1
|
Bannister AJ, Schneider R, Varga-Weisz P. Editorial: Colyn Crane-Robinson (1935-2023). Nucleic Acids Res 2023; 51:7709-7713. [PMID: 37493596 PMCID: PMC10450191 DOI: 10.1093/nar/gkad625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/27/2023] Open
Affiliation(s)
- Andrew J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Center Munich, Munich, Germany
- Faculty of Biology, Ludwig Maximilian University (LMU) of Munich, Munich, Germany
| | - Patrick Varga-Weisz
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- International Laboratory for Microbiome Host Epigenetics, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| |
Collapse
|
2
|
Farrelly LA, Zheng S, Schrode N, Topol A, Bhanu NV, Bastle RM, Ramakrishnan A, Chan JC, Cetin B, Flaherty E, Shen L, Gleason K, Tamminga CA, Garcia BA, Li H, Brennand KJ, Maze I. Chromatin profiling in human neurons reveals aberrant roles for histone acetylation and BET family proteins in schizophrenia. Nat Commun 2022; 13:2195. [PMID: 35459277 PMCID: PMC9033776 DOI: 10.1038/s41467-022-29922-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Schizophrenia (SZ) is a psychiatric disorder with complex genetic risk dictated by interactions between hundreds of risk variants. Epigenetic factors, such as histone posttranslational modifications (PTMs), have been shown to play critical roles in many neurodevelopmental processes, and when perturbed may also contribute to the precipitation of disease. Here, we apply an unbiased proteomics approach to evaluate combinatorial histone PTMs in human induced pluripotent stem cell (hiPSC)-derived forebrain neurons from individuals with SZ. We observe hyperacetylation of H2A.Z and H4 in neurons derived from SZ cases, results that were confirmed in postmortem human brain. We demonstrate that the bromodomain and extraterminal (BET) protein, BRD4, is a bona fide 'reader' of H2A.Z acetylation, and further provide evidence that BET family protein inhibition ameliorates transcriptional abnormalities in patient-derived neurons. Thus, treatments aimed at alleviating BET protein interactions with hyperacetylated histones may aid in the prevention or treatment of SZ.
Collapse
Affiliation(s)
- Lorna A Farrelly
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shuangping Zheng
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Nadine Schrode
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aaron Topol
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Natarajan V Bhanu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ryan M Bastle
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jennifer C Chan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bulent Cetin
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Erin Flaherty
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kelly Gleason
- Department of Psychiatry, University of Texas Southwestern Medical School, Dallas, TX, 75390, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical School, Dallas, TX, 75390, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Haitao Li
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Departments of Psychiatry and Genetics, Wu Tsai Institute, Yale School of Medicine, New Haven, CT, 065109, USA.
| | - Ian Maze
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Howard Hughes Medical Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| |
Collapse
|
3
|
Colino-Sanguino Y, Cornett EM, Moulder D, Smith GC, Hrit J, Cordeiro-Spinetti E, Vaughan RM, Krajewski K, Rothbart SB, Clark SJ, Valdés-Mora F. A Read/Write Mechanism Connects p300 Bromodomain Function to H2A.Z Acetylation. iScience 2019; 21:773-788. [PMID: 31727574 PMCID: PMC6889796 DOI: 10.1016/j.isci.2019.10.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 09/20/2019] [Accepted: 10/24/2019] [Indexed: 12/22/2022] Open
Abstract
Acetylation of the histone variant H2A.Z (H2A.Zac) occurs at active regulatory regions associated with gene expression. Although the Tip60 complex is proposed to acetylate H2A.Z, functional studies suggest additional enzymes are involved. Here, we show that p300 acetylates H2A.Z at multiple lysines. In contrast, we found that although Tip60 does not efficiently acetylate H2A.Z in vitro, genetic inhibition of Tip60 reduces H2A.Zac in cells. Importantly, we found that interaction between the p300-bromodomain and H4 acetylation (H4ac) enhances p300-driven H2A.Zac. Indeed, H2A.Zac and H4ac show high genomic overlap, especially at active promoters. We also reveal unique chromatin features and transcriptional states at enhancers correlating with co-occurrence or exclusivity of H4ac and H2A.Zac. We propose that differential H4 and H2A.Z acetylation signatures can also define the enhancer state. In conclusion, we show both Tip60 and p300 contribute to H2A.Zac and reveal molecular mechanisms of writer/reader crosstalk between H2A.Z and H4 acetylation through p300. p300 acetylates H2A.Z at multiple N-terminal lysine residues Interaction of p300 bromodomain with H4ac enhances H2A.Zac H2A.Zac and H4ac co-localize at active regulatory regions H4ac and H2A.Zac differential signature can define the enhancer state
Collapse
Affiliation(s)
- Yolanda Colino-Sanguino
- Histone Variants Group, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia
| | - Evan M Cornett
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David Moulder
- Histone Variants Group, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia
| | - Grady C Smith
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia
| | - Joel Hrit
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | | | - Robert M Vaughan
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia.
