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Abstract
Predicting regulatory potential from primary DNA sequences or transcription factor binding patterns is not possible. However, the annotation of the genome by chromatin proteins, histone modifications, and differential compaction is largely sufficient to reveal the locations of genes and their differential activity states. The Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are the central players in this cell type-specific chromatin organization. PcG function was originally viewed as being solely repressive and irreversible, as observed at the homeotic loci in flies and mammals. However, it is now clear that modular and reversible PcG function is essential at most developmental genes. Focusing mainly on recent advances, we review evidence for how PcG and TrxG patterns change dynamically during cell type transitions. The ability to implement cell type-specific transcriptional programming with exquisite fidelity is essential for normal development.
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Affiliation(s)
- Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Hyuckjoon Kang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA; ,
| | - Sandip De
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
| | - Judith A Kassis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA; ,
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52
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Differential regulation of lineage commitment in human and mouse primed pluripotent stem cells by the nucleosome remodelling and deacetylation complex. Stem Cell Res 2020; 46:101867. [PMID: 32535494 PMCID: PMC7347010 DOI: 10.1016/j.scr.2020.101867] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/04/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022] Open
Abstract
Differentiation of mammalian pluripotent cells involves large-scale changes in transcription and, among the molecules that orchestrate these changes, chromatin remodellers are essential to initiate, establish and maintain a new gene regulatory network. The Nucleosome Remodelling and Deacetylation (NuRD) complex is a highly conserved chromatin remodeller which fine-tunes gene expression in embryonic stem cells. While the function of NuRD in mouse pluripotent cells has been well defined, no study yet has defined NuRD function in human pluripotent cells. Here we find that while NuRD activity is required for lineage commitment from primed pluripotency in both human and mouse cells, the nature of this requirement is surprisingly different. While mouse embryonic stem cells (mESC) and epiblast stem cells (mEpiSC) require NuRD to maintain an appropriate differentiation trajectory as judged by gene expression profiling, human induced pluripotent stem cells (hiPSC) lacking NuRD fail to even initiate these trajectories. Further, while NuRD activity is dispensable for self-renewal of mESCs and mEpiSCs, hiPSCs require NuRD to maintain a stable self-renewing state. These studies reveal that failure to properly fine-tune gene expression and/or to reduce transcriptional noise through the action of a highly conserved chromatin remodeller can have different consequences in human and mouse pluripotent stem cells.
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53
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Pandya P, Isakov N. PICOT promotes T lymphocyte proliferation by down-regulating cyclin D2 expression. World J Immunol 2020; 10:1-12. [DOI: 10.5411/wji.v10.i1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 05/09/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
The mammalian protein kinase C-interacting cousin of thioredoxin (PICOT; also termed glutaredoxin 3) is a multi-domain monothiol glutaredoxin that is involved in a wide variety of signaling pathways and biological processes. PICOT is required for normal and transformed cell growth and is critical for embryonic development. Recent studies in T lymphocytes demonstrated that PICOT can translocate to the nucleus and interact with embryonic ectoderm development, a polycomb group protein and a core component of the polycomb repressive complex 2, which contributes to the maintenance of transcriptional repression and chromatin remodeling. Furthermore, PICOT was found to interact with chromatin-bound embryonic ectoderm development and alter the extent of histone 3 lysine 27 trimethylation at the promoter region of selected polycomb repressive complex 2 target genes. PICOT knockdown in Jurkat T cells led to increased histone 3 lysine 27 trimethylation at the promoter region of CCND2, a cell cycle-regulating gene which encodes the cyclin D2 protein. As a result, the expression levels of CCND2 mRNA and protein levels were reduced, concomitantly with inhibition of the cell growth rate. Analysis of multiple data sets from the Cancer Genome Atlas revealed that a high expression of PICOT correlated with a low expression of CCND2 in a large number of human cancers. In addition, this parameter correlated with poor patient survival, suggesting that the ratio between PICOT/CCND2 mRNA levels might serve as a predictor of patient survival in selected types of human cancer.
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Affiliation(s)
- Pinakin Pandya
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences and the Cancer Research Center, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
- Department of Computational and System biology, UPMC Hillman Cancer Center, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15232, United States
| | - Noah Isakov
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences and the Cancer Research Center, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
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54
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Schlag K, Steinhilber D, Karas M, Sorg BL. Analysis of proximal ALOX5 promoter binding proteins by quantitative proteomics. FEBS J 2020; 287:4481-4499. [PMID: 32096311 DOI: 10.1111/febs.15259] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/15/2019] [Accepted: 02/23/2020] [Indexed: 01/01/2023]
Abstract
5-Lipoxygenase (5-LO) is the initial enzyme in the biosynthesis of leukotrienes, which are mediators involved in pathophysiological conditions such as asthma and certain cancer types. Knowledge of proteins involved in 5-LO pathway regulation, including gene regulatory proteins, is needed to evaluate all options for therapeutic intervention in these diseases. Here, we present a mass spectrometric screening of ALOX5 promoter-interacting proteins, obtained by DNA pulldown and label-free quantitative mass spectrometry. Protein preparations from myeloid and B-lymphocytic cell lines were screened for promoter DNA interactors. Through statistical analysis, 66 proteins were identified as specific ALOX5 promotor binding proteins. Among those, the 15 most likely candidates for a prominent role in ALOX5 gene regulation are the known ALOX5 interactors Sp1 and Sp3, the related factor Sp2, two Krüppel-like factors (KLF13 and KLF16) and six other zinc finger proteins (MAZ, PRDM10, VEZF1, ZBTB7A, ZNF281 and ZNF579). Intriguingly, we also identified two helicases (BLM and DHX36) and the proteins hnRNPD and hnRNPK, which are, together with the protein MAZ, known to interact with DNA G-quadruplex structures. As G-quadruplexes are implicated in gene regulation, spectroscopic and antibody-based methods were used to confirm their presence within the GC-rich sequence of the ALOX5 promoter. In summary, we have systematically characterized the interactome of the ALOX5 promoter, identifying several zinc finger proteins as novel potential ALOX5 gene regulators. Further, we have shown that the ALOX5 promoter can form DNA G-quadruplex structures, which may play a functional role in ALOX5 gene regulation.
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Affiliation(s)
- Katharina Schlag
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
| | - Bernd L Sorg
- Institute of Pharmaceutical Chemistry/ZAFES, Goethe-University, Frankfurt am Main, Germany
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55
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Splicing and Chromatin Factors Jointly Regulate Epidermal Differentiation. Cell Rep 2019; 25:1292-1303.e5. [PMID: 30380419 DOI: 10.1016/j.celrep.2018.10.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/04/2018] [Accepted: 10/03/2018] [Indexed: 12/21/2022] Open
Abstract
Epidermal homeostasis requires balanced progenitor cell proliferation and loss of differentiated cells from the epidermal surface. During this process, cells undergo major changes in their transcriptional programs to accommodate new cellular functions. We found that transcriptional and post-transcriptional mechanisms underlying these changes jointly control genes involved in cell adhesion, a key process in epidermal maintenance. Using siRNA-based perturbation screens, we identified DNA and/or RNA binding regulators of epidermal differentiation. Computational modeling and experimental validation identified functional interactions between the matrin-type 2 zinc-finger protein ZMAT2 and the epigenetic modifiers ING5, SMARCA5, BRD1, UHRF1, BPTF, and SMARCC2. ZMAT2 is an interactor of the pre-spliceosome that is required to keep cells in an undifferentiated, proliferative state. RNA immunoprecipitation and transcriptome-wide RNA splicing analysis showed that ZMAT2 associates with and regulates transcripts involved in cell adhesion in conjunction with ING5. Thus, joint control by splicing regulation, histone, and DNA modification is important to maintain epidermal cells in an undifferentiated state.
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56
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Elías-Villalobos A, Toullec D, Faux C, Séveno M, Helmlinger D. Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes in yeast. Nat Commun 2019; 10:5237. [PMID: 31748520 PMCID: PMC6868236 DOI: 10.1038/s41467-019-13243-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022] Open
Abstract
Transcription initiation involves the coordinated activities of large multimeric complexes, but little is known about their biogenesis. Here we report several principles underlying the assembly and topological organization of the highly conserved SAGA and NuA4 co-activator complexes, which share the Tra1 subunit. We show that Tra1 contributes to the overall integrity of NuA4, whereas, within SAGA, it specifically controls the incorporation of the de-ubiquitination module (DUB), as part of an ordered assembly pathway. Biochemical and functional analyses reveal the mechanism by which Tra1 specifically interacts with either SAGA or NuA4. Finally, we demonstrate that Hsp90 and its cochaperone TTT promote Tra1 de novo incorporation into both complexes, indicating that Tra1, the sole pseudokinase of the PIKK family, shares a dedicated chaperone machinery with its cognate kinases. Overall, our work brings mechanistic insights into the assembly of transcriptional complexes and reveals the contribution of dedicated chaperones to this process. Transcription initiation involves the coordinated assembly and activity of large multimeric complexes. Here the authors report on the chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes in fission yeast, providing insight into the de novo assembly of transcriptional complexes and the contribution of dedicated chaperones to this process.
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Affiliation(s)
| | - Damien Toullec
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | - Céline Faux
- CRBM, CNRS, University of Montpellier, Montpellier, France
| | - Martial Séveno
- BioCampus Montpellier, CNRS, INSERM, University of Montpellier, Montpellier, France
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57
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Chammas P, Mocavini I, Di Croce L. Engaging chromatin: PRC2 structure meets function. Br J Cancer 2019; 122:315-328. [PMID: 31708574 PMCID: PMC7000746 DOI: 10.1038/s41416-019-0615-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/24/2019] [Indexed: 01/01/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2) is a key epigenetic multiprotein complex involved in the regulation of gene expression in metazoans. PRC2 is formed by a tetrameric core that endows the complex with histone methyltransferase activity, allowing it to mono-, di- and tri-methylate histone H3 on lysine 27 (H3K27me1/2/3); H3K27me3 is a hallmark of facultative heterochromatin. The core complex of PRC2 is bound by several associated factors that are responsible for modulating its targeting specificity and enzymatic activity. Depletion and/or mutation of the subunits of this complex can result in severe developmental defects, or even lethality. Furthermore, mutations of these proteins in somatic cells can be drivers of tumorigenesis, by altering the transcriptional regulation of key tumour suppressors or oncogenes. In this review, we present the latest results from structural studies that have characterised PRC2 composition and function. We compare this information with data and literature for both gain-of function and loss-of-function missense mutations in cancers to provide an overview of the impact of these mutations on PRC2 activity.
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Affiliation(s)
- Paul Chammas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Ivano Mocavini
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona, 08003, Spain
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona, 08003, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain. .,ICREA, Pg Lluis Companys 23, Barcelona, 08010, Spain.
