101
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Draime A, Bridoux L, Belpaire M, Pringels T, Tys J, Rezsohazy R. PRDM14, a putative histone methyl-transferase, interacts with and decreases the stability and activity of the HOXA1 transcription factor. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:534-542. [PMID: 29471045 DOI: 10.1016/j.bbagrm.2018.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 11/18/2022]
Abstract
Understanding how the activity of transcription factors like HOX proteins is regulated remains a widely open question. In a recent screen for proteins interacting with HOXA1, we identified a PRDM protein family member, PRDM14, which is known to be transiently co-expressed with HOXA1 in epiblast cells before their specification towards somatic versus germ cell fate. Here, we confirm PRDM14 is an interactor of HOXA1 and we identify the homeodomain of HOXA1 as well as the PR domain and Zinc fingers of PRDM14 to be required for the interaction. An 11-His repeat of HOXA1 previously highlighted to contribute to HOXA1-mediated protein-protein interactions is also involved. At a functional level, we provide evidence that HOXA1 displays an unexpectedly long half-life and demonstrate that PRDM14 can reduce the stability and affect the transcriptional activity of HOXA1.
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Affiliation(s)
- Amandine Draime
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Laure Bridoux
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Magali Belpaire
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Tamara Pringels
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - Janne Tys
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium
| | - René Rezsohazy
- Animal Molecular and Cellular Biology Group, Institut des Sciences de la Vie (ISV), Université catholique de Louvain, place Croix du Sud 5, 1348 Louvain-la-Neuve, Belgium.
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102
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Diagouraga B, Clément JAJ, Duret L, Kadlec J, de Massy B, Baudat F. PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites. Mol Cell 2018; 69:853-865.e6. [PMID: 29478809 DOI: 10.1016/j.molcel.2018.01.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/09/2018] [Accepted: 01/24/2018] [Indexed: 01/06/2023]
Abstract
The programmed formation of hundreds of DNA double-strand breaks (DSBs) is essential for proper meiosis and fertility. In mice and humans, the location of these breaks is determined by the meiosis-specific protein PRDM9, through the DNA-binding specificity of its zinc-finger domain. PRDM9 also has methyltransferase activity. Here, we show that this activity is required for H3K4me3 and H3K36me3 deposition and for DSB formation at PRDM9-binding sites. By analyzing mice that express two PRDM9 variants with distinct DNA-binding specificities, we show that each variant generates its own set of H3K4me3 marks independently from the other variant. Altogether, we reveal several basic principles of PRDM9-dependent DSB site determination, in which an excess of sites are designated through PRDM9 binding and subsequent histone methylation, from which a subset is selected for DSB formation.
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Affiliation(s)
| | | | - Laurent Duret
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villeurbanne, France
| | - Jan Kadlec
- Université Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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103
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Pan MR, Hsu MC, Chen LT, Hung WC. Orchestration of H3K27 methylation: mechanisms and therapeutic implication. Cell Mol Life Sci 2018; 75:209-223. [PMID: 28717873 PMCID: PMC5756243 DOI: 10.1007/s00018-017-2596-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/06/2017] [Accepted: 07/13/2017] [Indexed: 01/08/2023]
Abstract
Histone proteins constitute the core component of the nucleosome, the basic unit of chromatin. Chemical modifications of histone proteins affect their interaction with genomic DNA, the accessibility of recognized proteins, and the recruitment of enzymatic complexes to activate or diminish specific transcriptional programs to modulate cellular response to extracellular stimuli or insults. Methylation of histone proteins was demonstrated 50 years ago; however, the biological significance of each methylated residue and the integration between these histone markers are still under intensive investigation. Methylation of histone H3 on lysine 27 (H3K27) is frequently found in the heterochromatin and conceives a repressive marker that is linked with gene silencing. The identification of enzymes that add or erase the methyl group of H3K27 provides novel insights as to how this histone marker is dynamically controlled under different circumstances. Here we summarize the methyltransferases and demethylases involved in the methylation of H3K27 and show the new evidence by which the H3K27 methylation can be established via an alternative mechanism. Finally, the progress of drug development targeting H3K27 methylation-modifying enzymes and their potential application in cancer therapy are discussed.
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Affiliation(s)
- Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Ming-Chuan Hsu
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
| | - Li-Tzong Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan
- Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, 704, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 804, Taiwan
| | - Wen-Chun Hung
- National Institute of Cancer Research, National Health Research Institutes, Tainan, 704, Taiwan.
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 804, Taiwan.
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104
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Moriya C, Taniguchi H, Nagatoishi S, Igarashi H, Tsumoto K, Imai K. PRDM14 directly interacts with heat shock proteins HSP90α and glucose-regulated protein 78. Cancer Sci 2017; 109:373-383. [PMID: 29178343 PMCID: PMC5797828 DOI: 10.1111/cas.13458] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/16/2017] [Accepted: 11/21/2017] [Indexed: 12/22/2022] Open
Abstract
PRDM14 is overexpressed in various cancers and can regulate cancer phenotype under certain conditions. Inhibiting PRDM14 expression in breast and pancreatic cancers has been reported to reduce cancer stem‐like phenotypes, which are associated with aggressive tumor properties. Therefore, PRDM14 is considered a promising target for cancer therapy. To develop a pharmaceutical treatment, the mechanism and interacting partners of PRDM14 need to be clarified. Here, we identified the proteins interacting with PRDM14 in triple‐negative breast cancer (TNBC) cells, which do not express the three most common types of receptor (estrogen receptors, progesterone receptors, and HER2). We obtained 13 candidates that were pulled down with PRDM14 in TNBC HCC1937 cells and identified them by mass spectrometry. Two candidates—glucose‐regulated protein 78 (GRP78) and heat shock protein 90‐α (HSP90α)—were confirmed in immunoprecipitation assay in two TNBC cell lines (HCC1937 and MDA‐MB231). Surface plasmon resonance analysis using GST‐PRDM14 showed that these two proteins directly interacted with PRDM14 and that the interactions required the C‐terminal region of PRDM14, which includes zinc finger motifs. We also confirmed the interactions in living cells by NanoLuc luciferase‐based bioluminescence resonance energy transfer (NanoBRET) assay. Moreover, HSP90 inhibitors (17DMAG and HSP990) significantly decreased breast cancer stem‐like CD24− CD44+ and side population (SP) cells in HCC1937 cells, but not in PRDM14 knockdown HCC1937 cells. The combination of the GRP78 inhibitor HA15 and PRDM14 knockdown significantly decreased cell proliferation and SP cell number in HCC1937 cells. These results suggest that HSP90α and GRP78 interact with PRDM14 and participate in cancer regulation.
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Affiliation(s)
- Chiharu Moriya
- Center for Antibody and Vaccine Therapy, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Taniguchi
- Center for Antibody and Vaccine Therapy, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Project Division of Advanced Biopharmaceutical Science, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hisayoshi Igarashi
- Center for Antibody and Vaccine Therapy, Research Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan.,Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kohzoh Imai
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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105
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Mitani T, Yabuta Y, Ohta H, Nakamura T, Yamashiro C, Yamamoto T, Saitou M, Kurimoto K. Principles for the regulation of multiple developmental pathways by a versatile transcriptional factor, BLIMP1. Nucleic Acids Res 2017; 45:12152-12169. [PMID: 28981894 PMCID: PMC5716175 DOI: 10.1093/nar/gkx798] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/30/2017] [Indexed: 11/14/2022] Open
Abstract
Single transcription factors (TFs) regulate multiple developmental pathways, but the underlying mechanisms remain unclear. Here, we quantitatively characterized the genome-wide occupancy profiles of BLIMP1, a key transcriptional regulator for diverse developmental processes, during the development of three germ-layer derivatives (photoreceptor precursors, embryonic intestinal epithelium and plasmablasts) and the germ cell lineage (primordial germ cells). We identified BLIMP1-binding sites shared among multiple developmental processes, and such sites were highly occupied by BLIMP1 with a stringent recognition motif and were located predominantly in promoter proximities. A subset of bindings common to all the lineages exhibited a new, strong recognition sequence, a GGGAAA repeat. Paradoxically, however, the shared/common bindings had only a slight impact on the associated gene expression. In contrast, BLIMP1 occupied more distal sites in a cell type-specific manner; despite lower occupancy and flexible sequence recognitions, such bindings contributed effectively to the repression of the associated genes. Recognition motifs of other key TFs in BLIMP1-binding sites had little impact on the expression-level changes. These findings suggest that the shared/common sites might serve as potential reservoirs of BLIMP1 that functions at the specific sites, providing the foundation for a unified understanding of the genome regulation by BLIMP1, and, possibly, TFs in general.
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Affiliation(s)
- Tadahiro Mitani
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukihiro Yabuta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroshi Ohta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomonori Nakamura
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Chika Yamashiro
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,AMED-CREST, AMED 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.,Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuki Kurimoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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106
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Boström J, Sramkova Z, Salašová A, Johard H, Mahdessian D, Fedr R, Marks C, Medalová J, Souček K, Lundberg E, Linnarsson S, Bryja V, Sekyrova P, Altun M, Andäng M. Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells. PLoS One 2017; 12:e0188772. [PMID: 29228002 PMCID: PMC5724894 DOI: 10.1371/journal.pone.0188772] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/13/2017] [Indexed: 01/01/2023] Open
Abstract
The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchronized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development. Furthermore, the cell cycle synchronizes with the circadian clock, providing a possible link between developmental transcriptional networks and the cell cycle. In conclusion we find that cell cycle synchronized transcriptional patterns are temporally compartmentalized and more complex than previously anticipated, involving genes, which control cell identity and development.
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Affiliation(s)
- Johan Boström
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Zuzana Sramkova
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Alena Salašová
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Helena Johard
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Diana Mahdessian
- Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, Sweden
| | - Radek Fedr
- Department of Cytokinetics, Institute of Biophysics CAS, v.v.i., Královopolská 135, Brno, Czech Republic
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne’s University Hospital in Brno, Brno, Czech Republic
| | - Carolyn Marks
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jiřina Medalová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Karel Souček
- Department of Cytokinetics, Institute of Biophysics CAS, v.v.i., Královopolská 135, Brno, Czech Republic
- International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne’s University Hospital in Brno, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Emma Lundberg
- Science for Life Laboratory, KTH—Royal Institute of Technology, Stockholm, Sweden
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petra Sekyrova
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- * E-mail: (PS); (MAl); (MAn)
| | - Mikael Altun
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (PS); (MAl); (MAn)
| | - Michael Andäng
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- * E-mail: (PS); (MAl); (MAn)
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107
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Weidner CI, Lin Q, Birkhofer C, Gerstenmaier U, Kaifie A, Kirschner M, Bruns H, Balabanov S, Trummer A, Stockklausner C, Höchsmann B, Schrezenmeier H, Wlodarski M, Panse J, Brümmendorf TH, Beier F, Wagner W. DNA methylation in PRDM8 is indicative for dyskeratosis congenita. Oncotarget 2017; 7:10765-72. [PMID: 26909595 PMCID: PMC4905437 DOI: 10.18632/oncotarget.7458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/09/2016] [Indexed: 02/06/2023] Open
Abstract
Dyskeratosis congenita (DKC) is associated with impaired telomere maintenance and with clinical features of premature aging. In this study, we analysed global DNA methylation (DNAm) profiles of DKC patients. Age-associated DNAm changes were not generally accelerated in DKC, but there were significant differences to DNAm patterns of healthy controls, particularly in CpG sites related to an internal promoter region of PR domain containing 8 (PRDM8). Notably, the same genomic region was also hypermethylated in aplastic anemia (AA) – another bone marrow failure syndrome. Site-specific analysis of DNAm level in PRDM8 with pyrosequencing and MassARRAY validated aberrant hypermethylation in 11 DKC patients and 27 AA patients. Telomere length, measured by flow-FISH, did not directly correlate with DNAm in PRDM8. Therefore the two methods may be complementary to also identify patients with still normal telomere length. In conclusion, blood of DKC patients reveals aberrant DNAm patterns, albeit age-associated DNAm patterns are not generally accelerated. Aberrant hypermethylation is particularly observed in PRDM8 and this may support identification and classification of bone marrow failure syndromes.
