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Burenkova OV, Grigorenko EL. The role of epigenetic mechanisms in the long-term effects of early-life adversity and mother-infant relationship on physiology and behavior of offspring in laboratory rats and mice. Dev Psychobiol 2024; 66:e22479. [PMID: 38470450 PMCID: PMC10959231 DOI: 10.1002/dev.22479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/23/2024] [Accepted: 02/16/2024] [Indexed: 03/13/2024]
Abstract
Maternal care during the early postnatal period of altricial mammals is a key factor in the survival and adaptation of offspring to environmental conditions. Natural variations in maternal care and experimental manipulations with maternal-child relationships modeling early-life adversity (ELA) in laboratory rats and mice have a strong long-term influence on the physiology and behavior of offspring in rats and mice. This literature review is devoted to the latest research on the role of epigenetic mechanisms in these effects of ELA and mother-infant relationship, with a focus on the regulation of hypothalamic-pituitary-adrenal axis and brain-derived neurotrophic factor. An important part of this review is dedicated to pharmacological interventions and epigenetic editing as tools for studying the causal role of epigenetic mechanisms in the development of physiological and behavioral profiles. A special section of the manuscript will discuss the translational potential of the discussed research.
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Affiliation(s)
- Olga V. Burenkova
- Department of Psychology, University of Houston, Houston, Texas, USA
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, Texas, USA
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Elena L. Grigorenko
- Department of Psychology, University of Houston, Houston, Texas, USA
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, Texas, USA
- Center for Cognitive Sciences, Sirius University of Science and Technology, Sochi, Russia
- Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Child Study Center, Yale University, New Haven, Connecticut, USA
- Research Administration, Moscow State University for Psychology and Education, Moscow, Russia
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2
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Fottner M, Heimgärtner J, Gantz M, Mühlhofer R, Nast-Kolb T, Lang K. Site-Specific Protein Labeling and Generation of Defined Ubiquitin-Protein Conjugates Using an Asparaginyl Endopeptidase. J Am Chem Soc 2022; 144:13118-13126. [PMID: 35850488 PMCID: PMC9335880 DOI: 10.1021/jacs.2c02191] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Asparaginyl endopeptidases
(AEPs) have recently been widely utilized
for peptide and protein modification. Labeling is however restricted
to protein termini, severely limiting flexibility and scope in creating
diverse conjugates as needed for therapeutic and diagnostic applications.
Here, we use genetic code expansion to site-specifically modify target
proteins with an isopeptide-linked glycylglycine moiety that serves
as an acceptor nucleophile in AEP-mediated transpeptidation with various
probes containing a tripeptidic recognition motif. Our approach allows
simple and flexible labeling of recombinant proteins at any internal
site and leaves a minimal, entirely peptidic footprint (NGG) in the
conjugation product. We show site-specific labeling of diverse target
proteins with various biophysical probes, including dual labeling
at an internal site and the N-terminus. Furthermore, we harness AEP-mediated
transpeptidation for generation of ubiquitin- and ubiquitin-like-modifier
conjugates bearing a native isopeptide bond and only one point mutation
in the linker region.
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Affiliation(s)
- Maximilian Fottner
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Johannes Heimgärtner
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Maximilian Gantz
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Rahel Mühlhofer
- Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Timon Nast-Kolb
- Center for Protein Assemblies (CPA) and Lehrstuhl für Biophysik (E27), Physics Department, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Kathrin Lang
- Laboratory for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences (D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland.,Department of Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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3
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Toralova T, Kinterova V, Chmelikova E, Kanka J. The neglected part of early embryonic development: maternal protein degradation. Cell Mol Life Sci 2020; 77:3177-3194. [PMID: 32095869 PMCID: PMC11104927 DOI: 10.1007/s00018-020-03482-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 01/24/2020] [Accepted: 02/07/2020] [Indexed: 12/28/2022]
Abstract
The degradation of maternally provided molecules is a very important process during early embryogenesis. However, the vast majority of studies deals with mRNA degradation and protein degradation is only a very little explored process yet. The aim of this article was to summarize current knowledge about the protein degradation during embryogenesis of mammals. In addition to resuming of known data concerning mammalian embryogenesis, we tried to fill the gaps in knowledge by comparison with facts known about protein degradation in early embryos of non-mammalian species. Maternal protein degradation seems to be driven by very strict rules in terms of specificity and timing. The degradation of some maternal proteins is certainly necessary for the normal course of embryonic genome activation (EGA) and several concrete proteins that need to be degraded before major EGA have been already found. Nevertheless, the most important period seems to take place even before preimplantation development-during oocyte maturation. The defects arisen during this period seems to be later irreparable.
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Affiliation(s)
- Tereza Toralova
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
| | - Veronika Kinterova
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic.
- Department of Veterinary Sciences, Czech University of Life Sciences in Prague, Prague, Czech Republic.
| | - Eva Chmelikova
- Department of Veterinary Sciences, Czech University of Life Sciences in Prague, Prague, Czech Republic
| | - Jiri Kanka
- Laboratory of Developmental Biology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Libechov, Czech Republic
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4
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Braxton CN, Quartner E, Pawloski W, Fushman D, Cropp TA. Ubiquitin Chains Bearing Genetically Encoded Photo-Cross-Linkers Enable Efficient Covalent Capture of (Poly)ubiquitin-Binding Domains. Biochemistry 2019; 58:883-886. [PMID: 30668904 DOI: 10.1021/acs.biochem.8b01089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ubiquitin-mediated signaling pathways regulate essentially every aspect of cell biology in eukaryotes. Ubiquitin receptors typically contain ubiquitin-binding domains (UBDs) that have the ability to recognize monomeric ubiquitin (Ub) and polymeric Ub (polyUb) chains. However, how signaling specificity is achieved remains poorly understood, and many of the UBDs that selectively recognize polyUb chains of particular linkages still need to be identified and characterized. Here we report the incorporation of a genetically encoded photo-cross-linker, p-benzoyl-l-phenylalanine (Bpa), into recombinant Ub and enzymatically synthesized polyUb chains. This allows photo-cross-linking (covalent bond formation) of monoUb and K48- and K63-linked diUb chains to UBDs. This approach provides a framework for understanding Ub cellular signaling through the capture and identification of (poly)Ub-binding proteins.