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58
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C10ORF12 modulates PRC2 histone methyltransferase activity and H3K27me3 levels. Acta Pharmacol Sin 2019; 40:1457-1465. [PMID: 31186533 DOI: 10.1038/s41401-019-0247-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/05/2019] [Indexed: 01/03/2023] Open
Abstract
The polycomb repressive complex 2 (PRC2) catalyzes the methylation of histone H3 on lysine 27 (H3K27) to generate trimethyl-H3K27 (H3K27me3) marks, thereby leading to a repressive chromatin state that inhibits gene expression. C10ORF12 was recently identified as a novel PRC2 interactor. Here, we show that C10ORF12 specifically interacts with PRC2 through its middle region (positions 619-718). C10ORF12 significantly enhances the histone methyltransferase activity of PRC2 in vitro and dramatically increases the total H3K27me3 levels in HeLa cells. C10ORF12 also antagonizes Jarid2, which is an auxiliary factor of the PRC2.2 subcomplex, to promote increased H3K27me3 levels in HeLa cells. Moreover, C10ORF12 alters the substrate preference of PRC2. These results indicate that C10ORF12 functions as a positive regulator of PRC2 and facilitates PRC2-mediated H3K27me3 modification of chromatin. These findings provide new insight into the roles of C10ORF12 in regulating the activity of the PRC2 complex.
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59
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Hale R, Sandakly S, Shipley J, Walters Z. Epigenetic Targets in Synovial Sarcoma: A Mini-Review. Front Oncol 2019; 9:1078. [PMID: 31681608 PMCID: PMC6813544 DOI: 10.3389/fonc.2019.01078] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/30/2019] [Indexed: 01/25/2023] Open
Abstract
Synovial Sarcomas (SS) are a type of Soft Tissue Sarcoma (STS) and represent 8-10% of all STS cases. Although SS can arise at any age, it typically affects younger individuals aged 15-35 and is therefore part of both pediatric and adult clinical practices. SS occurs primarily in the limbs, often near joints, but can present anywhere. It is characterized by the recurrent pathognomonic chromosomal translocation t(X;18)(p11.2;q11.2) that most frequently fuses SSX1 or SSX2 genes with SS18. This leads to the expression of the SS18-SSX fusion protein, which causes disturbances in several interacting multiprotein complexes such as the SWItch/Sucrose Non-Fermentable (SWI/SNF) complex, also known as the BAF complex and the Polycomb Repressive Complex 1 and 2 (PRC1 and PRC2). Furthermore, this promotes widespread epigenetic rewiring, leading to aberrant gene expression that drives the pathogenesis of SS. Good prognoses are characterized predominantly by small tumor size and young patient age. Whereas, high tumor grade and an increased genomic complexity of the tumor constitute poor prognostic factors. The current therapeutic strategy relies on chemotherapy and radiotherapy, the latter of which can lead to chronic side effects for pediatric patients. We will focus on the known roles of SWI/SNF, PRC1, and PRC2 as the main effectors of the SS18-SSX-mediated genome modifications and we present existing biological rationale for potential therapeutic targets and treatment strategies.
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Affiliation(s)
- Ryland Hale
- Translational Epigenomics Team, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sami Sandakly
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Janet Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
| | - Zoë Walters
- Translational Epigenomics Team, Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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60
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Leighton G, Williams DC. The Methyl-CpG-Binding Domain 2 and 3 Proteins and Formation of the Nucleosome Remodeling and Deacetylase Complex. J Mol Biol 2019:S0022-2836(19)30599-6. [PMID: 31626804 DOI: 10.1016/j.jmb.2019.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 12/13/2022]
Abstract
The Nucleosome Remodeling and Deacetylase (NuRD) complex uniquely combines both deacetylase and remodeling enzymatic activities in a single macromolecular complex. The methyl-CpG-binding domain 2 and 3 (MBD2 and MBD3) proteins provide a critical structural link between the deacetylase and remodeling components, while MBD2 endows the complex with the ability to selectively recognize methylated DNA. Hence, NuRD combines three major arms of epigenetic gene regulation. Research over the past few decades has revealed much of the structural basis driving formation of this complex and started to uncover the functional roles of NuRD in epigenetic gene regulation. However, we have yet to fully understand the molecular and biophysical basis for methylation-dependent chromatin remodeling and transcription regulation by NuRD. In this review, we discuss the structural information currently available for the complex, the role MBD2 and MBD3 play in forming and recruiting the complex to methylated DNA, and the biological functions of NuRD.
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Affiliation(s)
- Gage Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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61
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Joosten J, Miesen P, Taşköprü E, Pennings B, Jansen PWTC, Huynen MA, Vermeulen M, Van Rij RP. The Tudor protein Veneno assembles the ping-pong amplification complex that produces viral piRNAs in Aedes mosquitoes. Nucleic Acids Res 2019; 47:2546-2559. [PMID: 30566680 PMCID: PMC6411831 DOI: 10.1093/nar/gky1266] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/28/2018] [Accepted: 12/10/2018] [Indexed: 11/21/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) comprise a class of small RNAs best known for suppressing transposable elements in germline tissues. The vector mosquito Aedes aegypti encodes seven PIWI genes, four of which are somatically expressed. This somatic piRNA pathway generates piRNAs from viral RNA during infection with cytoplasmic RNA viruses through ping-pong amplification by the PIWI proteins Ago3 and Piwi5. Yet, additional insights into the molecular mechanisms mediating non-canonical piRNA production are lacking. TUDOR-domain containing (Tudor) proteins facilitate piRNA biogenesis in Drosophila melanogaster and other model organisms. We thus hypothesized that Tudor proteins are required for viral piRNA production and performed a knockdown screen targeting all A. aegypti Tudor genes. Knockdown of the Tudor genes AAEL012437, Vreteno, Yb, SMN and AAEL008101-RB resulted in significantly reduced viral piRNA levels, with AAEL012437-depletion having the strongest effect. This protein, which we named Veneno, associates directly with Ago3 in an sDMA-dependent manner and localizes in cytoplasmic foci reminiscent of piRNA processing granules of Drosophila. Veneno-interactome analyses reveal a network of co-factors including the orthologs of the Drosophila piRNA pathway components Vasa and Yb, which in turn interacts with Piwi5. We propose that Veneno assembles a multi-protein complex for ping-pong dependent piRNA production from viral RNA.
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Affiliation(s)
- Joep Joosten
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ezgi Taşköprü
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Bas Pennings
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Ronald P Van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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62
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Abstract
Polycomb repressive complex 2 (PRC2) is a conserved chromatin regulator that is responsible for the methylation of histone H3 lysine 27 (H3K27). PRC2 is essential for normal development and its loss of function thus results in a range of developmental phenotypes. Here, we review the latest advances in our understanding of mammalian PRC2 activity and present an updated summary of the phenotypes associated with its loss of function in mice. We then discuss recent studies that have highlighted regulatory interplay between the modifications laid down by PRC2 and other chromatin modifiers, including NSD1 and DNMT3A. Finally, we propose a model in which the dysregulation of these modifications at intergenic regions is a shared molecular feature of genetically distinct but highly phenotypically similar overgrowth syndromes in humans.
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Affiliation(s)
- Orla Deevy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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63
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Capponi S, Stöffler N, Irimia M, Van Schaik FMA, Ondik MM, Biniossek ML, Lehmann L, Mitschke J, Vermunt MW, Creyghton MP, Graybiel AM, Reinheckel T, Schilling O, Blencowe BJ, Crittenden JR, Timmers HTM. Neuronal-specific microexon splicing of TAF1 mRNA is directly regulated by SRRM4/nSR100. RNA Biol 2019; 17:62-74. [PMID: 31559909 PMCID: PMC6948980 DOI: 10.1080/15476286.2019.1667214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Neuronal microexons represent the most highly conserved class of alternative splicing events and their timed expression shapes neuronal biology, including neuronal commitment and differentiation. The six-nt microexon 34ʹ is included in the neuronal form of TAF1 mRNA, which encodes the largest subunit of the basal transcription factor TFIID. In this study, we investigate the tissue distribution of TAF1-34ʹ mRNA and protein and the mechanism responsible for its neuronal-specific splicing. Using isoform-specific RNA probes and antibodies, we observe that canonical TAF1 and TAF1-34ʹ have different distributions in the brain, which distinguish proliferating from post-mitotic neurons. Knockdown and ectopic expression experiments demonstrate that the neuronal-specific splicing factor SRRM4/nSR100 promotes the inclusion of microexon 34ʹ into TAF1 mRNA, through the recognition of UGC sequences in the poly-pyrimidine tract upstream of the regulated microexon. These results show that SRRM4 regulates temporal and spatial expression of alternative TAF1 mRNAs to generate a neuronal-specific TFIID complex.
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Affiliation(s)
- Simona Capponi
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Nadja Stöffler
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Manuel Irimia
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frederik M A Van Schaik
- Molecular Cancer Research and Stem Cells, Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mercedes M Ondik
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lisa Lehmann
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Mitschke
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marit W Vermunt
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Menno P Creyghton
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ann M Graybiel
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas Reinheckel
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, and German Cancer Consortium (DKTK) partner site Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Faculty of Medicine-University of Freiburg, Freiburg, Germany
| | - Benjamin J Blencowe
- Donnelly Centre and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jill R Crittenden
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - H Th Marc Timmers
- German Cancer Consortium (DKTK) partner site Freiburg, German Cancer Research Center (DKFZ) and Department of Urology, Medical Center-University of Freiburg, Freiburg, Germany
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64
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Pandya P, Jethva M, Rubin E, Birnbaum RY, Braiman A, Isakov N. PICOT binding to chromatin-associated EED negatively regulates cyclin D2 expression by increasing H3K27me3 at the CCND2 gene promoter. Cell Death Dis 2019; 10:685. [PMID: 31527584 PMCID: PMC6746821 DOI: 10.1038/s41419-019-1935-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/08/2019] [Accepted: 08/27/2019] [Indexed: 12/14/2022]
Abstract
Protein kinase C (PKC)-interacting cousin of thioredoxin (PICOT; also termed glutaredoxin 3 (Grx3; Glrx3)) is a ubiquitous protein that can interact with the embryonic ectoderm development (EED) protein via each of its two C-terminal PICOT/Grx homology domains. Since EED is a Polycomb-Group protein and a core component of the polycomb repressive complex 2 (PRC2), we tested the involvement of PICOT in the regulation of PRC2-mediated H3 lysine 27 trimethylation (H3K27me3), transcription and translation of selected PRC2 target genes. A fraction of the cellular PICOT protein was found in the nuclei of leukemia cell lines, where it was associated with the chromatin. In addition, PICOT coimmunoprecipitated with chromatin-residing EED derived from Jurkat and COS-7 cell nuclei. PICOT knockdown led to a reduced H3K27me3 mark and a decrease in EED and EZH2 at the CCND2 gene promoter. In agreement, PICOT-deficient T cells exhibited a significant increase in CCND2 mRNA and protein expression. Since elevated expression levels of PICOT were reported in several different tumors and correlated in the current studies with decreased transcription and translation of the CCND2 gene, we tested whether this opposite correlation exists in human cancers. Data from the Cancer Genome Atlas (TCGA) database indicated statistically significant negative correlation between PICOT and CCND2 in eight different human tumors where the highest correlation was in lung (p = 8.67E−10) and pancreatic (p = 1.06E−5) adenocarcinoma. Furthermore, high expression of PICOT and low expression of CCND2 correlated with poor patient survival in five different types of human tumors. The results suggest that PICOT binding to chromatin-associated EED modulates the H3K27me3 level at the CCND2 gene promoter which may be one of the potential mechanisms for regulation of cyclin D2 expression in tumors. These findings also indicate that a low PICOT/CCND2 expression ratio might serve as a good predictor of patient survival in selected human cancers.
