau E, Jochem M, Dieterich C, Krijgsveld J. PEPseq quantifies transcriptome-wide changes in protein occupancy and reveals selective translational repression after translational stress. Nucleic Acids Res 2023; 51:e79. [PMID: 37395449 PMCID: PMC10415142 DOI: 10.1093/nar/gkad557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/24/2023] [Accepted: 06/30/2023] [Indexed: 07/04/2023] Open
Abstract
Post-transcriptional gene regulation is accomplished by the interplay of the transcriptome with RNA-binding proteins, which occurs in a dynamic manner in response to altered cellular conditions. Recording the combined occupancy of all proteins binding to the transcriptome offers the opportunity to interrogate if a particular treatment leads to any interaction changes, pointing to sites in RNA that undergo post-transcriptional regulation. Here, we establish a method to monitor protein occupancy in a transcriptome-wide fashion by RNA sequencing. To this end, peptide-enhanced pull-down for RNA sequencing (or PEPseq) uses metabolic RNA labelling with 4-thiouridine (4SU) for light-induced protein-RNA crosslinking, and N-hydroxysuccinimide (NHS) chemistry to isolate protein-crosslinked RNA fragments across all long RNA biotypes. We use PEPseq to investigate changes in protein occupancy during the onset of arsenite-induced translational stress in human cells and reveal an increase of protein interactions in the coding region of a distinct set of mRNAs, including mRNAs coding for the majority of cytosolic ribosomal proteins. We use quantitative proteomics to demonstrate that translation of these mRNAs remains repressed during the initial hours of recovery after arsenite stress. Thus, we present PEPseq as a discovery platform for the unbiased investigation of post-transcriptional regulation.
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Affiliation(s)
- Jakob Trendel
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Etienne Boileau
- Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Germany
| | - Marco Jochem
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research) Partner Site Heidelberg/Mannheim, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Medical Faculty, Heidelberg, Germany
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Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze MW, Krijgsveld J. The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest. Cell 2019; 176:391-403.e19. [PMID: 30528433 DOI: 10.1016/j.cell.2018.11.004] [Citation(s) in RCA: 229] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/21/2018] [Accepted: 10/31/2018] [Indexed: 12/21/2022]
Abstract
Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here, we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes and use this to characterize the sub-proteomes that interact with coding and non-coding RNAs (ncRNAs) and to identify hundreds of protein-RNA interfaces. Exploiting the quantitative nature of XRNAX, we observe drastic remodeling of the RNA-bound proteome during arsenite-induced stress, distinct from autophagy-related changes in the total proteome. In addition, we combine XRNAX with crosslinking immunoprecipitation sequencing (CLIP-seq) to validate the interaction of ncRNA with lamin B1 and EXOSC2. Thus, XRNAX is a resourceful approach to study structural and compositional aspects of protein-RNA interactions to address fundamental questions in RNA-biology.
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Affiliation(s)
- Jakob Trendel
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany
| | - Rastislav Horos
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany
| | - Ananth Prakash
- European Molecular Biology Laboratory, European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany; Heidelberg University, Medical Faculty, Im Neuenheimer Feld 672, Heidelberg, Germany.
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Nötzold L, Frank L, Gandhi M, Polycarpou-Schwarz M, Groß M, Gunkel M, Beil N, Erfle H, Harder N, Rohr K, Trendel J, Krijgsveld J, Longerich T, Schirmacher P, Boutros M, Erhardt S, Diederichs S. The long non-coding RNA LINC00152 is essential for cell cycle progression through mitosis in HeLa cells. Sci Rep 2017; 7:2265. [PMID: 28536419 PMCID: PMC5442156 DOI: 10.1038/s41598-017-02357-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/10/2017] [Indexed: 12/28/2022] Open
Abstract
In recent years, long non-coding RNA (lncRNA) research has identified essential roles of these transcripts in virtually all physiological cellular processes including tumorigenesis, but their functions and molecular mechanisms are poorly understood. In this study, we performed a high-throughput siRNA screen targeting 638 lncRNAs deregulated in cancer entities to analyse their impact on cell division by using time-lapse microscopy. We identified 26 lncRNAs affecting cell morphology and cell cycle including LINC00152. This transcript was ubiquitously expressed in many human cell lines and its RNA levels were significantly upregulated in lung, liver and breast cancer tissues. A comprehensive sequence analysis of LINC00152 revealed a highly similar paralog annotated as MIR4435-2HG and several splice variants of both transcripts. The shortest and most abundant isoform preferentially localized to the cytoplasm. Cells depleted of LINC00152 arrested in prometaphase of mitosis and showed reduced cell viability. In RNA affinity purification (RAP) studies, LINC00152 interacted with a network of proteins that were associated with M phase of the cell cycle. In summary, we provide new insights into the properties and biological function of LINC00152 suggesting that this transcript is crucial for cell cycle progression through mitosis and thus, could act as a non-coding oncogene.
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Affiliation(s)
- Linda Nötzold
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Excellence Cluster, Heidelberg University, 69120, Heidelberg, Germany.,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, 69129, Heidelberg, Germany
| | - Lukas Frank
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Minakshi Gandhi
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Maria Polycarpou-Schwarz
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Matthias Groß
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Manuel Gunkel
- ViroQuant-CellNetworks RNAi Screening Facility, BioQuant Center, Heidelberg University, 69120, Heidelberg, Germany
| | - Nina Beil
- ViroQuant-CellNetworks RNAi Screening Facility, BioQuant Center, Heidelberg University, 69120, Heidelberg, Germany
| | - Holger Erfle
- ViroQuant-CellNetworks RNAi Screening Facility, BioQuant Center, Heidelberg University, 69120, Heidelberg, Germany
| | - Nathalie Harder
- Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, Heidelberg University, BioQuant, IPMB, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.,Definiens AG, 80636, Munich, Germany
| | - Karl Rohr
- Department of Bioinformatics and Functional Genomics, Biomedical Computer Vision Group, Heidelberg University, BioQuant, IPMB, and German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Jakob Trendel
- German Cancer Research Center (DKFZ), Excellence Cluster CellNetworks, Heidelberg University, 69120, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117, Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Excellence Cluster CellNetworks, Heidelberg University, 69120, Heidelberg, Germany.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117, Heidelberg, Germany
| | - Thomas Longerich
- Institute of Pathology University Hospital RWTH Aachen, 52074, Aachen, Germany.,Institute of Pathology, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, 69120, Heidelberg, Germany
| | - Sylvia Erhardt
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Excellence Cluster, Heidelberg University, 69120, Heidelberg, Germany.,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, 69129, Heidelberg, Germany
| | - Sven Diederichs
- Division of RNA Biology & Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany. .,Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, 69129, Heidelberg, Germany. .,Institute of Pathology, University Hospital Heidelberg, 69120, Heidelberg, Germany. .,Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center - University of Freiburg, 79106, Freiburg, Germany. .,Faculty of Medicine, University of Freiburg, 79085, Freiburg, Germany. .,German Cancer Consortium (DKTK), 79104, Freiburg, Germany.
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