| | - Fátima Valdés-Mora
- Histone Variants Group, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, Australia; St. Vincent's Clinical School, University of NSW Sydney, Sydney, NSW, Australia.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Giaimo BD, Ferrante F, Herchenröther A, Hake SB, Borggrefe T. The histone variant H2A.Z in gene regulation. Epigenetics Chromatin 2019; 12:37. [PMID: 31200754 PMCID: PMC6570943 DOI: 10.1186/s13072-019-0274-9] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/23/2019] [Indexed: 01/04/2023] Open
Abstract
The histone variant H2A.Z is involved in several processes such as transcriptional control, DNA repair, regulation of centromeric heterochromatin and, not surprisingly, is implicated in diseases such as cancer. Here, we review the recent developments on H2A.Z focusing on its role in transcriptional activation and repression. H2A.Z, as a replication-independent histone, has been studied in several model organisms and inducible mammalian model systems. Its loading machinery and several modifying enzymes have been recently identified, and some of the long-standing discrepancies in transcriptional activation and/or repression are about to be resolved. The buffering functions of H2A.Z, as supported by genome-wide localization and analyzed in several dynamic systems, are an excellent example of transcriptional control. Posttranslational modifications such as acetylation and ubiquitination of H2A.Z, as well as its specific binding partners, are in our view central players in the control of gene expression. Understanding the key-mechanisms in either turnover or stabilization of H2A.Z-containing nucleosomes as well as defining the H2A.Z interactome will pave the way for therapeutic applications in the future.
Collapse
Affiliation(s)
| | - Francesca Ferrante
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Andreas Herchenröther
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, University of Giessen, Heinrich-Buff-Ring 58-62, 35392, Giessen, Germany
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany.
| |
Collapse
|
6
|
Role of lysozyme inhibitors in the virulence of avian pathogenic Escherichia coli. PLoS One 2012; 7:e45954. [PMID: 23049900 PMCID: PMC3458809 DOI: 10.1371/journal.pone.0045954] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 08/23/2012] [Indexed: 11/19/2022] Open
Abstract
Lysozymes are key effectors of the animal innate immunity system that kill bacteria by hydrolyzing peptidoglycan, their major cell wall constituent. Recently, specific inhibitors of the three major lysozyme families occuring in the animal kingdom (c-, g- and i-type) have been discovered in Gram-negative bacteria, and it has been proposed that these may help bacteria to evade lysozyme mediated lysis during interaction with an animal host. Escherichia coli produces two inhibitors that are specific for c-type lysozyme (Ivy, Inhibitor of vertebrate lysozyme; MliC, membrane bound lysozyme inhibitor of c-type lysozyme), and one specific for g-type lysozyme (PliG, periplasmic lysozyme inhibitor of g-type lysozyme). Here, we investigated the role of these lysozyme inhibitors in virulence of Avian Pathogenic E. coli (APEC) using a serum resistance test and a subcutaneous chicken infection model. Knock-out of mliC caused a strong reduction in serum resistance and in in vivo virulence that could be fully restored by genetic complementation, whereas ivy and pliG could be knocked out without effect on serum resistance and virulence. This is the first in vivo evidence for the involvement of lysozyme inhibitors in bacterial virulence. Remarkably, the virulence of a ivy mliC double knock-out strain was restored to almost wild-type level, and this strain also had a substantial residual periplasmic lysozyme inhibitory activity that was higher than that of the single knock-out strains. This suggests the existence of an additional periplasmic lysozyme inhibitor in this strain, and indicates a regulatory interaction in the expression of the different inhibitors.
