1
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Farley SJ, Grishok A, Zeldich E. Shaking up the silence: consequences of HMGN1 antagonizing PRC2 in the Down syndrome brain. Epigenetics Chromatin 2022; 15:39. [PMID: 36463299 PMCID: PMC9719135 DOI: 10.1186/s13072-022-00471-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/11/2022] [Indexed: 12/04/2022] Open
Abstract
Intellectual disability is a well-known hallmark of Down Syndrome (DS) that results from the triplication of the critical region of human chromosome 21 (HSA21). Major studies were conducted in recent years to gain an understanding about the contribution of individual triplicated genes to DS-related brain pathology. Global transcriptomic alterations and widespread changes in the establishment of neural lineages, as well as their differentiation and functional maturity, suggest genome-wide chromatin organization alterations in trisomy. High Mobility Group Nucleosome Binding Domain 1 (HMGN1), expressed from HSA21, is a chromatin remodeling protein that facilitates chromatin decompaction and is associated with acetylated lysine 27 on histone H3 (H3K27ac), a mark correlated with active transcription. Recent studies causatively linked overexpression of HMGN1 in trisomy and the development of DS-associated B cell acute lymphoblastic leukemia (B-ALL). HMGN1 has been shown to antagonize the activity of the Polycomb Repressive Complex 2 (PRC2) and prevent the deposition of histone H3 lysine 27 trimethylation mark (H3K27me3), which is associated with transcriptional repression and gene silencing. However, the possible ramifications of the increased levels of HMGN1 through the derepression of PRC2 target genes on brain cell pathology have not gained attention. In this review, we discuss the functional significance of HMGN1 in brain development and summarize accumulating reports about the essential role of PRC2 in the development of the neural system. Mechanistic understanding of how overexpression of HMGN1 may contribute to aberrant brain cell phenotypes in DS, such as altered proliferation of neural progenitors, abnormal cortical architecture, diminished myelination, neurodegeneration, and Alzheimer's disease-related pathology in trisomy 21, will facilitate the development of DS therapeutic approaches targeting chromatin.
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Affiliation(s)
- Sean J. Farley
- grid.189504.10000 0004 1936 7558Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Alla Grishok
- grid.189504.10000 0004 1936 7558Department of Biochemistry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA ,grid.189504.10000 0004 1936 7558Boston University Genome Science Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA USA
| | - Ella Zeldich
- Department of Anatomy and Neurobiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
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2
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Fulton SL, Wenderski W, Lepack AE, Eagle AL, Fanutza T, Bastle RM, Ramakrishnan A, Hays EC, Neal A, Bendl J, Farrelly LA, Al-Kachak A, Lyu Y, Cetin B, Chan JC, Tran TN, Neve RL, Roper RJ, Brennand KJ, Roussos P, Schimenti JC, Friedman AK, Shen L, Blitzer RD, Robison AJ, Crabtree GR, Maze I. Rescue of deficits by Brwd1 copy number restoration in the Ts65Dn mouse model of Down syndrome. Nat Commun 2022; 13:6384. [PMID: 36289231 PMCID: PMC9606253 DOI: 10.1038/s41467-022-34200-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/17/2022] [Indexed: 12/25/2022] Open
Abstract
With an incidence of ~1 in 800 births, Down syndrome (DS) is the most common chromosomal condition linked to intellectual disability worldwide. While the genetic basis of DS has been identified as a triplication of chromosome 21 (HSA21), the genes encoded from HSA21 that directly contribute to cognitive deficits remain incompletely understood. Here, we found that the HSA21-encoded chromatin effector, BRWD1, was upregulated in neurons derived from iPS cells from an individual with Down syndrome and brain of trisomic mice. We showed that selective copy number restoration of Brwd1 in trisomic animals rescued deficits in hippocampal LTP, cognition and gene expression. We demonstrated that Brwd1 tightly binds the BAF chromatin remodeling complex, and that increased Brwd1 expression promotes BAF genomic mistargeting. Importantly, Brwd1 renormalization rescued aberrant BAF localization, along with associated changes in chromatin accessibility and gene expression. These findings establish BRWD1 as a key epigenomic mediator of normal neurodevelopment and an important contributor to DS-related phenotypes.
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Affiliation(s)
- Sasha L Fulton
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford Medical School, Palo Alto, CA, 94305, USA
- Department of Genetics, Stanford Medical School, Palo Alto, CA, 94305, USA
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA, 94305, USA
| | - Ashley E Lepack
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Andrew L Eagle
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - Tomas Fanutza
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ryan M Bastle
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emma C Hays
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Arianna Neal
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jaroslav Bendl
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neuroepigenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lorna A Farrelly
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Amni Al-Kachak
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yang Lyu
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bulent Cetin
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jennifer C Chan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tina N Tran
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Rachael L Neve
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Randall J Roper
- Department of Biology, Indiana University-Purdue University, Indianapolis, IN, 46202, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Departments of Psychiatry and Genetics, Wu Tsai Institute, Yale School of Medicine, New Haven, CT, 065109, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Disease Neuroepigenomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- J.J. Peters Veterans Affairs Hospital, Bronx, NY, 10468, USA
| | - John C Schimenti
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Allyson K Friedman
- Department of Biological Sciences, City University of New York-Hunter College, New York, NY, 10065, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert D Blitzer
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alfred J Robison
- Department of Physiology, Michigan State University, East Lansing, MI, 48824, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford Medical School, Palo Alto, CA, 94305, USA
- Department of Genetics, Stanford Medical School, Palo Alto, CA, 94305, USA
- Department of Developmental Biology, Stanford Medical School, Palo Alto, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University, Palo Alto, CA, 94305, USA
| | - Ian Maze
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Howard Hughes Medical Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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3
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Li Z, Klein JA, Rampam S, Kurzion R, Campbell NB, Patel Y, Haydar TF, Zeldich E. Asynchronous excitatory neuron development in an isogenic cortical spheroid model of Down syndrome. Front Neurosci 2022; 16:932384. [PMID: 36161168 PMCID: PMC9504873 DOI: 10.3389/fnins.2022.932384] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022] Open
Abstract
The intellectual disability (ID) in Down syndrome (DS) is thought to result from a variety of developmental deficits such as alterations in neural progenitor division, neurogenesis, gliogenesis, cortical architecture, and reduced cortical volume. However, the molecular processes underlying these neurodevelopmental changes are still elusive, preventing an understanding of the mechanistic basis of ID in DS. In this study, we used a pair of isogenic (trisomic and euploid) induced pluripotent stem cell (iPSC) lines to generate cortical spheroids (CS) that model the impact of trisomy 21 on brain development. Cortical spheroids contain neurons, astrocytes, and oligodendrocytes and they are widely used to approximate early neurodevelopment. Using single cell RNA sequencing (scRNA-seq), we uncovered cell type-specific transcriptomic changes in the trisomic CS. In particular, we found that excitatory neuron populations were most affected and that a specific population of cells with a transcriptomic profile resembling layer IV cortical neurons displayed the most profound divergence in developmental trajectory between trisomic and euploid genotypes. We also identified candidate genes potentially driving the developmental asynchrony between trisomic and euploid excitatory neurons. Direct comparison between the current isogenic CS scRNA-seq data and previously published datasets revealed several recurring differentially expressed genes between DS and control samples. Altogether, our study highlights the power and importance of cell type-specific analyses within a defined genetic background, coupled with broader examination of mixed samples, to comprehensively evaluate cellular phenotypes in the context of DS.