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Affiliation(s)
- Courtney N Braxton
- Department of Chemistry , Virginia Commonwealth University , 1001 West Main Street , P.O. Box 842006, Richmond , Virginia 23284-2006 , United States
| | - Evan Quartner
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization , University of Maryland , College Park , Maryland 20742-3360 , United States
| | - Westley Pawloski
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization , University of Maryland , College Park , Maryland 20742-3360 , United States
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization , University of Maryland , College Park , Maryland 20742-3360 , United States
| | - T Ashton Cropp
- Department of Chemistry , Virginia Commonwealth University , 1001 West Main Street , P.O. Box 842006, Richmond , Virginia 23284-2006 , United States
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5
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Krajewski WA. Effects of DNA Superhelical Stress on the Stability of H2B-Ubiquitylated Nucleosomes. J Mol Biol 2018; 430:5002-5014. [PMID: 30267746 DOI: 10.1016/j.jmb.2018.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/27/2018] [Accepted: 09/21/2018] [Indexed: 01/31/2023]
Abstract
On the nucleosome level, histone posttranslational modifications function mainly as the regulatory signals; in addition, some posttranslational modifications can enhance nucleosome stochastic folding, which is restricted in "canonic" nucleosomes. Recently, it has been shown in vitro that symmetric or asymmetric nucleosome ubiquitylation at H2BK34 (and H2BK120, to a lesser extent) can destabilize one of the nucleosomal H2A-H2B dimers and promote nucleosome conversion to a hexasome particle [Krajewski et al. (2018). Nucleic Acids Res., 46, 7631-7642]. Such lability of H2Bub nucleosomes raises a question of whether they could accommodate transient changes in DNA torsional tensions, which are generated by virtually any process that manipulates DNA strands. Using positively or negatively supercoiled DNA minicircles and homogeneously-modified H2Bub histones, we have found that DNA topology could strongly and selectively affect nucleosome stability depending on its ubiquitylation state (here the term "nucleosome stability" means the nucleosome property to maintain its structural integrity and dynamics characteristic to "canonic" nucleosomes). The results point to a role for H2B ubiquitylation in amplifying or mitigating the effects of a DNA torque on the nucleosome stability and dynamics.
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Affiliation(s)
- Wladyslaw A Krajewski
- N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova str. 26, Moscow 119334, Russia.
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6
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Intracellular protein degradation: From a vague idea thru the lysosome and the ubiquitin-proteasome system and onto human diseases and drug targeting. Best Pract Res Clin Haematol 2017; 30:341-355. [DOI: 10.1016/j.beha.2017.09.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Doshi A, Sharma M, Prabha CR. Structural changes induced by L50P and I61T single mutations of ubiquitin affect cell cycle progression while impairing its regulatory and degradative functions in Saccharomyces cerevisiae. Int J Biol Macromol 2017; 99:128-140. [DOI: 10.1016/j.ijbiomac.2017.02.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/07/2017] [Accepted: 02/13/2017] [Indexed: 12/23/2022]
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8
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Xia Y, Yang W, Fa M, Li X, Wang Y, Jiang Y, Zheng Y, Lee JH, Li J, Lu Z. RNF8 mediates histone H3 ubiquitylation and promotes glycolysis and tumorigenesis. J Exp Med 2017; 214:1843-1855. [PMID: 28507061 PMCID: PMC5461008 DOI: 10.1084/jem.20170015] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/31/2017] [Accepted: 04/06/2017] [Indexed: 01/18/2023] Open
Abstract
Xia et al. show that EGF receptor activation results in the binding of the RNF8 forkhead-associated domain to pyruvate kinase M2-phosphorylated histone H3-T11, leading to histone H3 polyubiquitylation and degradation and subsequent gene expression for tumor cell glycolysis and proliferation. Disassembly of nucleosomes in which genomic DNA is packaged with histone regulates gene expression. However, the mechanisms underlying nucleosome disassembly for gene expression remain elusive. We show here that epidermal growth factor receptor activation results in the binding of the RNF8 forkhead-associated domain to pyruvate kinase M2–phosphorylated histone H3-T11, leading to K48-linked polyubiquitylation of histone H3 at K4 and subsequent proteasome-dependent protein degradation. In addition, H3 polyubiquitylation induces histone dissociation from chromatin, nucleosome disassembly, and binding of RNA polymerase II to MYC and CCND1 promoter regions for transcription. RNF8-mediated histone H3 polyubiquitylation promotes tumor cell glycolysis and proliferation and brain tumorigenesis. Our findings uncover the role of RNF8-mediated histone H3 polyubiquitylation in the regulation of histone H3 stability and chromatin modification, paving the way to gene expression regulation and tumorigenesis.
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Affiliation(s)
- Yan Xia
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Weiwei Yang
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ming Fa
- Genetivision Corporation, Houston, TX 77054
| | - Xinjian Li
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Yugang Wang
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Yuhui Jiang
- The Institute of Cell Metabolism and Disease, Shanghai Key Laboratory of Pancreatic Cancer, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China
| | - Yanhua Zheng
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Jong-Ho Lee
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Jing Li
- Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs of Minister of Education of China, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Zhimin Lu
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 .,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030.,The Cancer Biology Program, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030
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9
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Joo HY, Dai Q, Jones AE, Zhai L, Wang H. In vitro and in vivo assays for studying histone ubiquitination and deubiquitination. Methods Mol Biol 2015; 1288:213-30. [PMID: 25827882 DOI: 10.1007/978-1-4939-2474-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Posttranslational histone modifications play important roles in regulating chromatin structure and function (Rando, Curr Opin Genet Dev 22:148-155, 2012; Zentner and Henikoff, Nat Struct Mol Biol 20:259-266, 2013). One example of such modifications is histone ubiquitination, which occurs predominately on H2A and H2B. Recent studies have highlighted important regulatory roles of H2A ubiquitination in Polycomb group protein-mediated gene silencing and DNA damage repair (de Napoles et al., Dev Cell 7:663-676, 2004; Wang et al., Nature 431:873-878, 2004; Doil et al., Cell 136:435-446, 2009; Gatti et al., Cell Cycle 11:2538-2544, 2012; Mattiroli et al., Cell 150:1182-1195, 2012; Stewart et al., Cell 136:420-434, 2009; Bergink et al., Genes Dev 20:1343-1352, 2006; Facchino et al., J Neurosci 30:10096-10111, 2010; Ginjala et al., Mol Cell Biol 31:1972-1982, 2011; Ismail et al., J Cell Biol 191:45-60, 2010), H2B ubiquitination in transcription initiation and elongation (Xiao et al., Mol Cell Biol 25:637-651, 2005; Kao et al., Genes Dev 18:184-195, 2004; Pavri et al., Cell 125:703-717, 2006; Kim et al., Cell 137:459-471, 2009), pre-mRNA splicing (Jung et al. Genome Res 22:1026-1035, 2012; Shieh et al., BMC Genomics 12:627, 2011; Zhang et al., Genes Dev 27:1581-1595, 2013), nucleosome stabilities (Fleming et al., Mol Cell 31:57-66, 2008; Chandrasekharan et al., Proc Natl Acad Sci U S A 106:16686-16691, 2009), H3 methylation (Sun and Allis, Nature 418:104-108, 2002; Briggs et al., Nature 418:498, 2002; Dover et al., J Biol Chem 277:28368-28371, 2002; Ng et al., J Biol Chem 277:34655-34657, 2002), and DNA methylation (Sridhar et al., Nature 447:735-738, 2007). Here we describe methods for in vitro histone ubiquitination and deubiquitination assays. We also describe approaches to investigate the in vivo function of putative histone ubiquitin ligase(s) and deubiquitinase(s). These experimental procedures are largely based on our studies in mammalian cells. These methods should provide useful tools for studying this bulky histone modification.