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Affiliation(s)
- Carola I Weidner
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Aachen, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Qiong Lin
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Aachen, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | | | | | - Andrea Kaifie
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Heiko Bruns
- Department of Internal Medicine 5-Hematology/Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Stefan Balabanov
- Division of Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Arne Trummer
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Clemens Stockklausner
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Britta Höchsmann
- Institute of Transfusion Medicine, University of Ulm, Ulm, Germany.,Institute of Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen and University Hospital Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute of Transfusion Medicine, University of Ulm, Ulm, Germany.,Institute of Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen and University Hospital Ulm, Ulm, Germany
| | - Marcin Wlodarski
- Department of Pediatrics, Hematology and Oncology, University of Freiburg, Freiburg, Germany
| | - Jens Panse
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Aachen, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
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108
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Groman-Lupa S, Adewumi J, Park KU, Brzezinski JA. The Transcription Factor Prdm16 Marks a Single Retinal Ganglion Cell Subtype in the Mouse Retina. Invest Ophthalmol Vis Sci 2017; 58:5421-5433. [PMID: 29053761 PMCID: PMC5656415 DOI: 10.1167/iovs.17-22442] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/20/2017] [Indexed: 12/04/2022] Open
Abstract
Purpose Retinal ganglion cells (RGC) can be categorized into roughly 30 distinct subtypes. How these subtypes develop is poorly understood, in part because few unique subtype markers have been characterized. We tested whether the Prdm16 transcription factor is expressed by RGCs as a class or within particular ganglion cell subtypes. Methods Embryonic and mature retinal sections and flatmount preparations were examined by immunohistochemistry for Prdm16 and several other cell type-specific markers. To visualize the morphology of Prdm16+ cells, we utilized Thy1-YFP-H transgenic mice, where a small random population of RGCs expresses yellow fluorescent protein (YFP) throughout the cytoplasm. Results Prdm16 was expressed in the retina starting late in embryogenesis. Prdm16+ cells coexpressed the RGC marker Brn3a. These cells were arranged in an evenly spaced pattern and accounted for 2% of all ganglion cells. Prdm16+ cells coexpressed parvalbumin, but not calretinin, melanopsin, Smi32, or CART. This combination of marker expression and morphology data from Thy1-YFP-H mice suggested that the Prdm16+ cells represented a single ganglion cell subtype. Prdm16 also marked vascular endothelial cells and mural cells of retinal arterioles. Conclusions A single subtype of ganglion cell appears to be uniquely marked by Prdm16 expression. While the precise identity of these ganglion cells is unclear, they most resemble the G9 subtype described by Völgyi and colleagues in 2009. Future studies are needed to determine the function of these ganglion cells and whether Prdm16 regulates their development.
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Affiliation(s)
- Sergio Groman-Lupa
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
| | - Joseph Adewumi
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
| | - Joseph A. Brzezinski
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
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109
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Affiliation(s)
- Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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110
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Lai HC, Seal RP, Johnson JE. Making sense out of spinal cord somatosensory development. Development 2017; 143:3434-3448. [PMID: 27702783 DOI: 10.1242/dev.139592] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The spinal cord integrates and relays somatosensory input, leading to complex motor responses. Research over the past couple of decades has identified transcription factor networks that function during development to define and instruct the generation of diverse neuronal populations within the spinal cord. A number of studies have now started to connect these developmentally defined populations with their roles in somatosensory circuits. Here, we review our current understanding of how neuronal diversity in the dorsal spinal cord is generated and we discuss the logic underlying how these neurons form the basis of somatosensory circuits.
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Affiliation(s)
- Helen C Lai
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rebecca P Seal
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Jane E Johnson
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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111
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Bessodes N, Parain K, Bronchain O, Bellefroid EJ, Perron M. Prdm13 forms a feedback loop with Ptf1a and is required for glycinergic amacrine cell genesis in the Xenopus Retina. Neural Dev 2017; 12:16. [PMID: 28863786 PMCID: PMC5580440 DOI: 10.1186/s13064-017-0093-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 08/22/2017] [Indexed: 11/26/2022] Open
Abstract
Background Amacrine interneurons that modulate synaptic plasticity between bipolar and ganglion cells constitute the most diverse cell type in the retina. Most are inhibitory neurons using either GABA or glycine as neurotransmitters. Although several transcription factors involved in amacrine cell fate determination have been identified, mechanisms underlying amacrine cell subtype specification remain to be further understood. The Prdm13 histone methyltransferase encoding gene is a target of the transcription factor Ptf1a, an essential regulator of inhibitory neuron cell fate in the retina. Here, we have deepened our knowledge on its interaction with Ptf1a and investigated its role in amacrine cell subtype determination in the developing Xenopus retina. Methods We performed prdm13 gain and loss of function in Xenopus and assessed the impact on retinal cell fate determination using RT-qPCR, in situ hybridization and immunohistochemistry. Results We found that prdm13 in the amphibian Xenopus is expressed in few retinal progenitors and in about 40% of mature amacrine cells, predominantly in glycinergic ones. Clonal analysis in the retina reveals that prdm13 overexpression favours amacrine cell fate determination, with a bias towards glycinergic cells. Conversely, knockdown of prdm13 specifically inhibits glycinergic amacrine cell genesis. We also showed that, as in the neural tube, prdm13 is subjected to a negative autoregulation in the retina. Our data suggest that this is likely due to its ability to repress the expression of its inducer, ptf1a. Conclusions Our results demonstrate that Prdm13, downstream of Ptf1a, acts as an important regulator of glycinergic amacrine subtype specification in the Xenopus retina. We also reveal that Prdm13 regulates ptf1a expression through a negative feedback loop.
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Affiliation(s)
- Nathalie Bessodes
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), B-6041, Gosselies, Belgium.,Paris-Saclay Institute of Neuroscience, CNRS, Univ Paris Sud, Université Paris-Saclay, UMR 9197- Neuro-PSI, Bat. 445, 91405, ORSAY Cedex, France
| | - Karine Parain
- Paris-Saclay Institute of Neuroscience, CNRS, Univ Paris Sud, Université Paris-Saclay, UMR 9197- Neuro-PSI, Bat. 445, 91405, ORSAY Cedex, France
| | - Odile Bronchain
- Paris-Saclay Institute of Neuroscience, CNRS, Univ Paris Sud, Université Paris-Saclay, UMR 9197- Neuro-PSI, Bat. 445, 91405, ORSAY Cedex, France
| | - Eric J Bellefroid
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), B-6041, Gosselies, Belgium.
| | - Muriel Perron
- Paris-Saclay Institute of Neuroscience, CNRS, Univ Paris Sud, Université Paris-Saclay, UMR 9197- Neuro-PSI, Bat. 445, 91405, ORSAY Cedex, France. .,Centre d'Etude et de Recherche Thérapeutique en Ophtalmologie, Retina France, Orsay, France.
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112
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Mona B, Uruena A, Kollipara RK, Ma Z, Borromeo MD, Chang JC, Johnson JE. Repression by PRDM13 is critical for generating precision in neuronal identity. eLife 2017; 6. [PMID: 28850031 PMCID: PMC5576485 DOI: 10.7554/elife.25787] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/26/2017] [Indexed: 11/13/2022] Open
Abstract
The mechanisms that activate some genes while silencing others are critical to ensure precision in lineage specification as multipotent progenitors become restricted in cell fate. During neurodevelopment, these mechanisms are required to generate the diversity of neuronal subtypes found in the nervous system. Here we report interactions between basic helix-loop-helix (bHLH) transcriptional activators and the transcriptional repressor PRDM13 that are critical for specifying dorsal spinal cord neurons. PRDM13 inhibits gene expression programs for excitatory neuronal lineages in the dorsal neural tube. Strikingly, PRDM13 also ensures a battery of ventral neural tube specification genes such as Olig1, Olig2 and Prdm12 are excluded dorsally. PRDM13 does this via recruitment to chromatin by multiple neural bHLH factors to restrict gene expression in specific neuronal lineages. Together these findings highlight the function of PRDM13 in repressing the activity of bHLH transcriptional activators that together are required to achieve precise neuronal specification during mouse development.
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Affiliation(s)
- Bishakha Mona
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, United States
| | - Ana Uruena
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, United States
| | - Rahul K Kollipara
- McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, United States
| | - Zhenzhong Ma
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, United States
| | - Mark D Borromeo
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, United States
| | - Joshua C Chang
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, United States
| | - Jane E Johnson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, United States.,Department of Pharmacology, UT Southwestern Medical Center, Dallas, United States
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113
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Xue Y, Chen R, Du W, Yang F, Wei X. RIZ1 and histone methylation status in pituitary adenomas. Tumour Biol 2017; 39:1010428317711794. [PMID: 28718376 DOI: 10.1177/1010428317711794] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
RIZ1 displays strong tumor-suppressive activities, which has a potential histone methyltransferase activity. The objective of the study was to evaluate the level and the methylation status of RIZ1 and analyze its association with clinicopathological features and the histone in the pituitary adenomas. We found that RIZ1-positive cases were 11/50 and H-Scores 22.75 ± 11.83 in invasive pituitary adenomas and 26/53 and 66.3 ± 21.7 in non-invasive pituitary adenomas (χ2 = 8.182, p = 0.004). RIZ1 and C-myc showed the opposite trend in these cases. The methylation levels of RIZ1 were more than 50% in 30.4% (7/23) CpG sites through MALDI-TOF Mass array. There was significant difference (p < 0.01) in 4 CpG sites between invasive pituitary adenoma group and non-invasive pituitary adenoma group; furthermore, the relieved methylation levels of H3K4/H3K9 and enhanced methylation levels of H3K27 in the patients' serum were found. Furthermore, there was statistic difference of H3K4 and H3K27 methylation between invasive pituitary adenoma and non-invasive pituitary adenoma group (p < 0.01). The average progression-free survival in high RIZ1 group was 52.63 ± 7.62 months and 26.06 ± 4.23 months in low RIZ1 group (p < 0.05). Promoter region methylation of RIZ1 may play an important role in the epigenetic silencing of RIZ1 expression in pituitary adenomas, which may translate into important diagnostic and therapeutic applications.