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Affiliation(s)
- Zhen Li
- Center for Neuroscience Research, Children’s National Hospital, Washington, DC, United States
| | - Jenny A. Klein
- Center for Neuroscience Research, Children’s National Hospital, Washington, DC, United States
- Graduate Program for Neuroscience, Boston University, Boston, MA, United States
| | - Sanjeev Rampam
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Ronni Kurzion
- Department of Chemistry, Boston University, Boston, MA, United States
| | | | - Yesha Patel
- Department of Anatomy and Neurobiology, Boston University, Boston, MA, United States
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, United States
| | - Tarik F. Haydar
- Center for Neuroscience Research, Children’s National Hospital, Washington, DC, United States
| | - Ella Zeldich
- Department of Anatomy and Neurobiology, Boston University, Boston, MA, United States
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4
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Innocenti F, Fiorentino G, Cimadomo D, Soscia D, Garagna S, Rienzi L, Ubaldi FM, Zuccotti M. Maternal effect factors that contribute to oocytes developmental competence: an update. J Assist Reprod Genet 2022; 39:861-871. [PMID: 35165782 PMCID: PMC9051001 DOI: 10.1007/s10815-022-02434-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/09/2022] [Indexed: 11/30/2022] Open
Abstract
Oocyte developmental competence is defined as the capacity of the female gamete to be fertilized and sustain development to the blastocyst stage. Epigenetic reprogramming, a correct cell division pattern, and an efficient DNA damage response are all critical events that, before embryonic genome activation, are governed by maternally inherited factors such as maternal-effect gene (MEG) products. Although these molecules are stored inside the oocyte until ovulation and exert their main role during fertilization and preimplantation development, some of them are already functioning during folliculogenesis and oocyte meiosis resumption. This mini review summarizes the crucial roles played by MEGs during oocyte maturation, fertilization, and preimplantation development with a direct/indirect effect on the acquisition or maintenance of oocyte competence. Our aim is to inspire future research on a topic with potential clinical perspectives for the prediction and treatment of female infertility.
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Affiliation(s)
- Federica Innocenti
- GeneraLife IVF, Clinica Valle Giulia, via G. de Notaris, 2b, 00197, Rome, Italy
| | - Giulia Fiorentino
- Laboratory of Developmental Biology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.,Center for Health Technologies, University of Pavia, Pavia, Italy
| | - Danilo Cimadomo
- GeneraLife IVF, Clinica Valle Giulia, via G. de Notaris, 2b, 00197, Rome, Italy.
| | - Daria Soscia
- GeneraLife IVF, Clinica Valle Giulia, via G. de Notaris, 2b, 00197, Rome, Italy
| | - Silvia Garagna
- Laboratory of Developmental Biology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.,Center for Health Technologies, University of Pavia, Pavia, Italy
| | - Laura Rienzi
- GeneraLife IVF, Clinica Valle Giulia, via G. de Notaris, 2b, 00197, Rome, Italy
| | | | - Maurizio Zuccotti
- Laboratory of Developmental Biology, Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.,Center for Health Technologies, University of Pavia, Pavia, Italy
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5
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Muddassir M, Soni K, Sangani CB, Alarifi A, Afzal M, Abduh NAY, Duan Y, Bhadja P. Bromodomain and BET family proteins as epigenetic targets in cancer therapy: their degradation, present drugs, and possible PROTACs. RSC Adv 2021; 11:612-636. [PMID: 35746919 PMCID: PMC9133982 DOI: 10.1039/d0ra07971e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/28/2020] [Indexed: 12/27/2022] Open
Abstract
Alteration in the pattern of epigenetic marking leads to cancer, neurological disorders, inflammatory problems etc. These changes are due to aberration in histone modification enzymes that function as readers, writers and erasers. Bromodomains (BDs) and BET proteins that recognize acetylation of chromatin regulate gene expression. To block the function of any of these BrDs and/or BET protein can be a controlling agent in disorders such as cancer. BrDs and BET proteins are now emerging as targets for new therapeutic development. Traditional drugs like enzyme inhibitors and protein–protein inhibitors have many limitations. Recently Proteolysis-Targeting Chimeras (PROTACs) have become an advanced tool in therapeutic intervention as they remove disease causing proteins. This review provides an overview of the development and mechanisms of PROTACs for BRD and BET protein regulation in cancer and advanced possibilities of genetic technologies in therapeutics. Alteration in the pattern of epigenetic marking leads to cancer, neurological disorders, inflammatory problems etc.![]()
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Affiliation(s)
- Mohd. Muddassir
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Kunjal Soni
- Shri Maneklal M. Patel Institute of Sciences and Research
- Kadi Sarva Vishwavidyalaya University
- Gandhinagar
- India
| | - Chetan B. Sangani
- Shri Maneklal M. Patel Institute of Sciences and Research
- Kadi Sarva Vishwavidyalaya University
- Gandhinagar
- India
| | - Abdullah Alarifi
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Mohd. Afzal
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Naaser A. Y. Abduh
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Yongtao Duan
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases
- Zhengzhou Children's Hospital
- Zhengzhou University
- Zhengzhou 450018
- China
| | - Poonam Bhadja
- Arthropod Ecology and Biological Control Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Environment and Labour Safety
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6
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McLean KC, Mandal M. It Takes Three Receptors to Raise a B Cell. Trends Immunol 2020; 41:629-642. [PMID: 32451219 DOI: 10.1016/j.it.2020.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 12/14/2022]
Abstract
As the unique source of diverse immunoglobulin repertoires, B lymphocytes are an indispensable part of humoral immunity. B cell progenitors progress through sequential and mutually exclusive states of proliferation and recombination, coordinated by cytokines and chemokines. Mutations affecting the crucial pre-B cell checkpoint result in immunodeficiency, autoimmunity, and leukemia. This checkpoint was previously modeled by the signaling of two opposing receptors, IL-7R and the pre-BCR. We provide an update to this model in which three receptors, IL-7R, pre-BCR, and CXCR4, work in concert to coordinate both the proper positioning of B cell progenitors in the bone marrow (BM) microenvironment and their progression through the pre-B checkpoint. Furthermore, signaling initiated by all three receptors directly instructs cell fate and developmental progression.
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Affiliation(s)
- Kaitlin C McLean
- Section of Rheumatology, and Gwen Knapp Center for Lupus and Immunology Research, Department of Medicine, University of Chicago, IL 60637, USA
| | - Malay Mandal
- Section of Rheumatology, and Gwen Knapp Center for Lupus and Immunology Research, Department of Medicine, University of Chicago, IL 60637, USA.