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Affiliation(s)
- Pinakin Pandya
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences and the Cancer Research Center, Ben Gurion University of the Negev, P.O.B. 653, 84105, Beer Sheva, Israel
| | - Minesh Jethva
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences and the Cancer Research Center, Ben Gurion University of the Negev, P.O.B. 653, 84105, Beer Sheva, Israel
| | - Eitan Rubin
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences and the Cancer Research Center, Ben Gurion University of the Negev, P.O.B. 653, 84105, Beer Sheva, Israel
| | - Ramon Y Birnbaum
- Department of Life Sciences, Ben-Gurion University of the Negev, 84105, Beer-Sheva, Israel
| | - Alex Braiman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences and the Cancer Research Center, Ben Gurion University of the Negev, P.O.B. 653, 84105, Beer Sheva, Israel
| | - Noah Isakov
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences and the Cancer Research Center, Ben Gurion University of the Negev, P.O.B. 653, 84105, Beer Sheva, Israel.
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65
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Liu L, Li L, Ma C, Shi Y, Liu C, Xiao Z, Zhang Y, Tian F, Gao Y, Zhang J, Ying W, Wang PG, Zhang L. O-GlcNAcylation of Thr 12/Ser 56 in short-form O-GlcNAc transferase (sOGT) regulates its substrate selectivity. J Biol Chem 2019; 294:16620-16633. [PMID: 31527085 DOI: 10.1074/jbc.ra119.009085] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/11/2019] [Indexed: 02/05/2023] Open
Abstract
O-GlcNAcylation is a ubiquitous protein glycosylation playing different roles on variant proteins. O-GlcNAc transferase (OGT) is the unique enzyme responsible for the sugar addition to nucleocytoplasmic proteins. Recently, multiple O-GlcNAc sites have been observed on short-form OGT (sOGT) and nucleocytoplasmic OGT (ncOGT), both of which locate in the nucleus and cytoplasm in cell. Moreover, O-GlcNAcylation of Ser389 in ncOGT (1036 amino acids) affects its nuclear translocation in HeLa cells. To date, the major O-GlcNAcylation sites and their roles in sOGT remain unknown. Here, we performed LC-MS/MS and mutational analyses to seek the major O-GlcNAcylation site on sOGT. We identified six O-GlcNAc sites in the tetratricopeptide repeat domain in sOGT, with Thr12 and Ser56 being two "key" sites. Thr12 is a dominant O-GlcNAcylation site, whereas the modification of Ser56 plays a role in regulating sOGT O-GlcNAcylation, partly through Thr12 In vitro activity and pulldown assays demonstrated that O-GlcNAcylation does not affect sOGT activity but does affect sOGT-interacting proteins. In HEK293T cells, S56A bound to and hence glycosylated more proteins in contrast to T12A and WT sOGT. By proteomic and bioinformatics analyses, we found that T12A and S56A differed in substrate proteins (e.g. HNRNPU and PDCD6IP), which eventually affected cell cycle progression and/or cell proliferation. These findings demonstrate that O-GlcNAcylation modulates sOGT substrate selectivity and affects its role in the cell. The data also highlight the regulatory role of O-GlcNAcylation at Thr12 and Ser56.
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Affiliation(s)
- Li Liu
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Ling Li
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Cheng Ma
- Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Yangde Shi
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Congcong Liu
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Zikang Xiao
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Yong Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China.,West China-Washington Mitochondria and Metabolism Research Center, Key Laboratory of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fang Tian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Yang Gao
- School of medicine, Nankai University, Tianjin 300071, China
| | - Jie Zhang
- School of medicine, Nankai University, Tianjin 300071, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Peng George Wang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China.,Center for Diagnostics and Therapeutics, Department of Chemistry, Georgia State University, Atlanta, Georgia 30303
| | - Lianwen Zhang
- College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
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66
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Healy E, Mucha M, Glancy E, Fitzpatrick DJ, Conway E, Neikes HK, Monger C, Van Mierlo G, Baltissen MP, Koseki Y, Vermeulen M, Koseki H, Bracken AP. PRC2.1 and PRC2.2 Synergize to Coordinate H3K27 Trimethylation. Mol Cell 2019; 76:437-452.e6. [PMID: 31521505 DOI: 10.1016/j.molcel.2019.08.012] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/28/2019] [Accepted: 08/12/2019] [Indexed: 12/12/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is composed of EED, SUZ12, and EZH1/2 and mediates mono-, di-, and trimethylation of histone H3 at lysine 27. At least two independent subcomplexes exist, defined by their specific accessory proteins: PRC2.1 (PCL1-3, EPOP, and PALI1/2) and PRC2.2 (AEBP2 and JARID2). We show that PRC2.1 and PRC2.2 share the majority of target genes in mouse embryonic stem cells. The loss of PCL1-3 is sufficient to evict PRC2.1 from Polycomb target genes but only leads to a partial reduction of PRC2.2 and H3K27me3. Conversely, disruption of PRC2.2 function through the loss of either JARID2 or RING1A/B is insufficient to completely disrupt targeting of SUZ12 by PCLs. Instead, the combined loss of both PRC2.1 and PRC2.2 is required, leading to the global mislocalization of SUZ12. This supports a model in which the specific accessory proteins within PRC2.1 and PRC2.2 cooperate to direct H3K27me3 via both synergistic and independent mechanisms.
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Affiliation(s)
- Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Marlena Mucha
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Hannah K Neikes
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Craig Monger
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Guido Van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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67
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Schoenherr RM, Huang D, Voytovich UJ, Ivey RG, Kennedy JJ, Saul RG, Colantonio S, Roberts RR, Knotts JG, Kaczmarczyk JA, Perry C, Hewitt SM, Bocik W, Whiteley GR, Hiltke T, Boja ES, Rodriguez H, Whiteaker JR, Paulovich AG. A dataset describing a suite of novel antibody reagents for the RAS signaling network. Sci Data 2019; 6:160. [PMID: 31467290 PMCID: PMC6715692 DOI: 10.1038/s41597-019-0166-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
RAS genes are frequently mutated in cancer and have for decades eluded effective therapeutic attack. The National Cancer Institute's RAS Initiative has a focus on understanding pathways and discovering therapies for RAS-driven cancers. Part of these efforts is the generation of novel reagents to enable the quantification of RAS network proteins. Here we present a dataset describing the development, validation (following consensus principles developed by the broader research community), and distribution of 104 monoclonal antibodies (mAbs) enabling detection of 27 phosphopeptides and 69 unmodified peptides from 20 proteins in the RAS network. The dataset characterizes the utility of the antibodies in a variety of applications, including Western blotting, immunoprecipitation, protein array, immunohistochemistry, and targeted mass spectrometry. All antibodies and characterization data are publicly available through the CPTAC Antibody Portal, Panorama Public Repository, and/or PRIDE databases. These reagents will aid researchers in discerning pathways and measuring expression changes in the RAS signaling network.
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Affiliation(s)
| | - Dongqing Huang
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Richard G Ivey
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Richard G Saul
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rhonda R Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph G Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jan A Kaczmarczyk
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Candice Perry
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gordon R Whiteley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tara Hiltke
- National Cancer Institute, Bethesda, MD, USA
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68
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EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells. Nat Commun 2019; 10:3858. [PMID: 31451685 PMCID: PMC6710278 DOI: 10.1038/s41467-019-11800-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 08/06/2019] [Indexed: 12/18/2022] Open
Abstract
The Polycomb group of proteins is required for the proper orchestration of gene expression due to its role in maintaining transcriptional silencing. It is composed of several chromatin modifying complexes, including Polycomb Repressive Complex 2 (PRC2), which deposits H3K27me2/3. Here, we report the identification of a cofactor of PRC2, EZHIP (EZH1/2 Inhibitory Protein), expressed predominantly in the gonads. EZHIP limits the enzymatic activity of PRC2 and lessens the interaction between the core complex and its accessory subunits, but does not interfere with PRC2 recruitment to chromatin. Deletion of Ezhip in mice leads to a global increase in H3K27me2/3 deposition both during spermatogenesis and at late stages of oocyte maturation. This does not affect the initial number of follicles but is associated with a reduction of follicles in aging. Our results suggest that mature oocytes Ezhip-/- might not be fully functional and indicate that fertility is strongly impaired in Ezhip-/- females. Altogether, our study uncovers EZHIP as a regulator of chromatin landscape in gametes.
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69
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Ma H, Li R, Di X, Jin X, Wang Y, Lai B, Shi C, Ji M, Zhu X, Wang K. ITRAQ-based proteomic analysis reveals possible target-related proteins in human adrenocortical adenomas. BMC Genomics 2019; 20:655. [PMID: 31419939 PMCID: PMC6697928 DOI: 10.1186/s12864-019-6030-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/12/2019] [Indexed: 01/22/2023] Open
Abstract
Background Adrenocortical adenomas (ACAs) can lead to the autonomous secretion of aldosterone responsible for primary aldosteronism (PA), which is the most common form of secondary arterial hypertension. However, the authentic fundamental mechanisms underlying ACAs remain unclear. Objective Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics and bioinformatics analyses from etiological studies of ACAs were performed to screen the differentially expressed proteins (DEPs) and investigate the relevant mechanisms of their occurrence and development. Results could help determine therapeutic targets of clinical significance. Methods In the present study, iTRAQ-based proteomics was applied to analyze ACA tissue samples from normal adrenal cortex tissues adjacent to the tumor. Using proteins extracted from a panel of four pairs of ACA samples, we identified some upregulated proteins and other downregulated proteins in all four pairs of ACA samples compared with adjacent normal tissue. Subsequently, we predicted protein–protein interaction networks of three DEPs to determine the authentic functional factors in ACA. Results A total of 753 DEPs were identified, including 347 upregulated and 406 downregulated proteins. The expression of three upregulated proteins (E2F3, KRT6A, and ALDH1A2) was validated by Western blot in 24 ACA samples. Our data suggested that some DEPs might be important hallmarks during the development of ACA. Conclusions This study is the first proteomic research to investigate alterations in protein levels and affected pathways in ACA using the iTRAQ technique. Thus, this study not only provides a comprehensive dataset on overall protein changes but also sheds light on its potential molecular mechanism in human ACAs. Electronic supplementary material The online version of this article (10.1186/s12864-019-6030-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- He Ma
- Department of Respiratory Medicine, the Second Hospital of Jilin University, Changchun, China.,Department of Anesthesiology, the Second Hospital of Jilin University, Changchun, China
| | - Ranwei Li
- Department of Urinary Surgery, the Second Hospital of Jilin University, Changchun, China
| | - Xin Di
- Department of Respiratory Medicine, the Second Hospital of Jilin University, Changchun, China
| | - Xin Jin
- Department of Hematology, the Second Hospital of Jilin University, Changchun, China
| | - Yan Wang
- Department of Respiratory Medicine, the Second Hospital of Jilin University, Changchun, China
| | - Bingjie Lai
- Department of Intensive Care Unit, the Second Hospital of Jilin University, Changchun, China
| | - Cailian Shi
- Department of Anesthesiology, the Second Hospital of Jilin University, Changchun, China
| | - Mingxin Ji
- Department of Anesthesiology, the Second Hospital of Jilin University, Changchun, China
| | - Xinran Zhu
- Department of Anesthesiology, the Second Hospital of Jilin University, Changchun, China
| | - Ke Wang
- Department of Respiratory Medicine, the Second Hospital of Jilin University, Changchun, China.