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Affiliation(s)
- Yake Xue
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ruokun Chen
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Wei Du
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Fengdong Yang
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xinting Wei
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
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114
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Shimada IS, Acar M, Burgess RJ, Zhao Z, Morrison SJ. Prdm16 is required for the maintenance of neural stem cells in the postnatal forebrain and their differentiation into ependymal cells. Genes Dev 2017; 31:1134-1146. [PMID: 28698301 PMCID: PMC5538436 DOI: 10.1101/gad.291773.116] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 06/12/2017] [Indexed: 11/24/2022]
Abstract
Shimada et al. demonstrate that Prdm16 is required for neural stem cell maintenance and neurogenesis in the adult lateral ventricle subventricular zone and dentate gyrus. Prdm16 is also required for the formation of ciliated ependymal cells in the lateral ventricle. We and others showed previously that PR domain-containing 16 (Prdm16) is a transcriptional regulator required for stem cell function in multiple fetal and neonatal tissues, including the nervous system. However, Prdm16 germline knockout mice died neonatally, preventing us from testing whether Prdm16 is also required for adult stem cell function. Here we demonstrate that Prdm16 is required for neural stem cell maintenance and neurogenesis in the adult lateral ventricle subventricular zone and dentate gyrus. We also discovered that Prdm16 is required for the formation of ciliated ependymal cells in the lateral ventricle. Conditional Prdm16 deletion during fetal development using Nestin-Cre prevented the formation of ependymal cells, disrupting cerebrospinal fluid flow and causing hydrocephalus. Postnatal Prdm16 deletion using Nestin-CreERT2 did not cause hydrocephalus or prevent the formation of ciliated ependymal cells but caused defects in their differentiation. Prdm16 was required in neural stem/progenitor cells for the expression of Foxj1, a transcription factor that promotes ependymal cell differentiation. These studies show that Prdm16 is required for adult neural stem cell maintenance and neurogenesis as well as the formation of ependymal cells.
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Affiliation(s)
- Issei S Shimada
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Melih Acar
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Bahcesehir University, School of Medicine, Istanbul 34734, Turkey
| | - Rebecca J Burgess
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Zhiyu Zhao
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Sean J Morrison
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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115
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Rolev K, O'Donovan DG, Georgiou C, Rajan MS, Chittka A. Identification of Prdm genes in human corneal endothelium. Exp Eye Res 2017; 159:114-122. [PMID: 28228349 PMCID: PMC5451076 DOI: 10.1016/j.exer.2017.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 02/01/2017] [Accepted: 02/16/2017] [Indexed: 12/12/2022]
Abstract
Corneal endothelial cells (CECs) are essential for maintaining corneal stromal hydration and ensuring its transparency, which is necessary for normal vision. Dysfunction of CECs leads to stromal decompensation, loss of transparency and corneal blindness. Corneal endothelium has low proliferative potential compared to surface epithelial cells leading to poor regeneration of CEC following injury. Additionally, the tissue exhibits age related decline in endothelial cell density with re-organisation of the cell layer, but no regeneration. The mechanisms which control proliferation and differentiation of neural crest derived CEC progenitors are yet to be clearly elucidated. Prdm (Positive regulatory domain) family of transcriptional regulators and chromatin modifiers are important for driving differentiation of a variety of cellular types. Many Prdm proteins are expressed in specific precursor cell populations and are necessary for their progression to a fully differentiated phenotype. In the present work, we sought to identify members of the Prdm gene family which are specifically expressed in human (h) CECs with a view to begin addressing their potential roles in CEC biology, focussing especially on Prdm 4 and 5 genes. By performing semi-quantitative reverse transcription coupled to PCR amplification we found that in addition to Prdm4 and Prdm5, Prdm2 and Prdm10 genes are expressed in hCECs. We further found that cultured primary hCECs or immortalised HCEC-12 cells express all of the Prdm genes found in CECs, but also express additional Prdm transcripts. This difference is most pronounced between Prdm gene expression patterns of CECs isolated from healthy human corneas and immortalised HCEC-12 cells. We further investigated Prdm 4 and Prdm 5 protein expression in cultured primary hCECs and HCEC-12 cells as well as in a human cadaveric whole cornea. Both Prdm 4 and Prdm 5 are expressed in human corneal endothelium, primary hCECs and in HCECs-12 cells, characterised by expression of the Na+/K+-ATPase. We observed that both proteins exhibit cytosolic (intracellular, but non-nuclear and distinct from extracellular fluid) as well as nuclear localisation within the endothelial layer, with Prdm 5 being more concentrated in the nuclei of the endothelial cells than Prdm 4. Thus, our work identifies novel Prdm genes specifically expressed in corneal endothelial cells which may be important in the control of CEC differentiation and proliferation.
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Affiliation(s)
- Kostadin Rolev
- Anglia Ruskin University, Department of Biomedical and Forensic Sciences and the Vision & Eye Research Unit, Cambridge CB1 1PT, United Kingdom.
| | - Dominic G O'Donovan
- Dept. of Histopathology, Cambridge University Hospitals, Hills Road, Cambridge, Cambridgeshire CB2 0QQ, United Kingdom.
| | - Christiana Georgiou
- The Wolfson Institute for Biomedical Research, Division of Medicine, UCL, Gower St, London WC1E 6BT, United Kingdom.
| | - Madhavan S Rajan
- Anglia Ruskin University, Department of Biomedical and Forensic Sciences and the Vision & Eye Research Unit, Cambridge CB1 1PT, United Kingdom; Department of Ophthalmology, Cambridge University Hospitals, Hills Road, Cambridge, Cambridgeshire CB2 0QQ, United Kingdom.
| | - Alexandra Chittka
- The Wolfson Institute for Biomedical Research, Division of Medicine, UCL, Gower St, London WC1E 6BT, United Kingdom.
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116
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Imai Y, Baudat F, Taillepierre M, Stanzione M, Toth A, de Massy B. The PRDM9 KRAB domain is required for meiosis and involved in protein interactions. Chromosoma 2017; 126:681-695. [PMID: 28527011 PMCID: PMC5688218 DOI: 10.1007/s00412-017-0631-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 12/31/2022]
Abstract
PR domain-containing protein 9 (PRDM9) is a major regulator of the localization of meiotic recombination hotspots in the human and mouse genomes. This role involves its DNA-binding domain, which is composed of a tandem array of zinc fingers, and PRDM9-dependent trimethylation of histone H3 at lysine 4. PRDM9 is a member of the PRDM family of transcription regulators, but unlike other family members, it contains a Krüppel-associated box (KRAB)-related domain that is predicted to be a potential protein interaction domain. Here, we show that truncation of the KRAB domain of mouse PRDM9 leads to loss of PRDM9 function and altered meiotic prophase and gametogenesis. In addition, we identified proteins that interact with the KRAB domain of PRDM9 in yeast two-hybrid assay screens, particularly CXXC1, a member of the COMPASS complex. We also show that CXXC1 interacts with IHO1, an essential component of the meiotic double-strand break (DSB) machinery. As CXXC1 is orthologous to Saccharomyces cerevisiae Spp1 that links DSB sites to the DSB machinery on the chromosome axis, we propose that these molecular interactions involved in the regulation of meiotic DSB formation are conserved in mouse meiosis.
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Affiliation(s)
- Yukiko Imai
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 141 rue de la cardonille, 34396, Montpellier cedex 05, France
| | - Frédéric Baudat
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 141 rue de la cardonille, 34396, Montpellier cedex 05, France
| | | | - Marcello Stanzione
- Faculty of Medicine at the TU Dresden, Institute of Physiological Chemistry, Fetscherstraße 74, 01307, Dresden, Germany
| | - Attila Toth
- Faculty of Medicine at the TU Dresden, Institute of Physiological Chemistry, Fetscherstraße 74, 01307, Dresden, Germany
| | - Bernard de Massy
- Institut de Génétique Humaine UMR9002 CNRS-Université de Montpellier, 141 rue de la cardonille, 34396, Montpellier cedex 05, France.
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117
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Hyun K, Jeon J, Park K, Kim J. Writing, erasing and reading histone lysine methylations. Exp Mol Med 2017; 49:e324. [PMID: 28450737 PMCID: PMC6130214 DOI: 10.1038/emm.2017.11] [Citation(s) in RCA: 706] [Impact Index Per Article: 100.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 02/08/2023] Open
Abstract
Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and globular domains of histones and their levels are precisely balanced by the action of methyltransferases ('writers') and demethylases ('erasers'). In addition, distinct effector proteins ('readers') recognize specific methyl-lysines in a manner that depends on the neighboring amino-acid sequence and methylation state. Misregulation of histone lysine methylation has been implicated in several cancers and developmental defects. Therefore, histone lysine methylation has been considered a potential therapeutic target, and clinical trials of several inhibitors of this process have shown promising results. A more detailed understanding of histone lysine methylation is necessary for elucidating complex biological processes and, ultimately, for developing and improving disease treatments. This review summarizes enzymes responsible for histone lysine methylation and demethylation and how histone lysine methylation contributes to various biological processes.
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Affiliation(s)
- Kwangbeom Hyun
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongcheol Jeon
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Kihyun Park
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jaehoon Kim
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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118
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Zhu Z, Wang H, Wei Y, Meng F, Liu Z, Zhang Z. Downregulation of PRDM1 promotes cellular invasion and lung cancer metastasis. Tumour Biol 2017; 39:1010428317695929. [DOI: 10.1177/1010428317695929] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The zinc-finger transcription factor PRDM1 (PR domain containing 1) plays key roles in the development of malignant lymphoma, leukaemia and some non-haematopoietic cancers, including breast cancer, colorectal cancer and glioma. However, little is known regarding the function of PRDM1 in the progression of lung cancer. Here, we found that PRDM1 is expressed in normal human lung epithelium but is downregulated in lung cancer cells. Decreased expression of PRDM1 correlates with poor prognosis in lung cancer. Depletion of PRDM1 in lung cancer cells promotes cellular invasion and anoikis resistance in vitro and lung metastasis in vivo. PRDM1 is silenced by an ectopically expressed lymphocyte-specific transcription factor Aiolos. The transcription of these two genes is negatively correlated in 206 lung epithelial cell lines. Our results indicate that PRDM1 functions as a tumour suppressor in lung cancer.
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Affiliation(s)
- Zhiyan Zhu
- Department of Immunology, Tianjin Medical University, Tianjin, China
- Tianjin Research Center of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Hao Wang
- Department of Immunology, Tianjin Medical University, Tianjin, China
| | - Yiliang Wei
- Department of Immunology, Tianjin Medical University, Tianjin, China
| | - Fanrong Meng
- Department of Immunology, Tianjin Medical University, Tianjin, China
| | - Zhe Liu
- Department of Immunology, Tianjin Medical University, Tianjin, China
| | - Zhenfa Zhang
- Department of Lung Cancer, Lung Cancer Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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119
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Discovery and characterisation of the automethylation properties of PRDM9. Biochem J 2017; 474:971-982. [PMID: 28126738 DOI: 10.1042/bcj20161067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/16/2017] [Accepted: 01/25/2017] [Indexed: 11/17/2022]
Abstract
We have previously characterised the histone lysine methyltransferase properties of PRDM9, a member of the PRDM family of putative transcriptional regulators. PRDM9 displays broad substrate recognition and methylates a range of histone substrates, including octamers, core histone proteins, and peptides. In the present study, we show that PRDM9 performs intramolecular automethylation on multiple lysine residues localised to a lysine-rich region on the post-SET (suppressor of variegation 3-9, enhancer of zeste and trithorax) domain. PRDM9 automethylation is abolished by a single active-site mutation, C321P, also known to disrupt interactions with S-adenosylmethionine. We have taken an initial step towards tool compound generation through rational design of a substrate-mimic, peptidic inhibitor of PRDM9 automethylation. The discovery of automethylation in PRDM9 adds a new dimension to our understanding of PRDM9 enzymology.