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7
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Small Molecules Targeting the Specific Domains of Histone-Mark Readers in Cancer Therapy. Molecules 2020; 25:molecules25030578. [PMID: 32013155 PMCID: PMC7037402 DOI: 10.3390/molecules25030578] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
Epigenetic modifications (or epigenetic tags) on DNA and histones not only alter the chromatin structure, but also provide a recognition platform for subsequent protein recruitment and enable them to acquire executive instructions to carry out specific intracellular biological processes. In cells, different epigenetic-tags on DNA and histones are often recognized by the specific domains in proteins (readers), such as bromodomain (BRD), chromodomain (CHD), plant homeodomain (PHD), Tudor domain, Pro-Trp-Trp-Pro (PWWP) domain and malignant brain tumor (MBT) domain. Recent accumulating data reveal that abnormal intracellular histone modifications (histone marks) caused by tumors can be modulated by small molecule-mediated changes in the activity of the above domains, suggesting that small molecules targeting histone-mark reader domains may be the trend of new anticancer drug development. Here, we summarize the protein domains involved in histone-mark recognition, and introduce recent research findings about small molecules targeting histone-mark readers in cancer therapy.
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8
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Zaware N, Zhou MM. Bromodomain biology and drug discovery. Nat Struct Mol Biol 2019; 26:870-879. [PMID: 31582847 DOI: 10.1038/s41594-019-0309-8] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022]
Abstract
The bromodomain (BrD) is a conserved structural module found in chromatin- and transcription-associated proteins that acts as the primary reader for acetylated lysine residues. This basic activity endows BrD proteins with versatile functions in the regulation of protein-protein interactions mediating chromatin-templated gene transcription, DNA recombination, replication and repair. Consequently, BrD proteins are involved in the pathogenesis of numerous human diseases. In this Review, we highlight our current understanding of BrD biology, and discuss the latest development of small-molecule inhibitors targeting BrDs as emerging epigenetic therapies for cancer and inflammatory disorders.
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Affiliation(s)
- Nilesh Zaware
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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9
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Zainal Abidin S, Fam SZ, Chong CE, Abdullah S, Cheah PS, Nordin N, Ling KH. miR-3099 promotes neurogenesis and inhibits astrogliogenesis during murine neural development. Gene 2019; 697:201-212. [PMID: 30769142 DOI: 10.1016/j.gene.2019.02.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 12/29/2022]
Abstract
MicroRNA-3099 is highly expressed during neuronal differentiation and development of the central nervous system. Here we characterised the role of miR-3099 during neural differentiation and embryonic brain development using a stable and regulatable mouse embryonic stem cell culture system for miR-3099 expression and in utero electroporation of miR-3099 expression construct into E15.5 embryonic mouse brains. In the in vitro system, miR-3099 overexpression upregulated gene related to neuronal markers such as Tuj1, NeuN, Gat1, vGluT1 and vGluT2. In contrast, gene related to astrocyte markers (Gfap, S100β and Slc1a3) were suppressed upon overexpression of miR-3099. Furthermore, miR-3099 overexpression between E15.5 and E18.5 mouse embryonic brains led to disorganised neuronal migration potentially due to significantly decreased Gfap+ cells. Collectively, our results indicated that miR-3099 plays a role in modulating and regulating expression of key markers involved in neuronal differentiation. In silico analysis was also performed to identify miR-3099 homologues in the human genome, and candidates were validated by stem-loop RT-qPCR. Analysis of the miR-3099 seed sequence AGGCUA against human transcriptomes revealed that a potential miRNA, mds21 (Chr21:39186698-39186677) (GenBank accession ID: MK521584), was 100% identical to the miR-3099 seed sequence. Mds21 expression was observed and validated in various human cell lines (293FT, human Wharton's jelly and dental pulp mesenchymal stem cells, and MCF-7, MDA-MB-231, C-Sert, SW780, RT112, 5637, EJ28 and SH-SY5Y cells), with the highest levels detected in human mesenchymal stem cell lines. The analysis validated mds21 as a novel miRNA and a novel homologue of miR-3099 in the human genome.
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Affiliation(s)
- Shahidee Zainal Abidin
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Sze-Zheng Fam
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Chan-Eng Chong
- Department of Genetics and Molecular Pathology, SA Pathology and University of South Australia Alliance, Adelaide, South Australia, Australia
| | - Syahril Abdullah
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Pike-See Cheah
- Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Norshariza Nordin
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - King-Hwa Ling
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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10
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Mandal M, Maienschein-Cline M, Maffucci P, Veselits M, Kennedy DE, McLean KC, Okoreeh MK, Karki S, Cunningham-Rundles C, Clark MR. BRWD1 orchestrates epigenetic landscape of late B lymphopoiesis. Nat Commun 2018; 9:3888. [PMID: 30250168 PMCID: PMC6155124 DOI: 10.1038/s41467-018-06165-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/20/2018] [Indexed: 12/30/2022] Open
Abstract
Transcription factor (TF) networks determine cell fate in hematopoiesis. However, how TFs cooperate with other regulatory mechanisms to instruct transcription remains poorly understood. Here we show that in small pre-B cells, the lineage restricted epigenetic reader BRWD1 closes early development enhancers and opens the enhancers of late B lymphopoiesis to TF binding. BRWD1 regulates over 7000 genes to repress proliferative and induce differentiation programs. However, BRWD1 does not regulate the expression of TFs required for B lymphopoiesis. Hypogammaglobulinemia patients with BRWD1 mutations have B-cell transcriptional profiles and enhancer landscapes similar to those observed in Brwd1-/- mice. These data indicate that, in both mice and humans, BRWD1 is a master orchestrator of enhancer accessibility that cooperates with TF networks to drive late B-cell development. B-cell development is tightly regulated by transcription programs that are coordinated by transcription factors (TF) and locus accessibility. Here the authors show that, in mice and humans, the epigenetic reader BRWD1 inhibits and promotes the accessibility of enhancers for early and late B lymphopoiesis, respectively.
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Affiliation(s)
- Malay Mandal
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA.
| | - Mark Maienschein-Cline
- Core for Research Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Patrick Maffucci
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Margaret Veselits
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Domenick E Kennedy
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Kaitlin C McLean
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Michael K Okoreeh
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA
| | - Sophiya Karki
- Department of Research Biology, Genentech, South San Francisco, California, USA
| | - Charlotte Cunningham-Rundles
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Division of Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marcus R Clark
- Department of Medicine, Section of Rheumatology and Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, Illinois, USA.
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11
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Fujisawa T, Filippakopoulos P. Functions of bromodomain-containing proteins and their roles in homeostasis and cancer. Nat Rev Mol Cell Biol 2017; 18:246-262. [PMID: 28053347 DOI: 10.1038/nrm.2016.143] [Citation(s) in RCA: 381] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bromodomains (BRDs) are evolutionarily conserved protein-protein interaction modules that are found in a wide range of proteins with diverse catalytic and scaffolding functions and are present in most tissues. BRDs selectively recognize and bind to acetylated Lys residues - particularly in histones - and thereby have important roles in the regulation of gene expression. BRD-containing proteins are frequently dysregulated in cancer, they participate in gene fusions that generate diverse, frequently oncogenic proteins, and many cancer-causing mutations have been mapped to the BRDs themselves. Importantly, BRDs can be targeted by small-molecule inhibitors, which has stimulated many translational research projects that seek to attenuate the aberrant functions of BRD-containing proteins in disease.