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70
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van Mierlo G, Veenstra GJC, Vermeulen M, Marks H. The Complexity of PRC2 Subcomplexes. Trends Cell Biol 2019; 29:660-671. [PMID: 31178244 DOI: 10.1016/j.tcb.2019.05.004] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is a multisubunit protein complex essential for the development of multicellular organisms. Recruitment of PRC2 to target genes, followed by deposition and propagation of its catalytic product histone H3 lysine 27 trimethylation (H3K27me3), are key to the spatiotemporal control of developmental gene expression. Recent breakthrough studies have uncovered unexpected roles for substoichiometric PRC2 subunits in these processes. Here, we elaborate on how the facultative PRC2 subunits regulate catalytic activity, locus-specific PRC2 binding, and propagation of H3K27me3, and how this affects chromatin structure, gene expression, and cell fate.
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Affiliation(s)
- Guido van Mierlo
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen 6525GA, The Netherlands; Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen 6525GA, The Netherlands
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen 6500HB, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen 6525GA, The Netherlands; Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University, Nijmegen 6525GA, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen 6525GA, The Netherlands.
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71
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Fursova NA, Blackledge NP, Nakayama M, Ito S, Koseki Y, Farcas AM, King HW, Koseki H, Klose RJ. Synergy between Variant PRC1 Complexes Defines Polycomb-Mediated Gene Repression. Mol Cell 2019; 74:1020-1036.e8. [PMID: 31029541 PMCID: PMC6561741 DOI: 10.1016/j.molcel.2019.03.024] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 03/21/2019] [Indexed: 01/30/2023]
Abstract
The Polycomb system modifies chromatin and plays an essential role in repressing gene expression to control normal mammalian development. However, the components and mechanisms that define how Polycomb protein complexes achieve this remain enigmatic. Here, we use combinatorial genetic perturbation coupled with quantitative genomics to discover the central determinants of Polycomb-mediated gene repression in mouse embryonic stem cells. We demonstrate that canonical Polycomb repressive complex 1 (PRC1), which mediates higher-order chromatin structures, contributes little to gene repression. Instead, we uncover an unexpectedly high degree of synergy between variant PRC1 complexes, which is fundamental to gene repression. We further demonstrate that variant PRC1 complexes are responsible for distinct pools of H2A monoubiquitylation that are associated with repression of Polycomb target genes and silencing during X chromosome inactivation. Together, these discoveries reveal a new variant PRC1-dependent logic for Polycomb-mediated gene repression.
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Affiliation(s)
- Nadezda A Fursova
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Manabu Nakayama
- Laboratory of Medical Omics Research, Department of Frontier Research and Development, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Anca M Farcas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; AMED-CREST, Japanese Agency for Medical Research and Development, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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72
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Will T, Helms V. Differential analysis of combinatorial protein complexes with CompleXChange. BMC Bioinformatics 2019; 20:300. [PMID: 31159772 PMCID: PMC6547514 DOI: 10.1186/s12859-019-2852-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 04/26/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although a considerable number of proteins operate as multiprotein complexes and not on their own, organism-wide studies so far are only able to quantify individual proteins or protein-coding genes in a condition-specific manner for a sizeable number of samples, but not their assemblies. Consequently, there exist large amounts of transcriptomic data and an increasing amount of data on proteome abundance, but quantitative knowledge on complexomes is missing. This deficiency impedes the applicability of the powerful tool of differential analysis in the realm of macromolecular complexes. Here, we present a pipeline for differential analysis of protein complexes based on predicted or manually assigned complexes and inferred complex abundances, which can be easily applied on a whole-genome scale. RESULTS We observed for simulated data that results obtained by our complex abundance estimation algorithm were in better agreement with the ground truth and physicochemically more reasonable compared to previous efforts that used linear programming while running in a fraction of the time. The practical usability of the method was assessed in the context of transcription factor complexes in human monocyte and lymphoblastoid samples. We demonstrated that our new method is robust against false-positive detection and reports deregulated complexomes that can only be partially explained by differential analysis of individual protein-coding genes. Furthermore we showed that deregulated complexes identified by the tool potentially harbor significant yet unused information content. CONCLUSIONS CompleXChange allows to analyze deregulation of the protein complexome on a whole-genome scale by integrating a plethora of input data that is already available. A platform-independent Java binary, a user guide with example data and the source code are freely available at https://sourceforge.net/projects/complexchange/ .
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Affiliation(s)
- Thorsten Will
- Center for Bioinformatics, Saarland University, Campus E2.1, Saarbrücken, 66123, Germany.,Graduate School of Computer Science, Saarland University, Campus E1.3, Saarbrücken, 66123, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Campus E2.1, Saarbrücken, 66123, Germany.
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73
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Qu W, Du M, Yang F, Mai Z, Zhang C, Lin F, Ma Y, Chen T. Gaussian FRET two-hybrid assays for determining the stoichiometry of hetero-oligomeric complexes in single living cells. Biochem Biophys Res Commun 2019; 512:492-497. [DOI: 10.1016/j.bbrc.2019.03.089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 03/15/2019] [Indexed: 10/27/2022]
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74
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Burgold T, Barber M, Kloet S, Cramard J, Gharbi S, Floyd R, Kinoshita M, Ralser M, Vermeulen M, Reynolds N, Dietmann S, Hendrich B. The Nucleosome Remodelling and Deacetylation complex suppresses transcriptional noise during lineage commitment. EMBO J 2019; 38:embj.2018100788. [PMID: 31036553 PMCID: PMC6576150 DOI: 10.15252/embj.2018100788] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/30/2019] [Accepted: 04/02/2019] [Indexed: 12/11/2022] Open
Abstract
Multiprotein chromatin remodelling complexes show remarkable conservation of function amongst metazoans, even though components present in invertebrates are often found as multiple paralogous proteins in vertebrate complexes. In some cases, these paralogues specify distinct biochemical and/or functional activities in vertebrate cells. Here, we set out to define the biochemical and functional diversity encoded by one such group of proteins within the mammalian Nucleosome Remodelling and Deacetylation (NuRD) complex: Mta1, Mta2 and Mta3. We find that, in contrast to what has been described in somatic cells, MTA proteins are not mutually exclusive within embryonic stem (ES) cell NuRD and, despite subtle differences in chromatin binding and biochemical interactions, serve largely redundant functions. ES cells lacking all three MTA proteins exhibit complete NuRD loss of function and are viable, allowing us to identify a previously unreported function for NuRD in reducing transcriptional noise, which is essential for maintaining a proper differentiation trajectory during early stages of lineage commitment.
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Affiliation(s)
- Thomas Burgold
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Michael Barber
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Susan Kloet
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, The Netherlands
| | - Julie Cramard
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sarah Gharbi
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Robin Floyd
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Masaki Kinoshita
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Meryem Ralser
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, The Netherlands
| | - Nicola Reynolds
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sabine Dietmann
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Brian Hendrich
- Wellcome- MRC Stem Cell Institute, University of Cambridge, Cambridge, UK .,Department of Biochemistry, University of Cambridge, Cambridge, UK
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75
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Ignatova VV, Jansen PWTC, Baltissen MP, Vermeulen M, Schneider R. The interactome of a family of potential methyltransferases in HeLa cells. Sci Rep 2019; 9:6584. [PMID: 31036863 PMCID: PMC6488577 DOI: 10.1038/s41598-019-43010-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
Human methytransferase like proteins (METTL) are part of a large protein family characterized by the presence of binding domains for S-adenosyl methionine, a co-substrate for methylation reactions. Despite the fact that members of this protein family were shown or predicted to be DNA, RNA or protein methyltransferases, most METTL proteins are still poorly characterized. Identification of complexes in which these potential enzymes act could help to understand their function(s) and substrate specificities. Here we systematically studied interacting partners of METTL protein family members in HeLa cells using label-free quantitative mass spectrometry. We found that, surprisingly, many of the METTL proteins appear to function outside of stable complexes whereas others including METTL7B, METTL8 and METTL9 have high-confidence interaction partners. Our study is the first systematic and comprehensive overview of the interactome of METTL protein family that can provide a crucial resource for further studies of these potential novel methyltransferases.
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Affiliation(s)
- Valentina V Ignatova
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 30, 6525 GA, Nijmegen, The Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 30, 6525 GA, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 30, 6525 GA, Nijmegen, The Netherlands.
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany.
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76
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Tracey LJ, Brooke-Bisschop T, Jansen PWTC, Campos EI, Vermeulen M, Justice MJ. The Pluripotency Regulator PRDM14 Requires Hematopoietic Regulator CBFA2T3 to Initiate Leukemia in Mice. Mol Cancer Res 2019; 17:1468-1479. [PMID: 31015254 DOI: 10.1158/1541-7786.mcr-18-1327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/07/2019] [Accepted: 04/19/2019] [Indexed: 12/20/2022]
Abstract
PR domain-containing 14 (Prdm14) is a pluripotency regulator central to embryonic stem cell identity and primordial germ cell specification. Genomic regions containing PRDM14 are often amplified leading to misexpression in human cancer. Prdm14 expression in mouse hematopoietic stem cells (HSC) leads to progenitor cell expansion prior to the development of T-cell acute lymphoblastic leukemia (T-ALL), consistent with PRDM14's role in cancer initiation. Here, we demonstrate mechanistic insight into PRDM14-driven leukemias in vivo. Mass spectrometry revealed novel PRDM14-protein interactions including histone H1, RNA-binding proteins, and the master hematopoietic regulator CBFA2T3. In mouse leukemic cells, CBFA2T3 and PRDM14 associate independently of the related ETO family member CBFA2T2, PRDM14's primary protein partner in pluripotent cells. CBFA2T3 plays crucial roles in HSC self-renewal and lineage commitment, and participates in oncogenic translocations in acute myeloid leukemia. These results suggest a model whereby PRDM14 recruits CBFA2T3 to DNA, leading to gene misregulation causing progenitor cell expansion and lineage perturbations preceding T-ALL development. Strikingly, Prdm14-induced T-ALL does not occur in mice deficient for Cbfa2t3, demonstrating that Cbfa2t3 is required for leukemogenesis. Moreover, T-ALL develops in Cbfa2t3 heterozygotes with a significantly longer latency, suggesting that PRDM14-associated T-ALL is sensitive to Cbfa2t3 levels. Our study highlights how an oncogenic protein uses a native protein in progenitor cells to initiate leukemia, providing insight into PRDM14-driven oncogenesis in other cell types. IMPLICATIONS: The pluripotency regulator PRDM14 requires the master hematopoietic regulator CBFA2T3 to initiate leukemia in progenitor cells, demonstrating an oncogenic role for CBFA2T3 and providing an avenue for targeting cancer-initiating cells.
