1
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Carpenter BS, Scott A, Goldin R, Chavez SR, Rodriguez JD, Myrick DA, Curlee M, Schmeichel KL, Katz DJ. SPR-1/CoREST facilitates the maternal epigenetic reprogramming of the histone demethylase SPR-5/LSD1. Genetics 2023; 223:6992629. [PMID: 36655746 PMCID: PMC9991509 DOI: 10.1093/genetics/iyad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/07/2022] [Accepted: 12/09/2022] [Indexed: 01/20/2023] Open
Abstract
Maternal reprogramming of histone methylation is critical for reestablishing totipotency in the zygote, but how histone-modifying enzymes are regulated during maternal reprogramming is not well characterized. To address this gap, we asked whether maternal reprogramming by the H3K4me1/2 demethylase SPR-5/LSD1/KDM1A, is regulated by the chromatin co-repressor protein, SPR-1/CoREST, in Caenorhabditis elegans and mice. In C. elegans, SPR-5 functions as part of a reprogramming switch together with the H3K9 methyltransferase MET-2. By examining germline development, fertility, and gene expression in double mutants between spr-1 and met-2, as well as fertility in double mutants between spr-1 and spr-5, we find that loss of SPR-1 results in a partial loss of SPR-5 maternal reprogramming function. In mice, we generated a separation of function Lsd1 M448V point mutation that compromises CoREST binding, but only slightly affects LSD1 demethylase activity. When maternal LSD1 in the oocyte is derived exclusively from this allele, the progeny phenocopy the increased perinatal lethality that we previously observed when LSD1 was reduced maternally. Together, these data are consistent with CoREST having a conserved function in facilitating maternal LSD1 epigenetic reprogramming.
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Affiliation(s)
- Brandon S Carpenter
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Alyssa Scott
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Robert Goldin
- Uniformed Services University School of Medicine, Bethesda, MD 20814, USA
| | - Sindy R Chavez
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Juan D Rodriguez
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dexter A Myrick
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Marcus Curlee
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Karen L Schmeichel
- Natural Sciences Division, Oglethorpe University, Atlanta, GA 30319, USA
| | - David J Katz
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
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2
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Ryan KC, Ashkavand Z, Sarasija S, Laboy JT, Samarakoon R, Norman KR. Increased mitochondrial calcium uptake and concomitant mitochondrial activity by presenilin loss promotes mTORC1 signaling to drive neurodegeneration. Aging Cell 2021; 20:e13472. [PMID: 34499406 PMCID: PMC8520713 DOI: 10.1111/acel.13472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/21/2021] [Accepted: 08/05/2021] [Indexed: 12/21/2022] Open
Abstract
Metabolic dysfunction and protein aggregation are common characteristics that occur in age‐related neurodegenerative disease. However, the mechanisms underlying these abnormalities remain poorly understood. We have found that mutations in the gene encoding presenilin in Caenorhabditis elegans, sel‐12, results in elevated mitochondrial activity that drives oxidative stress and neuronal dysfunction. Mutations in the human presenilin genes are the primary cause of familial Alzheimer's disease. Here, we demonstrate that loss of SEL‐12/presenilin results in the hyperactivation of the mTORC1 pathway. This hyperactivation is caused by elevated mitochondrial calcium influx and, likely, the associated increase in mitochondrial activity. Reducing mTORC1 activity improves proteostasis defects and neurodegenerative phenotypes associated with loss of SEL‐12 function. Consistent with high mTORC1 activity, we find that SEL‐12 loss reduces autophagosome formation, and this reduction is prevented by limiting mitochondrial calcium uptake. Moreover, the improvements of proteostasis and neuronal defects in sel‐12 mutants due to mTORC1 inhibition require the induction of autophagy. These results indicate that mTORC1 hyperactivation exacerbates the defects in proteostasis and neuronal function in sel‐12 mutants and demonstrate a critical role of presenilin in promoting neuronal health.
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Affiliation(s)
- Kerry C. Ryan
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
| | - Zahra Ashkavand
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
| | - Shaarika Sarasija
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
| | - Jocelyn T. Laboy
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
| | - Rohan Samarakoon
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
| | - Kenneth R. Norman
- Department of Regenerative and Cancer Cell Biology Albany Medical College Albany New York USA
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3
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Wei CC, Yen PL, Chaikritsadakarn A, Huang CW, Chang CH, Liao VHC. Parental CuO nanoparticles exposure results in transgenerational toxicity in Caenorhabditis elegans associated with possible epigenetic regulation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 203:111001. [PMID: 32888585 DOI: 10.1016/j.ecoenv.2020.111001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/05/2020] [Accepted: 07/04/2020] [Indexed: 05/21/2023]
Abstract
Environmental nanomaterials contamination is a great concern for organisms including human. Copper oxide nanoparticles (CuO NPs) are widely used in a huge range of applications which might pose potential risk to organisms. This study investigated the in vivo transgenerational toxicity on development and reproduction with parental CuO NPs exposure in the nematode Caenorhabditis elegans. The results showed that CuO NPs (150 mg/L) significantly reduced the body length of parental C. elegans (P0). Only about 1 mg/L Cu2+ (~0.73%) were detected from 150 mg/L CuO NPs in 0.5X K-medium after 48 h. In transgenerational assays, CuO NPs (150 mg/L) parental exposure significantly induced developmental and reproductive toxicity in non-exposed C. elegans progeny (CuO NPs free) on body length (F1) and brood size (F1 and F2), respectively. In contrast, parental exposure to Cu2+ (1 mg/L) did not cause transgenerational toxicity on growth and reproduction. This suggests that the transgenerational toxicity was mostly attributed to the particulate form of CuO NPs. Moreover, qRT-PCR results showed that the mRNA levels of met-2 and spr-5 genes were significantly decreased at P0 and F1 upon only maternal exposure to CuO NPs (150 mg/L), suggesting the observed transgenerational toxicity was associated with possible epigenetic regulation in C. elegans.
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Affiliation(s)
- Chia-Cheng Wei
- Institute of Food Safety and Health, National Taiwan University, No. 17, Xuzhou Rd., Taipei, 100, Taiwan; Department of Public Health, National Taiwan University, No. 17, Xuzhou Rd., Taipei, 100, Taiwan
| | - Pei-Ling Yen
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 106, Taiwan
| | - Amornrat Chaikritsadakarn
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 106, Taiwan
| | - Chi-Wei Huang
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 106, Taiwan
| | - Chun-Han Chang
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 106, Taiwan
| | - Vivian Hsiu-Chuan Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 106, Taiwan.
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4
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Coutinho Carneiro V, de Abreu da Silva IC, Amaral MS, Pereira ASA, Silveira GO, Pires DDS, Verjovski-Almeida S, Dekker FJ, Rotili D, Mai A, Lopes-Torres EJ, Robaa D, Sippl W, Pierce RJ, Borrello MT, Ganesan A, Lancelot J, Thiengo S, Fernandez MA, Vicentino ARR, Mourão MM, Coelho FS, Fantappié MR. Pharmacological inhibition of lysine-specific demethylase 1 (LSD1) induces global transcriptional deregulation and ultrastructural alterations that impair viability in Schistosoma mansoni. PLoS Negl Trop Dis 2020; 14:e0008332. [PMID: 32609727 PMCID: PMC7329083 DOI: 10.1371/journal.pntd.0008332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
Treatment and control of schistosomiasis still rely on only one effective drug, praziquantel (PZQ) and, due to mass treatment, the increasing risk of selecting for schistosome strains that are resistant to PZQ has alerted investigators to the urgent need to develop novel therapeutic strategies. The histone-modifying enzymes (HMEs) represent promising targets for the development of epigenetic drugs against Schistosoma mansoni. In the present study, we targeted the S. mansoni lysine-specific demethylase 1 (SmLSD1), a transcriptional corepressor, using a novel and selective synthetic inhibitor, MC3935, which was used to treat schistosomula and adult worms in vitro. By using cell viability assays and optical and electron microscopy, we showed that treatment with MC3935 affected parasite motility, egg-laying, tegument, and cellular organelle structures, culminating in the death of schistosomula and adult worms. In silico molecular modeling and docking analysis suggested that MC3935 binds to the catalytic pocket of SmLSD1. Western blot analysis revealed that MC3935 inhibited SmLSD1 demethylation activity of H3K4me1/2. Knockdown of SmLSD1 by RNAi recapitulated MC3935 phenotypes in adult worms. RNA-Seq analysis of MC3935-treated parasites revealed significant differences in gene expression related to critical biological processes. Collectively, our findings show that SmLSD1 is a promising drug target for the treatment of schistosomiasis and strongly support the further development and in vivo testing of selective schistosome LSD1 inhibitors.
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Affiliation(s)
- Vitor Coutinho Carneiro
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabel Caetano de Abreu da Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Adriana S. A. Pereira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Gilbert Oliveira Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | | | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan, AV Groningen, Netherlands
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Eduardo José Lopes-Torres
- Laboratório de Helmintologia Romero Lascasas Porto, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dina Robaa
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Germany
| | - Raymond J. Pierce
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Centre d’Infection et d’Immunité de Lille, Lille, France
| | - M. Teresa Borrello
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - A. Ganesan
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Julien Lancelot
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Silvana Thiengo
- Laboratório de Malacologia, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Monica Ammon Fernandez
- Laboratório de Malacologia, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Amanda Roberta Revoredo Vicentino
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marina Moraes Mourão
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Fernanda Sales Coelho
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Marcelo Rosado Fantappié
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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5
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Zullo JM, Drake D, Aron L, O'Hern P, Dhamne SC, Davidsohn N, Mao CA, Klein WH, Rotenberg A, Bennett DA, Church GM, Colaiácovo MP, Yankner BA. Regulation of lifespan by neural excitation and REST. Nature 2019; 574:359-364. [PMID: 31619788 PMCID: PMC6893853 DOI: 10.1038/s41586-019-1647-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 09/18/2019] [Indexed: 12/27/2022]
Abstract
The mechanisms that extend lifespan in humans are poorly understood. Here we show that extended longevity in humans is associated with a distinct transcriptome signature in the cerebral cortex that is characterized by downregulation of genes related to neural excitation and synaptic function. In Caenorhabditis elegans, neural excitation increases with age and inhibition of excitation globally, or in glutamatergic or cholinergic neurons, increases longevity. Furthermore, longevity is dynamically regulated by the excitatory-inhibitory balance of neural circuits. The transcription factor REST is upregulated in humans with extended longevity and represses excitation-related genes. Notably, REST-deficient mice exhibit increased cortical activity and neuronal excitability during ageing. Similarly, loss-of-function mutations in the C. elegans REST orthologue genes spr-3 and spr-4 elevate neural excitation and reduce the lifespan of long-lived daf-2 mutants. In wild-type worms, overexpression of spr-4 suppresses excitation and extends lifespan. REST, SPR-3, SPR-4 and reduced excitation activate the longevity-associated transcription factors FOXO1 and DAF-16 in mammals and worms, respectively. These findings reveal a conserved mechanism of ageing that is mediated by neural circuit activity and regulated by REST.