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Affiliation(s)
- Takao Fujisawa
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford
| | - Panagis Filippakopoulos
- Ludwig Institute for Cancer Research, Old Road Campus Research Building, Roosevelt Drive, Oxford.,Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
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12
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Gentile G, Ceccarelli M, Micheli L, Tirone F, Cavallaro S. Functional Genomics Identifies Tis21-Dependent Mechanisms and Putative Cancer Drug Targets Underlying Medulloblastoma Shh-Type Development. Front Pharmacol 2016; 7:449. [PMID: 27965576 PMCID: PMC5127835 DOI: 10.3389/fphar.2016.00449] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/09/2016] [Indexed: 12/11/2022] Open
Abstract
We have recently generated a novel medulloblastoma (MB) mouse model with activation of the Shh pathway and lacking the MB suppressor Tis21 (Patched1+/-/Tis21KO ). Its main phenotype is a defect of migration of the cerebellar granule precursor cells (GCPs). By genomic analysis of GCPs in vivo, we identified as drug target and major responsible of this defect the down-regulation of the promigratory chemokine Cxcl3. Consequently, the GCPs remain longer in the cerebellum proliferative area, and the MB frequency is enhanced. Here, we further analyzed the genes deregulated in a Tis21-dependent manner (Patched1+/-/Tis21 wild-type vs. Ptch1+/-/Tis21 knockout), among which are a number of down-regulated tumor inhibitors and up-regulated tumor facilitators, focusing on pathways potentially involved in the tumorigenesis and on putative new drug targets. The data analysis using bioinformatic tools revealed: (i) a link between the Shh signaling and the Tis21-dependent impairment of the GCPs migration, through a Shh-dependent deregulation of the clathrin-mediated chemotaxis operating in the primary cilium through the Cxcl3-Cxcr2 axis; (ii) a possible lineage shift of Shh-type GCPs toward retinal precursor phenotype, i.e., the neural cell type involved in group 3 MB; (iii) the identification of a subset of putative drug targets for MB, involved, among the others, in the regulation of Hippo signaling and centrosome assembly. Finally, our findings define also the role of Tis21 in the regulation of gene expression, through epigenetic and RNA processing mechanisms, influencing the fate of the GCPs.
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Affiliation(s)
- Giulia Gentile
- Institute of Neurological Sciences, National Research Council Catania, Italy
| | - Manuela Ceccarelli
- Institute of Cell Biology and Neurobiology, National Research Council, Fondazione Santa Lucia Rome, Italy
| | - Laura Micheli
- Institute of Cell Biology and Neurobiology, National Research Council, Fondazione Santa Lucia Rome, Italy
| | - Felice Tirone
- Institute of Cell Biology and Neurobiology, National Research Council, Fondazione Santa Lucia Rome, Italy
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13
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Where Environment Meets Cognition: A Focus on Two Developmental Intellectual Disability Disorders. Neural Plast 2016; 2016:4235898. [PMID: 27547454 PMCID: PMC4980517 DOI: 10.1155/2016/4235898] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/03/2016] [Indexed: 11/22/2022] Open
Abstract
One of the most challenging questions in neuroscience is to dissect how learning and memory, the foundational pillars of cognition, are grounded in stable, yet plastic, gene expression states. All known epigenetic mechanisms such as DNA methylation and hydroxymethylation, histone modifications, chromatin remodelling, and noncoding RNAs regulate brain gene expression, both during neurodevelopment and in the adult brain in processes related to cognition. On the other hand, alterations in the various components of the epigenetic machinery have been linked to well-known causes of intellectual disability disorders (IDDs). Two examples are Down Syndrome (DS) and Fragile X Syndrome (FXS), where global and local epigenetic alterations lead to impairments in synaptic plasticity, memory, and learning. Since epigenetic modifications are reversible, it is theoretically possible to use epigenetic drugs as cognitive enhancers for the treatment of IDDs. Epigenetic treatments act in a context specific manner, targeting different regions based on cell and state specific chromatin accessibility, facilitating the establishment of the lost balance. Here, we discuss epigenetic studies of IDDs, focusing on DS and FXS, and the use of epidrugs in combinatorial therapies for IDDs.
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14
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Histone reader BRWD1 targets and restricts recombination to the Igk locus. Nat Immunol 2015; 16:1094-103. [PMID: 26301565 PMCID: PMC4575638 DOI: 10.1038/ni.3249] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/15/2015] [Indexed: 12/12/2022]
Abstract
B lymphopoiesis requires that immunoglobulin genes be accessible to the RAG1-RAG2 recombinase. However, the RAG proteins bind widely to open chromatin suggesting that additional mechanisms must restrict RAG-mediated DNA cleavage. Here, we demonstrate developmental downregulation of interleukin 7 (IL-7) receptor signaling in small pre-B cells induced expression of the bromodomain family member BRWD1, which was recruited to a specific epigenetic landscape at Igk dictated by pre-BCR-dependent Erk activation. BRWD1 enhanced RAG recruitment, increased gene accessibility and positioned nucleosomes 5′ to each Jκ recombination signal sequence. BRWD1 thus targets recombination to Igk and places recombination within the context of signaling cascades that control B cell development. Our findings provide a paradigm in which, at any particular antigen receptor locus, specialized mechanisms enforce lineage and stage specific recombination.
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15
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Pattabiraman S, Baumann C, Guisado D, Eppig JJ, Schimenti JC, De La Fuente R. Mouse BRWD1 is critical for spermatid postmeiotic transcription and female meiotic chromosome stability. ACTA ACUST UNITED AC 2014; 208:53-69. [PMID: 25547156 PMCID: PMC4284233 DOI: 10.1083/jcb.201404109] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Exhibiting sexually dimorphic roles in mice, BRWD1 is essential for proper meiotic chromosome condensation and telomere structure during oogenesis and for haploid-specific gene transcription during postmeiotic sperm differentiation. Postmeiotic gene expression is essential for development and maturation of sperm and eggs. We report that the dual bromodomain-containing protein BRWD1, which is essential for both male and female fertility, promotes haploid spermatid–specific transcription but has distinct roles in oocyte meiotic progression. Brwd1 deficiency caused down-regulation of ∼300 mostly spermatid-specific transcripts in testis, including nearly complete elimination of those encoding the protamines and transition proteins, but was not associated with global epigenetic changes in chromatin, which suggests that BRWD1 acts selectively. In females, Brwd1 ablation caused severe chromosome condensation and structural defects associated with abnormal telomere structure but only minor changes in gene expression at the germinal vesicle stage, including more than twofold overexpression of the histone methyltransferase MLL5 and LINE-1 elements transposons. Thus, loss of BRWD1 function interferes with the completion of oogenesis and spermatogenesis through sexually dimorphic mechanisms: it is essential in females for epigenetic control of meiotic chromosome stability and in males for haploid gene transcription during postmeiotic sperm differentiation.