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Affiliation(s)
- Heui-Yun Joo
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Kaul Human Genetics Building 402A, 720 20th Street South, Birmingham, 35294, AL, USA
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10
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Cai F, Chen P, Chen L, Biskup E, Liu Y, Chen PC, Chang JF, Jiang W, Jing Y, Chen Y, Jin H, Chen S. Human RAD6 promotes G1-S transition and cell proliferation through upregulation of cyclin D1 expression. PLoS One 2014; 9:e113727. [PMID: 25409181 PMCID: PMC4237501 DOI: 10.1371/journal.pone.0113727] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/28/2014] [Indexed: 11/19/2022] Open
Abstract
Protein ubiquitinylation regulates protein stability and activity. RAD6, an E2 ubiquitin-conjugating enzyme, which that has been substantially biochemically characterized, functions in a number of biologically relevant pathways, including cell cycle progression. In this study, we show that RAD6 promotes the G1-S transition and cell proliferation by regulating the expression of cyclin D1 (CCND1) in human cells. Furthermore, our data indicate that RAD6 influences the transcription of CCND1 by increasing monoubiquitinylation of histone H2B and trimethylation of H3K4 in the CCND1 promoter region. Our study presents, for the first time, an evidence for the function of RAD6 in cell cycle progression and cell proliferation in human cells, raising the possibility that RAD6 could be a new target for molecular diagnosis and prognosis in cancer therapeutics.
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Affiliation(s)
- Fengfeng Cai
- School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Research Center for Translational Medicine at East Hospital, Tongji University, Shanghai, P. R. China
| | - Ping Chen
- School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Research Center for Translational Medicine at East Hospital, Tongji University, Shanghai, P. R. China
| | - Li Chen
- School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Research Center for Translational Medicine at East Hospital, Tongji University, Shanghai, P. R. China
| | - Ewelina Biskup
- Department of Oncology, University Hospital of Basel, Basel, Switzerland
| | - Yan Liu
- College of Life Sciences, Hebei United University, Tangshan, Hebei Province, P. R. China
- The Cancer Institute, Tangshan People’s Hospital, Tangshan, Hebei Province, P. R. China
| | - Pei-Chao Chen
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou, Zhejiang Province, P. R. China
| | - Jian-Feng Chang
- School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Research Center for Translational Medicine at East Hospital, Tongji University, Shanghai, P. R. China
| | - Wenjie Jiang
- School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Research Center for Translational Medicine at East Hospital, Tongji University, Shanghai, P. R. China
| | - Yuanya Jing
- School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Research Center for Translational Medicine at East Hospital, Tongji University, Shanghai, P. R. China
| | - Youwei Chen
- School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Research Center for Translational Medicine at East Hospital, Tongji University, Shanghai, P. R. China
| | - Hui Jin
- Department of Biochemistry and Molecular Cell Biology, School of Medcine, Shanghai Jiao Tong University, Shanghai, P. R. China
- * E-mail: (SC); (HJ)
| | - Su Chen
- School of Life Sciences and Technology, Department of Breast Surgery of Yangpu Hospital, Research Center for Translational Medicine at East Hospital, Tongji University, Shanghai, P. R. China
- * E-mail: (SC); (HJ)
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11
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Wu L, Li L, Zhou B, Qin Z, Dou Y. H2B ubiquitylation promotes RNA Pol II processivity via PAF1 and pTEFb. Mol Cell 2014; 54:920-931. [PMID: 24837678 DOI: 10.1016/j.molcel.2014.04.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/24/2014] [Accepted: 04/08/2014] [Indexed: 12/16/2022]
Abstract
Histone H2B ubiquitination plays an important role in transcription regulation. It has been shown that H2B ubiquitination is regulated by multiple upstream events associated with elongating RNA polymerase. Here we demonstrate that H2B K34 ubiquitylation by the MOF-MSL complex is part of the protein networks involved in early steps of transcription elongation. Knocking down MSL2 in the MOF-MSL complex affects not only global H2BK34ub, but also multiple cotranscriptionally regulated histone modifications. More importantly, we show that the MSL, PAF1, and RNF20/40 complexes are recruited and stabilized at active gene promoters by direct binary interactions. The stabilized complexes serve to regulate chromatin association of pTEFb through a positive feedback loop and facilitate Pol II transition during early transcription elongation. Results from our biochemical studies are underscored by genome-wide analyses that show high RNA Pol II processivity and transcription activity at MSL target genes.
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Affiliation(s)
- Lipeng Wu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Li Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Bo Zhou
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhaohui Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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12
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Kim K, Lee B, Kim J, Choi J, Kim JM, Xiong Y, Roeder RG, An W. Linker Histone H1.2 cooperates with Cul4A and PAF1 to drive H4K31 ubiquitylation-mediated transactivation. Cell Rep 2013; 5:1690-703. [PMID: 24360965 DOI: 10.1016/j.celrep.2013.11.038] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 10/18/2013] [Accepted: 11/21/2013] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence suggests that linker histone H1 can influence distinct cellular processes by acting as a gene-specific regulator. However, the mechanistic basis underlying such H1 specificity and whether H1 acts in concert with other chromatin-altering activities remain unclear. Here, we show that one of the H1 subtypes, H1.2, stably interacts with Cul4A E3 ubiquitin ligase and PAF1 elongation complexes and that such interaction potentiates target gene transcription via induction of H4K31 ubiquitylation, H3K4me3, and H3K79me2. H1.2, Cul4A, and PAF1 are functionally cooperative because their individual knockdown results in the loss of the corresponding histone marks and the deficiency of target gene transcription. H1.2 interacts with the serine 2-phosphorylated form of RNAPII, and we argue that it recruits the Cul4A and PAF1 complexes to target genes by bridging the interaction between the Cul4A and PAF1 complexes. These data define an expanded role for H1 in regulating gene transcription and illustrate its dependence on the elongation competence of RNAPII.
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Affiliation(s)
- Kyunghwan Kim
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Bomi Lee
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Jaehoon Kim
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Jongkyu Choi
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Jin-Man Kim
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA
| | - Yue Xiong
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Woojin An
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, University of Southern California, Keck School of Medicine, Los Angeles, CA 90089, USA.