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Affiliation(s)
- Lauren J Tracey
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Travis Brooke-Bisschop
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pascal W T C Jansen
- Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Eric I Campos
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michiel Vermeulen
- Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, the Netherlands
| | - Monica J Justice
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
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77
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Del Gaudio N, Di Costanzo A, Liu NQ, Conte L, Migliaccio A, Vermeulen M, Martens JHA, Stunnenberg HG, Nebbioso A, Altucci L. BRD9 binds cell type-specific chromatin regions regulating leukemic cell survival via STAT5 inhibition. Cell Death Dis 2019; 10:338. [PMID: 31000698 PMCID: PMC6472371 DOI: 10.1038/s41419-019-1570-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/21/2019] [Accepted: 04/04/2019] [Indexed: 02/07/2023]
Abstract
Leukemia is characterized by genetic and epigenetic mutations resulting in selection of cancer cells, which are unable to differentiate. Although genetic alterations are difficult to target, the epigenome is intrinsically dynamic and readily offers new therapeutic strategies. Thus, identifying cancer-specific context-dependent targets and unraveling their biological function may open up new therapeutic perspectives. Here we identify bromodomain-containing protein 9 (BRD9) as a critical target required in acute myeloid leukemia (AML). We show that BRD9 is overexpressed in AML cells including ex vivo primary blasts compared with CD34+ cells. By targeting BRD9 expression in AML, we observed an alteration in proliferation and survival, ultimately resulting in the induction of apoptosis. Intriguingly, genome-wide profiling revealed that BRD9 binds enhancer regions in a cell type-specific manner, regulating cell type-related processes. We unveil a novel BRD9-sustained STAT5 pathway activation via regulation of SOCS3 expression levels. Our findings identify a previously undescribed BRD9-STAT5 axis as critical for leukemia maintenance, suggesting BRD9 as a potential therapeutic target.
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Affiliation(s)
- Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy.
| | - Antonella Di Costanzo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Ning Qing Liu
- Division Gene Regulation, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Lidio Conte
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Antimo Migliaccio
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, 6525 GA, Nijmegen, The Netherlands
| | - Joost H A Martens
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy.,Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, 6525 GA, Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, 6525 GA, Nijmegen, The Netherlands
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy.
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78
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Furlan C, Dirks RAM, Thomas PC, Jones RC, Wang J, Lynch M, Marks H, Vermeulen M. Miniaturised interaction proteomics on a microfluidic platform with ultra-low input requirements. Nat Commun 2019; 10:1525. [PMID: 30948724 PMCID: PMC6449397 DOI: 10.1038/s41467-019-09533-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/15/2019] [Indexed: 01/17/2023] Open
Abstract
Essentially all cellular processes are orchestrated by protein-protein interactions (PPIs). In recent years, affinity purification coupled to mass spectrometry (AP-MS) has been the preferred method to identify cellular PPIs. Here we present a microfluidic-based AP-MS workflow, called on-chip AP-MS, to identify PPIs using minute amounts of input material. By using this automated platform we purify the human Cohesin, CCC and Mediator complexes from as little as 4 micrograms of input lysate, representing a 50─100-fold downscaling compared to regular microcentrifuge tube-based protocols. We show that our platform can be used to affinity purify tagged baits as well as native cellular proteins and their interaction partners. As such, our method holds great promise for future biological and clinical AP-MS applications in which sample amounts are limited.
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Affiliation(s)
- Cristina Furlan
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, 6525 GA, The Netherlands
| | - René A M Dirks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, 6525 GA, The Netherlands
| | - Peter C Thomas
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Robert C Jones
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Jing Wang
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Mark Lynch
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Hendrik Marks
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, 6525 GA, The Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, 6525 GA, The Netherlands.
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79
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Laugesen A, Højfeldt JW, Helin K. Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation. Mol Cell 2019; 74:8-18. [PMID: 30951652 PMCID: PMC6452890 DOI: 10.1016/j.molcel.2019.03.011] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/12/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
The polycomb repressive complex 2 (PRC2) is a chromatin-associated methyltransferase catalyzing mono-, di-, and trimethylation of lysine 27 on histone H3 (H3K27). This activity is required for normal organismal development and maintenance of gene expression patterns to uphold cell identity. PRC2 function is often deregulated in disease and is a promising candidate for therapeutic targeting in cancer. In this review, we discuss the molecular mechanisms proposed to take part in modulating PRC2 recruitment and shaping H3K27 methylation patterns across the genome. This includes consideration of factors influencing PRC2 residence time on chromatin and PRC2 catalytic activity with a focus on the mechanisms giving rise to regional preferences and differential deposition of H3K27 methylation. We further discuss existing evidence for functional diversity between distinct subsets of PRC2 complexes with the aim of extracting key concepts and highlighting major open questions toward a more complete understanding of PRC2 function.
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Affiliation(s)
- Anne Laugesen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Jonas Westergaard Højfeldt
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA.
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80
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Sharifi Tabar M, Mackay JP, Low JKK. The stoichiometry and interactome of the Nucleosome Remodeling and Deacetylase (NuRD) complex are conserved across multiple cell lines. FEBS J 2019; 286:2043-2061. [DOI: 10.1111/febs.14800] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/27/2018] [Accepted: 03/01/2019] [Indexed: 12/13/2022]
Affiliation(s)
| | - Joel P. Mackay
- School of Life and Environmental Sciences University of Sydney Australia
| | - Jason K. K. Low
- School of Life and Environmental Sciences University of Sydney Australia
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81
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Zhang Q, McKenzie NJ, Warneford-Thomson R, Gail EH, Flanigan SF, Owen BM, Lauman R, Levina V, Garcia BA, Schittenhelm RB, Bonasio R, Davidovich C. RNA exploits an exposed regulatory site to inhibit the enzymatic activity of PRC2. Nat Struct Mol Biol 2019; 26:237-247. [PMID: 30833789 DOI: 10.1038/s41594-019-0197-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 01/29/2019] [Indexed: 12/18/2022]
Abstract
Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that maintains cell identity during development in multicellular organisms by marking repressed genes and chromatin domains. In addition to four core subunits, PRC2 comprises multiple accessory subunits that vary in their composition during cellular differentiation and define two major holo-PRC2 complexes: PRC2.1 and PRC2.2. PRC2 binds to RNA, which inhibits its enzymatic activity, but the mechanism of RNA-mediated inhibition of holo-PRC2 is poorly understood. Here we present in vivo and in vitro protein-RNA interaction maps and identify an RNA-binding patch within the allosteric regulatory site of human and mouse PRC2, adjacent to the methyltransferase center. RNA-mediated inhibition of holo-PRC2 is relieved by allosteric activation of PRC2 by H3K27me3 and JARID2-K116me3 peptides. Both holo-PRC2.1 and holo-PRC2.2 bind RNA, providing a unified model to explain how RNA and allosteric stimuli antagonistically regulate the enzymatic activity of PRC2.
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Affiliation(s)
- Qi Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Nicholas J McKenzie
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Robert Warneford-Thomson
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Graduate Group in Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Emma H Gail
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Sarena F Flanigan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Brady M Owen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Richard Lauman
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Graduate Group in Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Vitalina Levina
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Benjamin A Garcia
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ralf B Schittenhelm
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.,Monash Biomedical Proteomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. .,Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia. .,EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging, Clayton, Victoria, Australia.
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82
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Dittmar G, Hernandez DP, Kowenz-Leutz E, Kirchner M, Kahlert G, Wesolowski R, Baum K, Knoblich M, Hofstätter M, Muller A, Wolf J, Reimer U, Leutz A. PRISMA: Protein Interaction Screen on Peptide Matrix Reveals Interaction Footprints and Modifications- Dependent Interactome of Intrinsically Disordered C/EBPβ. iScience 2019; 13:351-370. [PMID: 30884312 PMCID: PMC6424098 DOI: 10.1016/j.isci.2019.02.026] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/20/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022] Open
Abstract
CCAAT enhancer-binding protein beta (C/EBPβ) is a pioneer transcription factor that specifies cell differentiation. C/EBPβ is intrinsically unstructured, a molecular feature common to many proteins involved in signal processing and epigenetics. The structure of C/EBPβ differs depending on alternative translation initiation and multiple post-translational modifications (PTM). Mutation of distinct PTM sites in C/EBPβ alters protein interactions and cell differentiation, suggesting that a C/EBPβ PTM indexing code determines epigenetic outcomes. Herein, we systematically explored the interactome of C/EBPβ using an array technique based on spot-synthesized C/EBPβ-derived linear tiling peptides with and without PTM, combined with mass spectrometric proteomic analysis of protein interactions. We identified interaction footprints of ∼1,300 proteins in nuclear extracts, many with chromatin modifying, chromatin remodeling, and RNA processing functions. The results suggest that C/EBPβ acts as a multi-tasking molecular switchboard, integrating signal-dependent modifications and structural plasticity to orchestrate interactions with numerous protein complexes directing cell fate and function.
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Affiliation(s)
- Gunnar Dittmar
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; BIH Core Facility Proteomics, Robert-Roessle Strasse 10, 10125 Berlin, Germany.
| | - Daniel Perez Hernandez
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; BIH Core Facility Proteomics, Robert-Roessle Strasse 10, 10125 Berlin, Germany
| | - Elisabeth Kowenz-Leutz
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Marieluise Kirchner
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; BIH Core Facility Proteomics, Robert-Roessle Strasse 10, 10125 Berlin, Germany
| | - Günther Kahlert
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Radoslaw Wesolowski
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Katharina Baum
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Maria Knoblich
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Maria Hofstätter
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Arnaud Muller
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Jana Wolf
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; Humboldt-University of Berlin, Institute of Biology, 10115 Berlin, Germany.