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Affiliation(s)
- Shrivatsav Pattabiraman
- Department of Biomedical Sciences and Center for Vertebrate Genomics, Cornell University, College of Veterinary Medicine, Ithaca, NY 14853 Department of Biomedical Sciences and Center for Vertebrate Genomics, Cornell University, College of Veterinary Medicine, Ithaca, NY 14853
| | - Claudia Baumann
- Department of Physiology and Pharmacology, University of Georgia College of Veterinary Medicine, Athens, GA 30602
| | - Daniela Guisado
- Department of Biomedical Sciences and Center for Vertebrate Genomics, Cornell University, College of Veterinary Medicine, Ithaca, NY 14853 Department of Biomedical Sciences and Center for Vertebrate Genomics, Cornell University, College of Veterinary Medicine, Ithaca, NY 14853
| | | | - John C Schimenti
- Department of Biomedical Sciences and Center for Vertebrate Genomics, Cornell University, College of Veterinary Medicine, Ithaca, NY 14853 Department of Biomedical Sciences and Center for Vertebrate Genomics, Cornell University, College of Veterinary Medicine, Ithaca, NY 14853
| | - Rabindranath De La Fuente
- Department of Physiology and Pharmacology, University of Georgia College of Veterinary Medicine, Athens, GA 30602
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16
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Dekker AD, De Deyn PP, Rots MG. Epigenetics: The neglected key to minimize learning and memory deficits in Down syndrome. Neurosci Biobehav Rev 2014; 45:72-84. [DOI: 10.1016/j.neubiorev.2014.05.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/04/2014] [Accepted: 05/13/2014] [Indexed: 10/25/2022]
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17
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Functional transcriptome analysis of the postnatal brain of the Ts1Cje mouse model for Down syndrome reveals global disruption of interferon-related molecular networks. BMC Genomics 2014; 15:624. [PMID: 25052193 PMCID: PMC4124147 DOI: 10.1186/1471-2164-15-624] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/16/2014] [Indexed: 12/25/2022] Open
Abstract
Background The Ts1Cje mouse model of Down syndrome (DS) has partial triplication of mouse chromosome 16 (MMU16), which is partially homologous to human chromosome 21. These mice develop various neuropathological features identified in DS individuals. We analysed the effect of partial triplication of the MMU16 segment on global gene expression in the cerebral cortex, cerebellum and hippocampus of Ts1Cje mice at 4 time-points: postnatal day (P)1, P15, P30 and P84. Results Gene expression profiling identified a total of 317 differentially expressed genes (DEGs), selected from various spatiotemporal comparisons, between Ts1Cje and disomic mice. A total of 201 DEGs were identified from the cerebellum, 129 from the hippocampus and 40 from the cerebral cortex. Of these, only 18 DEGs were identified as common to all three brain regions and 15 were located in the triplicated segment. We validated 8 selected DEGs from the cerebral cortex (Brwd1, Donson, Erdr1, Ifnar1, Itgb8, Itsn1, Mrps6 and Tmem50b), 18 DEGs from the cerebellum (Atp5o, Brwd1, Donson, Dopey2, Erdr1, Hmgn1, Ifnar1, Ifnar2, Ifngr2, Itgb8, Itsn1, Mrps6, Paxbp1, Son, Stat1, Tbata, Tmem50b and Wrb) and 11 DEGs from the hippocampus (Atp5o, Brwd1, Cbr1, Donson, Erdr1, Itgb8, Itsn1, Morc3, Son, Tmem50b and Wrb). Functional clustering analysis of the 317 DEGs identified interferon-related signal transduction as the most significantly dysregulated pathway in Ts1Cje postnatal brain development. RT-qPCR and western blotting analysis showed both Ifnar1 and Stat1 were over-expressed in P84 Ts1Cje cerebral cortex and cerebellum as compared to wild type littermates. Conclusions These findings suggest over-expression of interferon receptor may lead to over-stimulation of Jak-Stat signaling pathway which may contribute to the neuropathology in Ts1Cje or DS brain. The role of interferon mediated activation or inhibition of signal transduction including Jak-Stat signaling pathway has been well characterized in various biological processes and disease models including DS but information pertaining to the role of this pathway in the development and function of the Ts1Cje or DS brain remains scarce and warrants further investigation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-624) contains supplementary material, which is available to authorized users.
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18
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Bryois J, Buil A, Evans DM, Kemp JP, Montgomery SB, Conrad DF, Ho KM, Ring S, Hurles M, Deloukas P, Davey Smith G, Dermitzakis ET. Cis and trans effects of human genomic variants on gene expression. PLoS Genet 2014; 10:e1004461. [PMID: 25010687 PMCID: PMC4091791 DOI: 10.1371/journal.pgen.1004461] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/12/2014] [Indexed: 11/18/2022] Open
Abstract
Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation. In order to detect genetic variations affecting gene expression, we performed association analysis of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with gene expression measured in 869 lymphoblastoid cell lines of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort in cis and in trans. We discovered that 3,534 genes (false discovery rate (FDR) = 5%) are affected by an expression quantitative trait locus (eQTL) in cis and 48 genes are affected in trans. We observed that CNVs are more likely to be eQTLs than SNPs. In addition, we found that variants associated to complex traits and diseases are enriched for trans-eQTLs and that trans-eQTLs are enriched for cis-eQTLs. As a variant affecting both a gene in cis and in trans suggests that the cis gene is functionally linked to the trans gene expression, we looked specifically for trans effects of cis-eQTLs. We discovered that 26 cis-eQTLs are associated to 92 genes in trans with the cis-eQTLs of the transcriptions factors BATF3 and HMX2 affecting the most genes. We then explored if the variation of the level of expression of the cis genes were causally affecting the level of expression of the trans genes and discovered several causal relationships between variation in the level of expression of the cis gene and variation of the level of expression of the trans gene. This analysis shows that a large sample size allows the discovery of secondary effects of human variations on gene expression that can be used to construct short directed gene regulatory networks.
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Affiliation(s)
- Julien Bryois
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - David M. Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - John P. Kemp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Stephen B. Montgomery
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Department of Pathology and Genetics, Stanford University, Stanford, California, United States of America
| | | | - Karen M. Ho
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kindom
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
- Center of Excellence for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
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Domains of genome-wide gene expression dysregulation in Down's syndrome. Nature 2014; 508:345-50. [PMID: 24740065 DOI: 10.1038/nature13200] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 03/04/2014] [Indexed: 12/27/2022]
Abstract
Trisomy 21 is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in trisomy 21, and to eliminate the noise of genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of monozygotic twins discordant for trisomy 21. Here we show that the differential expression between the twins is organized in domains along all chromosomes that are either upregulated or downregulated. These gene expression dysregulation domains (GEDDs) can be defined by the expression level of their gene content, and are well conserved in induced pluripotent stem cells derived from the twins' fibroblasts. Comparison of the transcriptome of the Ts65Dn mouse model of Down's syndrome and normal littermate mouse fibroblasts also showed GEDDs along the mouse chromosomes that were syntenic in human. The GEDDs correlate with the lamina-associated (LADs) and replication domains of mammalian cells. The overall position of LADs was not altered in trisomic cells; however, the H3K4me3 profile of the trisomic fibroblasts was modified and accurately followed the GEDD pattern. These results indicate that the nuclear compartments of trisomic cells undergo modifications of the chromatin environment influencing the overall transcriptome, and that GEDDs may therefore contribute to some trisomy 21 phenotypes.