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Affiliation(s)
- Joseph M Zullo
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Derek Drake
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Liviu Aron
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Patrick O'Hern
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sameer C Dhamne
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Noah Davidsohn
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chai-An Mao
- Department of Ophthalmology and Visual Science, The University of Texas McGovern Medical School, Houston, TX, USA
| | - William H Klein
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander Rotenberg
- F. M. Kirby Neurobiology Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Bruce A Yankner
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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6
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Giaimo BD, Ferrante F, Vallejo DM, Hein K, Gutierrez-Perez I, Nist A, Stiewe T, Mittler G, Herold S, Zimmermann T, Bartkuhn M, Schwarz P, Oswald F, Dominguez M, Borggrefe T. Histone variant H2A.Z deposition and acetylation directs the canonical Notch signaling response. Nucleic Acids Res 2019; 46:8197-8215. [PMID: 29986055 PMCID: PMC6144792 DOI: 10.1093/nar/gky551] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 06/28/2018] [Indexed: 02/04/2023] Open
Abstract
A fundamental as yet incompletely understood feature of Notch signal transduction is a transcriptional shift from repression to activation that depends on chromatin regulation mediated by transcription factor RBP-J and associated cofactors. Incorporation of histone variants alter the functional properties of chromatin and are implicated in the regulation of gene expression. Here, we show that depletion of histone variant H2A.Z leads to upregulation of canonical Notch target genes and that the H2A.Z-chaperone TRRAP/p400/Tip60 complex physically associates with RBP-J at Notch-dependent enhancers. When targeted to RBP-J-bound enhancers, the acetyltransferase Tip60 acetylates H2A.Z and upregulates Notch target gene expression. Importantly, the Drosophila homologs of Tip60, p400 and H2A.Z modulate Notch signaling response and growth in vivo. Together, our data reveal that loading and acetylation of H2A.Z are required to assure tight control of canonical Notch activation.
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Affiliation(s)
- Benedetto Daniele Giaimo
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany.,Spemann Graduate School of Biology and Medicine (SGBM), Albertstrasse 19A, 79104 Freiburg, Germany
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Diana M Vallejo
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Kerstin Hein
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Irene Gutierrez-Perez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany
| | - Gerhard Mittler
- Max-Planck-Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Susanne Herold
- Department of Internal Medicine II, Universities Giessen & Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Tobias Zimmermann
- Bioinformatics and Systems Biology, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany
| | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany
| | - Peggy Schwarz
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Franz Oswald
- University Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Maria Dominguez
- Instituto de Neurociencias, Consejo Superior de Investigaciones Cientificas and Universidad Miguel Hernández, Campus de Sant Joan, Apartado 18, 03550 Sant Joan, Alicante, Spain
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
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7
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Monestime CM, Taibi A, Gates KP, Jiang K, Sirotkin HI. CoRest1 regulates neurogenesis in a stage‐dependent manner. Dev Dyn 2019; 248:918-930. [DOI: 10.1002/dvdy.86] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/31/2022] Open
Affiliation(s)
| | - Andrew Taibi
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
| | - Keith P. Gates
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
| | - Karen Jiang
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
| | - Howard I. Sirotkin
- Department of Neurobiology and BehaviorStony Brook University Stony Brook New York
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8
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Li SW, How CM, Liao VHC. Prolonged exposure of di(2-ethylhexyl) phthalate induces multigenerational toxic effects in Caenorhabditis elegans. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:260-266. [PMID: 29627549 DOI: 10.1016/j.scitotenv.2018.03.355] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/29/2018] [Accepted: 03/29/2018] [Indexed: 06/08/2023]
Abstract
The plasticizer di(2-ethylhexyl) phthalate (DEHP) is an emerging organic contaminant that has represented a risk for organisms present in the environment. However, there is still limited information regarding DEHP-induced multigenerational toxicity and the underlying mechanisms. In this study we investigated the multigenerational toxic effects including locomotive behaviors and reproduction upon prolonged DEHP exposure (from larval L1 to adult) and the underlying mechanisms in the nematode Caenorhabditis elegans. The multigenerational effects were examined over 6 generations (F0-F5) with only parental C. elegans (F0) was exposed to DEHP from larval L1 to adults (72h), and the subsequent offsprings (F1-F5) were grown under DEHP-free conditions. The results showed that prolonged exposure (72h) to various concentrations of DEHP caused dose-dependent locomotive impairments and reproduction defects in C. elegans and that a concentration of 0.2mg/L DEHP was enough to cause such sublethal effects. The results showed that after prolonged exposure to DEHP in the F0 generation, abnormal locomotive behaviors such as reduced body bends and head thrashes were observed from generations F0 to F5. Additionally, prolonged exposure to DEHP (20mg/L) in F0 significantly reduced total brood size in F0, and this parental exposure was sufficient to cause multigenerational reproductive toxicity in the offspring generations (F1-F5) as well. Furthermore, the expressions of reproduction-related genes such as vit-2 and vit-6 were down-regulated by about 20% until F3, and the expression of H3Kme2 demethylase, spr-5, was downregulated in F1 by about 40%. Results from this study demonstrate that prolonged exposure to DEHP only at F0 adversely affected reproduction and locomotive behaviors in C. elegans across generations and might be associated with inadequate vitellogenin production and malfunction of H3Kme2 demethylase. This study implies that parentally prolonged exposure to DEHP caused multigenerational defects in both reproduction and locomotive behaviors raising the potential health and ecological risk.
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Affiliation(s)
- Shang-Wei Li
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Chun Ming How
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Vivian Hsiu-Chuan Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei 10617, Taiwan.
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9
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Kim HM, Beese-Sims SE, Colaiácovo MP. Fanconi Anemia FANCM/FNCM-1 and FANCD2/FCD-2 Are Required for Maintaining Histone Methylation Levels and Interact with the Histone Demethylase LSD1/SPR-5 in Caenorhabditis elegans. Genetics 2018; 209:409-423. [PMID: 29588287 PMCID: PMC5972417 DOI: 10.1534/genetics.118.300823] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/22/2018] [Indexed: 11/18/2022] Open
Abstract
The histone demethylase LSD1 was originally discovered by removing methyl groups from di- and monomethylated histone H3 lysine 4 (H3K4me2/1). Several studies suggest that LSD1 plays roles in meiosis as well as in the epigenetic regulation of fertility given that, in its absence, there is evidence of a progressive accumulation of H3K4me2 and increased sterility through generations. In addition to the progressive sterility phenotype observed in the mutants, growing evidence for the importance of histone methylation in the regulation of DNA damage repair has attracted more attention to the field in recent years. However, we are still far from understanding the mechanisms by which histone methylation is involved in DNA damage repair, and only a few studies have focused on the roles of histone demethylases in germline maintenance. Here, we show that the histone demethylase LSD1/CeSPR-5 interacts with the Fanconi anemia (FA) protein FANCM/CeFNCM-1 using biochemical, cytological, and genetic analyses. LSD1/CeSPR-5 is required for replication stress-induced S phase-checkpoint activation, and its absence suppresses the embryonic lethality and larval arrest observed in fncm-1 mutants. FANCM/CeFNCM-1 relocalizes upon hydroxyurea exposure and colocalizes with FANCD2/CeFCD-2 and LSD1/CeSPR-5, suggesting coordination between this histone demethylase and FA components to resolve replication stress. Surprisingly, the FA pathway is required for H3K4me2 maintenance, regardless of the presence of replication stress. Our study reveals a connection between FA and epigenetic maintenance and therefore provides new mechanistic insight into the regulation of histone methylation in DNA repair.
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Affiliation(s)
- Hyun-Min Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- School of Pharmaceutical Science and Technology, Tianjin University, 300072, China
| | - Sara E Beese-Sims
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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10
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Xu T, Park SS, Giaimo BD, Hall D, Ferrante F, Ho DM, Hori K, Anhezini L, Ertl I, Bartkuhn M, Zhang H, Milon E, Ha K, Conlon KP, Kuick R, Govindarajoo B, Zhang Y, Sun Y, Dou Y, Basrur V, Elenitoba-Johnson KS, Nesvizhskii AI, Ceron J, Lee CY, Borggrefe T, Kovall RA, Rual JF. RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1. EMBO J 2017; 36:3232-3249. [PMID: 29030483 PMCID: PMC5666606 DOI: 10.15252/embj.201796525] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 08/31/2017] [Accepted: 09/12/2017] [Indexed: 12/21/2022] Open
Abstract
Notch signaling is an evolutionarily conserved signal transduction pathway that is essential for metazoan development. Upon ligand binding, the Notch intracellular domain (NOTCH ICD) translocates into the nucleus and forms a complex with the transcription factor RBPJ (also known as CBF1 or CSL) to activate expression of Notch target genes. In the absence of a Notch signal, RBPJ acts as a transcriptional repressor. Using a proteomic approach, we identified L3MBTL3 (also known as MBT1) as a novel RBPJ interactor. L3MBTL3 competes with NOTCH ICD for binding to RBPJ. In the absence of NOTCH ICD, RBPJ recruits L3MBTL3 and the histone demethylase KDM1A (also known as LSD1) to the enhancers of Notch target genes, leading to H3K4me2 demethylation and to transcriptional repression. Importantly, in vivo analyses of the homologs of RBPJ and L3MBTL3 in Drosophila melanogaster and Caenorhabditis elegans demonstrate that the functional link between RBPJ and L3MBTL3 is evolutionarily conserved, thus identifying L3MBTL3 as a universal modulator of Notch signaling in metazoans.
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Affiliation(s)
- Tao Xu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sung-Soo Park
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Daniel Hall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Diana M Ho
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Kazuya Hori
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Lucas Anhezini
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Iris Ertl
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Giessen, Germany
| | - Honglai Zhang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eléna Milon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kimberly Ha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kevin P Conlon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rork Kuick
- Center for Cancer Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Brandon Govindarajoo
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zhang
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yuqing Sun
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yali Dou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Julian Ceron
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cheng-Yu Lee
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
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11
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Porter RS, Murata-Nakamura Y, Nagasu H, Kim HG, Iwase S. Transcriptome Analysis Revealed Impaired cAMP Responsiveness in PHF21A-Deficient Human Cells. Neuroscience 2017; 370:170-180. [PMID: 28571721 DOI: 10.1016/j.neuroscience.2017.05.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/08/2017] [Accepted: 05/19/2017] [Indexed: 12/16/2022]
Abstract
Potocki-Shaffer Syndrome is a rare neurodevelopmental syndrome associated with microdeletion of a region of Chromosome 11p11.2. Genetic evidence has implicated haploinsufficiency of PHF21A, a gene that encodes a histone-binding protein, as the likely cause of intellectual disability and craniofacial abnormalities in Potocki-Shaffer Syndrome. However, the molecular consequences of reduced PHF21A expression remain elusive. In this study, we analyzed by RNA-Sequencing (RNA-Seq) two patient-derived cell lines with heterozygous loss of PHF21A compared to unaffected individuals and identified 1,885 genes that were commonly misregulated. The patient cells displayed down-regulation of key pathways relevant to learning and memory, including Cyclic Adenosine Monophosphate (cAMP)-signaling pathway genes. We found that PHF21A is required for full induction of a luciferase reporter carrying cAMP-responsive elements (CRE) following stimulation by the cAMP analog, forskolin. Finally, PHF21A-deficient patient-derived cells exhibited a delayed induction of immediate early genes following forskolin stimulation. These results suggest that an impaired response to cAMP signaling might be involved in the pathology of PHF21A deficiency. This article is part of a Special Issue entitled: [SI: Molecules & Cognition].