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13
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Fonseca GJ, Cohen MJ, Nichols AC, Barrett JW, Mymryk JS. Viral retasking of hBre1/RNF20 to recruit hPaf1 for transcriptional activation. PLoS Pathog 2013; 9:e1003411. [PMID: 23785282 PMCID: PMC3681745 DOI: 10.1371/journal.ppat.1003411] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 04/25/2013] [Indexed: 12/25/2022] Open
Abstract
Upon infection, human adenovirus (HAdV) must activate the expression of its early genes to reprogram the cellular environment to support virus replication. This activation is orchestrated in large part by the first HAdV gene expressed during infection, early region 1A (E1A). E1A binds and appropriates components of the cellular transcriptional machinery to modulate cellular gene transcription and activate viral early genes transcription. Previously, we identified hBre1/RNF20 as a target for E1A. The interaction between E1A and hBre1 antagonizes the innate antiviral response by blocking H2B monoubiquitination, a chromatin modification necessary for the interferon (IFN) response. Here, we describe a second distinct role for the interaction of E1A with hBre1 in transcriptional activation of HAdV early genes. Furthermore, we show that E1A changes the function of hBre1 from a ubiquitin ligase involved in substrate selection to a scaffold which recruits hPaf1 as a means to stimulate transcription and transcription-coupled histone modifications. By using hBre1 to recruit hPaf1, E1A is able to optimally activate viral early transcription and begin the cycle of viral replication. The ability of E1A to target hBre1 to simultaneously repress cellular IFN dependent transcription while activating viral transcription, represents an elegant example of the incredible economy of action accomplished by a viral regulatory protein through a single protein interaction.
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Affiliation(s)
- Gregory J. Fonseca
- Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Michael J. Cohen
- Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
| | - Anthony C. Nichols
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
- Department of Oncology, University of Western Ontario, London, Ontario, Canada
| | - John W. Barrett
- Department of Otolaryngology-Head and Neck Surgery, University of Western Ontario, London, Ontario, Canada
| | - Joe S. Mymryk
- Department of Microbiology & Immunology, University of Western Ontario, London, Ontario, Canada
- Department of Oncology, University of Western Ontario, London, Ontario, Canada
- London Regional Cancer Program and Lawson Health Research Institute, London, Ontario, Canada
- * E-mail:
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14
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ASH2L regulates ubiquitylation signaling to MLL: trans-regulation of H3 K4 methylation in higher eukaryotes. Mol Cell 2013; 49:1108-20. [PMID: 23453805 DOI: 10.1016/j.molcel.2013.01.033] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 12/18/2012] [Accepted: 01/23/2013] [Indexed: 12/23/2022]
Abstract
Crosstalk between H2B ubiquitylation (H2Bub) and H3 K4 methylation plays important roles in coordinating functions of diverse cofactors during transcription activation. The underlying mechanism for this trans-tail signaling pathway is poorly defined in higher eukaryotes. Here, we show the following: (1) ASH2L in the MLL complex is essential for H2Bub-dependent H3 K4 methylation. Deleting or mutating K99 of the N-terminal winged helix (WH) motif in ASH2L abrogates H2Bub-dependent regulation. (2) Crosstalk can occur in trans and does not require ubiquitin to be on nucleosomes or histones to exert regulatory effects. (3) trans-regulation by ubiquitin promotes MLL activity for all three methylation states. (4) MLL3, an MLL homolog, does not respond to H2Bub, highlighting regulatory specificity for MLL family histone methyltransferases. Altogether, our results potentially expand the classic histone crosstalk to nonhistone proteins, which broadens the scope of chromatin regulation by ubiquitylation signaling.
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15
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Ciechanover A. Intracellular protein degradation: from a vague idea through the lysosome and the ubiquitin-proteasome system and onto human diseases and drug targeting. Bioorg Med Chem 2013; 21:3400-10. [PMID: 23485445 DOI: 10.1016/j.bmc.2013.01.056] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 01/03/2013] [Indexed: 01/30/2023]
Abstract
Between the 1950s and 1980s, scientists were focusing mostly on how the genetic code is transcribed to RNA and translated to proteins, but how proteins are degraded has remained a neglected research area. With the discovery of the lysosome by Christian de Duve it was assumed that cellular proteins are degraded within this organelle. Yet, several independent lines of experimental evidence strongly suggested that intracellular proteolysis is largely non-lysosomal, but the mechanisms involved remained obscure. The discovery of the ubiquitin-proteasome system resolved the enigma. We now recognize that degradation of intracellular proteins is involved in regulation of a broad array of cellular processes, such as cell cycle and division, regulation of transcription factors, and assurance of the cellular quality control. Not surprisingly, aberrations in the system have been implicated in the pathogenesis of human disease, such as malignancies and neurodegenerative disorders, which led subsequently to an increasing effort to develop mechanism-based drugs.
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Affiliation(s)
- Aaron Ciechanover
- Cancer and Vascular Biology Research Center, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Efron Street, Bat Galim, PO Box 9649, Haifa 31096, Israel.
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16
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Maity AK, Saha P. The histone acetyl transferase LdHAT1 fromLeishmania donovaniis regulated by S-phase cell cycle kinase. FEMS Microbiol Lett 2012; 336:57-63. [DOI: 10.1111/j.1574-6968.2012.02656.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 07/25/2012] [Accepted: 08/03/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Anup Kumar Maity
- Crystallography and Molecular Biology Division; Saha Institute of Nuclear Physics; Kolkata; India
| | - Partha Saha
- Crystallography and Molecular Biology Division; Saha Institute of Nuclear Physics; Kolkata; India
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17
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Sansó M, Lee KM, Viladevall L, Jacques PÉ, Pagé V, Nagy S, Racine A, St. Amour CV, Zhang C, Shokat KM, Schwer B, Robert F, Fisher RP, Tanny JC. A positive feedback loop links opposing functions of P-TEFb/Cdk9 and histone H2B ubiquitylation to regulate transcript elongation in fission yeast. PLoS Genet 2012; 8:e1002822. [PMID: 22876190 PMCID: PMC3410854 DOI: 10.1371/journal.pgen.1002822] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 05/24/2012] [Indexed: 11/25/2022] Open
Abstract
Transcript elongation by RNA polymerase II (RNAPII) is accompanied by conserved patterns of histone modification. Whereas histone modifications have established roles in transcription initiation, their functions during elongation are not understood. Mono-ubiquitylation of histone H2B (H2Bub1) plays a key role in coordinating co-transcriptional histone modification by promoting site-specific methylation of histone H3. H2Bub1 also regulates gene expression through an unidentified, methylation-independent mechanism. Here we reveal bidirectional communication between H2Bub1 and Cdk9, the ortholog of metazoan positive transcription elongation factor b (P-TEFb), in the fission yeast Schizosaccharomyces pombe. Chemical and classical genetic analyses indicate that lowering Cdk9 activity or preventing phosphorylation of its substrate, the transcription processivity factor Spt5, reduces H2Bub1 in vivo. Conversely, mutations in the H2Bub1 pathway impair Cdk9 recruitment to chromatin and decrease Spt5 phosphorylation. Moreover, an Spt5 phosphorylation-site mutation, combined with deletion of the histone H3 Lys4 methyltransferase Set1, phenocopies morphologic and growth defects due to H2Bub1 loss, suggesting independent, partially redundant roles for Cdk9 and Set1 downstream of H2Bub1. Surprisingly, mutation of the histone H2B ubiquitin-acceptor residue relaxes the Cdk9 activity requirement in vivo, and cdk9 mutations suppress cell-morphology defects in H2Bub1-deficient strains. Genome-wide analyses by chromatin immunoprecipitation also demonstrate opposing effects of Cdk9 and H2Bub1 on distribution of transcribing RNAPII. Therefore, whereas mutual dependence of H2Bub1 and Spt5 phosphorylation indicates positive feedback, mutual suppression by cdk9 and H2Bub1-pathway mutations suggests antagonistic functions that must be kept in balance to regulate elongation. Loss of H2Bub1 disrupts that balance and leads to deranged gene expression and aberrant cell morphologies, revealing a novel function of a conserved, co-transcriptional histone modification. Modification of histone proteins is an important transcriptional regulatory mechanism in eukaryotic cells. Although various histone modifications are found primarily within the coding regions of transcribed genes, how they influence transcription elongation remains unclear. Among these modifications is mono-ubiquitylation of histone H2B (H2Bub1), which is needed for co-transcriptional methylation of histone H3 at specific sites. Here we show that H2Bub1 and Cdk9, the kinase component of positive transcription elongation factor b (P-TEFb), are jointly regulated by a positive feedback loop: Cdk9 activity is needed for co-transcriptional H2Bub1, and H2Bub1 in turn stimulates Cdk9 activity toward one of its major substrates, the conserved elongation factor Spt5. We provide genetic evidence that the combined action of H2Bub1 on Spt5 phosphorylation and histone methylation accounts for the gene-regulatory effects of this modification. Surprisingly, our genetic and genome-wide studies indicate that P-TEFb and H2Bub1 act in opposition on elongating RNA polymerase. We suggest that the positive feedback linking P-TEFb and H2Bub1 helps to maintain a balance between their opposing actions. These results highlight a novel regulatory role for a conserved histone modification during transcription elongation.