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83
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Andrews D, Oliviero G, De Chiara L, Watson A, Rochford E, Wynne K, Kennedy C, Clerkin S, Doyle B, Godson C, Connell P, O'Brien C, Cagney G, Crean J. Unravelling the transcriptional responses of TGF‐β: Smad3 and EZH2 constitute a regulatory switch that controls neuroretinal epithelial cell fate specification. FASEB J 2019; 33:6667-6681. [DOI: 10.1096/fj.201800566rr] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Darrell Andrews
- Diabetes Complications Research CentreUniversity College Dublin Dublin Ireland
- UCD School of Medicine and Medical ScienceUniversity College Dublin Dublin Ireland
| | - Giorgio Oliviero
- National Institute for Bioprocessing Research and TrainingUniversity College Dublin Dublin Ireland
| | - Letizia De Chiara
- Department of Biomedical, Experimental, and Clinical SciencesCentro di Eccellenza DeNotheUniversity of Florence Florence Italy
| | - Ariane Watson
- Systems Biology IrelandUniversity College Dublin Dublin Ireland
| | - Emily Rochford
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - Kieran Wynne
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - Ciaran Kennedy
- Diabetes Complications Research CentreUniversity College Dublin Dublin Ireland
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - Shane Clerkin
- Diabetes Complications Research CentreUniversity College Dublin Dublin Ireland
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - Benjamin Doyle
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - Catherine Godson
- Diabetes Complications Research CentreUniversity College Dublin Dublin Ireland
- UCD School of Medicine and Medical ScienceUniversity College Dublin Dublin Ireland
| | - Paul Connell
- UCD School of Medicine and Medical ScienceUniversity College Dublin Dublin Ireland
- Department of OphthalmologyMater Misericordiae University Hospital Dublin Ireland
| | - Colm O'Brien
- UCD School of Medicine and Medical ScienceUniversity College Dublin Dublin Ireland
- Department of OphthalmologyMater Misericordiae University Hospital Dublin Ireland
| | - Gerard Cagney
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
| | - John Crean
- Diabetes Complications Research CentreUniversity College Dublin Dublin Ireland
- University College Dublin (UCD) School of Biomolecular and Biomedical ScienceConway Institute of Biomolecular and Biomedical ScienceUniversity College Dublin Dublin Ireland
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84
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van Oorschot R, Hansen M, Koornneef JM, Marneth AE, Bergevoet SM, van Bergen MGJM, van Alphen FPJ, van der Zwaan C, Martens JHA, Vermeulen M, Jansen PWTC, Baltissen MPA, Gorkom BAPLV, Janssen H, Jansen JH, von Lindern M, Meijer AB, van den Akker E, van der Reijden BA. Molecular mechanisms of bleeding disorderassociated GFI1B Q287* mutation and its affected pathways in megakaryocytes and platelets. Haematologica 2019; 104:1460-1472. [PMID: 30655368 PMCID: PMC6601108 DOI: 10.3324/haematol.2018.194555] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 01/09/2019] [Indexed: 12/13/2022] Open
Abstract
Dominant-negative mutations in the transcription factor Growth Factor Independence-1B (GFI1B), such as GFI1BQ287*, cause a bleeding disorder characterized by a plethora of megakaryocyte and platelet abnormalities. The deregulated molecular mechanisms and pathways are unknown. Here we show that both normal and Q287* mutant GFI1B interacted most strongly with the lysine specific demethylase-1 – REST corepressor - histone deacetylase (LSD1-RCOR-HDAC) complex in megakaryoblasts. Sequestration of this complex by GFI1BQ287* and chemical separation of GFI1B from LSD1 induced abnormalities in normal megakaryocytes comparable to those seen in patients. Megakaryocytes derived from GFI1BQ287*-induced pluripotent stem cells also phenocopied abnormalities seen in patients. Proteome studies on normal and mutant-induced pluripotent stem cell-derived megakaryocytes identified a multitude of deregulated pathways downstream of GFI1BQ287* including cell division and interferon signaling. Proteome studies on platelets from GFI1BQ287* patients showed reduced expression of proteins implicated in platelet function, and elevated expression of proteins normally downregulated during megakaryocyte differentiation. Thus, GFI1B and LSD1 regulate a broad developmental program during megakaryopoiesis, and GFI1BQ287* deregulates this program through LSD1-RCOR-HDAC sequestering.
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Affiliation(s)
- Rinske van Oorschot
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen
| | - Marten Hansen
- Department of Hematopoiesis, Sanquin Research-Academic Medical Center Landsteiner Laboratory, Amsterdam
| | | | - Anna E Marneth
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen
| | - Saskia M Bergevoet
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen
| | - Maaike G J M van Bergen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen
| | | | | | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen
| | - Marijke P A Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud University Nijmegen, Radboud Institute for Molecular Life Sciences, Nijmegen
| | | | - Hans Janssen
- Department of Biochemistry, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research-Academic Medical Center Landsteiner Laboratory, Amsterdam
| | | | - Emile van den Akker
- Department of Hematopoiesis, Sanquin Research-Academic Medical Center Landsteiner Laboratory, Amsterdam
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen
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85
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Induction and Suppression of NF-κB Signalling by a DNA Virus of Drosophila. J Virol 2019; 93:JVI.01443-18. [PMID: 30404807 DOI: 10.1128/jvi.01443-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/29/2018] [Indexed: 12/12/2022] Open
Abstract
Interactions between the insect immune system and RNA viruses have been extensively studied in Drosophila, in which RNA interference, NF-κB, and JAK-STAT pathways underlie antiviral immunity. In response to RNA interference, insect viruses have convergently evolved suppressors of this pathway that act by diverse mechanisms to permit viral replication. However, interactions between the insect immune system and DNA viruses have received less attention, primarily because few Drosophila-infecting DNA virus isolates are available. In this study, we used a recently isolated DNA virus of Drosophila melanogaster, Kallithea virus (KV; family Nudiviridae), to probe known antiviral immune responses and virus evasion tactics in the context of DNA virus infection. We found that fly mutants for RNA interference and immune deficiency (Imd), but not Toll, pathways are more susceptible to Kallithea virus infection. We identified the Kallithea virus-encoded protein gp83 as a potent inhibitor of Toll signalling, suggesting that Toll mediates antiviral defense against Kallithea virus infection but that it is suppressed by the virus. We found that Kallithea virus gp83 inhibits Toll signalling through the regulation of NF-κB transcription factors. Furthermore, we found that gp83 of the closely related Drosophila innubila nudivirus (DiNV) suppresses D. melanogaster Toll signalling, suggesting an evolutionarily conserved function of Toll in defense against DNA viruses. Together, these results provide a broad description of known antiviral pathways in the context of DNA virus infection and identify the first Toll pathway inhibitor in a Drosophila virus, extending the known diversity of insect virus-encoded immune inhibitors.IMPORTANCE Coevolution of multicellular organisms and their natural viruses may lead to an intricate relationship in which host survival requires effective immunity and virus survival depends on evasion of such responses. Insect antiviral immunity and reciprocal virus immunosuppression tactics have been well studied in Drosophila melanogaster, primarily during RNA, but not DNA, virus infection. Therefore, we describe interactions between a recently isolated Drosophila DNA virus (Kallithea virus [KV]) and immune processes known to control RNA viruses, such as RNA interference (RNAi) and Imd pathways. We found that KV suppresses the Toll pathway and identified gp83 as a KV-encoded protein that underlies this suppression. This immunosuppressive ability is conserved in another nudivirus, suggesting that the Toll pathway has conserved antiviral activity against DNA nudiviruses, which have evolved suppressors in response. Together, these results indicate that DNA viruses induce and suppress NF-κB responses, and they advance the application of KV as a model to study insect immunity.
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86
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Brien GL, Remillard D, Shi J, Hemming ML, Chabon J, Wynne K, Dillon ET, Cagney G, Van Mierlo G, Baltissen MP, Vermeulen M, Qi J, Fröhling S, Gray NS, Bradner JE, Vakoc CR, Armstrong SA. Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma. eLife 2018; 7:41305. [PMID: 30431433 PMCID: PMC6277197 DOI: 10.7554/elife.41305] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/11/2018] [Indexed: 12/14/2022] Open
Abstract
Synovial sarcoma tumours contain a characteristic fusion protein, SS18-SSX, which drives disease development. Targeting oncogenic fusion proteins presents an attractive therapeutic opportunity. However, SS18-SSX has proven intractable for therapeutic intervention. Using a domain-focused CRISPR screen we identified the bromodomain of BRD9 as a critical functional dependency in synovial sarcoma. BRD9 is a component of SS18-SSX containing BAF complexes in synovial sarcoma cells; and integration of BRD9 into these complexes is critical for cell growth. Moreover BRD9 and SS18-SSX co-localize extensively on the synovial sarcoma genome. Remarkably, synovial sarcoma cells are highly sensitive to a novel small molecule degrader of BRD9, while other sarcoma subtypes are unaffected. Degradation of BRD9 induces downregulation of oncogenic transcriptional programs and inhibits tumour progression in vivo. We demonstrate that BRD9 supports oncogenic mechanisms underlying the SS18-SSX fusion in synovial sarcoma and highlight targeted degradation of BRD9 as a potential therapeutic opportunity in this disease.
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Affiliation(s)
- Gerard L Brien
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - David Remillard
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Junwei Shi
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Matthew L Hemming
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Jonathon Chabon
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Eugène T Dillon
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Guido Van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jun Qi
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Stefan Fröhling
- German Cancer Consortium, Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Translational Oncology, National Center for Tumor Diseases Heidelberg and German Cancer Research Center, Heidelberg, Germany
| | - Nathanael S Gray
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - James E Bradner
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | | | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
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87
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NuRD-interacting protein ZFP296 regulates genome-wide NuRD localization and differentiation of mouse embryonic stem cells. Nat Commun 2018; 9:4588. [PMID: 30389936 PMCID: PMC6214896 DOI: 10.1038/s41467-018-07063-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 10/10/2018] [Indexed: 12/02/2022] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex plays an important role in gene expression regulation, stem cell self-renewal, and lineage commitment. However, little is known about the dynamics of NuRD during cellular differentiation. Here, we study these dynamics using genome-wide profiling and quantitative interaction proteomics in mouse embryonic stem cells (ESCs) and neural progenitor cells (NPCs). We find that the genomic targets of NuRD are highly dynamic during differentiation, with most binding occurring at cell-type specific promoters and enhancers. We identify ZFP296 as an ESC-specific NuRD interactor that also interacts with the SIN3A complex. ChIP-sequencing in Zfp296 knockout (KO) ESCs reveals decreased NuRD binding both genome-wide and at ZFP296 binding sites, although this has little effect on the transcriptome. Nevertheless, Zfp296 KO ESCs exhibit delayed induction of lineage-specific markers upon differentiation to embryoid bodies. In summary, we identify an ESC-specific NuRD-interacting protein which regulates genome-wide NuRD binding and cellular differentiation. The NuRD complex plays an important role in regulating lineage commitment and cell fate during early embryonic development. Here the authors present an integrative analysis of MBD3/NuRD composition and binding in mouse embryonic stem cells and neural progenitor cells, providing a molecular basis for genome-wide NuRD localization
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88
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Mor N, Rais Y, Sheban D, Peles S, Aguilera-Castrejon A, Zviran A, Elinger D, Viukov S, Geula S, Krupalnik V, Zerbib M, Chomsky E, Lasman L, Shani T, Bayerl J, Gafni O, Hanna S, Buenrostro JD, Hagai T, Masika H, Vainorius G, Bergman Y, Greenleaf WJ, Esteban MA, Elling U, Levin Y, Massarwa R, Merbl Y, Novershtern N, Hanna JH. Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency. Cell Stem Cell 2018; 23:412-425.e10. [PMID: 30122475 DOI: 10.1016/j.stem.2018.07.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/19/2018] [Accepted: 07/10/2018] [Indexed: 01/08/2023]
Abstract
Mbd3, a member of nucleosome remodeling and deacetylase (NuRD) co-repressor complex, was previously identified as an inhibitor for deterministic induced pluripotent stem cell (iPSC) reprogramming, where up to 100% of donor cells successfully complete the process. NuRD can assume multiple mutually exclusive conformations, and it remains unclear whether this deterministic phenotype can be attributed to a specific Mbd3/NuRD subcomplex. Moreover, since complete ablation of Mbd3 blocks somatic cell proliferation, we aimed to explore functionally relevant alternative ways to neutralize Mbd3-dependent NuRD activity. We identify Gatad2a, a NuRD-specific subunit, whose complete deletion specifically disrupts Mbd3/NuRD repressive activity on the pluripotency circuitry during iPSC differentiation and reprogramming without ablating somatic cell proliferation. Inhibition of Gatad2a facilitates deterministic murine iPSC reprogramming within 8 days. We validate a distinct molecular axis, Gatad2a-Chd4-Mbd3, within Mbd3/NuRD as being critical for blocking reestablishment of naive pluripotency and further highlight signaling-dependent and post-translational modifications of Mbd3/NuRD that influence its interactions and assembly.