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Affiliation(s)
- Robert S Porter
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | | | - Hajime Nagasu
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Hyung-Goo Kim
- Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA 30912, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
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12
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REST corepressors RCOR1 and RCOR2 and the repressor INSM1 regulate the proliferation-differentiation balance in the developing brain. Proc Natl Acad Sci U S A 2017; 114:E406-E415. [PMID: 28049845 DOI: 10.1073/pnas.1620230114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The transcriptional events that lead to the cessation of neural proliferation, and therefore enable the production of proper numbers of differentiated neurons and glia, are still largely uncharacterized. Here, we report that the transcription factor Insulinoma-associated 1 (INSM1) forms complexes with RE1 Silencing Transcription factor (REST) corepressors RCOR1 and RCOR2 in progenitors in embryonic mouse brain. Mice lacking both RCOR1 and RCOR2 in developing brain die perinatally and generate an abnormally high number of neural progenitors at the expense of differentiated neurons and oligodendrocyte precursor cells. In addition, Rcor1/2 deletion detrimentally affects complex morphological processes such as closure of the interganglionic sulcus. We find that INSM1, a transcription factor that induces cell-cycle arrest, is coexpressed with RCOR1/2 in a subset of neural progenitors and forms complexes with RCOR1/2 in embryonic brain. Further, the Insm1-/- mouse phenocopies predominant brain phenotypes of the Rcor1/2 knockout. A large number of genes are concordantly misregulated in both knockout genotypes, and a majority of the down-regulated genes are targets of REST. Rest transcripts are up-regulated in both knockouts, and reducing transcripts to control levels in the Rcor1/2 knockout partially rescues the defect in interganglionic sulcus closure. Our findings indicate that an INSM1/RCOR1/2 complex controls the balance of proliferation and differentiation during brain development.
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13
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The silent information regulator 1 (Sirt1) is a positive regulator of the Notch pathway in Drosophila. Biochem J 2016; 473:4129-4143. [DOI: 10.1042/bcj20160563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/26/2016] [Accepted: 09/12/2016] [Indexed: 02/07/2023]
Abstract
The silent information regulator 1 (Sirt1) has been shown to have negative effects on the Notch pathway in several contexts. We bring evidence that Sirt1 has a positive effect on Notch activation in Drosophila, in the context of sensory organ precursor specification and during wing development. The phenotype of Sirt1 mutant resembles weak Notch loss-of-function phenotypes, and genetic interactions of Sirt1 with the components of the Notch pathway also suggest a positive role for Sirt1 in Notch signalling. Sirt1 is necessary for the efficient activation of enhancer of split [E(spl)] genes by Notch in S2N cells. Additionally, the Notch-dependent response of several E(spl) genes is sensitive to metabolic stress caused by 2-deoxy-d-glucose treatment, in a Sirt1-dependent manner. We found Sirt1 associated with several proteins involved in Notch repression as well as activation, including the cofactor exchange factor Ebi (TBL1), the RLAF/LAF histone chaperone complex and the Tip60 acetylation complex. Moreover, Sirt1 participates in the deacetylation of the CSL transcription factor Suppressor of Hairless. The role of Sirt1 in Notch signalling is, therefore, more complex than previously recognized, and its diverse effects may be explained by a plethora of Sirt1 substrates involved in the regulation of Notch signalling.
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14
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Maiques-Diaz A, Somervaille TCP. LSD1: biologic roles and therapeutic targeting. Epigenomics 2016; 8:1103-16. [PMID: 27479862 PMCID: PMC5066116 DOI: 10.2217/epi-2016-0009] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/27/2016] [Indexed: 12/13/2022] Open
Abstract
LSD1 (KDM1A; BHC110; AOF2) was the first protein reported to exhibit histone demethylase activity and has since been shown to have multiple essential roles in mammalian biology. Given its enzymatic activity and its high-level expression in many human malignancies, a significant recent focus has been the development of pharmacologic inhibitors. Here we summarize structural and biochemical knowledge of this important epigenetic regulator, with a particular emphasis on the functional and preclinical studies in oncology that have provided justification for the evaluation of tranylcypromine derivative LSD1 inhibitors in early phase clinical trials.
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Affiliation(s)
- Alba Maiques-Diaz
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
| | - Tim CP Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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15
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Magalhães LG, Morais ER, Machado CB, Gomes MS, Cabral FJ, Souza JM, Soares CS, Sá RG, Castro-Borges W, Rodrigues V. Uncovering Notch pathway in the parasitic flatworm Schistosoma mansoni. Parasitol Res 2016; 115:3951-61. [PMID: 27344453 DOI: 10.1007/s00436-016-5161-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/01/2016] [Indexed: 01/19/2023]
Abstract
Several signaling molecules that govern development in higher animals have been identified in the parasite Schistosoma mansoni, including the transforming growth factor β, protein tyrosine kinases, nuclear hormone receptors, among others. The Notch pathway is a highly conserved signaling mechanism which is involved in a wide variety of developmental processes including embryogenesis and oogenesis in worms and flies. Here we aimed to provide the molecular reconstitution of the Notch pathway in S. mansoni using the available transcriptome and genome databases. Our results also revealed the presence of the transcripts coded for SmNotch, SmSu(H), SmHes, and the gamma-secretase complex (SmNicastrin, SmAph-1, and SmPen-2), throughout all the life stages analyzed. Besides, it was observed that the viability and separation of adult worm pairs were not affected by treatment with N-[N(3,5)-difluorophenacetyl)-L-Alanyl]-S-phenylglycine t-butyl ester (DAPT), a Notch pathway inhibitor. Moreover, DAPT treatment decreased the production of phenotypically normal eggs and arrested their development in culture. Our results also showed a significant decrease in SmHes transcript levels in both adult worms and eggs treated with DAPT. These results provide, for the first time, functional validation of the Notch pathway in S. mansoni and suggest its involvement in parasite oogenesis and embryogenesis. Given the complexity of the Notch pathway, further experiments shall highlight the full repertoire of Notch-mediated cellular processes throughout the S. mansoni life cycle.
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Affiliation(s)
- Lizandra G Magalhães
- Núcleo de Pesquisa em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, Avenida, Dr Armando Salles de Oliveira, 201 Franca, SP, Brazil.
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
| | - Enyara R Morais
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Carla B Machado
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Matheus S Gomes
- Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Patos de Minas, MG, Brazil
| | - Fernanda J Cabral
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Julia M Souza
- Núcleo de Pesquisa em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, Avenida, Dr Armando Salles de Oliveira, 201 Franca, SP, Brazil
| | - Cláudia S Soares
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Renata G Sá
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - William Castro-Borges
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, Brazil
| | - Vanderlei Rodrigues
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
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16
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Lopez CI, Saud KE, Aguilar R, Berndt FA, Cánovas J, Montecino M, Kukuljan M. The chromatin modifying complex CoREST/LSD1 negatively regulates notch pathway during cerebral cortex development. Dev Neurobiol 2016; 76:1360-1373. [PMID: 27112428 DOI: 10.1002/dneu.22397] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/19/2016] [Accepted: 04/22/2016] [Indexed: 12/22/2022]
Abstract
The development of the cerebral cortex is a dynamic and coordinated process in which cell division, cell death, migration, and differentiation must be highly regulated to acquire the final architecture and functional competence of the mature organ. Notch pathway is an important regulator of differentiation and it is essential to maintain neural stem cell (NSC) pool. Here, we studied the role of epigenetic modulators such as lysine-specific demethylase 1 (LSD1) and its interactor CoREST in the regulation of the Notch pathway activity during the development of the cerebral cortex. We found that CoREST and LSD1 interact in vitro with RBPJ-κ in the repressor complex and these proteins are released upon overexpression of Notch intracellular domain (NICD). We corroborated LSD1 and RBPJ-κ interaction in developing cerebral cortex and also found that LSD1 binds to the hes1 promoter. Knock-down of CoREST and LSD1 by in utero electroporation increases Hes1 expression in vivo and decreases Ngn2. Interestingly, we found a functional interaction between CoREST and LSD1 with Notch pathway. This conclusion is based on the observation that both the defects in neuronal migration and the increase in the number of cells expressing Sox2 and Tbr2 were associated to the knock-down of either CoREST or LSD1 and were reversed by the loss of Notch. These results demonstrate that CoREST and LSD1 downregulate the Notch pathway in the developing cerebral cortex, thus suggesting a role of epigenetic regulation in the fine tuning of cell differentiation. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 76: 1360-1373, 2016.
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Affiliation(s)
- Cecilia I Lopez
- Faculty of Medicine, Program in Physiology and Biophysics, Institute for Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Biomedical Neuroscience Institute (BNI), Universidad de Chile, Santiago, Chile
| | - Katherine E Saud
- Faculty of Medicine, Program in Physiology and Biophysics, Institute for Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Biomedical Neuroscience Institute (BNI), Universidad de Chile, Santiago, Chile
| | - Rodrigo Aguilar
- Faculty of Biological Sciences and Faculty of Medicine, Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andre's Bello, Santiago, Chile
| | - F Andrés Berndt
- Faculty of Medicine, Program in Physiology and Biophysics, Institute for Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Biomedical Neuroscience Institute (BNI), Universidad de Chile, Santiago, Chile
| | - José Cánovas
- Faculty of Medicine, Program in Physiology and Biophysics, Institute for Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Biomedical Neuroscience Institute (BNI), Universidad de Chile, Santiago, Chile
| | - Martín Montecino
- Faculty of Biological Sciences and Faculty of Medicine, Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andre's Bello, Santiago, Chile
| | - Manuel Kukuljan
- Faculty of Medicine, Program in Physiology and Biophysics, Institute for Biomedical Sciences, Universidad de Chile, Santiago, Chile.,Faculty of Medicine, Biomedical Neuroscience Institute (BNI), Universidad de Chile, Santiago, Chile
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17
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Stefanakis N, Carrera I, Hobert O. Regulatory Logic of Pan-Neuronal Gene Expression in C. elegans. Neuron 2015; 87:733-50. [PMID: 26291158 DOI: 10.1016/j.neuron.2015.07.031] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 07/01/2015] [Accepted: 07/20/2015] [Indexed: 01/03/2023]
Abstract
While neuronal cell types display an astounding degree of phenotypic diversity, most if not all neuron types share a core panel of terminal features. However, little is known about how pan-neuronal expression patterns are genetically programmed. Through an extensive analysis of the cis-regulatory control regions of a battery of pan-neuronal C. elegans genes, including genes involved in synaptic vesicle biology and neuropeptide signaling, we define a common organizational principle in the regulation of pan-neuronal genes in the form of a surprisingly complex array of seemingly redundant, parallel-acting cis-regulatory modules that direct expression to broad, overlapping domains throughout the nervous system. These parallel-acting cis-regulatory modules are responsive to a multitude of distinct trans-acting factors. Neuronal gene expression programs therefore fall into two fundamentally distinct classes. Neuron-type-specific genes are generally controlled by discrete and non-redundantly acting regulatory inputs, while pan-neuronal gene expression is controlled by diverse, coincident and seemingly redundant regulatory inputs.