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20
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Regulatory role of the 90-kDa-heat-shock protein (Hsp90) and associated factors on gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:71-87. [DOI: 10.1016/j.bbagrm.2013.12.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 12/23/2013] [Accepted: 12/26/2013] [Indexed: 12/31/2022]
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21
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Barbieri I, Cannizzaro E, Dawson MA. Bromodomains as therapeutic targets in cancer. Brief Funct Genomics 2013; 12:219-30. [DOI: 10.1093/bfgp/elt007] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Ramshackle (Brwd3) promotes light-induced ubiquitylation of Drosophila Cryptochrome by DDB1-CUL4-ROC1 E3 ligase complex. Proc Natl Acad Sci U S A 2013; 110:4980-5. [PMID: 23479607 DOI: 10.1073/pnas.1303234110] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cryptochrome (CRY) is the primary circadian photoreceptor in Drosophila. It resets the circadian clock by promoting light-induced degradation of the clock proteins Timeless and Period, as well as its own proteolysis. The E3 ligases that ubiquitylate Timeless and Period before degradation are known and it is known that Drosophila (d) CRY is degraded by the ubiquitin-proteasome system as well. To identify the E3 ligase for dCRY we screened candidates in S2 cells by RNAi. Knockdown of each of the 25 putative F-box proteins identified by bioinformatics did not attenuate the light-induced degradation of dCRY. However, knockdown of a WD40 protein, Bromodomain and WD repeat domain containing 3 (Brwd3) (CG31132/Ramshackle) caused strong attenuation of dCRY degradation following light exposure. We found that BRWD3 functions as a Damage-specific DNA binding protein 1 (DDB1)- and CULLIN (CUL)4-associated factor in a Cullin4-RING Finger E3 Ligase (CRL4) that mediates light-dependent binding of dCRY to CUL4-ROC1-DDB1-BRWD3, inducing ubiquitylation of dCRY and its light-induced degradation. Thus, this study identifies a light-activated E3 ligase complex essential for light-mediated CRY degradation in Drosophila cells.
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Heubeck B, Wendler O, Bumm K, Schäfer R, Müller-Vogt U, Häusler M, Meese E, Iro H, Steinhart H. Tumor-associated antigenic pattern in squamous cell carcinomas of the head and neck – Analysed by SEREX. Eur J Cancer 2013; 49:e1-7. [PMID: 16837193 DOI: 10.1016/j.ejca.2005.09.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 09/06/2005] [Indexed: 11/22/2022]
Abstract
Most immuno-therapeutic approaches are based on tumor-associated antigens and many newly identified proteins have led to trials exploiting their possible therapeutic applicability. So far only limited information on the antigenic profile of head and neck squamous cell carcinomas (HNSCC) exists. Serological analysis of tumor antigens by recombinant cDNA expression cloning (SEREX) was used to identify the immunogenic patterns in our HNSCC patient collective. A cDNA expression library derived from a pharynx HNSCC case was screened with autologous and heterologous sera. Thirty-seven positive clones coding for 17 immunoreactive gene products, which elicited an in vivo tumor response, were found. Results were confirmed and extended by expression analysis using RT-PCR and in situ-hybridisation. The protein-sequence of five clones exists so far only hypothetically. Of all identified proteins only KIAA0530 has previously been associated with a HNSCC related immune response. All other proteins have not yet been described in a context with HNSCC antigenic patterns. Antibodies against a heat shock transcription factor 2 (HSF2) were found in 2 out of 10 sera from HNSCC patients. In summary, using the SEREX technique, we isolated 17 immunogenic antigens in HNSCC's and confirmed the clinical relevance of KIAA0530. Further analysis concerning their feasibility as target structures for an immunotherapy approach is currently conducted.
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Affiliation(s)
- Bernd Heubeck
- Department of Otorhinolaryngology Head and Neck Surgery, University of Erlangen-Nuremberg, Waldstrasse 1, 91054 Erlangen, Germany.
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24
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Filippakopoulos P, Knapp S. The bromodomain interaction module. FEBS Lett 2012; 586:2692-704. [DOI: 10.1016/j.febslet.2012.04.045] [Citation(s) in RCA: 281] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 04/20/2012] [Accepted: 04/20/2012] [Indexed: 01/05/2023]
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25
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Filippakopoulos P, Picaud S, Mangos M, Keates T, Lambert JP, Barsyte-Lovejoy D, Felletar I, Volkmer R, Müller S, Pawson T, Gingras AC, Arrowsmith C, Knapp S. Histone recognition and large-scale structural analysis of the human bromodomain family. Cell 2012; 149:214-31. [PMID: 22464331 PMCID: PMC3326523 DOI: 10.1016/j.cell.2012.02.013] [Citation(s) in RCA: 1212] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 10/16/2011] [Accepted: 01/13/2012] [Indexed: 12/18/2022]
Abstract
Bromodomains (BRDs) are protein interaction modules that specifically recognize ε-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resolution crystal structures, covering all BRD families. Comprehensive crossfamily structural analysis identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences. We further uncovered a structural mechanism for the simultaneous binding and recognition of diverse diacetyl-containing peptides by BRD4. These data provide a foundation for structure-based drug design of specific inhibitors for this emerging target family.
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Affiliation(s)
- Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Maria Mangos
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Tracy Keates
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Jean-Philippe Lambert
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ildiko Felletar
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Rudolf Volkmer
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Hessische Str. 3-4, 10115 Berlin, Germany
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
| | - Tony Pawson
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Anne-Claude Gingras
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
- Ontario Cancer Institute, Campbell Family Cancer Research Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
- Department of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK
- Department of Biochemistry and Molecular Biology, George Washington University, School of Medicine and Health Sciences, 2300 Eye Street, NW, Suite 530, Washington, DC, 20037, USA
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Sanchez-Mut J, Huertas D, Esteller M. Aberrant epigenetic landscape in intellectual disability. PROGRESS IN BRAIN RESEARCH 2012; 197:53-71. [DOI: 10.1016/b978-0-444-54299-1.00004-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME, Ballon G, Yang SN, Weinhold N, Reimers M, Clozel T, Luttrop K, Ekstrom TJ, Frank J, Vasanthakumar A, Godley LA, Michor F, Elemento O, Melnick A. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood 2011; 118:3559-69. [PMID: 21828137 PMCID: PMC3186332 DOI: 10.1182/blood-2011-06-357996] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 07/29/2011] [Indexed: 11/20/2022] Open
Abstract
The phenotype of germinal center (GC) B cells includes the unique ability to tolerate rapid proliferation and the mutagenic actions of activation induced cytosine deaminase (AICDA). Given the importance of epigenetic patterning in determining cellular phenotypes, we examined DNA methylation and the role of DNA methyltransferases in the formation of GCs. DNA methylation profiling revealed a marked shift in DNA methylation patterning in GC B cells versus resting/naive B cells. This shift included significant differential methylation of 235 genes, with concordant inverse changes in gene expression affecting most notably genes of the NFkB and MAP kinase signaling pathways. GC B cells were predominantly hypomethylated compared with naive B cells and AICDA binding sites were highly overrepresented among hypomethylated loci. GC B cells also exhibited greater DNA methylation heterogeneity than naive B cells. Among DNA methyltransferases (DNMTs), only DNMT1 was significantly up-regulated in GC B cells. Dnmt1 hypomorphic mice displayed deficient GC formation and treatment of mice with the DNA methyltransferase inhibitor decitabine resulted in failure to form GCs after immune stimulation. Notably, the GC B cells of Dnmt1 hypomorphic animals showed evidence of increased DNA damage, suggesting dual roles for DNMT1 in DNA methylation and double strand DNA break repair.