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Affiliation(s)
- Nofar Mor
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Yoach Rais
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel.
| | - Daoud Sheban
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel; Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Shani Peles
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | | | - Asaf Zviran
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel; New York Genome Center, New York, NY, USA
| | - Dalia Elinger
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Viukov
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Shay Geula
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Vladislav Krupalnik
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Mirie Zerbib
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Elad Chomsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Lior Lasman
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Tom Shani
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Jonathan Bayerl
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Ohad Gafni
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Suhair Hanna
- Department of Pediatrics, Rambam Health Care Campus, Haifa, Israel
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Tzachi Hagai
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Hagit Masika
- Department of Developmental Biology and Cancer Research, Hebrew University, Jerusalem, Israel
| | | | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Hebrew University, Jerusalem, Israel
| | - William J Greenleaf
- Department of Genetics, Stanford University, Palo Alto, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Miguel A Esteban
- Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ulrich Elling
- Institute of Molecular Biotechnology (IMBA), Vienna, Austria
| | - Yishai Levin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Rada Massarwa
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Novershtern
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel.
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel.
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89
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Su Q, Hu F, Ge X, Lei J, Yu S, Wang T, Zhou Q, Mei C, Shi Y. Structure of the human PKD1-PKD2 complex. Science 2018; 361:science.aat9819. [DOI: 10.1126/science.aat9819] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022]
Abstract
Mutations in two genes, PKD1 and PKD2, account for most cases of autosomal dominant polycystic kidney disease, one of the most common monogenetic disorders. Here we report the 3.6-angstrom cryo–electron microscopy structure of truncated human PKD1-PKD2 complex assembled in a 1:3 ratio. PKD1 contains a voltage-gated ion channel (VGIC) fold that interacts with PKD2 to form the domain-swapped, yet noncanonical, transient receptor potential (TRP) channel architecture. The S6 helix in PKD1 is broken in the middle, with the extracellular half, S6a, resembling pore helix 1 in a typical TRP channel. Three positively charged, cavity-facing residues on S6b may block cation permeation. In addition to the VGIC, a five–transmembrane helix domain and a cytosolic PLAT domain were resolved in PKD1. The PKD1-PKD2 complex structure establishes a framework for dissecting the function and disease mechanisms of the PKD proteins.
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90
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Draycheva A, Lee S, Wintermeyer W. Cotranslational protein targeting to the membrane: Nascent-chain transfer in a quaternary complex formed at the translocon. Sci Rep 2018; 8:9922. [PMID: 29967439 PMCID: PMC6028451 DOI: 10.1038/s41598-018-28262-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/20/2018] [Indexed: 11/29/2022] Open
Abstract
Membrane proteins in bacteria are cotranslationally inserted into the plasma membrane through the SecYEG translocon. Ribosomes exposing the signal-anchor sequence (SAS) of a membrane protein are targeted to the translocon by the signal recognition particle (SRP) pathway. SRP scans translating ribosomes and forms high-affinity targeting complexes with those exposing a SAS. Recognition of the SAS activates SRP for binding to its receptor, FtsY, which, in turn, is primed for SRP binding by complex formation with SecYEG, resulting in a quaternary targeting complex. Here we examine the effect of SecYEG docking to ribosome-nascent-chain complexes (RNCs) on SRP binding and SAS transfer, using SecYEG embedded in phospholipid-containing nanodiscs and monitoring FRET between fluorescence-labeled constituents of the targeting complex. SecYEG–FtsY binding to RNC–SRP complexes lowers the affinity of SRP to both ribosome and FtsY, indicating a general weakening of the complex due to partial binding competition near the ribosomal peptide exit. The rearrangement of the quaternary targeting complex to the pre-transfer complex requires an at least partially exposed SAS. The presence of SecYEG-bound FtsY and the length of the nascent chain strongly influence nascent-chain transfer from SRP to the translocon and repositioning of SRP in the post-transfer complex.
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Affiliation(s)
- Albena Draycheva
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Sejeong Lee
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,Chemistry Research Laboratory, University of Oxford, OX1 3TA, Oxford, UK
| | - Wolfgang Wintermeyer
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
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91
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Targeted deletion of the AAA-ATPase Ruvbl1 in mice disrupts ciliary integrity and causes renal disease and hydrocephalus. Exp Mol Med 2018; 50:1-17. [PMID: 29959317 PMCID: PMC6026120 DOI: 10.1038/s12276-018-0108-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 03/12/2018] [Accepted: 03/16/2018] [Indexed: 02/06/2023] Open
Abstract
Ciliopathies comprise a large number of hereditary human diseases and syndromes caused by mutations resulting in dysfunction of either primary or motile cilia. Both types of cilia share a similar architecture. While primary cilia are present on most cell types, expression of motile cilia is limited to specialized tissues utilizing ciliary motility. We characterized protein complexes of ciliopathy proteins and identified the conserved AAA-ATPase Ruvbl1 as a common novel component. Here, we demonstrate that Ruvbl1 is crucial for the development and maintenance of renal tubular epithelium in mice: both constitutive and inducible deletion in tubular epithelial cells result in renal failure with tubular dilatations and fewer ciliated cells. Moreover, inducible deletion of Ruvbl1 in cells carrying motile cilia results in hydrocephalus, suggesting functional relevance in both primary and motile cilia. Cilia of Ruvbl1-negative cells lack crucial proteins, consistent with the concept of Ruvbl1-dependent cytoplasmic pre-assembly of ciliary protein complexes. A protein involved in building and maintaining thin protrusions from cell surfaces called cilia is implicated in “ciliopathies”, diseases in which ciliary function is disrupted. These include polycystic kidney disease and disorders collectively known as ciliary dyskinesias. “Primary cilia” perform sensory functions, detecting external chemical and physical signals and initiating responses within cells. In addition, “motile cilia” beat rhythmically to move fluids surrounding cells. Researchers in Germany and the Netherlands, led by Bernhard Schermer and Max C. Liebau at the University of Cologne, studied a protein called Ruvbl1, known to interact with DNA and other proteins. The researchers found it is crucial for the functioning of both types of cilia. Deleting the gene for Ruvbl1 in mice caused kidney failure and a build-up of fluid in the brain known as hydrocephalus. The research could help understand and ultimately treat ciliopathies.
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92
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Di Silvestre D, Bergamaschi A, Bellini E, Mauri P. Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World. Proteomes 2018; 6:proteomes6020027. [PMID: 29865292 PMCID: PMC6027444 DOI: 10.3390/proteomes6020027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/26/2022] Open
Abstract
The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.
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Affiliation(s)
- Dario Di Silvestre
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Andrea Bergamaschi
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - Edoardo Bellini
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
| | - PierLuigi Mauri
- Institute for Biomedical Technologies-National Research Council; F.lli Cervi 93, 20090 Segrate, Milan, Italy.
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93
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Perino M, van Mierlo G, Karemaker ID, van Genesen S, Vermeulen M, Marks H, van Heeringen SJ, Veenstra GJC. MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding. Nat Genet 2018; 50:1002-1010. [DOI: 10.1038/s41588-018-0134-8] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 04/06/2018] [Indexed: 01/09/2023]
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94
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Hicks JA, Li L, Matsui M, Chu Y, Volkov O, Johnson KC, Corey DR. Human GW182 Paralogs Are the Central Organizers for RNA-Mediated Control of Transcription. Cell Rep 2018; 20:1543-1552. [PMID: 28813667 DOI: 10.1016/j.celrep.2017.07.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/10/2017] [Accepted: 07/20/2017] [Indexed: 01/21/2023] Open
Abstract
In the cytoplasm, small RNAs can control mammalian translation by regulating the stability of mRNA. In the nucleus, small RNAs can also control transcription and splicing. The mechanisms for RNA-mediated nuclear regulation are not understood and remain controversial, hindering the effective application of nuclear RNAi and investigation of its natural regulatory roles. Here, we reveal that the human GW182 paralogs TNRC6A/B/C are central organizing factors critical to RNA-mediated transcriptional activation. Mass spectrometry of purified nuclear lysates followed by experimental validation demonstrates that TNRC6A interacts with proteins involved in protein degradation, RNAi, the CCR4-NOT complex, the mediator complex, and histone-modifying complexes. Functional analysis implicates TNRC6A, NAT10, MED14, and WDR5 in RNA-mediated transcriptional activation. These findings describe protein complexes capable of bridging RNA-mediated sequence-specific recognition of noncoding RNA transcripts with the regulation of gene transcription.
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Affiliation(s)
- Jessica A Hicks
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Liande Li
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Masayuki Matsui
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Yongjun Chu
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Oleg Volkov
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - Krystal C Johnson
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA
| | - David R Corey
- Departments of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390-9041, USA.