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120
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Strunk D, Weber P, Röthlisberger B, Filges I. Autism and intellectual disability in a patient with two microdeletions in 6q16: a contiguous gene deletion syndrome? Mol Cytogenet 2016; 9:88. [PMID: 27980676 PMCID: PMC5135825 DOI: 10.1186/s13039-016-0299-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/21/2016] [Indexed: 01/19/2023] Open
Abstract
Background Copy number variations play a significant role in the aetiology of developmental disabilities including non-syndromic intellectual disability and autism. Case presentation We describe a 19-year old patient with intellectual disability and autism for whom chromosomal microarray (CMA) analysis showed the unusual finding of two de novo microdeletions in cis position on chromosome 6q16.1q16.2 and 6q16.3. The two deletions span 10 genes, including FBXL4, POU3F2, PRDM13, CCNC, COQ3 and GRIK2. We compared phenotypes of patients with similar deletions and looked at the involvement of the genes in neuronal networks in order to determine the pathogenicity of our patient’s deletions. Conclusions We suggest that both deletions on 6q are causing his disease phenotype since they harbour several genes which are implicated in pathways of neuronal development and function. Further studies regarding the interaction between PRDM13 and GRIK2 specifically may be interesting.
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Affiliation(s)
- Daniela Strunk
- Medical Genetics, University Hospital Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland
| | - Peter Weber
- Division of Neuropediatrics and Developmental Pediatrics, University Children's Hospital, Spitalstrasse 33, CH-4056 Basel, Switzerland
| | - Benno Röthlisberger
- Medical Genetics, Department of Laboratory Medicine, Cantonal Hospital Aarau, Tellstrasse, CH-5001 Aarau, Switzerland
| | - Isabel Filges
- Medical Genetics, University Hospital Basel and University of Basel, Schönbeinstrasse 40, CH-4031 Basel, Switzerland
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121
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Optimization of the optical transparency of rodent tissues by modified PACT-based passive clearing. Exp Mol Med 2016; 48:e274. [PMID: 27909337 PMCID: PMC5192069 DOI: 10.1038/emm.2016.105] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/22/2016] [Accepted: 06/27/2016] [Indexed: 12/11/2022] Open
Abstract
Recently, a bio-electrochemical technique known as CLARITY was reported for three-dimensional phenotype mapping within transparent tissues, allowing clearer whole-body and organ visualization with CB-perfusion (CUBIC) and leading to the development of whole-body clearing and transparency of intact tissues with the PACT (passive clarity technique) and PARS (perfusion-assisted agent release in situ) methodologies. We evaluated the structure–function relationships in circuits of the whole central nervous system (CNS) and various internal organs using improved methods with optimized passive clarity. Thus, in the present study, we aimed to improve the original PACT procedure and passive clearing protocols for different intact rodent tissues. We determined the optimal conditions for the passive clarity method that allowed the production of a transparent whole CNS by clearing the brain and spinal cord, as well as various organs. We also improved the tissue transparency using mPACT (modified PACT), a method for direct passive clearing, and whole perfusion-based PARS-mPACT, a method for fusion clearing, and we identified the appropriate experimental conditions. These optimized methods can be used for easy and economical high-resolution mapping and phenotyping of normal and pathological elements within intact tissues.
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122
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Rehimi R, Nikolic M, Cruz-Molina S, Tebartz C, Frommolt P, Mahabir E, Clément-Ziza M, Rada-Iglesias A. Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations. Cell Rep 2016; 17:3062-3076. [DOI: 10.1016/j.celrep.2016.11.046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/05/2016] [Accepted: 11/14/2016] [Indexed: 12/21/2022] Open
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123
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Carlson SM, Gozani O. Nonhistone Lysine Methylation in the Regulation of Cancer Pathways. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026435. [PMID: 27580749 DOI: 10.1101/cshperspect.a026435] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Proteins are regulated by an incredible array of posttranslational modifications (PTMs). Methylation of lysine residues on histone proteins is a PTM with well-established roles in regulating chromatin and epigenetic processes. The recent discovery that hundreds and likely thousands of nonhistone proteins are also methylated at lysine has opened a tremendous new area of research. Major cellular pathways involved in cancer, such as growth signaling and the DNA damage response, are regulated by lysine methylation. Although the field has developed quickly in recent years many fundamental questions remain to be addressed. We review the history and molecular functions of lysine methylation. We then discuss the enzymes that catalyze methylation of lysine residues, the enzymes that remove lysine methylation, and the cancer pathways known to be regulated by lysine methylation. The rest of the article focuses on two open questions that we suggest as a roadmap for future research. First is understanding the large number of candidate methyltransferase and demethylation enzymes whose enzymatic activity is not yet defined and which are potentially associated with cancer through genetic studies. Second is investigating the biological processes and cancer mechanisms potentially regulated by the multitude of lysine methylation sites that have been recently discovered.
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Affiliation(s)
- Scott M Carlson
- Department of Biology, Stanford University, Stanford, California 94305
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, California 94305
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124
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Gunnar E, Bivik C, Starkenberg A, Thor S. sequoia controls the type I>0 daughter proliferation switch in the developing Drosophila nervous system. Development 2016; 143:3774-3784. [PMID: 27578794 DOI: 10.1242/dev.139998] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/22/2016] [Indexed: 01/16/2023]
Abstract
Neural progenitors typically divide asymmetrically to renew themselves, while producing daughters with more limited potential. In the Drosophila embryonic ventral nerve cord, neuroblasts initially produce daughters that divide once to generate two neurons/glia (type I proliferation mode). Subsequently, many neuroblasts switch to generating daughters that differentiate directly (type 0). This programmed type I>0 switch is controlled by Notch signaling, triggered at a distinct point of lineage progression in each neuroblast. However, how Notch signaling onset is gated was unclear. We recently identified Sequoia (Seq), a C2H2 zinc-finger transcription factor with homology to Drosophila Tramtrack (Ttk) and the positive regulatory domain (PRDM) family, as important for lineage progression. Here, we find that seq mutants fail to execute the type I>0 daughter proliferation switch and also display increased neuroblast proliferation. Genetic interaction studies reveal that seq interacts with the Notch pathway, and seq furthermore affects expression of a Notch pathway reporter. These findings suggest that seq may act as a context-dependent regulator of Notch signaling, and underscore the growing connection between Seq, Ttk, the PRDM family and Notch signaling.
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Affiliation(s)
- Erika Gunnar
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping SE-58185, Sweden
| | - Caroline Bivik
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping SE-58185, Sweden
| | - Annika Starkenberg
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping SE-58185, Sweden
| | - Stefan Thor
- Department of Clinical and Experimental Medicine, Linkoping University, Linkoping SE-58185, Sweden
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125
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Lan X, Gao H, Wang F, Feng J, Bai J, Zhao P, Cao L, Gui S, Gong L, Zhang Y. Whole-exome sequencing identifies variants in invasive pituitary adenomas. Oncol Lett 2016; 12:2319-2328. [PMID: 27698795 PMCID: PMC5038494 DOI: 10.3892/ol.2016.5029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/18/2016] [Indexed: 12/24/2022] Open
Abstract
Pituitary adenomas exhibit a wide range of behaviors. The prediction of invasion or malignant behavior in pituitary adenomas remains challenging. The objective of the present study was to identify the genetic abnormalities associated with invasion in sporadic pituitary adenomas. In the present study, the exomes of six invasive pituitary adenomas (IPA) and six non-invasive pituitary adenomas (nIPA) were sequenced by whole-exome sequencing. Variants were confirmed by dideoxynucleotide sequencing, and candidate driver genes were assessed in an additional 28 pituitary adenomas. A total of 15 identified variants were mainly associated with angiogenesis, metabolism, cell cycle phase, cellular component organization, cytoskeleton and biogenesis immune at a cellular level, including 13 variants that occurred as single nucleotide variants and 2 that comprised of insertions. The messenger RNA (mRNA) levels of diffuse panbronchiolitis critical region 1 (DPCR1), KIAA0226, myxovirus (influenza virus) resistance, proline-rich protein BstNI subfamily 3, PR domain containing 2, with ZNF domain, RIZ1 (PRDM2), PR domain containing 8 (PRDM8), SPANX family member N2 (SPANXN2), TRIO and F-actin binding protein and zinc finger protein 717 in IPA specimens were 50% decreased compared with nIPA specimens. In particular, DPCR1, PRDM2, PRDM8 and SPANXN2 mRNA levels in IPA specimens were approximately four-fold lower compared with nIPA specimens (P=0.003, 0.007, 0.009 and 0.004, respectively). By contrast, the mRNA levels of dentin sialophospho protein, EGF like domain, multiple 7 (EGFL7), low density lipoprotein receptor-related protein 1B and dynein, axonemal, assembly factor 1 (LRRC50) were increased in IPA compared with nIPA specimens (P=0.041, 0.037, 0.022 and 0.013, respectively). Furthermore, decreased PRDM2 expression was associated with tumor recurrence. The findings of the present study indicate that DPCR1, EGFL7, the PRDM family and LRRC50 in pituitary adenomas are modifiers of tumorigenesis, and most likely contribute to the development of oncocytic change and to the invasive tumor phenotype.
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Affiliation(s)
- Xiaolei Lan
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China; Department of Neurosurgery, The Affiliated Hospital of Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Hua Gao
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Fei Wang
- Department of Neurosurgery, Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Jie Feng
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Jiwei Bai
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Peng Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 200050, P.R. China
| | - Lei Cao
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Songbai Gui
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 200050, P.R. China
| | - Lei Gong
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Yazhuo Zhang
- Key Laboratory of Central Nervous System Injury Research, Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, P.R. China
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126
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Wei Y, Cui YF, Tong HL, Zhang WW, Yan YQ. MicroRNA-2400 promotes bovine preadipocyte proliferation. Biochem Biophys Res Commun 2016; 478:1054-9. [PMID: 27514450 DOI: 10.1016/j.bbrc.2016.08.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/06/2016] [Indexed: 11/27/2022]
Abstract
MicroRNAs (miRNAs) play critical roles in the proliferation of bovine preadipocytes. miR-2400 is a novel and unique miRNA from bovines. In the present study, we separated and identified preadipocytes from bovine samples. miR-2400 overexpression increased the rate of preadipocyte proliferation, which was analyzed with a combination of EdU and flow cytometry. Simultaneously, functional genes related to proliferation (PCNA, CCND2, CCNB1) were also increased, which was detected by real-time PCR. Furthermore, luciferase reporter assays showed that miR-2400 bound directly to the 3'untranslated regions (3'UTRs) of PRDM11 mRNA. These data suggested that miR-2400 could promote preadipocyte proliferation by targeting PRDM11.