Collapse
|
7
|
Sarkies P, Murat P, Phillips LG, Patel KJ, Balasubramanian S, Sale JE. FANCJ coordinates two pathways that maintain epigenetic stability at G-quadruplex DNA. Nucleic Acids Res 2011; 40:1485-98. [PMID: 22021381 PMCID: PMC3287192 DOI: 10.1093/nar/gkr868] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We have previously reported that DT40 cells deficient in the Y-family polymerase REV1 are defective in replicating G-quadruplex DNA. In vivo this leads to uncoupling of DNA synthesis from redeposition of histones displaced ahead of the replication fork, which in turn leads to loss of transcriptional repression due to failure to recycle pre-existing repressive histone post-translational modifications. Here we report that a similar process can also affect transcriptionally active genes, leading to their deactivation. We use this finding to develop an assay based on loss of expression of a cell surface marker to monitor epigenetic instability at the level of single cells. This assay allows us to demonstrate G4 DNA motif-associated epigenetic instability in mutants of three helicases previously implicated in the unwinding of G-quadruplex structures, FANCJ, WRN and BLM. Transcriptional profiling of DT40 mutants reveals that FANCJ coordinates two independent mechanisms to maintain epigenetic stability near G4 DNA motifs that are dependent on either REV1 or on the WRN and BLM helicases, suggesting a model in which efficient in vivo replication of G-quadruplexes often requires the established 5'-3'-helicase activity of FANCJ acting in concert with either a specialized polymerase or helicase operating in the opposite polarity.
Collapse
Affiliation(s)
- Peter Sarkies
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | | | | | | | | | | |
Collapse
|
8
|
Sarkies P, Reams C, Simpson LJ, Sale JE. Epigenetic instability due to defective replication of structured DNA. Mol Cell 2011; 40:703-13. [PMID: 21145480 PMCID: PMC3145961 DOI: 10.1016/j.molcel.2010.11.009] [Citation(s) in RCA: 221] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 07/30/2010] [Accepted: 09/10/2010] [Indexed: 01/22/2023]
Abstract
The accurate propagation of histone marks during chromosomal replication is proposed to rely on the tight coupling of replication with the recycling of parental histones to the daughter strands. Here, we show in the avian cell line DT40 that REV1, a key regulator of DNA translesion synthesis at the replication fork, is required for the maintenance of repressive chromatin marks and gene silencing in the vicinity of DNA capable of forming G-quadruplex (G4) structures. We demonstrate a previously unappreciated requirement for REV1 in replication of G4 forming sequences and show that transplanting a G4 forming sequence into a silent locus leads to its derepression in REV1-deficient cells. Together, our observations support a model in which failure to maintain processive DNA replication at G4 DNA in REV1-deficient cells leads to uncoupling of DNA synthesis from histone recycling, resulting in localized loss of repressive chromatin through biased incorporation of newly synthesized histones.
Collapse
Affiliation(s)
- Peter Sarkies
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Charlie Reams
- University of Cambridge Computer Laboratory, William Gates Building, 15, J.J. Thomson Avenue, Cambridge CB3 0FD, UK
| | - Laura J. Simpson
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Julian E. Sale
- Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
- Corresponding author
| |
Collapse
|
9
|
Ishibashi T, Dryhurst D, Rose KL, Shabanowitz J, Hunt DF, Ausió J. Acetylation of vertebrate H2A.Z and its effect on the structure of the nucleosome. Biochemistry 2009; 48:5007-17. [PMID: 19385636 DOI: 10.1021/bi900196c] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Purified histone H2A.Z from chicken erythrocytes and a sodium butyrate-treated chicken erythroleukemic cell line was used as a model system to identify the acetylation sites (K4, K7, K11, K13, and K15) and quantify their distribution in this vertebrate histone variant. To understand the role played by acetylation in the modulation of the H2A.Z nucleosome core particle (NCP) stability and conformation, an extensive analysis was conducted on NCPs reconstituted from acetylated forms of histones, including H2A.Z and recombinant H2A.Z (K/Q) acetylation mimic mutants. Although the overall global acetylation of core histones destabilizes the NCP, we found that H2A.Z stabilizes the NCP regardless of its state of acetylation. Interestingly and quite unexpectedly, we found that the change in NCP conformation induced by global histone acetylation is dependent on H2A/H2A.Z acetylation. This suggests that acetylated H2A variants act synergistically with the acetylated forms of the core histone complement to alter the particle conformation. Furthermore, the simultaneous occurrence of H2A.Z and H2A in heteromorphic NCPs that most likely occurs in vivo slightly destabilizes the NCP, but only in the presence of acetylation.