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95
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Conway E, Jerman E, Healy E, Ito S, Holoch D, Oliviero G, Deevy O, Glancy E, Fitzpatrick DJ, Mucha M, Watson A, Rice AM, Chammas P, Huang C, Pratt-Kelly I, Koseki Y, Nakayama M, Ishikura T, Streubel G, Wynne K, Hokamp K, McLysaght A, Ciferri C, Di Croce L, Cagney G, Margueron R, Koseki H, Bracken AP. A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities. Mol Cell 2018; 70:408-421.e8. [PMID: 29628311 DOI: 10.1016/j.molcel.2018.03.005] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 01/11/2018] [Accepted: 03/02/2018] [Indexed: 12/18/2022]
Abstract
The polycomb repressive complex 2 (PRC2) consists of core subunits SUZ12, EED, RBBP4/7, and EZH1/2 and is responsible for mono-, di-, and tri-methylation of lysine 27 on histone H3. Whereas two distinct forms exist, PRC2.1 (containing one polycomb-like protein) and PRC2.2 (containing AEBP2 and JARID2), little is known about their differential functions. Here, we report the discovery of a family of vertebrate-specific PRC2.1 proteins, "PRC2 associated LCOR isoform 1" (PALI1) and PALI2, encoded by the LCOR and LCORL gene loci, respectively. PALI1 promotes PRC2 methyltransferase activity in vitro and in vivo and is essential for mouse development. Pali1 and Aebp2 define mutually exclusive, antagonistic PRC2 subtypes that exhibit divergent H3K27-tri-methylation activities. The balance of these PRC2.1/PRC2.2 activities is required for the appropriate regulation of polycomb target genes during differentiation. PALI1/2 potentially link polycombs with transcriptional co-repressors in the regulation of cellular identity during development and in cancer.
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Affiliation(s)
- Eric Conway
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Emilia Jerman
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evan Healy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Daniel Holoch
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS UMR 3215, INSERM U934, 75248 Paris Cedex 05, France
| | - Giorgio Oliviero
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Orla Deevy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eleanor Glancy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Marlena Mucha
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Ariane Watson
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Alan M Rice
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Paul Chammas
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Christine Huang
- Department of Structural Biology, Genentech, San Francisco, CA 94080, USA
| | - Indigo Pratt-Kelly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Yoko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Manabu Nakayama
- Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan
| | - Tomoyuki Ishikura
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Gundula Streubel
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Kieran Wynne
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Karsten Hokamp
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Aoife McLysaght
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Claudio Ciferri
- Chromosome Engineering Team, Department of Technology Development, Kazusa DNA Research Institute, Kisarazu 292-0818, Japan
| | - Luciano Di Croce
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003 Barcelona, Spain; ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin 4, Ireland
| | - Raphaël Margueron
- Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS UMR 3215, INSERM U934, 75248 Paris Cedex 05, France
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Adrian P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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96
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Pines A, Dijk M, Makowski M, Meulenbroek EM, Vrouwe MG, van der Weegen Y, Baltissen M, French PJ, van Royen ME, Luijsterburg MS, Mullenders LH, Vermeulen M, Vermeulen W, Pannu NS, van Attikum H. TRiC controls transcription resumption after UV damage by regulating Cockayne syndrome protein A. Nat Commun 2018. [PMID: 29531219 PMCID: PMC5847541 DOI: 10.1038/s41467-018-03484-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Transcription-blocking DNA lesions are removed by transcription-coupled nucleotide excision repair (TC-NER) to preserve cell viability. TC-NER is triggered by the stalling of RNA polymerase II at DNA lesions, leading to the recruitment of TC-NER-specific factors such as the CSA–DDB1–CUL4A–RBX1 cullin–RING ubiquitin ligase complex (CRLCSA). Despite its vital role in TC-NER, little is known about the regulation of the CRLCSA complex during TC-NER. Using conventional and cross-linking immunoprecipitations coupled to mass spectrometry, we uncover a stable interaction between CSA and the TRiC chaperonin. TRiC’s binding to CSA ensures its stability and DDB1-dependent assembly into the CRLCSA complex. Consequently, loss of TRiC leads to mislocalization and depletion of CSA, as well as impaired transcription recovery following UV damage, suggesting defects in TC-NER. Furthermore, Cockayne syndrome (CS)-causing mutations in CSA lead to increased TRiC binding and a failure to compose the CRLCSA complex. Thus, we uncover CSA as a TRiC substrate and reveal that TRiC regulates CSA-dependent TC-NER and the development of CS. An integrated network of chaperones and protein degradation machineries called the proteostasis network (PN) is required to maintain protein homeostasis. Here the authors show that one of the components of the PN, the chaperonin TRiC, interacts with the core transcription-coupled nucleotide excision repair protein CSA to ensure its assembly into the CRLCSA complex.
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Affiliation(s)
- Alex Pines
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands.,Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Madelon Dijk
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands
| | - Matthew Makowski
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Elisabeth M Meulenbroek
- Department of Biophysical Structural Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Mischa G Vrouwe
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands
| | - Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands
| | - Marijke Baltissen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Pim J French
- Department of Neurology, Cancer Treatment Screening Facility (CTSF), Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Cancer Treatment Screening Facility (CTSF), Erasmus Optical Imaging Centre (OIC), Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands
| | - Leon H Mullenders
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Cancer Genomics Netherlands, Erasmus University Medical Center, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Navraj S Pannu
- Department of Biophysical Structural Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, Leiden, 2333 ZC, The Netherlands.
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97
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Højfeldt JW, Laugesen A, Willumsen BM, Damhofer H, Hedehus L, Tvardovskiy A, Mohammad F, Jensen ON, Helin K. Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2. Nat Struct Mol Biol 2018; 25:225-232. [PMID: 29483650 PMCID: PMC5842896 DOI: 10.1038/s41594-018-0036-6] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/18/2018] [Indexed: 01/07/2023]
Abstract
Polycomb repressive complex 2 (PRC2) catalyzes methylation on lysine 27 of histone H3 (H3K27) and is required for maintaining transcriptional patterns and cellular identity, but the specification and maintenance of genomic PRC2 binding and H3K27 methylation patterns remain incompletely understood. Epigenetic mechanisms have been proposed, wherein pre-existing H3K27 methylation directs recruitment and regulates the catalytic activity of PRC2 to support its own maintenance. Here we investigate whether such mechanisms are required for specifying H3K27 methylation patterns in mouse embryonic stem cells (mESCs). Through re-expression of PRC2 subunits in PRC2-knockout cells that have lost all H3K27 methylation, we demonstrate that methylation patterns can be accurately established de novo. We find that regional methylation kinetics correlate with original methylation patterns even in their absence, and specification of the genomic PRC2 binding pattern is retained and specifically dependent on the PRC2 core subunit SUZ12. Thus, the H3K27 methylation patterns in mESCs are not dependent on self-autonomous epigenetic inheritance.
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Affiliation(s)
- Jonas W Højfeldt
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Laugesen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Berthe M Willumsen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Helene Damhofer
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lin Hedehus
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrey Tvardovskiy
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Faizaan Mohammad
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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98
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Di Costanzo A, Del Gaudio N, Conte L, Dell'Aversana C, Vermeulen M, de Thé H, Migliaccio A, Nebbioso A, Altucci L. The HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia. Oncogene 2018; 37:2559-2572. [PMID: 29467492 PMCID: PMC5945585 DOI: 10.1038/s41388-018-0143-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/15/2017] [Accepted: 12/24/2017] [Indexed: 12/31/2022]
Abstract
Polycomb group (PcG) proteins regulate transcription, playing a key role in stemness and differentiation. Deregulation of PcG members is known to be involved in cancer pathogenesis. Emerging evidence suggests that CBX2, a member of the PcG protein family, is overexpressed in several human tumors, correlating with lower overall survival. Unraveling the mechanisms regulating CBX2 expression may thus provide a promising new target for anticancer strategies. Here we show that the HDAC inhibitor SAHA regulates CBX2 stability via a SUMO-triggered ubiquitin-mediated pathway in leukemia. We identify CBX4 and RNF4 as the E3 SUMO and E3 ubiquitin ligase, respectively, and describe the specific molecular mechanism regulating CBX2 protein stability. Finally, we show that CBX2-depleted leukemic cells display impaired proliferation, underscoring its critical role in regulating leukemia cell tumorogenicity. Our results show that SAHA affects CBX2 stability, revealing a potential SAHA-mediated anti-leukemic activity though SUMO2/3 pathway.
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Affiliation(s)
- Antonella Di Costanzo
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy.
| | - Nunzio Del Gaudio
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Lidio Conte
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Carmela Dell'Aversana
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6500 HB, Nijmegen, The Netherlands
| | - Hugues de Thé
- INSERM Unite ́ Mixte de Recherche 944, Equipe labellisée par la Ligue Nationale contre le Cancer, Institut Universitaire d'Hématologie, Hôpital St. Louis, Paris Cedex 10, France
| | - Antimo Migliaccio
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Angela Nebbioso
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy
| | - Lucia Altucci
- Department of Biochemistry, Biophysics and General Pathology, University of Campania "Luigi Vanvitelli", Vico L. De Crecchio 7, 80138, Napoli, Italy.
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99
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The JAZF1-SUZ12 fusion protein disrupts PRC2 complexes and impairs chromatin repression during human endometrial stromal tumorogenesis. Oncotarget 2018; 8:4062-4078. [PMID: 27845897 PMCID: PMC5354813 DOI: 10.18632/oncotarget.13270] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/29/2016] [Indexed: 11/27/2022] Open
Abstract
The Polycomb repressive complex 2 (PRC2), which contains three core proteins EZH2, EED and SUZ12, controls chromatin compaction and transcription repression through trimethylation of lysine 27 on histone 3. The (7;17)(p15;q21) chromosomal translocation present in most cases of endometrial stromal sarcomas (ESSs) results in the in-frame fusion of the JAZF1 and SUZ12 genes. We have investigated whether and how the fusion protein JAZF1-SUZ12 functionally alters PRC2. We found that the fusion protein exists at high levels in ESS containing the t(7;17). Co-transient transfection assay indicated JAZF1-SUZ12 destabilized PRC2 components EZH2 and EED, resulting in decreased histone methyl transferase (HMT) activity, which was confirmed by in vitro studies using reconstituted PRC2 and nucleosome array substrates. We also demonstrated the PRC2 containing the fusion protein decreased the binding affinity to target chromatin loci. In addition, we found that trimethylation of H3K27 was decreased in ESS samples with the t(7;17), but there was no detectable change in H3K9 in these tissues. Moreover, re-expression of SUZ12 in Suz12 (−/−) ES cells rescued the neuronal differentiation while the fusion protein failed to restore this function and enhanced cell proliferation. In summary, our studies reveal that JAZF1-SUZ12 fusion protein disrupts the PRC2 complex, abolishes HMT activity and subsequently activates chromatin/genes normally repressed by PRC2. Such dyesfunction of PRC2 inhibits normal neural differentiation of ES cell and increases cell proliferation. Related changes induced by the JAZF-SUZ12 protein in endometrial stromal cells may explain the oncogenic effect of the t(7;17) in ESS.
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100
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Kuhlmann L, Cummins E, Samudio I, Kislinger T. Cell-surface proteomics for the identification of novel therapeutic targets in cancer. Expert Rev Proteomics 2018; 15:259-275. [DOI: 10.1080/14789450.2018.1429924] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Laura Kuhlmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Emma Cummins
- The Centre for Drug Research and Development, Division of Biologics, Vancouver, Canada
| | - Ismael Samudio
- The Centre for Drug Research and Development, Division of Biologics, Vancouver, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
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