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Affiliation(s)
- Nikolaos Stefanakis
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA
| | - Ines Carrera
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA
| | - Oliver Hobert
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY, USA.
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18
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Vandamme J, Sidoli S, Mariani L, Friis C, Christensen J, Helin K, Jensen ON, Salcini AE. H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans. Nucleic Acids Res 2015; 43:9694-710. [PMID: 26476455 PMCID: PMC4787770 DOI: 10.1093/nar/gkv1063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/01/2015] [Indexed: 12/05/2022] Open
Abstract
Genome-wide analyses in Caenorhabditis elegans show that post-translational modifications (PTMs) of histones are evolutionary conserved and distributed along functionally distinct genomic domains. However, a global profile of PTMs and their co-occurrence on the same histone tail has not been described in this organism. We used mass spectrometry based middle-down proteomics to analyze histone H3 N-terminal tails from C. elegans embryos for the presence, the relative abundance and the potential cross-talk of co-existing PTMs. This analysis highlighted that the lysine 23 of histone H3 (H3K23) is extensively modified by methylation and that tri-methylated H3K9 (H3K9me3) is exclusively detected on histone tails with di-methylated H3K23 (H3K23me2). Chromatin immunoprecipitation approaches revealed a positive correlation between H3K23me2 and repressive marks. By immunofluorescence analyses, H3K23me2 appears differentially regulated in germ and somatic cells, in part by the action of the histone demethylase JMJD-1.2. H3K23me2 is enriched in heterochromatic regions, localizing in H3K9me3 and heterochromatin protein like-1 (HPL-1)-positive foci. Biochemical analyses indicated that HPL-1 binds to H3K23me2 and interacts with a conserved CoREST repressive complex. Thus, our study suggests that H3K23me2 defines repressive domains and contributes to organizing the genome in distinct heterochromatic regions during embryogenesis.
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Affiliation(s)
- Julien Vandamme
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Simone Sidoli
- Centre for Epigenetics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Luca Mariani
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Carsten Friis
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Jesper Christensen
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark The Danish Stem Cell Centre (Danstem), University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Ole N Jensen
- Centre for Epigenetics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Anna Elisabetta Salcini
- Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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19
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Peng Y, Cooper SK, Li Y, Mei JM, Qiu S, Borchert GL, Donald SP, Kung HF, Phang JM. Ornithine-δ-Aminotransferase Inhibits Neurogenesis During Xenopus Embryonic Development. Invest Ophthalmol Vis Sci 2015; 56:2486-97. [PMID: 25783604 DOI: 10.1167/iovs.15-16509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE In humans, deficiency of ornithine-δ-aminotransferase (OAT) results in progressive degeneration of the neural retina (gyrate atrophy) with blindness in the fourth decade. In this study, we used the Xenopus embryonic developmental model to study functions of the OAT gene on embryonic development. METHODS We cloned and sequenced full-length OAT cDNA from Xenopus oocytes (X-OAT) and determined X-OAT expression in various developmental stages of Xenopus embryos and in a variety of adult tissues. The phenotype, gene expression of neural developmental markers, and enzymatic activity were detected by gain-of-function and loss-of-function manipulations. RESULTS We showed that X-OAT is essential for Xenopus embryonic development, and overexpression of X-OAT produces a ventralized phenotype characterized by a small head, lack of axial structure, and defective expression of neural developmental markers. Using X-OAT mutants based on mutations identified in humans, we found that substitution of both Arg 180 and Leu 402 abrogated both X-OAT enzymatic activity and ability to modulate the developmental phenotype. Neurogenesis is inhibited by X-OAT during Xenopus embryonic development. CONCLUSIONS Neurogenesis is inhibited by X-OAT during Xenopus embryonic development, but it is essential for Xenopus embryonic development. The Arg 180 and Leu 402 are crucial for these effects of the OAT molecule in development.
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Affiliation(s)
- Ying Peng
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sandra K Cooper
- Basic Research Program, Leidos, Inc., National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland, United States
| | - Yi Li
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jay M Mei
- Metabolism and Cancer Susceptibility Section, Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland, United States
| | - Shuwei Qiu
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Gregory L Borchert
- Basic Research Program, Leidos, Inc., National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland, United States
| | - Steven P Donald
- Metabolism and Cancer Susceptibility Section, Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland, United States
| | - Hsiang-Fu Kung
- State Key Laboratory of Oncology in Southern China, and Centre for Emerging Infectious Diseases, the Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - James M Phang
- Metabolism and Cancer Susceptibility Section, Basic Research Laboratory, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland, United States
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20
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Differential properties of transcriptional complexes formed by the CoREST family. Mol Cell Biol 2014; 34:2760-70. [PMID: 24820421 DOI: 10.1128/mcb.00083-14] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mammalian genomes harbor three CoREST genes. rcor1 encodes CoREST (CoREST1), and the paralogues rcor2 and rcor3 encode CoREST2 and CoREST3, respectively. Here, we describe specific properties of transcriptional complexes formed by CoREST proteins with the histone demethylase LSD1/KDM1A and histone deacetylases 1 and 2 (HDAC1/2) and the finding that all three CoRESTs are expressed in the adult rat brain. CoRESTs interact equally strongly with LSD1/KDM1A. Structural analysis shows that the overall conformation of CoREST3 is similar to that of CoREST1 complexed with LSD1/KDM1A. Nonetheless, transcriptional repressive capacity of CoREST3 is lower than that of CoREST1, which correlates with the observation that CoREST3 leads to a reduced LSD1/KDM1A catalytic efficiency. Also, CoREST2 shows a lower transcriptional repression than CoREST1, which is resistant to HDAC inhibitors. CoREST2 displays lower interaction with HDAC1/2, which is barely present in LSD1/KDM1A-CoREST2 complexes. A nonconserved leucine in the first SANT domain of CoREST2 severely weakens its association with HDAC1/2. Furthermore, CoREST2 mutants with increased HDAC1/2 interaction and those without HDAC1/2 interaction exhibit equivalent transcriptional repression capacities, indicating that CoREST2 represses in an HDAC-independent manner. In conclusion, differences among CoREST proteins are instrumental in the modulation of protein-protein interactions and catalytic activities of LSD1/KDM1A-CoREST-HDAC complexes, fine-tuning gene expression regulation.
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Meier K, Brehm A. Chromatin regulation: how complex does it get? Epigenetics 2014; 9:1485-95. [PMID: 25482055 PMCID: PMC4622878 DOI: 10.4161/15592294.2014.971580] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/18/2014] [Accepted: 09/29/2014] [Indexed: 12/16/2022] Open
Abstract
Gene transcription is tightly regulated at different levels to ensure that the transcriptome of the cell is appropriate for developmental stage and cell type. The chromatin state in which a gene is embedded determines its expression level to a large extent. Activation or repression of transcription is typically accomplished by the recruitment of chromatin-associated multisubunit protein complexes that combine several molecular tools, such as histone-binding and chromatin-modifying activities. Recent biochemical purifications of such complexes have revealed a substantial diversity. On the one hand, complexes that were thought to be unique have been revealed to be part of large complex families. On the other hand, protein subunits that were thought to only exist in separate complexes have been shown to coexist in novel assemblies. In this review we discuss our current knowledge of repressor complexes that contain MBT domain proteins and/or the CoREST co-repressor and use them as a paradigm to illustrate the unexpected heterogeneity and tool sharing of chromatin regulating protein complexes. These recent insights also challenge the ways we define and think about protein complexes in general.
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Key Words
- ATP, adenosine triphosphate
- BAP, brahma associated protein
- BHC80, BRAF-histone deacetylase complex 80
- BRG1, brahma Related Gene 1
- CHD, chromo domain helicase DNA binding
- CoREST
- CoREST REST, corepressor
- DNA, deoxyribonucleic acid
- DNMT, DNA methyltransferase
- DP-1, dimerization partner 1
- E2F, E2 transcription Factor
- ELM2, EGL-27 and MTA1 homology 2
- ES cell, embryonic stem cells
- H, histone
- HDAC, histone deacetylas
- HMTase, histone methylase
- HP1, heterochromatin protein 1
- K, lysine
- L3MBTL, lethal 3 malignant brain tumor-like
- LINT, l(3)mbt interacting
- LSD1, lysine-specific demethylase 1
- Lint-1, l(3)mbt interacting 1
- MBT protein
- MBT, malignant brain tumor
- MBTS, malignant brain tumor signature
- NPA1, nucleosome assembly protein
- NRSF, neural-restrictive silencing factor
- NuRD, nucleosome remodeling and deacetylase
- PBAP, polybromo-associated BAP
- PHD, plant homeo domain
- PRC1, polycomb repressive complex 1
- PRE, polycomb responsive element
- Pc, polycomb
- PcG, polycomb group
- Ph, polyhomeotic
- Pho, pleiohomeotic
- PhoRC, Pho repressive complex
- Psc, posterior sex combs
- RB, retinoblastoma
- REST, repressor element 1 silencing transcription factor
- RNA, ribonucleic acid
- Rpd3, reduced potassium dependency 3
- SANT, SWI/ADA2/N-CoR/TFIIIB
- SCML, sex combs on midleg-like
- SLC, SFMBT1, LSD1, CoREST
- SWH, Salvador-Warts-Hippo
- SWI/SNF, switching defective/sucrose non-fermenting
- Sce, sex combs extra
- Scm, sex combs on midleg
- Sfmbt, Scm-related gene containing 4 mbt domains
- TSS, transcription start site
- YY1, ying-yang 1
- ZNF, zinc finger
- complex family
- dL(3)mbt, Drosophila Lethal 3 malignant brain tumor
- hBRM, human Brahma
- l(3)mbt, lethal 3 malignant brain tumor
- protein complex
- transcriptional regulation
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Affiliation(s)
- Karin Meier
- Institut für Molekularbiologie und Tumorforschung; Philipps-Universität Marburg; Marburg, Germany
- Instituto de Fisiología Celular; Departamento de Genética Molecular; Universidad Nacional Autónoma de México; México City, México
| | - Alexander Brehm
- Institut für Molekularbiologie und Tumorforschung; Philipps-Universität Marburg; Marburg, Germany
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SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state during passage through the germ line. Proc Natl Acad Sci U S A 2014; 111:9509-14. [PMID: 24979765 DOI: 10.1073/pnas.1321843111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The Caenorhabditis elegans LSD1 H3K4me2 demethylase SPR-5 reprograms epigenetic transcriptional memory during passage through the germ line. Here we show that mutants in the H3K9me2 methyltransferase, met-2, result in transgenerational epigenetic effects that parallel spr-5 mutants. In addition, we find that spr-5;met-2 double mutants have a synergistic effect on sterility, H3K4me2, and spermatogenesis expression. These results implicate MET-2 as a second histone-modifying enzyme in germ-line reprogramming and suggest a model in which SPR-5 and MET-2 function cooperatively to reestablish an epigenetic ground state required for the continued immortality of the C. elegans germ line. Without SPR-5 and MET-2, we find that the ability to express spermatogenesis genes is transgenerationally passed on to the somatic cells of the subsequent generation. This indicates that H3K4me2 may act in the maintenance of cell fate. Finally, we demonstrate that reducing H3K4me2 causes a large increase in H3K9me2 added by the SPR-5;MET-2 reprogramming mechanism. This finding suggests a novel histone code interaction in which the input chromatin environment dictates the output chromatin state. Taken together, our results provide evidence for a broader reprogramming mechanism in which multiple enzymes coordinately regulate histone information during passage through the germ line.