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Affiliation(s)
- Yao Wei
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Ya Feng Cui
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Hui Li Tong
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Wei Wei Zhang
- College of Life Sciences and Agriculture & Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Yun Qin Yan
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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127
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Wang L, Ding QQ, Gao SS, Yang HJ, Wang M, Shi Y, Cheng BF, Bi JJ, Feng ZW. PRDM5 promotes the proliferation and invasion of murine melanoma cells through up-regulating JNK expression. Cancer Med 2016; 5:2558-66. [PMID: 27485778 PMCID: PMC5055150 DOI: 10.1002/cam4.846] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 06/30/2016] [Accepted: 07/07/2016] [Indexed: 12/21/2022] Open
Abstract
PRDM (PRDI-BF1 and RIZ domain-containing) proteins constitute a family of zinc finger proteins and play important roles in multiple cellular processes by acting as epigenetic modifiers. PRDM5 is a recently identified member of the PRDM family and may function as a tumor suppressor in several types of cancer. However, the role of PRDM5 in murine melanoma remains largely unknown. In our study, effect of PRDM5 on murine melanoma cells was determined and results showed that PRDM5 overexpression significantly promoted proliferation, migration, and invasion of murine melanoma B16F10 cells. Consistently, silencing of PRDM5 expression significantly inhibited proliferation, invasion, and migration of B16F10 cells. In vivo study also showed that PRDM5 silencing significantly inhibited the growth and metastasis of melanoma in mice. PRDM5 was then found to increase the expression and activation of JNK in B16F10 cells. JNK silencing significantly reduced PRDM5-mediated up-regulation of JNK expression and blocked the PRDM5-induced proliferation and invasion of B16F10 cells. To further verify the involvement of JNK signaling in PRDM5-induced progression of B16F10 cells, a specific JNK inhibitor was employed to inhibit the JNK signaling pathway, and results showed that PRDM5-induced proliferation and invasion of B16F10 cells were abolished. We conclude that PRDM5 promotes the proliferation and invasion of murine melanoma cells through up-regulating JNK expression and strategies targeting PRDM5 may be promising for the therapy of melanoma.
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Affiliation(s)
- Lei Wang
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Qiong-Qiong Ding
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Shan-Shan Gao
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Hai-Jie Yang
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Mian Wang
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Yu Shi
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Bin-Feng Cheng
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Jia-Jia Bi
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China
| | - Zhi-Wei Feng
- College of Life Science and Technology, Xinxiang Medical University, Xinxiang, China. ,
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128
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BLIMP-1/BLMP-1 and Metastasis-Associated Protein Regulate Stress Resistant Development in Caenorhabditis elegans. Genetics 2016; 203:1721-32. [PMID: 27334271 DOI: 10.1534/genetics.116.190793] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/14/2016] [Indexed: 01/17/2023] Open
Abstract
Environmental stress triggers multilevel adaptations in animal development that depend in part on epigenetic mechanisms. In response to harsh environmental conditions and pheromone signals, Caenorhabditis elegans larvae become the highly stress-resistant and long-lived dauer. Despite extensive studies of dauer formation pathways that integrate specific environmental cues and appear to depend on transcriptional reprogramming, the role of epigenetic regulation in dauer development has remained unclear. Here we report that BLMP-1, the BLIMP-1 ortholog, regulates dauer formation via epigenetic pathways; in the absence of TGF-β signaling (in daf-7 mutants), lack of blmp-1 caused lethality. Using this phenotype, we screened 283 epigenetic factors, and identified lin-40, a homolog of metastasis-associate protein 1 (MTA1) as an interactor of BLMP-1 The interaction between LIN-40 and BLMP-1 is conserved because mammalian homologs for both MTA1 and BLIMP-1 could also interact. From microarray studies, we identified several downstream target genes of blmp-1: npr-3, nhr-23, ptr-4, and sams-1 Among them S-adenosyl methionine synthase (SAMS-1), is the key enzyme for production of SAM used in histone methylation. Indeed, blmp-1 is necessary for controlling histone methylation level in daf-7 mutants, suggesting BLMP-1 regulates the expression of SAMS-1, which in turn may regulate histone methylation and dauer formation. Our results reveal a new interaction between BLMP-1/BLIMP-1 and LIN-40/MTA1, as well as potential epigenetic downstream pathways, whereby these proteins cooperate to regulate stress-specific developmental adaptations.
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129
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Tunbak H, Georgiou C, Guan C, Richardson WD, Chittka A. Zinc fingers 1, 2, 5 and 6 of transcriptional regulator, PRDM4, are required for its nuclear localisation. Biochem Biophys Res Commun 2016; 474:388-394. [PMID: 27125459 DOI: 10.1016/j.bbrc.2016.04.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 04/24/2016] [Indexed: 11/17/2022]
Abstract
PRDM4 is a member of the PRDM family of transcriptional regulators which control various aspects of cellular differentiation and proliferation. PRDM proteins exert their biological functions both in the cytosol and the nucleus of cells. All PRDM proteins are characterised by the presence of two distinct structural motifs, the PR/SET domain and the zinc finger (ZF) motifs. We previously observed that deletion of all six zinc fingers found in PRDM4 leads to its accumulation in the cytosol, whereas overexpressed full length PRDM4 is found predominantly in the nucleus. Here, we investigated the requirements for single zinc fingers in the nuclear localisation of PRDM4. We demonstrate that ZF's 1, 2, 5 and 6 contribute to the accumulation of PRDM4 in the nucleus. Their effect is additive as deleting either ZF1-2 or ZF 5-6 redistributes PRDM4 protein from being almost exclusively nuclear to cytosolic and nuclear. We investigated the potential mechanism of nuclear shuttling of PRDM4 via the importin α/β-mediated pathway and find that PRDM4 nuclear targeting is independent of α/β-mediated nuclear import.
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Affiliation(s)
- Hale Tunbak
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK.
| | - Christiana Georgiou
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK.
| | - Cui Guan
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
| | - William David Richardson
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK.
| | - Alexandra Chittka
- The Wolfson Institute for Biomedical Research, University College London, Gower Street, London WC1E 6BT, UK.
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130
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Blazer LL, Lima-Fernandes E, Gibson E, Eram MS, Loppnau P, Arrowsmith CH, Schapira M, Vedadi M. PR Domain-containing Protein 7 (PRDM7) Is a Histone 3 Lysine 4 Trimethyltransferase. J Biol Chem 2016; 291:13509-19. [PMID: 27129774 PMCID: PMC4919437 DOI: 10.1074/jbc.m116.721472] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 12/22/2022] Open
Abstract
PR domain-containing protein 7 (PRDM7) is a primate-specific histone methyltransferase that is the result of a recent gene duplication of PRDM9. The two proteins are highly homologous, especially in the catalytic PR/SET domain, where they differ by only three amino acid residues. Here we report that PRDM7 is an efficient methyltransferase that selectively catalyzes the trimethylation of H3 lysine 4 (H3K4) both in vitro and in cells. Through selective mutagenesis we have dissected the functional roles of each of the three divergent residues between the PR domains of PRDM7 and PRDM9. These studies indicate that after a single serine to tyrosine mutation at residue 357 (S357Y), PRDM7 regains the substrate specificities and catalytic activities similar to its evolutionary predecessor, including the ability to efficiently methylate H3K36.
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Affiliation(s)
- Levi L Blazer
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Evelyne Lima-Fernandes
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Elisa Gibson
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Mohammad S Eram
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Cheryl H Arrowsmith
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, and
| | - Matthieu Schapira
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Masoud Vedadi
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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131
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Joubert BR, Felix JF, Yousefi P, Bakulski KM, Just AC, Breton C, Reese SE, Markunas CA, Richmond RC, Xu CJ, Küpers LK, Oh SS, Hoyo C, Gruzieva O, Söderhäll C, Salas LA, Baïz N, Zhang H, Lepeule J, Ruiz C, Ligthart S, Wang T, Taylor JA, Duijts L, Sharp GC, Jankipersadsing SA, Nilsen RM, Vaez A, Fallin MD, Hu D, Litonjua AA, Fuemmeler BF, Huen K, Kere J, Kull I, Munthe-Kaas MC, Gehring U, Bustamante M, Saurel-Coubizolles MJ, Quraishi BM, Ren J, Tost J, Gonzalez JR, Peters MJ, Håberg SE, Xu Z, van Meurs JB, Gaunt TR, Kerkhof M, Corpeleijn E, Feinberg AP, Eng C, Baccarelli AA, Benjamin Neelon SE, Bradman A, Merid SK, Bergström A, Herceg Z, Hernandez-Vargas H, Brunekreef B, Pinart M, Heude B, Ewart S, Yao J, Lemonnier N, Franco OH, Wu MC, Hofman A, McArdle W, Van der Vlies P, Falahi F, Gillman MW, Barcellos LF, Kumar A, Wickman M, Guerra S, Charles MA, Holloway J, Auffray C, Tiemeier HW, Smith GD, Postma D, Hivert MF, Eskenazi B, Vrijheid M, Arshad H, Antó JM, Dehghan A, Karmaus W, Annesi-Maesano I, Sunyer J, Ghantous A, Pershagen G, Holland N, Murphy SK, DeMeo DL, Burchard EG, Ladd-Acosta C, Snieder H, Nystad W, Koppelman GH, Relton CL, Jaddoe VWV, Wilcox A, Melén E, London SJ. DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis. Am J Hum Genet 2016; 98:680-96. [PMID: 27040690 PMCID: PMC4833289 DOI: 10.1016/j.ajhg.2016.02.019] [Citation(s) in RCA: 587] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/20/2016] [Indexed: 02/07/2023] Open
Abstract
Epigenetic modifications, including DNA methylation, represent a potential mechanism for environmental impacts on human disease. Maternal smoking in pregnancy remains an important public health problem that impacts child health in a myriad of ways and has potential lifelong consequences. The mechanisms are largely unknown, but epigenetics most likely plays a role. We formed the Pregnancy And Childhood Epigenetics (PACE) consortium and meta-analyzed, across 13 cohorts (n = 6,685), the association between maternal smoking in pregnancy and newborn blood DNA methylation at over 450,000 CpG sites (CpGs) by using the Illumina 450K BeadChip. Over 6,000 CpGs were differentially methylated in relation to maternal smoking at genome-wide statistical significance (false discovery rate, 5%), including 2,965 CpGs corresponding to 2,017 genes not previously related to smoking and methylation in either newborns or adults. Several genes are relevant to diseases that can be caused by maternal smoking (e.g., orofacial clefts and asthma) or adult smoking (e.g., certain cancers). A number of differentially methylated CpGs were associated with gene expression. We observed enrichment in pathways and processes critical to development. In older children (5 cohorts, n = 3,187), 100% of CpGs gave at least nominal levels of significance, far more than expected by chance (p value < 2.2 × 10(-16)). Results were robust to different normalization methods used across studies and cell type adjustment. In this large scale meta-analysis of methylation data, we identified numerous loci involved in response to maternal smoking in pregnancy with persistence into later childhood and provide insights into mechanisms underlying effects of this important exposure.