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Affiliation(s)
- Miriam Sansó
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Karen M. Lee
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Laia Viladevall
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | | | - Viviane Pagé
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
| | - Stephen Nagy
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
| | - Ariane Racine
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
| | - Courtney V. St. Amour
- Programs in Biochemistry, Cell and Molecular Biology, Weill Cornell Medical College, New York, New York, United States of America
| | - Chao Zhang
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Kevan M. Shokat
- Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California, United States of America
| | - Beate Schwer
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, United States of America
| | - François Robert
- Institut de Recherches Cliniques de Montréal, Montréal, Canada
| | - Robert P. Fisher
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail: (RPF); (JCT)
| | - Jason C. Tanny
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Canada
- * E-mail: (RPF); (JCT)
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18
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Lai MY, Zhang D, Laronde-Leblanc N, Fushman D. Structural and biochemical studies of the open state of Lys48-linked diubiquitin. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:2046-56. [PMID: 22542781 DOI: 10.1016/j.bbamcr.2012.04.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 04/10/2012] [Accepted: 04/11/2012] [Indexed: 01/05/2023]
Abstract
Ubiquitin (Ub) is a small protein highly conserved among eukaryotes and involved in practically all aspects of eukaryotic cell biology. Polymeric chains assembled from covalently-linked Ub monomers function as molecular signals in the regulation of a host of cellular processes. Our previous studies have shown that the predominant state of Lys48-linked di- and tetra-Ub chains at near-physiological conditions is a closed conformation, in which the Ub-Ub interface is formed by the hydrophobic surface residues of the adjacent Ub units. Because these very residues are involved in (poly)Ub interactions with the majority of Ub-binding proteins, their sequestration at the Ub-Ub interface renders the closed conformation of polyUb binding incompetent. Thus the existence of open conformation(s) and the interdomain motions opening and closing the Ub-Ub interface is critical for the recognition of Lys48-linked polyUb by its receptors. Knowledge of the conformational properties of a polyUb signal is essential for our understanding of its specific recognition by various Ub-receptors. Despite their functional importance, open states of Lys48-linked chains are poorly characterized. Here we report a crystal structure of the open state of Lys48-linked di-Ub. Moreover, using NMR, we examined interactions of the open state of this chain (at pH4.5) with a Lys48-linkage-selective receptor, the UBA2 domain of a shuttle protein hHR23a. Our results show that di-Ub binds UBA2 in the same mode and with comparable affinity as the closed state. Our data suggest a mechanism for polyUb signal recognition, whereby Ub-binding proteins select specific conformations out of the available ensemble of polyUb chain conformations. This article is part of a Special Issue entitled: Ubiquitin Drug Discovery and Diagnostics.
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Affiliation(s)
- Ming-Yih Lai
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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19
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Ciechanover A. Intracellular Protein Degradation: From a Vague Idea through the Lysosome and the Ubiquitin-Proteasome System and onto Human Diseases and Drug Targeting. Rambam Maimonides Med J 2012; 3:e0001. [PMID: 23908826 PMCID: PMC3707415 DOI: 10.5041/rmmj.10068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Between the 1950s and 1980s, scientists were focusing mostly on how the genetic code was transcribed to RNA and translated to proteins, but how proteins were degraded had remained a neglected research area. With the discovery of the lysosome by Christian de Duve it was assumed that cellular proteins are degraded within this organelle. Yet, several independent lines of experimental evidence strongly suggested that intracellular proteolysis was largely non-lysosomal, but the mechanisms involved have remained obscure. The discovery of the ubiquitin-proteasome system resolved the enigma. We now recognize that degradation of intracellular proteins is involved in regulation of a broad array of cellular processes, such as cell cycle and division, regulation of transcription factors, and assurance of the cellular quality control. Not surprisingly, aberrations in the system have been implicated in the pathogenesis of human disease, such as malignancies and neurodegenerative disorders, which led subsequently to an increasing effort to develop mechanism-based drugs.
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20
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Castañeda C, Liu J, Chaturvedi A, Nowicka U, Cropp TA, Fushman D. Nonenzymatic assembly of natural polyubiquitin chains of any linkage composition and isotopic labeling scheme. J Am Chem Soc 2011; 133:17855-68. [PMID: 21962295 PMCID: PMC3226840 DOI: 10.1021/ja207220g] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Polymeric chains made of a small protein ubiquitin act as molecular signals regulating a variety of cellular processes controlling essentially all aspects of eukaryotic biology. Uncovering the mechanisms that allow differently linked polyubiquitin chains to serve as distinct molecular signals requires the ability to make these chains with the native connectivity, defined length, linkage composition, and in sufficient quantities. This, however, has been a major impediment in the ubiquitin field. Here, we present a robust, efficient, and widely accessible method for controlled iterative nonenzymatic assembly of polyubiquitin chains using recombinant ubiquitin monomers as the primary building blocks. This method uses silver-mediated condensation reaction between the C-terminal thioester of one ubiquitin and the ε-amine of a specific lysine on the other ubiquitin. We augment the nonenzymatic approaches developed recently by using removable orthogonal amine-protecting groups, Alloc and Boc. The use of bacterially expressed ubiquitins allows cost-effective isotopic enrichment of any individual monomer in the chain. We demonstrate that our method yields completely natural polyubiquitin chains (free of mutations and linked through native isopeptide bonds) of essentially any desired length, linkage composition, and isotopic labeling scheme, and in milligram quantities. Specifically, we successfully made Lys11-linked di-, tri-, and tetra-ubiquitins, Lys33-linked diubiquitin, and a mixed-linkage Lys33,Lys11-linked triubiquitin. We also demonstrate the ability to obtain, by high-resolution NMR, residue-specific information on ubiquitin units at any desired position in such chains. This method opens up essentially endless possibilities for rigorous structural and functional studies of polyubiquitin signals.