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Hale JJ, Amin NM, George C, Via Z, Shi H, Liu J. A role of the LIN-12/Notch signaling pathway in diversifying the non-striated egg-laying muscles in C. elegans. Dev Biol 2014; 389:137-48. [PMID: 24512688 PMCID: PMC3981933 DOI: 10.1016/j.ydbio.2014.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/27/2014] [Accepted: 02/01/2014] [Indexed: 01/19/2023]
Abstract
The proper formation and function of an organ is dependent on the specification and integration of multiple cell types and tissues. An example of this is the Caenorhabditis elegans hermaphrodite egg-laying system, which requires coordination between the vulva, uterus, neurons, and musculature. While the genetic constituents of the first three components have been well studied, little is known about the molecular mechanisms underlying the specification of the egg-laying musculature. The egg-laying muscles are non-striated in nature and consist of sixteen cells, four each of type I and type II vulval muscles and uterine muscles. These 16 non-striated muscles exhibit distinct morphology, location, synaptic connectivity and function. Using an RNAi screen targeting the putative transcription factors in the C. elegans genome, we identified a number of novel factors important for the diversification of these different types of egg-laying muscles. In particular, we found that RNAi knockdown of lag-1, which encodes the sole C. elegans ortholog of the transcription factor CSL (CBF1, Suppressor of Hairless, LAG-1), an effector of the LIN-12/Notch pathway, led to the production of extra type I vulval muscles. Similar phenotypes were also observed in animals with down-regulation of the Notch receptor LIN-12 and its DSL (Delta, Serrate, LAG-2) ligand LAG-2. The extra type I vulval muscles in animals with reduced LIN-12/Notch signaling resulted from a cell fate transformation of type II vulval muscles to type I vulval muscles. We showed that LIN-12/Notch was activated in the undifferentiated type II vulval muscle cells by LAG-2/DSL that is likely produced by the anchor cell (AC). Our findings provide additional evidence highlighting the roles of LIN-12/Notch signaling in coordinating the formation of various components of the functional C. elegans egg-laying system. We also identify multiple new factors that play critical roles in the proper specification of the different types of egg-laying muscles.
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Affiliation(s)
- Jared J Hale
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States
| | - Nirav M Amin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States
| | - Carolyn George
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States
| | - Zachary Via
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States
| | - Herong Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States
| | - Jun Liu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, United States.
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Alvares SM, Mayberry GA, Joyner EY, Lakowski B, Ahmed S. H3K4 demethylase activities repress proliferative and postmitotic aging. Aging Cell 2014; 13:245-53. [PMID: 24134677 PMCID: PMC4020274 DOI: 10.1111/acel.12166] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2013] [Indexed: 12/16/2022] Open
Abstract
Homeostasis of postmitotic and proliferating cells is maintained by pathways that repress stress. We found that the Caenorhabditis elegans histone 3 lysine 4 (H3K4) demethylases RBR-2 and SPR-5 promoted postmitotic longevity of stress-resistant daf-2 adults, altered pools of methylated H3K4, and promoted silencing of some daf-2 target genes. In addition, RBR-2 and SPR-5 were required for germ cell immortality at a high temperature. Transgenerational proliferative aging was enhanced for spr-5; rbr-2 double mutants, suggesting that these histone demethylases may function sequentially to promote germ cell immortality by targeting distinct H3K4 methyl marks. RBR-2 did not play a comparable role in the maintenance of quiescent germ cells in dauer larvae, implying that it represses stress that occurs as a consequence of germ cell proliferation, rather than stress that accumulates in nondividing cells. We propose that H3K4 demethylase activities promote the maintenance of chromatin states during stressful growth conditions, thereby repressing postmitotic aging of somatic cells as well as proliferative aging of germ cells.
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Affiliation(s)
- Stacy M. Alvares
- Department of Genetics University of North Carolina Chapel Hill NC 27599‐3280USA
- SPIRE Postdoctoral Fellowship Program University of North Carolina Chapel Hill NC 27599‐3280USA
| | - Gaea A. Mayberry
- Department of Biology University of North Carolina Chapel Hill NC 27599‐3280USA
| | - Ebony Y. Joyner
- Department of Natural Sciences Fayetteville State University Fayetteville NC 28301‐4298USA
| | - Bernard Lakowski
- Department of Neuroscience Institut Pasteur 75724 Paris Cedex 15 France
| | - Shawn Ahmed
- Department of Genetics University of North Carolina Chapel Hill NC 27599‐3280USA
- Department of Biology University of North Carolina Chapel Hill NC 27599‐3280USA
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Lu T, Aron L, Zullo J, Pan Y, Kim H, Chen Y, Yang TH, Kim HM, Drake D, Liu XS, Bennett DA, Colaiácovo MP, Yankner BA. REST and stress resistance in ageing and Alzheimer's disease. Nature 2014; 507:448-54. [PMID: 24670762 PMCID: PMC4110979 DOI: 10.1038/nature13163] [Citation(s) in RCA: 520] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 02/21/2014] [Indexed: 12/13/2022]
Abstract
Human neurons are functional over an entire lifetime, yet the mechanisms that preserve function and protect against neurodegeneration during aging are unknown. Here we show that induction of the repressor element 1-silencing transcription/neuron-restrictive silencer factor (REST/NRSF) is a universal feature of normal aging in human cortical and hippocampal neurons. REST is lost, however, in mild cognitive impairment (MCI) and Alzheimer’s disease (AD). Chromatin immunoprecipitation with deep sequencing (ChIP-seq) and expression analysis show that REST represses genes that promote cell death and AD pathology, and induces the expression of stress response genes. Moreover, REST potently protects neurons from oxidative stress and amyloid β-protein (Aβ) toxicity, and conditional deletion of REST in the mouse brain leads to age-related neurodegeneration. A functional ortholog of REST, C. elegans SPR-4, also protects against oxidative stress and Aβ toxicity. During normal aging, REST is induced in part by cell non-autonomous Wnt signaling. However, in AD, frontotemporal dementia and dementia with Lewy bodies, REST is lost from the nucleus and appears in autophagosomes together with pathologic misfolded proteins. Finally, REST levels during aging are closely correlated with cognitive preservation and longevity. Thus, the activation state of REST may distinguish neuroprotection from neurodegeneration in the aging brain.
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Affiliation(s)
- Tao Lu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Liviu Aron
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph Zullo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ying Pan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Haeyoung Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yiwen Chen
- Department of Biostatistics and Computational Biology, Dana-Faber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - Tun-Hsiang Yang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hyun-Min Kim
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Derek Drake
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Faber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois 60612, USA
| | - Monica P Colaiácovo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Bruce A Yankner
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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SACY-1 DEAD-Box helicase links the somatic control of oocyte meiotic maturation to the sperm-to-oocyte switch and gamete maintenance in Caenorhabditis elegans. Genetics 2012; 192:905-28. [PMID: 22887816 PMCID: PMC3522166 DOI: 10.1534/genetics.112.143271] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In sexually reproducing animals, oocytes arrest at diplotene or diakinesis and resume meiosis (meiotic maturation) in response to hormones. In Caenorhabditis elegans, major sperm protein triggers meiotic resumption through a mechanism involving somatic Gαs–adenylate cyclase signaling and soma-to-germline gap-junctional communication. Using genetic mosaic analysis, we show that the major effector of Gαs–adenylate cyclase signaling, protein kinase A (PKA), is required in gonadal sheath cells for oocyte meiotic maturation and dispensable in the germ line. This result rules out a model in which cyclic nucleotides must transit through sheath-oocyte gap junctions to activate PKA in the germ line, as proposed in vertebrate systems. We conducted a genetic screen to identify regulators of oocyte meiotic maturation functioning downstream of Gαs–adenylate cyclase–PKA signaling. We molecularly identified 10 regulatory loci, which include essential and nonessential factors. sacy-1, which encodes a highly conserved DEAD-box helicase, is an essential germline factor that negatively regulates meiotic maturation. SACY-1 is a multifunctional protein that establishes a mechanistic link connecting the somatic control of meiotic maturation to germline sex determination and gamete maintenance. Modulatory factors include multiple subunits of a CoREST-like complex and the TWK-1 two-pore potassium channel. These factors are not absolutely required for meiotic maturation or its negative regulation in the absence of sperm, but function cumulatively to enable somatic control of meiotic maturation. This work provides insights into the genetic control of meiotic maturation signaling in C. elegans, and the conserved factors identified here might inform analysis in other systems through either homology or analogy.
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Domanitskaya E, Schüpbach T. CoREST acts as a positive regulator of Notch signaling in the follicle cells of Drosophila melanogaster. J Cell Sci 2012; 125:399-410. [PMID: 22331351 DOI: 10.1242/jcs.089797] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The Notch signaling pathway plays important roles in a variety of developmental events. The context-dependent activities of positive and negative modulators dramatically increase the diversity of cellular responses to Notch signaling. In a screen for mutations affecting the Drosophila melanogaster follicular epithelium, we isolated a mutation in CoREST that disrupts the Notch-dependent mitotic-to-endocycle switch of follicle cells at stage 6 of oogenesis. We show that Drosophila CoREST positively regulates Notch signaling, acting downstream of the proteolytic cleavage of Notch but upstream of Hindsight activity; the Hindsight gene is a Notch target that coordinates responses in the follicle cells. We show that CoREST genetically interacts with components of the Notch repressor complex, Hairless, C-terminal Binding Protein and Groucho. In addition, we demonstrate that levels of H3K27me3 and H4K16 acetylation are dramatically increased in CoREST mutant follicle cells. Our data indicate that CoREST acts as a positive modulator of the Notch pathway in the follicular epithelium as well as in wing tissue, and suggests a previously unidentified role for CoREST in the regulation of Notch signaling. Given its high degree of conservation among species, CoREST probably also functions as a regulator of Notch-dependent cellular events in other organisms.