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Affiliation(s)
- Rita Shaknovich
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
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Abstract
Acetylation of lysine residues is a post-translational modification with broad relevance
to cellular signalling and disease biology. Enzymes that ‘write’
(histone acetyltransferases, HATs) and ‘erase’ (histone deacetylases,
HDACs) acetylation sites are an area of extensive research in current drug development,
but very few potent inhibitors that modulate the ‘reading process’
mediated by acetyl lysines have been described. The principal readers of
ɛ-N-acetyl lysine (Kac) marks are
bromodomains (BRDs), which are a diverse family of evolutionary conserved
protein-interaction modules. The conserved BRD fold contains a deep, largely hydrophobic
acetyl lysine binding site, which represents an attractive pocket for the development of
small, pharmaceutically active molecules. Proteins that contain BRDs have been implicated
in the development of a large variety of diseases. Recently, two highly potent and
selective inhibitors that target BRDs of the BET (bromodomains and extra-terminal) family
provided compelling data supporting targeting of these BRDs in inflammation and in an
aggressive type of squamous cell carcinoma. It is likely that BRDs will emerge alongside
HATs and HDACs as interesting targets for drug development for the large number of
diseases that are caused by aberrant acetylation of lysine residues.
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Wang YH, Huang ML. Organogenesis and tumorigenesis: insight from the JAK/STAT pathway in the Drosophila eye. Dev Dyn 2011; 239:2522-33. [PMID: 20737505 PMCID: PMC2972639 DOI: 10.1002/dvdy.22394] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Janus kinase (JAK) signal transducer and activator of transcription (STAT) pathway is one of the main signaling pathways in eukaryotic cells. This pathway is used during diverse growth and developmental processes in multiple tissues to control cell proliferation, differentiation, survival, and apoptosis. In addition to its role during development, the JAK/STAT pathway has also been implicated in tumorigenesis. Drosophila melanogaster is a powerful genetic tool, and its eyes have been used extensively as a platform to study signaling pathways. Many reports have demonstrated that the JAK/STAT pathway plays pleiotropic roles in Drosophila eye development. Its functions and activation are decided by its interplay with other signal pathways and the epigenetic status. In this review, we focus on the functions and regulation of the JAK/STAT pathway during eye development and provide some insights into the study of this pathway in tumorigenesis. Developmental Dynamics 239:2522–2533, 2010. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Ying-Hsuan Wang
- Department of Life Science and Institute of Molecular Biology, National Chung-Cheng University, Chia-Yi, Taiwan
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Birge LM, Pitts ML, Richard BH, Wilkinson GS. Length polymorphism and head shape association among genes with polyglutamine repeats in the stalk-eyed fly, Teleopsis dalmanni. BMC Evol Biol 2010; 10:227. [PMID: 20663190 PMCID: PMC3055267 DOI: 10.1186/1471-2148-10-227] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 07/27/2010] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Polymorphisms of single amino acid repeats (SARPs) are a potential source of genetic variation for rapidly evolving morphological traits. Here, we characterize variation in and test for an association between SARPs and head shape, a trait under strong sexual selection, in the stalk-eyed fly, Teleopsis dalmanni. Using an annotated expressed sequence tag database developed from eye-antennal imaginal disc tissues in T. dalmanni we identified 98 genes containing nine or more consecutive copies of a single amino acid. We then quantify variation in length and allelic diversity for 32 codon and 15 noncodon repeat regions in a large outbred population. We also assessed the frequency with which amino acid repeats are either gained or lost by identifying sequence similarities between T. dalmanni SARP loci and their orthologs in Drosophila melanogaster. Finally, to identify SARP containing genes that may influence head development we conducted a two-generation association study after assortatively mating for extreme relative eyespan. RESULTS We found that glutamine repeats occur more often than expected by amino acid abundance among 3,400 head development genes in T. dalmanni and D. melanogaster. Furthermore, glutamine repeats occur disproportionately in transcription factors. Loci with glutamine repeats exhibit heterozygosities and allelic diversities that do not differ from noncoding dinucleotide microsatellites, including greater variation among X-linked than autosomal regions. In the majority of cases, repeat tracts did not overlap between T. dalmanni and D. melanogaster indicating that large glutamine repeats are gained or lost frequently during Dipteran evolution. Analysis of covariance reveals a significant effect of parental genotype on mean progeny eyespan, with body length as a covariate, at six SARP loci [CG33692, ptip, band4.1 inhibitor LRP interactor, corto, 3531953:1, and ecdysone-induced protein 75B (Eip75B)]. Mixed model analysis of covariance using the eyespan of siblings segregating for repeat length variation confirms that significant genotype-phenotype associations exist for at least one sex at five of these loci and for one gene, CG33692, longer repeats were associated with longer relative eyespan in both sexes. CONCLUSION Among genes expressed during head development in stalk-eyed flies, long codon repeats typically contain glutamine, occur in transcription factors and exhibit high levels of heterozygosity. Furthermore, the presence of significant associations within families between repeat length and head shape indicates that six genes, or genes linked to them, contribute genetic variation to the development of this extremely sexually dimorphic trait.
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Affiliation(s)
- Leanna M Birge
- Department of Biology, University of Maryland, College Park, MD 20742 USA
- University College London, Research Department of Genetics, Evolution and Environment, Wolfson House, 4 Stephenson Way, London, NW1 2HE, UK
| | - Marie L Pitts
- Department of Biology, The College of William and Mary, Williamsburg, VA 23187 USA
| | - Baker H Richard
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024 USA
| | - Gerald S Wilkinson
- Department of Biology, University of Maryland, College Park, MD 20742 USA
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32
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Philipps DL, Wigglesworth K, Hartford SA, Sun F, Pattabiraman S, Schimenti K, Handel M, Eppig JJ, Schimenti JC. The dual bromodomain and WD repeat-containing mouse protein BRWD1 is required for normal spermiogenesis and the oocyte-embryo transition. Dev Biol 2008; 317:72-82. [PMID: 18353305 DOI: 10.1016/j.ydbio.2008.02.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 02/05/2008] [Accepted: 02/05/2008] [Indexed: 11/24/2022]
Abstract
A novel mutation, repro5, was isolated in a forward genetic screen for infertility mutations induced by ENU mutagenesis. Homozygous mutant mice were phenotypically normal but were infertile. Oocytes from mutant females appeared normal, but were severely maturation-defective in that they had reduced ability to progress to metaphase II (MII), and those reaching MII were unable to progress beyond the two pronuclei stage following in vitro fertilization (IVF). Mutant males exhibited defective spermiogenesis, resulting in oligoasthenoteratospermia. Genetic mapping, positional cloning, and complementation studies with a disruption allele led to the identification of a mutation in Brwd1 (Bromodomain and WD repeat domain containing 1) as the causative lesion. Bromodomain-containing proteins typically interact with regions of chromatin containing histones hyperacetylated at lysine residues, a characteristic of chromatin in early spermiogenesis before eventual replacement of histones by the protamines. Previous data indicated that Brwd1 is broadly expressed, encoding a putative transcriptional regulator that is believed to act on chromatin through interactions with the Brg1-dependent SWI/SNF chromatin-remodeling pathway. Brwd1 represents one of a small number of genes whose elimination disrupts gametogenesis in both sexes after the major events of meiotic prophase I have been completed.