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Affiliation(s)
- Carlos Castañeda
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, 20742, USA
| | - Jia Liu
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284
| | - Apurva Chaturvedi
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, 20742, USA
| | - Urszula Nowicka
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, 20742, USA
| | - T. Ashton Cropp
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, 20742, USA
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21
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A chemical-genetic screen to unravel the genetic network of CDC28/CDK1 links ubiquitin and Rad6-Bre1 to cell cycle progression. Proc Natl Acad Sci U S A 2011; 108:18748-53. [PMID: 22042866 DOI: 10.1073/pnas.1115885108] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Cyclin-dependent kinases (CDKs) control the eukaryotic cell cycle, and a single CDK, Cdc28 (also known as Cdk1), is necessary and sufficient for cell cycle regulation in the budding yeast Saccharomyces cerevisiae. Cdc28 regulates cell cycle-dependent processes such as transcription, DNA replication and repair, and chromosome segregation. To gain further insight into the functions of Cdc28, we performed a high-throughput chemical-genetic array (CGA) screen aimed at unraveling the genetic network of CDC28. We identified 107 genes that strongly genetically interact with CDC28. Although these genes serve multiple cellular functions, genes involved in cell cycle regulation, transcription, and chromosome metabolism were overrepresented. DOA1, which is involved in maintaining free ubiquitin levels, as well as the RAD6-BRE1 pathway, which is involved in transcription, displayed particularly strong genetic interactions with CDC28. We discovered that DOA1 is important for cell cycle entry by supplying ubiquitin. Furthermore, we found that the RAD6-BRE1 pathway functions downstream of DOA1/ubiquitin but upstream of CDC28, by promoting transcription of cyclins. These results link cellular ubiquitin levels and the Rad6-Bre1 pathway to cell cycle progression.
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22
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Wu L, Zee BM, Wang Y, Garcia BA, Dou Y. The RING finger protein MSL2 in the MOF complex is an E3 ubiquitin ligase for H2B K34 and is involved in crosstalk with H3 K4 and K79 methylation. Mol Cell 2011; 43:132-44. [PMID: 21726816 DOI: 10.1016/j.molcel.2011.05.015] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 03/22/2011] [Accepted: 05/13/2011] [Indexed: 01/31/2023]
Abstract
We demonstrate that RING finger protein MSL2 in the MOF-MSL complex is a histone ubiquitin E3 ligase. MSL2, together with MSL1, has robust histone ubiquitylation activity that mainly targets nucleosomal H2B on lysine 34 (H2B K34ub), a site within a conserved basic patch on H2B tail. H2B K34ub by MSL1/2 directly regulates H3 K4 and K79 methylation through trans-tail crosstalk both in vitro and in cells. The significance of MSL1/2-mediated histone H2B ubiquitylation is underscored by the facts that MSL1/2 activity is important for transcription activation at HOXA9 and MEIS1 loci and that this activity is evolutionarily conserved in the Drosophila dosage compensation complex. Altogether, these results indicate that the MOF-MSL complex possesses two distinct chromatin-modifying activities (i.e., H4 K16 acetylation and H2B K34 ubiquitylation) through MOF and MSL2 subunits. They also shed light on how an intricate network of chromatin-modifying enzymes functions coordinately in gene activation.
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Affiliation(s)
- Lipeng Wu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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23
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Conservation and divergence of the histone H2B monoubiquitination pathway from yeast to humans and plants. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11515-011-1000-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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24
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Ciechanover A. Intracellular protein degradation: from a vague idea thru the lysosome and the ubiquitin-proteasome system and onto human diseases and drug targeting. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:3-13. [PMID: 21435401 DOI: 10.1016/j.bbapap.2011.03.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Revised: 03/11/2011] [Accepted: 03/14/2011] [Indexed: 01/30/2023]
Abstract
Between the 1950s and 1980s, scientists were focusing mostly on how the genetic code was transcribed to RNA and translated to proteins, but how proteins were degraded had remained a neglected research area. With the discovery of the lysosome by Christian de Duve it was assumed that cellular proteins are degraded within this organelle. Yet, several independent lines of experimental evidence strongly suggested that intracellular proteolysis was largely non-lysosomal, but the mechanisms involved have remained obscure. The discovery of the ubiquitin-proteasome system resolved the enigma. We now recognize that degradation of intracellular proteins is involved in regulation of a broad array of cellular processes, such as cell cycle and division, regulation of transcription factors, and assurance of the cellular quality control. Not surprisingly, aberrations in the system have been implicated in the pathogenesis of human disease, such as malignancies and neurodegenerative disorders, which led subsequently to an increasing effort to develop mechanism-based drugs. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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Affiliation(s)
- Aaron Ciechanover
- Cancer and Vascular Biology research Center, Technion-Israel Institute of Technology, Haifa, Israel.
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25
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Chandrasekharan MB, Huang F, Sun ZW. Decoding the trans-histone crosstalk: methods to analyze H2B ubiquitination, H3 methylation and their regulatory factors. Methods 2011; 54:304-14. [PMID: 21392582 DOI: 10.1016/j.ymeth.2011.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 02/18/2011] [Accepted: 02/22/2011] [Indexed: 12/16/2022] Open
Abstract
Regulation of histone H3 lysine 4 and 79 methylation by histone H2B lysine 123 monoubiquitination is an evolutionarily conserved trans-histone crosstalk mechanism, which demonstrates a functional role for histone ubiquitination within the cell. The regulatory enzymes, factors and processes involved in the establishment and dynamic modulation of these modifications and their genome-wide distribution patterns have been determined in many model systems. Rapid progress in understanding this trans-histone crosstalk has been made using the standard experimental tools of chromatin biology in budding yeast (Saccharomyces cerevisiae), a highly tractable model organism. Here, we provide a set of modified and refined experimental procedures that can be used to gain further insights into the underlying mechanisms that govern this crosstalk in budding yeast. Importantly, the improved procedures and their underlying principles can also be applied to other model organisms. Methods presented here provide a rapid and efficient means to prepare enriched protein extracts to better preserve and assess the steady state levels of histones, non-histone proteins and their modifications. Improved chromatin immunoprecipitation and double immunoprecipitation protocols are provided to measure the occupancy and distribution of proteins and their modified forms at specific chromatin regions or loci. A quick and easy method to measure overall protein abundance and changes in protein-protein and protein-DNA interactions on native chromatin is also described.