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Affiliation(s)
- Elena Domanitskaya
- Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, Washington Road, Princeton, NJ 08544-1014, USA
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28
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Shaye DD, Greenwald I. OrthoList: a compendium of C. elegans genes with human orthologs. PLoS One 2011; 6:e20085. [PMID: 21647448 PMCID: PMC3102077 DOI: 10.1371/journal.pone.0020085] [Citation(s) in RCA: 302] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 04/18/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND C. elegans is an important model for genetic studies relevant to human biology and disease. We sought to assess the orthology between C. elegans and human genes to understand better the relationship between their genomes and to generate a compelling list of candidates to streamline RNAi-based screens in this model. RESULTS We performed a meta-analysis of results from four orthology prediction programs and generated a compendium, "OrthoList", containing 7,663 C. elegans protein-coding genes. Various assessments indicate that OrthoList has extensive coverage with low false-positive and false-negative rates. Part of this evaluation examined the conservation of components of the receptor tyrosine kinase, Notch, Wnt, TGF-ß and insulin signaling pathways, and led us to update compendia of conserved C. elegans kinases, nuclear hormone receptors, F-box proteins, and transcription factors. Comparison with two published genome-wide RNAi screens indicated that virtually all of the conserved hits would have been obtained had just the OrthoList set (∼38% of the genome) been targeted. We compiled Ortholist by InterPro domains and Gene Ontology annotation, making it easy to identify C. elegans orthologs of human disease genes for potential functional analysis. CONCLUSIONS We anticipate that OrthoList will be of considerable utility to C. elegans researchers for streamlining RNAi screens, by focusing on genes with apparent human orthologs, thus reducing screening effort by ∼60%. Moreover, we find that OrthoList provides a useful basis for annotating orthology and reveals more C. elegans orthologs of human genes in various functional groups, such as transcription factors, than previously described.
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Affiliation(s)
- Daniel D. Shaye
- Howard Hughes Medical Institute, Columbia University, College of Physicians and Surgeons, New York, New York, United States of America
| | - Iva Greenwald
- Howard Hughes Medical Institute, Columbia University, College of Physicians and Surgeons, New York, New York, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University, College of Physicians and Surgeons, New York, New York, United States of America
- Department of Genetics and Development, Columbia University, College of Physicians and Surgeons, New York, New York, United States of America
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29
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Zhang Y, Li Y. The Expanding Mi-2/NuRD Complexes: A Schematic Glance. PROTEOMICS INSIGHTS 2011. [DOI: 10.4137/pri.s6329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
This mini-review will schematically update the progress of the expanding Mi-2/Nucleosome Remodeling Deacetylase (NuRD) complexes in cancer and in normal development such as stemness, with a focus on mammals and the increasingly popular and powerful model organism Caenorhabditis elegans. The Mi-2/NuRD complexes control gene activity during the development of complex organisms. Every Mi-2/NuRD complex contains many different core polypeptides, which form distinct multifunctional complexes with specific context-dependent regulators. The Mi-2/NuRD complexes have unique ATP-dependent chromatin remodeling, histone deacetylase, demethylase activities and higher order chromatin organization. They can regulate the accessibility of transcription factors or repair proteins to DNA. In this review, we summarize our current knowleges in the composition, interaction and function of the subunits within the Mi-2/NuRD complex, the methodology used for the identification of Mi-2/NuRD complexes, as well as the clinical and therapeutic implications targeting the Mi-2/NuRD subunits.
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Affiliation(s)
- Yue Zhang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, 99 Brookline Avenue, Boston, MA 02215, USA
| | - Yinghua Li
- Department of Radiation Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
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Malik S, Bhaumik SR. Mixed lineage leukemia: histone H3 lysine 4 methyltransferases from yeast to human. FEBS J 2010; 277:1805-21. [PMID: 20236312 DOI: 10.1111/j.1742-4658.2010.07607.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The fourth lysine of histone H3 is post-translationally modified by a methyl group via the action of histone methyltransferase, and such a covalent modification is associated with transcriptionally active and/or repressed chromatin states. Thus, histone H3 lysine 4 methylation has a crucial role in maintaining normal cellular functions. In fact, misregulation of this covalent modification has been implicated in various types of cancer and other diseases. Therefore, a large number of studies over recent years have been directed towards histone H3 lysine 4 methylation and the enzymes involved in this covalent modification in eukaryotes ranging from yeast to human. These studies revealed a set of histone H3 lysine 4 methyltransferases with important cellular functions in different eukaryotes, as discussed here.
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Affiliation(s)
- Shivani Malik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
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Katz DJ, Edwards TM, Reinke V, Kelly WG. A C. elegans LSD1 demethylase contributes to germline immortality by reprogramming epigenetic memory. Cell 2009; 137:308-20. [PMID: 19379696 DOI: 10.1016/j.cell.2009.02.015] [Citation(s) in RCA: 242] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 11/14/2008] [Accepted: 02/06/2009] [Indexed: 10/20/2022]
Abstract
Epigenetic information undergoes extensive reprogramming in the germline between generations. This reprogramming may be essential to establish a developmental ground state in the zygote. We show that mutants in spr-5, the Caenorhabditis elegans ortholog of the H3K4me2 demethylase LSD1/KDM1, exhibit progressive sterility over many generations. This sterility correlates with the misregulation of spermatogenesis-expressed genes and transgenerational accumulation of the histone modification dimethylation of histone H3 on lysine 4 (H3K4me2). This suggests that H3K4me2 can serve as a stable epigenetic memory, and that erasure of H3K4me2 by LSD/KDM1 in the germline prevents the inappropriate transmission of this epigenetic memory from one generation to the next. Thus, our results provide direct mechanistic insights into the processes that are required for epigenetic reprogramming between generations.
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Affiliation(s)
- David J Katz
- Biology Department, Emory University, Atlanta, GA 30322, USA
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Gontijo AM, Aubert S, Roelens I, Lakowski B. Mutations in genes involved in nonsense mediated decay ameliorate the phenotype of sel-12 mutants with amber stop mutations in Caenorhabditis elegans. BMC Genet 2009; 10:14. [PMID: 19302704 PMCID: PMC2678165 DOI: 10.1186/1471-2156-10-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 03/20/2009] [Indexed: 11/29/2022] Open
Abstract
Background Presenilin proteins are part of a complex of proteins that can cleave many type I transmembrane proteins, including Notch Receptors and the Amyloid Precursor Protein, in the middle of the transmembrane domain. Dominant mutations in the human presenilin genes PS1 and PS2 lead to Familial Alzheimer's disease. Mutations in the Caenorhabditis elegans sel-12 presenilin gene cause a highly penetrant egg-laying defect due to reduction of signalling through the lin-12/Notch receptor. Mutations in six spr genes (for suppressor of presenilin) are known to strongly suppress sel-12. Mutations in most strong spr genes suppress sel-12 by de-repressing the transcription of the largely functionally equivalent hop-1 presenilin gene. However, how mutations in the spr-2 gene suppress sel-12 is unknown. Results We show that spr-2 mutations increase the levels of sel-12 transcripts with Premature translation Termination Codons (PTCs) in embryos and L1 larvae. mRNA transcripts from sel-12 alleles with PTCs undergo degradation by a process known as Nonsense Mediated Decay (NMD). However, spr-2 mutations do not appear to affect NMD. Mutations in the smg genes, which are required for NMD, can restore sel-12(PTC) transcript levels and ameliorate the phenotype of sel-12 mutants with amber PTCs. However, the phenotypic suppression of sel-12 by smg genes is nowhere near as strong as the effect of previously characterized spr mutations including spr-2. Consistent with this, we have identified only two mutations in smg genes among the more than 100 spr mutations recovered in genetic screens. Conclusion spr-2 mutations do not suppress sel-12 by affecting NMD of sel-12(PTC) transcripts and appear to have a novel mechanism of suppression. The fact that mutations in smg genes can ameliorate the phenotype of sel-12 alleles with amber PTCs suggests that some read-through of sel-12(amber) alleles occurs in smg backgrounds.
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Gómez AV, Galleguillos D, Maass JC, Battaglioli E, Kukuljan M, Andrés ME. CoREST represses the heat shock response mediated by HSF1. Mol Cell 2008; 31:222-31. [PMID: 18657505 DOI: 10.1016/j.molcel.2008.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Revised: 03/23/2008] [Accepted: 06/01/2008] [Indexed: 10/21/2022]
Abstract
The stress response in cells involves a rapid and transient transcriptional activation of stress genes. It has been shown that Hsp70 limits its own transcriptional activation functioning as a corepressor of heat shock factor 1 (HSF1) during the attenuation of the stress response. Here we show that the transcriptional corepressor CoREST interacts with Hsp70. Through this interaction, CoREST represses both HSF1-dependent and heat shock-dependent transcriptional activation of the hsp70 promoter. In cells expressing short hairpin RNAs directed against CoREST, Hsp70 cannot repress HSF1-dependent transcription. A reduction of CoREST levels also provoked a significant increase of Hsp70 protein levels and an increase of HSF1-dependent transactivation of hsp70 promoter. Via chromatin immunoprecipitation assays we show that CoREST is bound to the hsp70 gene promoter under basal conditions and that its binding increases during heat shock response. In conclusion, we demonstrated that CoREST is a key regulator of the heat shock stress response.
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Affiliation(s)
- Andrea V Gómez
- Millenium Nucleus in Stress and Addiction, Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8330025, Chile
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34
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Ouellet J, Li S, Roy R. Notch signalling is required for both dauer maintenance and recovery in C. elegans. Development 2008; 135:2583-92. [PMID: 18599512 DOI: 10.1242/dev.012435] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The Notch signalling pathway is conserved among higher metazoans and is used repeatedly throughout development to specify distinct cell fates among populations of equipotent cells. Mounting evidence suggests that Notch signalling may also be crucial in neuronal function in postmitotic, differentiated neurons. Here, we demonstrate a novel role for the canonical Notch signalling pathway in postmitotic neurons during a specialised ;diapause-like' post-embryonic developmental stage in C. elegans called dauer. Our data suggest that cell signalling downstream of the developmental decision to enter dauer leads to the activation of Notch-responding genes in postmitotic neurons. Consistent with this, we demonstrate that glp-1, one of the two C. elegans Notch receptors, and its ligand lag-2 are expressed in neurons during the dauer stage, and both genes are required to maintain this stage in a daf-7/TGFbeta dauer constitutive background. Our genetic data also suggest that a second Notch receptor, lin-12, functions upstream of, or in parallel with, insulin-like signalling components in response to replete growth conditions to promote dauer recovery. Based on our findings, cues associated with the onset of dauer ultimately trigger a glp-1-dependent Notch signalling cascade in neurons to maintain this developmental state. Then, as growth conditions improve, activation of the LIN-12 Notch receptor cooperates with the insulin-like signalling pathway to signal recovery from the dauer stage.