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Affiliation(s)
- Dana L Philipps
- Cornell University, College of Veterinary Medicine, Ithaca, NY 14850, USA
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Abu-Farha M, Lambert JP, Al-Madhoun AS, Elisma F, Skerjanc IS, Figeys D. The tale of two domains: proteomics and genomics analysis of SMYD2, a new histone methyltransferase. Mol Cell Proteomics 2007; 7:560-72. [PMID: 18065756 DOI: 10.1074/mcp.m700271-mcp200] [Citation(s) in RCA: 148] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Very little is known about SET- and MYND-containing protein 2 (SMYD2), a member of the SMYD protein family. However, the interest in better understanding the roles of SMYD2 has grown because of recent reports indicating that SMYD2 methylates p53 and histone H3. In this study, we present a combined proteomics and genomics study of SMYD2 designed to elucidate its molecular roles. We report the cytosolic and nuclear interactome of SMYD2 using a combination of immunoprecipitation coupled with high throughput MS, chromatin immunoprecipitation coupled with high throughput MS, and co-immunoprecipitation methods. In particular, we report that SMYD2 interacted with HSP90alpha independently of the SET and MYND domains, with EBP41L3 through the MYND domain, and with p53 through the SET domain. We demonstrated that the interaction of SMYD2 with HSP90alpha enhances SMYD2 histone methyltransferase activity and specificity for histone H3 at lysine 4 (H3K4) in vitro. Interestingly histone H3K36 methyltransferase activity was independent of its interaction with HSP90alpha similar to LSD1 dependence on the androgen receptor. We also showed that the SET domain is required for the methylation at H3K4. We demonstrated using a modified chromatin immunoprecipitation protocol that the SMYD2 gain of function leads to an increase in H3K4 methylation in vivo, whereas no observable levels of H3K36 were detected. We also report that the SMYD2 gain of function was correlated with the up-regulation of 37 and down-regulation of four genes, the majority of which are involved in the cell cycle, chromatin remodeling, and transcriptional regulation. TACC2 is one of the genes up-regulated as a result of SMYD2 gain of function. Up-regulation of TACC2 by SMYD2 occurred as a result of SMYD2 binding to the TACC2 promoter where it methylates H3K4. Furthermore the combination of the SMYD2 interactome with the gene expression data suggests that some of the genes regulated by SMYD2 are closely associated with SMYD2-interacting proteins.
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Affiliation(s)
- Mohamed Abu-Farha
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario K1H 8M5, Canada
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Bettencourt BR, Hogan CC, Nimali M. Polyglutamine expansion in Drosophila: thermal stress and Hsp70 as selective agents. J Biosci 2007; 32:537-47. [PMID: 17536173 DOI: 10.1007/s12038-007-0053-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Repetitive DNA sequences that encode polyglutamine tracts are prone to expansion and cause highly deleterious phenotypes of neurodegeneration. Despite this tendency,polyglutamine tracts ("polyQs") are conserved features of eukaryotic genomes. PolyQs are the most frequent protein-coding homotypic repeat in insect genomes, and are found predominantly in genes encoding transcription factors conserved from Drosophila through human. Although highly conserved across species, polyQ lengths vary widely within species. In D. melanogaster, polyQs in 25 genes have more alleles and higher heterozygosity than all other poly-amino acid tracts. The heat shock protein Hsp70 is a principal suppressor of polyQ expansions and may play a key role in modulating the phenotypes of the alleles that encode them. Hsp70 also promotes tolerance of natural thermal stress in Drosophila and diverse organisms,a role which may deplete the chaperone from buffering against polyQ toxicity. Thus in stressful environments, natural selection against long polyQ alleles more prone to expansion and deleterious phenotypes may be more effective. This hypothesis can be tested by measuring the phenotypic interactions between Hsp70 and polyQ transgenes in D. melanogaster undergoing natural thermal stress, an approach which integrates comparative genomics with experimental and ecological genetics.
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Affiliation(s)
- Brian R Bettencourt
- Department of Biological Sciences, University of Massachusetts Lowell, 1 University Ave., Lowell, MA 01854, USA.
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D'Costa A, Reifegerste R, Sierra S, Moses K. The Drosophila ramshackle gene encodes a chromatin-associated protein required for cell morphology in the developing eye. Mech Dev 2006; 123:591-604. [PMID: 16904300 DOI: 10.1016/j.mod.2006.06.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2005] [Revised: 06/26/2006] [Accepted: 06/28/2006] [Indexed: 12/21/2022]
Abstract
We have identified ramshackle (ram) as a dominant suppressor of hedgehog loss-of-function in the developing Drosophila eye. We have characterized the gene and it encodes a double bromodomain protein with eight WD40 repeats. The Ram protein is localized predominantly to polytene chromosome interbands and is required for the transcription of some genes. ram is an essential gene and null mutants die during larval life. In the developing retina, ram mutant cells have morphological defects including disrupted apical junctions, disorganized actin cytoskeletons and mislocalized nuclei, which are followed by delays in cell-cycle transitions and the expression of differentiation markers. ram is a conserved gene: its vertebrate homolog (WDR9), which lies in Down's Syndrome Critical region 2 (DCR2) is also known to be associated with Brahma-Related-Gene 1 (BRG1).
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Affiliation(s)
- Allison D'Costa
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322-3030, USA
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Huang H, Rastegar M, Bodner C, Goh SL, Rambaldi I, Featherstone M. MEIS C Termini Harbor Transcriptional Activation Domains That Respond to Cell Signaling. J Biol Chem 2005; 280:10119-27. [PMID: 15654074 DOI: 10.1074/jbc.m413963200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MEIS proteins form heteromeric DNA-binding complexes with PBX monomers and PBX.HOX heterodimers. We have shown previously that transcriptional activation by PBX.HOX is augmented by either protein kinase A (PKA) or the histone deacetylase inhibitor trichostatin A (TSA). To examine the contribution of MEIS proteins to this response, we used the chromatin immunoprecipitation assay to show that MEIS1 in addition to PBX1, HOXA1, and HOXB1 was recruited to a known PBX.HOX target, the Hoxb1 autoregulatory element following Hoxb1 transcriptional activation in P19 cells. Subsequent to TSA treatment, MEIS1 recruitment lagged behind that of HOX and PBX partners. MEIS1A also enhanced the transcriptional activation of a reporter construct bearing the Hoxb1 autoregulatory element after treatment with TSA. The MEIS1 homeodomain and protein-protein interaction with PBX contributed to this activity. We further mapped TSA-responsive and CREB-binding protein-dependent PKA-responsive transactivation domains to the MEIS1A and MEIS1B C termini. Fine mutation of the 56-residue MEIS1A C terminus revealed four discrete regions required for transcriptional activation function. All of the mutations impairing the response to TSA likewise reduced activation by PKA, implying a common mechanistic basis. C-terminal deletion of MEIS1 impaired transactivation without disrupting DNA binding or complex formation with HOX and PBX. Despite sequence similarity to MEIS and a shared ability to form heteromeric complexes with PBX and HOX partners, the PREP1 C terminus does not respond to TSA or PKA. Thus, MEIS C termini possess transcriptional regulatory domains that respond to cell signaling and confer functional differences between MEIS and PREP proteins.
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Affiliation(s)
- He Huang
- McGill Cancer Centre, McGill University, 3655 Promenade Sir William Osler, Montréal, Québec H3G 1Y6, Canada
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