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Affiliation(s)
- Mahesh B Chandrasekharan
- Department of Biochemistry and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, United States
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26
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Kumar B, Lecompte KG, Klein JM, Haas AL. Ser(120) of Ubc2/Rad6 regulates ubiquitin-dependent N-end rule targeting by E3{alpha}/Ubr1. J Biol Chem 2010; 285:41300-9. [PMID: 21041297 DOI: 10.1074/jbc.m110.169136] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In CHO cells, CDK1/2-dependent phosphorylation of Ubc2/Rad6 at Ser(120) stimulates its ubiquitin conjugating activity and can be replicated by a S120D point mutant (Sarcevic, B., Mawson, A., Baker, R. T., and Sutherland, R. L. (2002) EMBO J. 21, 2009-2018). In contrast, we find that ectopic expression of wild type Ubc2b but not Ubc2bS120D or Ubc2bS120A in T47D human breast cancer cells specifically stimulates N-end rule-dependent degradation but not the Ubc2-independent unfolded protein response pathway, indicating that the former is E2 limiting in vivo and likely down-regulated by Ser(120) phosphorylation, as modeled by the S120D point mutation. In vitro kinetic analysis shows the in vivo phenotype of Ubc2bS120D and Ubc2bS120A is not due to differences in activating enzyme-catalyzed E2 transthiolation. However, the Ser(120) mutants possess marked differences in their abilities to support in vitro conjugation by the N-end rule-specific E3α/Ubr1 ligase that presumably accounts for their in vivo effects. Initial rate kinetics of human E3α-catalyzed conjugation of the human α-lactalbumin N-end rule substrate shows Ubc2bS120D is 20-fold less active than wild type E2, resulting from an 8-fold increase in K(m) and a 2.5-fold decrease in V(max), the latter reflecting a decreased ability to support the initial step in target protein conjugation; Ubc2bS120A is 8-fold less active than wild type E2 due almost exclusively to a decrease in V(max), reflecting a defect in polyubiquitin chain elongation. These studies suggest a mechanism for the integrated regulation of diverse ubiquitin-dependent signaling pathways through E2 phosphorylation that yields differential effects on its cognate ligases.
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Affiliation(s)
- Brajesh Kumar
- Department of Biochemistry and Molecular Biology and the Stanley S Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112, USA
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27
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Chandrasekharan MB, Huang F, Sun ZW. Histone H2B ubiquitination and beyond: Regulation of nucleosome stability, chromatin dynamics and the trans-histone H3 methylation. Epigenetics 2010; 5:460-8. [PMID: 20523115 DOI: 10.4161/epi.5.6.12314] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Regulation of Set1-COMPASS-mediated H3K4 methylation and Dot1-mediated H3K79 methylation by H2BK123 ubiquitination (H2Bub1) is an evolutionarily conserved trans-histone crosstalk mechanism. How H2Bub1 impacts chromatin structure and affects Set1-COMPASS/Dot1 functions has not been fully defined. Ubiquitin was proposed to bind proteins to physically bridge H2Bub1 with Set1-COMPASS/Dot1. Alternatively, the bulky ubiquitin was thought to be a "wedge" that loosens the nucleosome for factor access. Contrary to the latter possibility, recent discoveries provide evidence for nucleosome stabilization by H2Bub1 via preventing the constant H2A-H2B eviction. Recent data has also uncovered a "docking-site" on H2B for Set1-COMPASS. Collectively, these findings invoke a model, where ubiquitin acts as a "glue" to bind the nucleosome together for supporting Set1-COMPASS/Dot1 functions. This review provides an overview of these novel findings. Additionally, how H2Bub1 and its deubiquitination might alter the chromatin dynamics during transcription is discussed. Possible models for nucleosome stabilization by ubiquitin are also provided.
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Affiliation(s)
- Mahesh B Chandrasekharan
- Department of Biochemistry and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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28
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Abstract
Traditionally, research has been reductionist, characterizing the individual components of biological systems. But new technologies have increased the size and scope of biological data, and systems approaches have broadened the view of how these components are interconnected. Here, we discuss how quantitative mapping of genetic interactions enhances our view of biological systems, allowing their deeper interrogation across different biological scales.
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Affiliation(s)
- Pedro Beltrao
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, CA 94158, USA
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29
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Cui L, Li W. Role of ubiquitination in meiotic recombination repair. SCIENCE CHINA-LIFE SCIENCES 2010; 53:447-54. [PMID: 20596910 DOI: 10.1007/s11427-010-0052-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 01/04/2010] [Indexed: 11/28/2022]
Abstract
Programmed and unprogrammed double-strand breaks (DSBs) often arise from such physiological requirements as meiotic recombination, and exogenous insults, such as ionizing radiation (IR). Due to deleterious impacts on genome stability, DSBs must be appropriately processed and repaired in a regulatory manner. Recent investigations have indicated that ubiquitination is a critical factor in DNA damage response and meiotic recombination repair. This review summarizes the effects of proteins and complexes associated with ubiquitination with regard to homologous recombination (HR)-dependent DSB repair.
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Affiliation(s)
- Li Cui
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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30
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The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. Cell 2010; 140:491-503. [PMID: 20178742 DOI: 10.1016/j.cell.2009.12.050] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 07/24/2009] [Accepted: 12/22/2009] [Indexed: 01/12/2023]
Abstract
Genetic and cell-based studies have implicated the PAF1 complex (PAF1C) in transcription-associated events, but there has been no evidence showing a direct role in facilitating transcription of a natural chromatin template. Here, we demonstrate an intrinsic ability of human PAF1C (hPAF1C) to facilitate activator (p53)- and histone acetyltransferase (p300)-dependent transcription elongation from a recombinant chromatin template in a biochemically defined RNA polymerase II transcription system. This represents a PAF1C function distinct from its established role in histone ubiquitylation and methylation. Importantly, we further demonstrate a strong synergy between hPAF1C and elongation factor SII/TFIIS and an underlying mechanism involving direct hPAF1C-SII interactions and cooperative binding to RNA polymerase II. Apart from a distinct PAF1C function, the present observations provide a molecular mechanism for the cooperative function of distinct transcription elongation factors in chromatin transcription.
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Kim J, Roeder RG. Direct Bre1-Paf1 complex interactions and RING finger-independent Bre1-Rad6 interactions mediate histone H2B ubiquitylation in yeast. J Biol Chem 2009; 284:20582-92. [PMID: 19531475 DOI: 10.1074/jbc.m109.017442] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Recent yeast genetic studies have implicated the ubiquitin-conjugating enzyme and ubiquitin ligase functions of yRad6 and yBre1, respectively, in H2B ubiquitylation. However, there have been no corresponding biochemical analyses demonstrating intrinsic enzyme activities of yRad6 and yBre1 or related mechanistic details. Here, we describe a robust in vitro chromatin ubiquitylation assay that involves purified H2B ubiquitylation factors and natural nucleosomes. Our results indicate that yRad6 has an in vitro ability to nonspecifically ubiquitylate all core histones in the absence of an ubiquitin ligase but that yBre1 functions, through direct interactions with yRad6, to direct the ubiquitin conjugating activity of yRad6 toward the physiological H2B ubiquitylation site. Moreover, a yRad6 domain mapping analysis shows that an intact UBC domain is required for binding to yBre1, whereas the C-terminal acidic tail domain that is not required for a stable yBre1-yRad6 interaction is necessary for full enzyme activity of yRad6. We also find that, analogous to heteromeric complex formation by BRE1 paralogues in other organisms, yBre1 forms a homo-multimeric complex. Of special significance, our detailed biochemical analyses further show that the yBre1 RING finger domain is essential for H2B ubiquitylation but, surprisingly, dispensable for interaction of yBre1 with yRad6. In further support of the genetically identified requirement of the RNA polymerase II-associated yPaf1 complex for H2B ubiquitylation, protein interaction studies reveal that a purified yPaf1 complex directly and selectively interacts with yBre1 and thus serves to link the H2B ubiquitylation and general transcription machineries. These studies provide a more detailed mechanistic basis for H2B ubiquitylation in yeast.