Collapse
Affiliation(s)
- Toyotaka Ishibashi
- Department of Biochemistry and Microbiology and The Center for Biomedical Research, University of Victoria, Petch Building, Victoria, BC, Canada V8W 3P6
| | | | | | | | | | | |
Collapse
|
10
|
Garner MM, Latimer KS, Mickley KA, Ritzman TK, Nordhausen RW. Histologic, immunohistochemical, and electron microscopic features of a unique pulmonary tumor in cockatiels (Nymphicus hollandicus): six cases. Vet Pathol 2009; 46:1100-8. [PMID: 19605913 DOI: 10.1354/vp.08-vp-0136-g-fl] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A unique form of pulmonary malignancy develops in cockatiels. This report describes the gross, histologic, electron microscopic, and immunohistochemical features of this tumor in 6 cockatiels. DNA in-situ hybridization for polyomavirus in the neoplasm was also performed. The tumor was comprised predominantly of compact sheets of anaplastic round to polygonal cells. All tumors had a high mitotic index, and had occasional large clear to slightly basophilic intranuclear inclusions that caused peripheral dispersal or complete masking of chromatin. Tumors were invasive but convincing metastases were not observed. Transmission electron microscopy identified intracytoplasmic intermediate filaments, desmosomes between cells, and intranuclear cytoplasmic invaginations corresponding to the intranuclear inclusions in light microscopic sections. Neoplastic cells stained positive for vimentin, lysozyme, and in 1 bird, pan cytokeratin. All 6 pulmonary neoplasms were negative for avian polyomavirus using the FN-19/FN-40 cocktail and the long VP-1 probe. We propose that these tumors may be poorly differentiated carcinomas of pulmonary or thymic origin.
Collapse
Affiliation(s)
- M M Garner
- Northwest ZooPath, Monroe, WA 98272, USA.
| | | | | | | | | |
Collapse
|
11
|
Wong MM, Cox LK, Chrivia JC. The chromatin remodeling protein, SRCAP, is critical for deposition of the histone variant H2A.Z at promoters. J Biol Chem 2007; 282:26132-9. [PMID: 17617668 DOI: 10.1074/jbc.m703418200] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Studies in Saccharomyces cerevisiae indicate the histone variant H2A.Z is deposited at promoters by the chromatin remodeling protein Swr1 and plays a critical role in the regulation of transcription. In higher eukaryotes, however, little is known about the distribution, method of deposition, and function of H2A.Z at promoters. Using biochemical studies, we demonstrated previously that SRCAP (SNF-2-related CREB-binding protein activator protein), the human ortholog of Swr1, could catalyze deposition of H2A.Z into nucleosomes. To address whether SRCAP directs H2A.Z deposition in vivo, promoters targeted by SRCAP were identified by a chromatin immunoprecipitation (ChIP)-on-chip assay. ChIP assays on a subset of these promoters confirmed the presence of SRCAP on inactive and active promoters. The highest levels of SRCAP were observed on the active SP-1, G3BP, and FAD synthetase promoters. Detailed analyses of these promoters indicate sites of SRCAP binding overlap or occur adjacent to the sites of H2A.Z deposition. Knockdown of SRCAP levels using siRNA resulted in loss of SRCAP at these promoters, decreased deposition of H2A.Z and acetylated H2A.Z, and a decrease in levels of SP-1, G3BP, and FAD synthetase mRNA. Thus, these studies provide the first evidence that SRCAP is recruited to promoters and is critical for the deposition of H2A.Z.
Collapse
Affiliation(s)
- Madeline M Wong
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, Saint Louis, Missouri 63104, USA
| | | | | |
Collapse
|
12
|
Razin SV, Iarovaia OV, Sjakste N, Sjakste T, Bagdoniene L, Rynditch AV, Eivazova ER, Lipinski M, Vassetzky YS. Chromatin domains and regulation of transcription. J Mol Biol 2007; 369:597-607. [PMID: 17466329 DOI: 10.1016/j.jmb.2007.04.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 03/27/2007] [Accepted: 04/02/2007] [Indexed: 12/20/2022]
Abstract
Compartmentalization and compaction of DNA in the nucleus is the characteristic feature of eukaryotic cells. A fully extended DNA molecule has to be compacted 100,000 times to fit within the nucleus. At the same time it is critical that various DNA regions remain accessible for interaction with regulatory factors and transcription/replication factories. This puzzle is solved at the level of DNA packaging in chromatin that occurs in several steps: rolling of DNA onto nucleosomes, compaction of nucleosome fiber with formation of the so-called 30 nm fiber, and folding of the latter into the giant (50-200 kbp) loops, fixed onto the protein skeleton, the nuclear matrix. The general assumption is that DNA folding in the cell nucleus cannot be uniform. It has been known for a long time that a transcriptionally active chromatin fraction is more sensitive to nucleases; this was interpreted as evidence for the less tight compaction of this fraction. In this review we summarize the latest results on structure of transcriptionally active chromatin and the mechanisms of transcriptional regulation in the context of chromatin dynamics. In particular the significance of histone modifications and the mechanisms controlling dynamics of chromatin domains are discussed as well as the significance of spatial organization of the genome for functioning of distant regulatory elements.
Collapse
Affiliation(s)
- Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | | | | | | | | | | | | | | | | |
Collapse
|