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Affiliation(s)
- Jimmy Ouellet
- Department of Biology, McGill University, Montréal, Québec, Canada
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35
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A Caenorhabditis elegans model for epithelial-neuronal transdifferentiation. Proc Natl Acad Sci U S A 2008; 105:3790-5. [PMID: 18308937 DOI: 10.1073/pnas.0712159105] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding transdifferentiation-the conversion of one differentiated cell type into another-is important from both basic science and clinical perspectives. In Caenorhabditis elegans, an epithelial cell named Y is initially part of the rectum but later appears to withdraw, migrate, and then become a motor neuron named PDA. Here, we show that this represents a bona fide transdifferentiation event: Y has epithelial hallmarks without detectable neural characteristics, and PDA has no residual epithelial characteristics. Using available mutants and laser microsurgery, we found that transdifferentiation does not depend on fusion with a neighboring cell or require migration of Y away from the rectum, that other rectal epithelial cells are not competent to transdifferentiate, and that transdifferentiation requires the EGL-5 and SEM-4 transcription factors and LIN-12/Notch signaling. Our results establish Y-to-PDA transdifferentiation as a genetically tractable model for deciphering the mechanisms underlying cellular plasticity in vivo.
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36
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Abstract
The discovery of an increasing number of histone demethylases has highlighted the dynamic nature of the regulation of histone methylation, a key chromatin modification that is involved in eukaryotic genome and gene regulation. A flurry of recent studies has offered glimpses into the specific biological roles of these enzymes and their potential connections to human diseases. These advances have also catalysed a resurgence of interest in epigenetic regulators as potential therapeutic targets.
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Affiliation(s)
- Yang Shi
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.
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37
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Saleque S, Kim J, Rooke HM, Orkin SH. Epigenetic regulation of hematopoietic differentiation by Gfi-1 and Gfi-1b is mediated by the cofactors CoREST and LSD1. Mol Cell 2007; 27:562-72. [PMID: 17707228 DOI: 10.1016/j.molcel.2007.06.039] [Citation(s) in RCA: 313] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 04/27/2007] [Accepted: 06/25/2007] [Indexed: 02/06/2023]
Abstract
Gfi-1 and Gfi-1b are homologous transcriptional repressors involved in diverse developmental contexts, including hematopoiesis and oncogenesis. Transcriptional repression by Gfi proteins requires the conserved SNAG domain. To elucidate the function of Gfi proteins, we purified Gfi-1b complexes and identified interacting proteins. Prominent among these is the corepressor CoREST, the histone demethylase LSD1, and HDACs 1 and 2. CoREST and LSD1 associate with Gfi-1/1b via the SNAG repression domain. Gfi-1b further recruits these cofactors to the majority of target gene promoters in vivo. Inhibition of CoREST and LSD1 perturbs differentiation of erythroid, megakaryocytic, and granulocytic cells as well as primary erythroid progenitors. LSD1 depletion derepresses Gfi targets in lineage-specific patterns, accompanied by enhanced histone 3 lysine 4 methylation at the respective promoters. Overall, we show that chromatin regulatory proteins CoREST and LSD1 mediate transcriptional repression by Gfi proteins. Lineage-restricted deployment of these cofactors through interaction with Gfi proteins controls hematopoietic differentiation.
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Affiliation(s)
- Shireen Saleque
- Division of Hematology-Oncology, Children's Hospital Boston, Boston, Harvard Medical School, Boston, MA 02115, USA
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38
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Klose RJ, Zhang Y. Regulation of histone methylation by demethylimination and demethylation. Nat Rev Mol Cell Biol 2007; 8:307-18. [PMID: 17342184 DOI: 10.1038/nrm2143] [Citation(s) in RCA: 621] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Histone methylation has important roles in regulating transcription, genome integrity and epigenetic inheritance. Historically, methylated histone arginine and lysine residues have been considered static modifications because of the low levels of methyl-group turnover in chromatin. The recent identification of enzymes that antagonize or remove histone methylation has changed this view and now the dynamic nature of these modifications is being appreciated. Here, we examine the enzymatic and structural basis for the mechanisms that these enzymes use to counteract histone methylation and provide insights into their substrate specificity and biological function.
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Affiliation(s)
- Robert J Klose
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7295, USA
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39
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Lee MG, Wynder C, Norman J, Shiekhattar R. Isolation and characterization of histone H3 lysine 4 demethylase-containing complexes. Methods 2007; 40:327-30. [PMID: 17101444 PMCID: PMC4682359 DOI: 10.1016/j.ymeth.2006.07.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2006] [Accepted: 07/16/2006] [Indexed: 12/21/2022] Open
Abstract
Histone methylation is involved in the regulation of many cellular processes. In the past 2 years, several histone demethylases including BHC110/LSD1 have been characterized. BHC110, the first known histone lysine demethylase, removes methyl groups from methylated histone H3 lysine 4 and has been found in many multi-protein complexes. Using one-step affinity purification, we have isolated enzymatically active BHC110-containing complexes. Here, we detail the methods used for the isolation and characterization of these histone demethylase complexes from a human stable cell line.
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Affiliation(s)
| | | | | | - Ramin Shiekhattar
- To whom correspondence should be addressed. Phone: (215) 898-3896, Fax: (215) 898-3986, E-mail:
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40
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Bender AM, Kirienko NV, Olson SK, Esko JD, Fay DS. lin-35/Rb and the CoREST ortholog spr-1 coordinately regulate vulval morphogenesis and gonad development in C. elegans. Dev Biol 2007; 302:448-62. [PMID: 17070797 PMCID: PMC1933485 DOI: 10.1016/j.ydbio.2006.09.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 08/28/2006] [Accepted: 09/30/2006] [Indexed: 11/21/2022]
Abstract
Using a genetic screen to identify genes that carry out redundant functions during development with lin-35/Rb, the C. elegans Retinoblastoma family ortholog, we have identified a mutation in spr-1. spr-1 encodes the C. elegans ortholog of human CoREST, a protein containing Myb-like SANT and ELM2 domains, which functions as part of a transcriptional regulatory complex. CoREST recruits mediators of transcriptional repression, including histone deacetylase, and demethylase, and interacts with the tumor suppression protein REST. spr-1/CoREST was previously shown in C. elegans to suppress defects associated with loss of the presenilin sel-12, which functions in the proteolytic processing of LIN-12/Notch. Here we show that lin-35 and spr-1 coordinately regulate several developmental processes in C. elegans including the ingression of vulval cells as well as germline proliferation. We also show that loss of lin-35 and spr-1 hypersensitizes animals to a reduction in LIN-12/Notch activity, leading to the generation of proximal germline tumors. This defect, which is observed in lin-35; spr-1; lin-12(RNAi) and lin-35; spr-1; hop-1(RNAi) triple mutants is likely due to a delay in the entry of germ cells into meiosis.
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Affiliation(s)
- Aaron M. Bender
- University of Wyoming, College of Agriculture, Department of Molecular Biology Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
| | - Natalia V. Kirienko
- University of Wyoming, College of Agriculture, Department of Molecular Biology Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
| | - Sara K. Olson
- Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla CA 92093
| | - Jeffery D. Esko
- Department of Cellular and Molecular Medicine, Glycobiology Research and Training Center, University of California, San Diego, La Jolla CA 92093
| | - David S Fay
- University of Wyoming, College of Agriculture, Department of Molecular Biology Dept 3944, 1000 E. University Avenue, Laramie, WY 82071
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41
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Lakowski B, Roelens I, Jacob S. CoREST-like complexes regulate chromatin modification and neuronal gene expression. J Mol Neurosci 2007; 29:227-39. [PMID: 17085781 DOI: 10.1385/jmn:29:3:227] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Revised: 11/30/1999] [Accepted: 02/03/2006] [Indexed: 12/29/2022]
Abstract
The mammalian CoREST ([co]repressor for element-1-silencing transcription factor) complex was first identified associated with the repressor for element-1 silencing transcription factor (REST)/neuronal restrictive silencing factor. The CoREST complex is a chromatin-modifying corepressor complex that acts with REST to regulate neuronal gene expression and neuronal stem cell fate. Components of a CoREST-like complex have been identified recently in Xenopus laevis, Caenorhabditis elegans, and Drosophila melanogaster. Like the mammalian complex, the Drosophila complex is required to regulate neuronal gene expression, whereas the C. elegans homologs regulate the expression of the hop-1 presenilin gene, suggesting an ancient conserved function of CoREST complexes in regulating neuronal gene expression.
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Affiliation(s)
- Bernard Lakowski
- Nematode Genetics Group, Department of Neuroscience, Pasteur Institute, 75724 Paris Cedex 15, France.
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42
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Kraemer B, Schellenberg GD. Using Caenorhabditis elegans models of neurodegenerative disease to identify neuroprotective strategies. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2007; 77:219-46. [PMID: 17178476 DOI: 10.1016/s0074-7742(06)77007-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Brian Kraemer
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle Division, Seattle, Washington 98108, USA
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43
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Nicolas E, Lee MG, Hakimi MA, Cam HP, Grewal SIS, Shiekhattar R. Fission Yeast Homologs of Human Histone H3 Lysine 4 Demethylase Regulate a Common Set of Genes with Diverse Functions. J Biol Chem 2006; 281:35983-8. [PMID: 16990277 DOI: 10.1074/jbc.m606349200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Schizosaccharomyces pombe contains two proteins, SWIRM1 and SWIRM2, with close homology to human histone H3 lysine 4 demethylase. Both proteins contain the amino oxidase catalytic domain and a recently described DNA interaction SWIRM domain. Here we describe the biochemical isolation and the functional characterization of SWIRM1 and SWIRM2. Our results indicate that while SWIRM2 is an essential gene, cells lacking SWIRM1 are viable. We found that SWIRM1 and SWIRM2 are stably associated in a multiprotein complex, but intriguingly, unlike their human counterpart, S. pombe SWIRM complex contains neither a histone deacetylase nor any detectable demethylase activity. Genome-wide chromatin immunoprecipitation unexpectedly showed the absence of both SWIRM proteins from heterochromatic domains. Instead, consistent with biochemical analyses, SWIRM1 and SWIRM2 co-localize to a common set of target gene promoters whose functions are implicated in diverse processes including mitochondrial metabolism and transcriptional regulation. Importantly, we show that SWIRM1 is not only required for optimum transcription of its target genes but also display a global role in regulation of antisense transcription.