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Affiliation(s)
- Bonnie R Joubert
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands
| | - Paul Yousefi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Kelly M Bakulski
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Allan C Just
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carrie Breton
- University of Southern California, Los Angeles, CA 90032, USA
| | - Sarah E Reese
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Christina A Markunas
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA; Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Cheng-Jian Xu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands
| | - Leanne K Küpers
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Cathrine Hoyo
- Department of Biological Sciences and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695-7633, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm 141 83, Sweden
| | - Lucas A Salas
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Nour Baïz
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Saint-Antoine Medical School, F75012 Paris, France
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Johanna Lepeule
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Institut Albert Bonniot, Institut National de la Santé et de le Recherche Médicale, University of Grenoble Alpes, Centre Hospitalier Universitaire de Grenoble, F-38000 Grenoble, France
| | - Carlos Ruiz
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Symen Ligthart
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Tianyuan Wang
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jack A Taylor
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Liesbeth Duijts
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands; Division of Neonatology, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands; Division of Respiratory Medicine, Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Soesma A Jankipersadsing
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Roy M Nilsen
- Department of Global Public Health and Primary Care, University of Bergen, Bergen 5018, Norway
| | - Ahmad Vaez
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; School of Medicine, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - M Daniele Fallin
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Bernard F Fuemmeler
- Department of Community and Family Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Karen Huen
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm 141 83, Sweden
| | - Inger Kull
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | | | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3508 TD, the Netherlands
| | - Mariona Bustamante
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Center for Genomic Regulation (CRG), Barcelona 08003, Spain
| | | | - Bilal M Quraishi
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Jie Ren
- University of Southern California, Los Angeles, CA 90032, USA
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, 91000 Evry, France
| | - Juan R Gonzalez
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Marjolein J Peters
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands
| | - Siri E Håberg
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo 0403, Norway
| | - Zongli Xu
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Joyce B van Meurs
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA, the Netherlands
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Marjan Kerkhof
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Andrew P Feinberg
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Andrea A Baccarelli
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Asa Bradman
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | | | - Bert Brunekreef
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3508 TD, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3508 TD, the Netherlands
| | - Mariona Pinart
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona 08003, Spain
| | - Barbara Heude
- INSERM, UMR 1153, Early Origin of the Child's Health And Development (ORCHAD) Team, Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS), Université Paris Descartes, 94807 Villejuif, France
| | - Susan Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Jin Yao
- University of Southern California, Los Angeles, CA 90032, USA
| | - Nathanaël Lemonnier
- Centre National de la Recherche Scientifique-École Normale Supérieure de Lyon-Université Claude Bernard (Lyon 1), Université de Lyon, European Institute for Systems Biology and Medicine 69007 Lyon, France
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Michael C Wu
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Wendy McArdle
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Pieter Van der Vlies
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Fahimeh Falahi
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Matthew W Gillman
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Lisa F Barcellos
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden; Department of Public Health Epidemiology, Unit of Chronic Disease Epidemiology, Swiss Tropical and Public Health Institute, Basel 4051, Switzerland; University of Basel, Basel 4001, Switzerland
| | - Magnus Wickman
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden; Sachs' Children's Hospital and Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm 171 77, Sweden
| | - Stefano Guerra
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain
| | - Marie-Aline Charles
- INSERM, UMR 1153, Early Origin of the Child's Health And Development (ORCHAD) Team, Centre de Recherche Épidémiologie et Statistique Sorbonne Paris Cité (CRESS), Université Paris Descartes, 94807 Villejuif, France
| | - John Holloway
- Faculty of Medicine, Clinical & Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK; Faculty of Medicine, Human Development & Health, University of Southampton, Southampton SO16 6YD, UK
| | - Charles Auffray
- Centre National de la Recherche Scientifique-École Normale Supérieure de Lyon-Université Claude Bernard (Lyon 1), Université de Lyon, European Institute for Systems Biology and Medicine 69007 Lyon, France
| | - Henning W Tiemeier
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Dirkje Postma
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands
| | - Marie-France Hivert
- Obesity Prevention Program, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Martine Vrijheid
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Hasan Arshad
- Faculty of Medicine, Clinical & Experimental Sciences, University of Southampton, Southampton SO16 6YD, UK
| | - Josep M Antó
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona 08003, Spain
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Isabella Annesi-Maesano
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Saint-Antoine Medical School, F75012 Paris, France
| | - Jordi Sunyer
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain; Hospital del Mar Medical Research Institute (IMIM), Barcelona 08003, Spain
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Nina Holland
- Center for Environmental Research and Children's Health (CERCH), School of Public Health, University of California Berkeley, Berkeley, CA 94720-7360, USA
| | - Susan K Murphy
- Departments of Obstetrics and Gynecology and Pathology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143-2911, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143-2911, USA
| | - Christine Ladd-Acosta
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Wenche Nystad
- Division of Mental and Physical Health, Norwegian Institute of Public Health, Oslo 0403, Norway
| | - Gerard H Koppelman
- GRIAC Research Institute Groningen, University of Groningen, University Medical Center Groningen, 9700 RB, the Netherlands; Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam 3000 CA, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, 3000 CA the Netherlands
| | - Allen Wilcox
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden; Sachs' Children's Hospital and Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm 171 77, Sweden
| | - Stephanie J London
- National Institute of Environmental Health Sciences, NIH, U.S. Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
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Liu C, Liu W, Fan L, Liu J, Li P, Zhang W, Gao J, Li Z, Zhang Q, Wang X. Sequences analyses and expression profiles in tissues and embryos of Japanese flounder (Paralichthys olivaceus) PRDM1. FISH PHYSIOLOGY AND BIOCHEMISTRY 2016; 42:467-482. [PMID: 26508172 DOI: 10.1007/s10695-015-0152-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/20/2015] [Indexed: 06/05/2023]
Abstract
PRDM1 (PRDI-BF1-RIZ1 homologous domain containing 1) appears to be a pleiotropic regulatory factor in various processes. It contains a PR (PRDI-BF1-RIZ1 homologous) domain protein and five zinc fingers. In the present study, a gene coding the homolog of prdm1 and the 5' regulatory region of prdm1 was identified from the Paralichthys olivaceus (denoted Po-prdm1). Results of real-time quantitative polymerase chain reaction amplification (RT-qPCR) and in situ hybridization (ISH) in embryos revealed that Po-prdm1 was highly expressed between the early gastrula and tail bud stages, with its expression peaking in the mid-gastrula stage, whereas the results of RT-qPCR and ISH in tissues demonstrated that Po-prdm1 transcripts were ubiquitously detected in all tissues, which indicates its pleiotropic function in multiple processes. ISH of gonadal tissues revealed that the transcripts were located in the nucleus and cytoplasm of the oocytes in the ovaries but only in the spermatogonia and not in the spermatocytes in the testes. The Po-prdm1 transcription factor binding sites and their conserved binding region among vertebrates were analyzed in this study. The combined results suggest that Po-PRDM1 has a conserved function in teleosts and mammals.
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Affiliation(s)
- Conghui Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Wei Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Lin Fan
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Jinxiang Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Peizhen Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Wei Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Jinning Gao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Zan Li
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Quanqi Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
| | - Xubo Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
- College of Marine Life Science, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China.
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133
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Zhang S, Malik Sharif S, Chen YC, Valente EM, Ahmed M, Sheridan E, Bennett C, Woods G. Clinical features for diagnosis and management of patients with PRDM12 congenital insensitivity to pain. J Med Genet 2016; 53:533-5. [PMID: 26975306 PMCID: PMC4975812 DOI: 10.1136/jmedgenet-2015-103646] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/31/2016] [Indexed: 12/18/2022]
Abstract
Background Congenital insensitivity to pain (CIP) is a rare extreme phenotype characterised by an inability to perceive pain present from birth due to lack of, or malfunction of, nociceptors. PRDM12 has recently been identified as a new gene that can cause CIP. The full phenotype and natural history have not yet been reported. Methods We have ascertained five adult patients and report their clinical features. Results Based on our findings, and those of previous patients, we describe the natural history of the PRDM12-CIP disorder, and derive diagnostic and management features to guide the clinical management of patients. Conclusions PRDM12-CIP is a distinct and diagnosable disorder, and requires specific clinical management to minimise predictable complications.
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Affiliation(s)
- Stella Zhang
- School of Clinical Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | | | - Ya-Chun Chen
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust, Cambridge, UK
| | - Enza-Maria Valente
- Section of Neurosciences, Department of Medicine and Surgery, University of Salerno, Italy
| | - Mushtaq Ahmed
- The Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Eamonn Sheridan
- The Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Christopher Bennett
- The Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Geoffrey Woods
- School of Clinical Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust, Cambridge, UK
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134
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Han Y, Lin Q. [Research Progress of PR Domain Zinc Finger Protein 14]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2016; 19:93-7. [PMID: 26903163 PMCID: PMC6015138 DOI: 10.3779/j.issn.1009-3419.2016.02.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
正性调节区锌指蛋白14(PR domain zinc finger protein 14, PRDM14)是PRDM家族中的重要成员,PRDM14基因对维持细胞的完整性和控制细胞的分化、生长及凋亡起着关键作用,在原始生殖细胞的形成、干细胞全能性的维持和其他组织器官的形成中都发挥了重要作用。PRDM14具有1个PR结构域和6个锌指结构,PRDM14参与了组蛋白的去乙酰化及甲基化过程,通过启动子区甲基化水平的改变参与肿瘤的形成。PRDM14异常甲基化能够引起染色质结构、DNA构象及DNA与蛋白质作用方式的改变,使基因的转录和表达受抑制,这些改变引起了肿瘤的发生、发展及转移。本文根据国内外发表的相关文献对PRDM14的研究现状进行综述。
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Affiliation(s)
- Yudong Han
- Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, China
| | - Qiang Lin
- Department of Thoracic Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200080, China
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135
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Thélie A, Desiderio S, Hanotel J, Quigley I, Van Driessche B, Rodari A, Borromeo MD, Kricha S, Lahaye F, Croce J, Cerda-Moya G, Ordoño Fernandez J, Bolle B, Lewis KE, Sander M, Pierani A, Schubert M, Johnson JE, Kintner CR, Pieler T, Van Lint C, Henningfeld KA, Bellefroid EJ, Van Campenhout C. Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus. Development 2016; 142:3416-28. [PMID: 26443638 DOI: 10.1242/dev.121871] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
V1 interneurons are inhibitory neurons that play an essential role in vertebrate locomotion. The molecular mechanisms underlying their genesis remain, however, largely undefined. Here, we show that the transcription factor Prdm12 is selectively expressed in p1 progenitors of the hindbrain and spinal cord in the frog embryo, and that a similar restricted expression profile is observed in the nerve cord of other vertebrates as well as of the cephalochordate amphioxus. Using frog, chick and mice, we analyzed the regulation of Prdm12 and found that its expression in the caudal neural tube is dependent on retinoic acid and Pax6, and that it is restricted to p1 progenitors, due to the repressive action of Dbx1 and Nkx6-1/2 expressed in the adjacent p0 and p2 domains. Functional studies in the frog, including genome-wide identification of its targets by RNA-seq and ChIP-Seq, reveal that vertebrate Prdm12 proteins act as a general determinant of V1 cell fate, at least in part, by directly repressing Dbx1 and Nkx6 genes. This probably occurs by recruiting the methyltransferase G9a, an activity that is not displayed by the amphioxus Prdm12 protein. Together, these findings indicate that Prdm12 promotes V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes, and suggest that this function might have only been acquired after the split of the vertebrate and cephalochordate lineages.
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Affiliation(s)
- Aurore Thélie
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Simon Desiderio
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Julie Hanotel
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Ian Quigley
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Anthony Rodari
- Laboratory of Molecular Virology, ULB, IBMM, Gosselies B-6041, Belgium
| | - Mark D Borromeo
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sadia Kricha
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - François Lahaye
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009), Observatoire Océanologique de Villefranche-sur-Mer, Villefranche-sur-Mer 06230, France
| | - Jenifer Croce
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009), Observatoire Océanologique de Villefranche-sur-Mer, Villefranche-sur-Mer 06230, France
| | - Gustavo Cerda-Moya
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Jesús Ordoño Fernandez
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Barbara Bolle
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Katharine E Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Maike Sander
- Departments of Pediatrics and Cellular and Molecular Medicine, Pediatric Diabetes Research Center, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Alessandra Pierani
- Génétique et développement du cortex cerebral, Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris Cedex 13 75205, France
| | - Michael Schubert
- Sorbonne Universités, UPMC Université Paris 06, CNRS UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (UMR 7009), Observatoire Océanologique de Villefranche-sur-Mer, Villefranche-sur-Mer 06230, France
| | - Jane E Johnson
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Christopher R Kintner
- Molecular Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tomas Pieler
- Department of Developmental Biochemistry, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University of Göttingen, 37077 Göttingen, Germany
| | - Carine Van Lint
- Laboratory of Molecular Virology, ULB, IBMM, Gosselies B-6041, Belgium
| | - Kristine A Henningfeld
- Department of Developmental Biochemistry, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University of Göttingen, 37077 Göttingen, Germany
| | - Eric J Bellefroid
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
| | - Claude Van Campenhout
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medecine (IBMM) and ULB Neuroscience Institute, Gosselies B-6041, Belgium
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136
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The role of PRDMs in cancer: one family, two sides. Curr Opin Genet Dev 2016; 36:83-91. [DOI: 10.1016/j.gde.2016.03.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/24/2016] [Indexed: 12/24/2022]
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137
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Nakamura T, Extavour CG. The transcriptional repressor Blimp-1 acts downstream of BMP signaling to generate primordial germ cells in the cricket Gryllus bimaculatus. Development 2016; 143:255-63. [DOI: 10.1242/dev.127563] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Segregation of the germ line from the soma is an essential event for transmission of genetic information across generations in all sexually reproducing animals. Although some well-studied systems such as Drosophila and Xenopus use maternally inherited germ determinants to specify germ cells, most animals, including mice, appear to utilize zygotic inductive cell signals to specify germ cells during later embryogenesis. Such inductive germ cell specification is thought to be an ancestral trait of Bilateria, but major questions remain as to the nature of an ancestral mechanism to induce germ cells, and how that mechanism evolved. We previously reported that BMP signaling-based germ cell induction is conserved in both the mouse Mus musculus and the cricket Gryllus bimaculatus, which is an emerging model organism for functional studies of induction-based germ cell formation. In order to gain further insight into the functional evolution of germ cell specification, here we examined the Gryllus ortholog of the transcription factor Blimp-1 (also known as Prdm1), which is a widely conserved bilaterian gene known to play a crucial role in the specification of germ cells in mice. Our functional analyses of the Gryllus Blimp-1 ortholog revealed that it is essential for Gryllus primordial germ cell development, and is regulated by upstream input from the BMP signaling pathway. This functional conservation of the epistatic relationship between BMP signaling and Blimp-1 in inductive germ cell specification between mouse and cricket supports the hypothesis that this molecular mechanism regulated primordial germ cell specification in a last common bilaterian ancestor.
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Affiliation(s)
- Taro Nakamura
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cassandra G. Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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138
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Chi J, Cohen P. The Multifaceted Roles of PRDM16: Adipose Biology and Beyond. Trends Endocrinol Metab 2016; 27:11-23. [PMID: 26688472 DOI: 10.1016/j.tem.2015.11.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 01/07/2023]
Abstract
The PRDM [PRDI-BFI (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1) homologous domain containing] protein family is involved in a spectrum of biological processes including cell fate determination and development. These proteins regulate transcription through intrinsic chromatin-modifying activity or by complexing with histone-modifying or other nuclear proteins. Studies have indicated crucial roles for PRDM16 in the determination and function of brown and beige fat as well as in hematopoiesis and cardiac development, highlighting the importance of PRDM16 in developmental processes in different tissues. More recently, PRDM16 mutations were also identified in humans. The substantial progress in understanding the mechanism underlying the action of PRDM16 in adipose biology may have relevance to other PRDM family members, and this new knowledge has the potential to be exploited for therapeutic benefit.
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Affiliation(s)
- Jingyi Chi
- The Rockefeller University, Laboratory of Molecular Metabolism, New York, NY 10065, USA
| | - Paul Cohen
- The Rockefeller University, Laboratory of Molecular Metabolism, New York, NY 10065, USA.
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139
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Boriack-Sjodin PA, Swinger KK. Protein Methyltransferases: A Distinct, Diverse, and Dynamic Family of Enzymes. Biochemistry 2015; 55:1557-69. [PMID: 26652298 DOI: 10.1021/acs.biochem.5b01129] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyltransferase proteins make up a superfamily of enzymes that add one or more methyl groups to substrates that include protein, DNA, RNA, and small molecules. The subset of proteins that act upon arginine and lysine side chains are characterized as epigenetic targets because of their activity on histone molecules and their ability to affect transcriptional regulation. However, it is now clear that these enzymes target other protein substrates, as well, greatly expanding their potential impact on normal and disease biology. Protein methyltransferases are well-characterized structurally. In addition to revealing the overall architecture of the subfamilies of enzymes, structures of complexes with substrates and ligands have permitted detailed analysis of biochemical mechanism, substrate recognition, and design of potent and selective inhibitors. This review focuses on how knowledge gained from structural studies has impacted the understanding of this large class of epigenetic enzymes.
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Affiliation(s)
- P Ann Boriack-Sjodin
- Epizyme, Inc. , 400 Technology Square, Cambridge, Massachusetts 02139, United States
| | - Kerren K Swinger
- Epizyme, Inc. , 400 Technology Square, Cambridge, Massachusetts 02139, United States
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140
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Wang JQ, Cao WG. Key Signaling Events for Committing Mouse Pluripotent Stem Cells to the Germline Fate. Biol Reprod 2015; 94:24. [PMID: 26674564 DOI: 10.1095/biolreprod.115.135095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 12/07/2015] [Indexed: 01/01/2023] Open
Abstract
The process of germline development carries genetic information and preparatory totipotency across generations. The last decade has witnessed remarkable successes in the generation of germline cells from mouse pluripotent stem cells, especially induced germline cells with the capacity for producing viable offspring, suggesting clinical applications of induced germline cells in humans. However, to date, the culture systems for germline induction with accurate sex-specific meiosis and epigenetic reprogramming have not been well-established. In this study, we primarily focus on the mouse model to discuss key signaling events for germline induction. We review mechanisms of competent regulators on primordial germ cell induction and discuss current achievements and difficulties in inducing sex-specific germline development. Furthermore, we review the developmental identities of mouse embryonic stem cells and epiblast stem cells under certain defined culture conditions as it relates to the differentiation process of becoming germline cells.
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Affiliation(s)
- Jian-Qi Wang
- Transgenic and Stem Cell Core, Institute of Animal Sciences and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wen-Guang Cao
- Transgenic and Stem Cell Core, Institute of Animal Sciences and Veterinary Medicine, Chinese Academy of Agricultural Sciences, Beijing, China
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141
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Vervoort M, Meulemeester D, Béhague J, Kerner P. Evolution of Prdm Genes in Animals: Insights from Comparative Genomics. Mol Biol Evol 2015; 33:679-96. [PMID: 26560352 PMCID: PMC4760075 DOI: 10.1093/molbev/msv260] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Prdm genes encode transcription factors with a subtype of SET domain known as the PRDF1-RIZ (PR) homology domain and a variable number of zinc finger motifs. These genes are involved in a wide variety of functions during animal development. As most Prdm genes have been studied in vertebrates, especially in mice, little is known about the evolution of this gene family. We searched for Prdm genes in the fully sequenced genomes of 93 different species representative of all the main metazoan lineages. A total of 976 Prdm genes were identified in these species. The number of Prdm genes per species ranges from 2 to 19. To better understand how the Prdm gene family has evolved in metazoans, we performed phylogenetic analyses using this large set of identified Prdm genes. These analyses allowed us to define 14 different subfamilies of Prdm genes and to establish, through ancestral state reconstruction, that 11 of them are ancestral to bilaterian animals. Three additional subfamilies were acquired during early vertebrate evolution (Prdm5, Prdm11, and Prdm17). Several gene duplication and gene loss events were identified and mapped onto the metazoan phylogenetic tree. By studying a large number of nonmetazoan genomes, we confirmed that Prdm genes likely constitute a metazoan-specific gene family. Our data also suggest that Prdm genes originated before the diversification of animals through the association of a single ancestral SET domain encoding gene with one or several zinc finger encoding genes.
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Affiliation(s)
- Michel Vervoort
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France Institut Universitaire de France, Paris, France
| | - David Meulemeester
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Julien Béhague
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Pierre Kerner
- Institut Jacques Monod, CNRS, UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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142
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Nady N, Gupta A, Ma Z, Swigut T, Koide A, Koide S, Wysocka J. ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation. eLife 2015; 4:e10150. [PMID: 26523391 PMCID: PMC4749557 DOI: 10.7554/elife.10150] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/01/2015] [Indexed: 01/15/2023] Open
Abstract
Prdm14 is a sequence-specific transcriptional regulator of embryonic stem cell (ESC) pluripotency and primordial germ cell (PGC) formation. It exerts its function, at least in part, through repressing genes associated with epigenetic modification and cell differentiation. Here, we show that this repressive function is mediated through an ETO-family co-repressor Mtgr1, which tightly binds to the pre-SET/SET domains of Prdm14 and co-occupies its genomic targets in mouse ESCs. We generated two monobodies, synthetic binding proteins, targeting the Prdm14 SET domain and demonstrate their utility, respectively, in facilitating crystallization and structure determination of the Prdm14-Mtgr1 complex, or as genetically encoded inhibitor of the Prdm14-Mtgr1 interaction. Structure-guided point mutants and the monobody abrogated the Prdm14-Mtgr1 association and disrupted Prdm14's function in mESC gene expression and PGC formation in vitro. Altogether, our work uncovers the molecular mechanism underlying Prdm14-mediated repression and provides renewable reagents for studying and controlling Prdm14 functions. DOI:http://dx.doi.org/10.7554/eLife.10150.001 In animals, there are many different types of cells that perform different roles. For example, stem cells divide to produce new cells that may then become other types of cells such as muscle or skin cells. Most stem cells can only produce a limited range of other cell types, except for a subset known as ‘pluripotent’ stem cells that can give rise to cells of any type in the body. A protein called Prdm14 helps to keep stem cells in a pluripotent state. In mouse embryos, Prdm14 binds to and represses particular genes that promote a process by which the stem cells can change into other cell types. If Prdm14 is missing from pluripotent stem cells, these cells become more sensitive to signals that encourage them to become other types of cells, which can lead to the loss of pluripotency. Prdm14 contains a region called the SET domain. In other proteins, this domain can alter how DNA is packaged to help switch particular genes on or off. However, such activity has not been found for the SET domain of Prdm14, raising questions about how it actually works. Here, Nady, Gupta et al. show that Prdm14 tightly interacts with a protein called Mtgr1, which belongs to a family of proteins known to be involved in leukemia. The loss of Mtgr1 also leads to the loss of pluripotency in mouse stem cells and disrupts the formation of reproductive stem cells. Furthermore, Mtgr1 binds to the same genes as Prdm14. Next, Nady, Gupta et al. made synthetic proteins, termed monobodies, that bind to the Prdm14 SET domain. One such monobody enabled the authors to determine the three-dimensional structure of Prdm1 and Mtgr1, which revealed that the SET domain of Prdm14 has many points of contact with Mtgr1. Importantly, interaction between the two partners is crucial for these proteins to maintain pluripotency and promote the production of reproductive stem cells. Altogether, these findings identify Mtgr1 as a key binding partner of Prdm14 in pluripotent stem cells and uncover a role for the SET domain in this interaction. A future challenge will be to understand the roles of these proteins in leukemia and other diseases. DOI:http://dx.doi.org/10.7554/eLife.10150.002
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Affiliation(s)
- Nataliya Nady
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Ziyang Ma
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States.,National Institute of Environmental Health Sciences, , United States.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
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143
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Nahorski MS, Chen YC, Woods CG. New Mendelian Disorders of Painlessness. Trends Neurosci 2015; 38:712-724. [DOI: 10.1016/j.tins.2015.08.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 08/28/2015] [Accepted: 08/31/2015] [Indexed: 02/08/2023]
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144
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Zannino DA, Sagerström CG. An emerging role for prdm family genes in dorsoventral patterning of the vertebrate nervous system. Neural Dev 2015; 10:24. [PMID: 26499851 PMCID: PMC4620005 DOI: 10.1186/s13064-015-0052-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/13/2015] [Indexed: 12/13/2022] Open
Abstract
The embryonic vertebrate neural tube is divided along its dorsoventral (DV) axis into eleven molecularly discrete progenitor domains. Each of these domains gives rise to distinct neuronal cell types; the ventral-most six domains contribute to motor circuits, while the five dorsal domains contribute to sensory circuits. Following the initial neurogenesis step, these domains also generate glial cell types—either astrocytes or oligodendrocytes. This DV pattern is initiated by two morphogens—Sonic Hedgehog released from notochord and floor plate and Bone Morphogenetic Protein produced in the roof plate—that act in concentration gradients to induce expression of genes along the DV axis. Subsequently, these DV-restricted genes cooperate to define progenitor domains and to control neuronal cell fate specification and differentiation in each domain. Many genes involved in this process have been identified, but significant gaps remain in our understanding of the underlying genetic program. Here we review recent work identifying members of the Prdm gene family as novel regulators of DV patterning in the neural tube. Many Prdm proteins regulate transcription by controlling histone modifications (either via intrinsic histone methyltransferase activity, or by recruiting histone modifying enzymes). Prdm genes are expressed in spatially restricted domains along the DV axis of the neural tube and play important roles in the specification of progenitor domains, as well as in the subsequent differentiation of motor neurons and various types of interneurons. Strikingly, Prdm proteins appear to function by binding to, and modulating the activity of, other transcription factors (particularly bHLH proteins). The identity of key transcription factors in DV patterning of the neural tube has been elucidated previously (e.g. the nkx, bHLH and pax families), but it now appears that an additional family is also required and that it acts in a potentially novel manner.