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Affiliation(s)
- Estelle Nicolas
- Laboratory of Molecular Cell Biology, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
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44
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Abstract
The genome of the nematode Caenorhabditis elegans contains homologs of several genes associated with familial Alzheimer's disease in humans. apl-1 encodes a transmembrane protein belonging to the amyloid precursor protein family, sel-12 and hop-1 are the two somatically expressed presenilin genes that resemble PS1 and PS2 on both a structural and a functional level. Mutations in the sel-12-encoded presenilin gene cause defective Notch/lin-12 signaling and result in reduced egg-laying, caused by cell specification and cell attachment defects. spr-1, spr-3, spr-4 and spr-5 were identified as the suppressors of the egg-laying defect of presenilin/sel-12 loss of function mutants in genetic suppressor screens. The corresponding proteins are C. elegans homologs of human REST, CoREST and LSD1, respectively. REST/NSRF (Re1 silencing transcription factor/neural-restrictive silencing factor) is a transcriptional repressor that blocks the expression of neuronal genes in non-neuronal tissues in vertebrates. CoREST is a conserved histone deacetylase and demethylase-containing co-repressor complex possessing a potential chromatin-modifying activity. It is recruited to the promoter via REST-mediated DNA binding. LSD1 is a flavin-dependent demethylase of histone H3. Mutations in spr-1, spr-3, spr-4 and spr-5 genes suppress the egg-laying phenotype of sel-12 loss of function mutants by derepressing the expression of the second C. elegans presenilin gene, hop-1.
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Affiliation(s)
- Agata Smialowska
- Bio3/Bioinformatics and Molecular Genetics, University of Freiburg, Freiburg, Germany
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45
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Lee MG, Wynder C, Bochar DA, Hakimi MA, Cooch N, Shiekhattar R. Functional interplay between histone demethylase and deacetylase enzymes. Mol Cell Biol 2006; 26:6395-402. [PMID: 16914725 PMCID: PMC1592851 DOI: 10.1128/mcb.00723-06] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Histone deacetylase (HDAC) inhibitors are a promising class of anticancer agents for the treatment of solid and hematological malignancies. The precise mechanism by which HDAC inhibitors mediate their effects on tumor cell growth, differentiation, and/or apoptosis is the subject of intense research. Previously we described a family of multiprotein complexes that contain histone deacetylase 1/2 (HDAC1/2) and the histone demethylase BHC110 (LSD1). Here we show that HDAC inhibitors diminish histone H3 lysine 4 (H3K4) demethylation by BHC110 in vitro. In vivo analysis revealed an increased H3K4 methylation concomitant with inhibition of nucleosomal deacetylation by HDAC inhibitors. Reconstitution of recombinant complexes revealed a functional connection between HDAC1 and BHC110 only when nucleosomal substrates were used. Importantly, while the enzymatic activity of BHC110 is required to achieve optimal deacetylation in vitro, in vivo analysis following ectopic expression of an enzymatically dead mutant of BHC110 (K661A) confirmed the functional cross talk between the demethylase and deacetylase enzymes. Our studies not only reveal an intimate link between the histone demethylase and deacetylase enzymes but also identify histone demethylation as a secondary target of HDAC inhibitors.
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Affiliation(s)
- Min Gyu Lee
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
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46
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Lee MG, Wynder C, Schmidt DM, McCafferty DG, Shiekhattar R. Histone H3 Lysine 4 Demethylation Is a Target of Nonselective Antidepressive Medications. ACTA ACUST UNITED AC 2006; 13:563-7. [PMID: 16793513 DOI: 10.1016/j.chembiol.2006.05.004] [Citation(s) in RCA: 334] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 05/11/2006] [Accepted: 05/15/2006] [Indexed: 11/19/2022]
Abstract
Demethylation of histone H3 lysine 4 is carried out by BHC110/LSD1, an enzyme with close homology to monoamine oxidases (MAO). Monoamine oxidase A or B are frequent targets of selective and nonselective small molecular inhibitors used for treatment of depression. Here we show that in contrast to selective monoamine oxidase inhibitors such as pargyline, nonselective monoamine oxidase inhibitors potently inhibit nucleosomal demethylation of histone H3 lysine 4. Tranylcypromine (brand name Parnate) displayed the best inhibitory activity with an IC50 of less than 2 microM. Treatment of P19 embryonal carcinoma cells with tranylcypromine resulted in global increase in H3K4 methylation as well as transcriptional derepression of two BHC110 target genes, Egr1 and the pluripotent stem cell marker Oct4. These results attest to the effectiveness of tranylcypromine as a small molecular inhibitor of histone demethylation.
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Affiliation(s)
- Min Gyu Lee
- The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
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47
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Bates EA, Victor M, Jones AK, Shi Y, Hart AC. Differential contributions of Caenorhabditis elegans histone deacetylases to huntingtin polyglutamine toxicity. J Neurosci 2006; 26:2830-8. [PMID: 16525063 PMCID: PMC6675170 DOI: 10.1523/jneurosci.3344-05.2006] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Expansion of a polyglutamine tract in the huntingtin protein causes neuronal degeneration and death in Huntington's disease patients, but the molecular mechanisms underlying polyglutamine-mediated cell death remain unclear. Previous studies suggest that expanded polyglutamine tracts alter transcription by sequestering glutamine rich transcriptional regulatory proteins, thereby perturbing their function. We tested this hypothesis in Caenorhabditis elegans neurons expressing a human huntingtin fragment with an expanded polyglutamine tract (Htn-Q150). Loss of function alleles and RNA interference (RNAi) were used to examine contributions of C. elegans cAMP response element-binding protein (CREB), CREB binding protein (CBP), and histone deacetylases (HDACs) to polyglutamine-induced neurodegeneration. Deletion of CREB (crh-1) or loss of one copy of CBP (cbp-1) enhanced polyglutamine toxicity in C. elegans neurons. Loss of function alleles and RNAi were then used to systematically reduce function of each C. elegans HDAC. Generally, knockdown of individual C. elegans HDACs enhanced Htn-Q150 toxicity, but knockdown of C. elegans hda-3 suppressed toxicity. Neuronal expression of hda-3 restored Htn-Q150 toxicity and suggested that C. elegans HDAC3 (HDA-3) acts within neurons to promote degeneration in response to Htn-Q150. Genetic epistasis experiments suggested that HDA-3 and CRH-1 (C. elegans CREB homolog) directly oppose each other in regulating transcription of genes involved in polyglutamine toxicity. hda-3 loss of function failed to suppress increased neurodegeneration in hda-1/+;Htn-Q150 animals, indicating that HDA-1 and HDA-3 have different targets with opposing effects on polyglutamine toxicity. Our results suggest that polyglutamine expansions perturb transcription of CREB/CBP targets and that specific targeting of HDACs will be useful in reducing associated neurodegeneration.
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48
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Shi YJ, Matson C, Lan F, Iwase S, Baba T, Shi Y. Regulation of LSD1 histone demethylase activity by its associated factors. Mol Cell 2005; 19:857-64. [PMID: 16140033 DOI: 10.1016/j.molcel.2005.08.027] [Citation(s) in RCA: 670] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Revised: 08/23/2005] [Accepted: 08/24/2005] [Indexed: 11/23/2022]
Abstract
LSD1 is a recently identified human lysine (K)-specific histone demethylase. LSD1 is associated with HDAC1/2; CoREST, a SANT domain-containing corepressor; and BHC80, a PHD domain-containing protein, among others. We show that CoREST endows LSD1 with the ability to demethylate nucleosomal substrates and that it protects LSD1 from proteasomal degradation in vivo. We find hyperacetylated nucleosomes less susceptible to CoREST/LSD1-mediated demethylation, suggesting that hypoacetylated nucleosomes may be the preferred physiological substrates. This raises the possibility that histone deacetylases and LSD1 may collaborate to generate a repressive chromatin environment. Consistent with this model, TSA treatment results in derepression of LSD1 target genes. While CoREST positively regulates LSD1 function, BHC80 inhibits CoREST/LSD1-mediated demethylation in vitro and may therefore confer negative regulation. Taken together, these findings suggest that LSD1-mediated histone demethylation is regulated dynamically in vivo. This is expected to have profound effects on gene expression under both physiological and pathological conditions.
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Affiliation(s)
- Yu-Jiang Shi
- Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
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49
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Jarriault S, Greenwald I. Evidence for functional redundancy between C. elegans ADAM proteins SUP-17/Kuzbanian and ADM-4/TACE. Dev Biol 2005; 287:1-10. [PMID: 16197940 PMCID: PMC1805470 DOI: 10.1016/j.ydbio.2005.08.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2005] [Revised: 08/01/2005] [Accepted: 08/05/2005] [Indexed: 11/30/2022]
Abstract
The ectodomain of LIN-12/Notch proteins is cleaved and shed upon ligand binding. In Caenorhabditis elegans, genetic evidence has implicated SUP-17, the ortholog of Drosophila Kuzbanian and mammalian ADAM10, as the protease that mediates this event. In mammals, however, biochemical evidence has implicated TACE, a different ADAM protein. We have investigated potential functional redundancy of sup-17 and the C. elegans ortholog of TACE, adm-4, by exploring their roles in cell fate decisions mediated by lin-12/Notch genes. We found that reduced adm-4 activity, like reduced sup-17 activity, suppresses an allele of glp-1 that encodes a constitutively active receptor. Furthermore, concomitant reduction of adm-4 and sup-17 activity causes the production of two anchor cells in the hermaphrodite gonad, instead of one--a phenotype associated with loss of lin-12 activity. Concomitant reduction of both sup-17 and adm-4 activity in hermaphrodites results in highly penetrant synthetic sterility, which appears to reflect a defect in the spermatheca. Expression of a truncated form of LIN-12 that mimics the product of ectodomain shedding rescues this fertility defect, suggesting that sup-17 and adm-4 may mediate ectodomain shedding of LIN-12 and/or GLP-1. Our results are consistent with the possibility that sup-17 and adm-4 are functionally redundant for at least a subset of LIN-12/Notch-mediated decisions in C. elegans.
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Affiliation(s)
- Sophie Jarriault
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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50
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Shi Y, Lan F, Matson C, Mulligan P, Whetstine JR, Cole PA, Casero RA, Shi Y. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2005; 119:941-53. [PMID: 15620353 DOI: 10.1016/j.cell.2004.12.012] [Citation(s) in RCA: 3053] [Impact Index Per Article: 160.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Revised: 11/11/2004] [Accepted: 12/10/2004] [Indexed: 12/13/2022]
Abstract
Posttranslational modifications of histone N-terminal tails impact chromatin structure and gene transcription. While the extent of histone acetylation is determined by both acetyltransferases and deacetylases, it has been unclear whether histone methylation is also regulated by enzymes with opposing activities. Here, we provide evidence that LSD1 (KIAA0601), a nuclear homolog of amine oxidases, functions as a histone demethylase and transcriptional corepressor. LSD1 specifically demethylates histone H3 lysine 4, which is linked to active transcription. Lysine demethylation occurs via an oxidation reaction that generates formaldehyde. Importantly, RNAi inhibition of LSD1 causes an increase in H3 lysine 4 methylation and concomitant derepression of target genes, suggesting that LSD1 represses transcription via histone demethylation. The results thus identify a histone demethylase conserved from S. pombe to human and reveal dynamic regulation of histone methylation by both histone methylases and demethylases.
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Affiliation(s)
- Yujiang Shi
- Department of Pathology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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