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Affiliation(s)
- Denise A Zannino
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St./LRB815, Worcester, MA, 01605-2324, USA.
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St./LRB815, Worcester, MA, 01605-2324, USA.
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145
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Sound of silence: the properties and functions of repressive Lys methyltransferases. Nat Rev Mol Cell Biol 2015. [PMID: 26204160 DOI: 10.1038/nrm4029] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The methylation of histone Lys residues by Lys methyltransferases (KMTs) regulates chromatin organization and either activates or represses gene expression, depending on the residue that is targeted. KMTs are emerging as key components in several cellular processes, and their deregulation is often associated with pathogenesis. Here, we review the current knowledge on the main KMTs that are associated with gene silencing: namely, those responsible for methylating histone H3 Lys 9 (H3K9), H3K27 and H4K20. We discuss their biochemical properties and the various mechanisms by which they are targeted to the chromatin and regulate gene expression, as well as new data on the interplay between them and other chromatin modifiers.
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146
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Role of PRDM16 and its PR domain in the epigenetic regulation of myogenic and adipogenic genes during transdifferentiation of C2C12 cells. Gene 2015; 570:191-8. [DOI: 10.1016/j.gene.2015.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/02/2015] [Accepted: 06/05/2015] [Indexed: 12/18/2022]
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147
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Baker CL, Petkova P, Walker M, Flachs P, Mihola O, Trachtulec Z, Petkov PM, Paigen K. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots. PLoS Genet 2015; 11:e1005512. [PMID: 26368021 PMCID: PMC4569383 DOI: 10.1371/journal.pgen.1005512] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/17/2015] [Indexed: 02/04/2023] Open
Abstract
Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape. During formation of sperm and eggs chromosomes exchange DNA in a process known as recombination, creating new combinations responsible for much of the enormous diversity in populations. In some mammals, including humans, the locations of recombination are chosen by a DNA-binding protein named PRDM9. Importantly, there are tens to hundreds of different variations of the Prdm9 gene (termed alleles), many of which are predicted to bind a unique DNA sequence. This high frequency of variation results in many individuals having two different copies of Prdm9, and several lines of evidence indicate that alleles compete to initiate recombination. In seeking to understand the mechanism of this competition we found that Prdm9 activity is sensitive to the number of gene copies present, suggesting that availability of this protein is a limiting factor during recombination. Moreover, we found that variant forms of PRDM9 protein can physically interact suggesting that when this happens one variant can influence which hotspots will become activated. Genetic crosses in mice support these observations; the presence of a dominant Prdm9 allele can completely suppress recombination at some locations. We conclude that allele-dominance of PRDM9 is a consequence of protein-protein interaction and competition for DNA binding in a limited pool of molecules, thus shaping the recombination landscape in natural populations.
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Affiliation(s)
- Christopher L. Baker
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Pavlina Petkova
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Michael Walker
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Petr Flachs
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, v. v. i., Prague, Czech Republic
| | - Ondrej Mihola
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, v. v. i., Prague, Czech Republic
| | - Zdenek Trachtulec
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, v. v. i., Prague, Czech Republic
| | - Petko M. Petkov
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Kenneth Paigen
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
- * E-mail:
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148
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Vieira Braga FA, Hertoghs KML, Kragten NAM, Doody GM, Barnes NA, Remmerswaal EBM, Hsiao CC, Moerland PD, Wouters D, Derks IAM, van Stijn A, Demkes M, Hamann J, Eldering E, Nolte MA, Tooze RM, ten Berge IJM, van Gisbergen KPJM, van Lier RAW. Blimp-1 homolog Hobit identifies effector-type lymphocytes in humans. Eur J Immunol 2015; 45:2945-58. [DOI: 10.1002/eji.201545650] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/16/2015] [Accepted: 07/13/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Felipe A. Vieira Braga
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
| | | | - Natasja A. M. Kragten
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - Gina M. Doody
- Section of Experimental Haematology; Leeds Institute of Cancer and Pathology; University of Leeds; Leeds UK
| | - Nicholas A. Barnes
- Section of Experimental Haematology; Leeds Institute of Cancer and Pathology; University of Leeds; Leeds UK
| | - Ester B. M. Remmerswaal
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
- Internal Medicine; Renal Transplant Unit; AMC; Amsterdam The Netherlands
| | - Cheng-Chih Hsiao
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | | | - Diana Wouters
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
| | | | - Amber van Stijn
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
- Internal Medicine; Renal Transplant Unit; AMC; Amsterdam The Netherlands
| | - Marc Demkes
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - Jörg Hamann
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - Eric Eldering
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - Martijn A. Nolte
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - Reuben M. Tooze
- Section of Experimental Haematology; Leeds Institute of Cancer and Pathology; University of Leeds; Leeds UK
| | | | - Klaas P. J. M. van Gisbergen
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
| | - René A. W. van Lier
- Department of Hematopoiesis; Sanquin Research and Landsteiner Laboratory AMC/UvA; Amsterdam The Netherlands
- Department of Experimental Immunology; AMC; Amsterdam The Netherlands
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149
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Direct and positive regulation of Caenorhabditis elegans bed-3 by PRDM1/BLIMP1 ortholog BLMP-1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1229-36. [DOI: 10.1016/j.bbagrm.2015.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/28/2015] [Accepted: 07/29/2015] [Indexed: 11/19/2022]
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150
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Inoue M, Iwai R, Yamanishi E, Yamagata K, Komabayashi-Suzuki M, Honda A, Komai T, Miyachi H, Kitano S, Watanabe C, Teshima W, Mizutani KI. Deletion of Prdm8 impairs development of upper-layer neocortical neurons. Genes Cells 2015; 20:758-70. [PMID: 26283595 DOI: 10.1111/gtc.12274] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 06/15/2015] [Indexed: 01/17/2023]
Abstract
Upper-layer (UL) neocortical neurons are the most prominent distinguishing features of the mammalian neocortex compared with those of the avian dorsal cortex and are vastly expanded in primates. However, little is known about the identities of the genes that control the specification of UL neurons. Here, we found that Prdm8, a member of the PR (PRDI-BF1 and RIZ homology) domain protein family, was specifically expressed in the postnatal UL neocortex, particular those in late-born RORß-positive layer IV neurons. We generated homozygous Prdm8 knockout (Prdm8 KO) mice and found that the deletion of Prdm8 causes growth retardation and a reduced brain weight, although the brain weight-to-body weight ratio is unchanged at postnatal day 8 (P8). Immunohistochemistry showed that the relative UL thickness, but not the thickness of the deep layer (DL), was significantly reduced in Prdm8 KO mice compared with wild-type (WT) mice. In addition, we found that a number of late-born Brn2-positive UL neurons were significantly decreased in Prdm8 KO mice. To identify genes regulated by Prdm8 during neocortical development, we compared expression profiling analysis in Prdm8 KO and WT mice, and identified some candidate genes. These results suggest that the proper expression of Prdm8 is required for the normal development and construction of UL neurons in the mammalian neocortex.
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Affiliation(s)
- Mayuko Inoue
- Laboratory of Neural Differentiation, Graduate School of Brain Science, Doshisha University, Kyoto, 619-0225, Japan.,Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
| | - Ryota Iwai
- Laboratory of Neural Differentiation, Graduate School of Brain Science, Doshisha University, Kyoto, 619-0225, Japan
| | - Emiko Yamanishi
- Laboratory of Neural Differentiation, Graduate School of Brain Science, Doshisha University, Kyoto, 619-0225, Japan
| | - Kazuyuki Yamagata
- Laboratory of Neural Differentiation, Graduate School of Brain Science, Doshisha University, Kyoto, 619-0225, Japan
| | - Mariko Komabayashi-Suzuki
- Laboratory of Neural Differentiation, Graduate School of Brain Science, Doshisha University, Kyoto, 619-0225, Japan
| | - Aya Honda
- Laboratory of Neural Differentiation, Graduate School of Brain Science, Doshisha University, Kyoto, 619-0225, Japan
| | - Tae Komai
- Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
| | - Hitoshi Miyachi
- Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
| | - Satsuki Kitano
- Institute for Virus Research, Kyoto University, Kyoto, 606-8507, Japan
| | - Chisato Watanabe
- Laboratory of Neural Differentiation, Graduate School of Brain Science, Doshisha University, Kyoto, 619-0225, Japan
| | - Waka Teshima
- Laboratory of Neural Differentiation, Graduate School of Brain Science, Doshisha University, Kyoto, 619-0225, Japan
| | - Ken-ichi Mizutani
- Laboratory of Neural Differentiation, Graduate School of Brain Science, Doshisha University, Kyoto, 619-0225, Japan.,Japan Science and Technology Agency, PRESTO, Saitama, 332-0012, Japan
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