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Affiliation(s)
- Jaehoon Kim
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York 10065, USA
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Thambirajah AA, Li A, Ishibashi T, Ausió J. New developments in post-translational modifications and functions of histone H2A variants. Biochem Cell Biol 2009; 87:7-17. [PMID: 19234519 DOI: 10.1139/o08-103] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Structural variability within histone families, such as H2A, can be achieved through 2 primary mechanisms: the expression of histone variants and the incorporation of chemical modifications. The histone H2A family contains several variants in addition to the canonical H2A forms. In this review, recent developments in the study of the heteromorphous variants H2A.X, H2A.Z, and macroH2A will be discussed. Particular focus will be given to the post-translational modifications (PTMs) of these variants, including phosphorylation, ubiquitination, acetylation, and methylation. The combination of the newly identified N- and C-terminal tail PTMs expands the multiplicity of roles that the individual H2A variants can perform. It is of additional interest that analogous sites within these different histone variants can be similarly modified. Whether this is a redundant function or a finely tuned one, designed to meet specific needs, remains to be elucidated.
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Affiliation(s)
- Anita A Thambirajah
- Department of Biochemistry and Microbiology and The Center for Biomedical Research, University of Victoria, Victoria, BCV8W3P6, Canada
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Dunham-Ems SM, Lee YW, Stachowiak EK, Pudavar H, Claus P, Prasad PN, Stachowiak MK. Fibroblast growth factor receptor-1 (FGFR1) nuclear dynamics reveal a novel mechanism in transcription control. Mol Biol Cell 2009; 20:2401-12. [PMID: 19261810 DOI: 10.1091/mbc.e08-06-0600] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Nuclear FGFR1 acts as a developmental gene regulator in cooperation with FGF-2, RSK1, and CREB-binding protein (CBP). FRAP analysis revealed three nuclear FGFR1 populations: i) a fast mobile, ii) a slower mobile population reflecting chromatin-bound FGFR1, and iii) an immobile FGFR1 population associated with the nuclear matrix. Factors (cAMP, CBP) that induce FGFR1-mediated gene activation shifted FGFR1 from the nuclear matrix (immobile) to chromatin (slow) and reduced the movement rate of the chromatin-bound population. Transcription inhibitors accelerated FGFR1 movement; the content of the chromatin-bound slow FGFR1 decreased, whereas the fast population increased. The transcriptional activation appears to involve conversion of the immobile matrix-bound and the fast nuclear FGFR1 into a slow chromatin-binding population through FGFR1's interaction with CBP, RSK1, and the high-molecular-weight form of FGF-2. Our findings support a general mechanism in which gene activation is governed by protein movement and collisions with other proteins and nuclear structures.
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Affiliation(s)
- Star M Dunham-Ems
- Department of Pathology and Anatomical Sciences, and Department of Chemistry, State University of New York, Buffalo, NY 14214, USA
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Dhawan R, Luo H, Foerster AM, Abuqamar S, Du HN, Briggs SD, Mittelsten Scheid O, Mengiste T. HISTONE MONOUBIQUITINATION1 interacts with a subunit of the mediator complex and regulates defense against necrotrophic fungal pathogens in Arabidopsis. THE PLANT CELL 2009; 21:1000-19. [PMID: 19286969 PMCID: PMC2671699 DOI: 10.1105/tpc.108.062364] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 02/11/2009] [Accepted: 02/26/2009] [Indexed: 05/17/2023]
Abstract
This work examines the role of the Arabidopsis thaliana RING E3 ligase, HISTONE MONOUBIQUITINATION1 (HUB1) in disease resistance. Loss-of-function alleles of HUB1 show increased susceptibility to the necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola, whereas HUB1 overexpression conferred resistance to B. cinerea. By contrast, responses to the bacterial pathogen Pseudomonas syringae are unaltered in hub1 plants. hub1 mutants have thinner cell walls but increased callose around an infection site. HUB1 acts independently of jasmonate, but ethylene (ET) responses and salicylate modulate the resistance of hub1 mutants to necrotrophic fungi. The ET response factor ETHYLENE INSENSITIVE2 is epistatic to HUB1 for A. brassicicola resistance but additive to HUB1 for B. cinerea resistance. HUB1 interacts with MED21, a subunit of the Arabidopsis Mediator, a conserved complex that regulates RNA polymerase II. RNA interference lines with reduced MED21 expression are highly susceptible to A. brassicicola and B. cinerea, whereas T-DNA insertion alleles are embryonic lethal, suggesting an essential role for MED21. However, HUB1-mediated histone H2B modification is independent of histone H3 and DNA methylation. In sum, histone H2B monoubiquitination is an important chromatin modification with regulatory roles in plant defense against necrotrophic fungi most likely through modulation of gene expression.
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Affiliation(s)
- Rahul Dhawan
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907-2054, USA
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Misri S, Pandita S, Kumar R, Pandita TK. Telomeres, histone code, and DNA damage response. Cytogenet Genome Res 2009; 122:297-307. [PMID: 19188699 DOI: 10.1159/000167816] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2008] [Indexed: 12/30/2022] Open
Abstract
Genomic stability is maintained by telomeres, the end terminal structures that protect chromosomes from fusion or degradation. Shortening or loss of telomeric repeats or altered telomere chromatin structure is correlated with telomere dysfunction such as chromosome end-to-end associations that could lead to genomic instability and gene amplification. The structure at the end of telomeres is such that its DNA differs from DNA double strand breaks (DSBs) to avoid nonhomologous end-joining (NHEJ), which is accomplished by forming a unique higher order nucleoprotein structure. Telomeres are attached to the nuclear matrix and have a unique chromatin structure. Whether this special structure is maintained by specific chromatin changes is yet to be thoroughly investigated. Chromatin modifications implicated in transcriptional regulation are thought to be the result of a code on the histone proteins (histone code). This code, involving phosphorylation, acetylation, methylation, ubiquitylation, and sumoylation of histones, is believed to regulate chromatin accessibility either by disrupting chromatin contacts or by recruiting non-histone proteins to chromatin. The histone code in which distinct histone tail-protein interactions promote engagement may be the deciding factor for choosing specific DSB repair pathways. Recent evidence suggests that such mechanisms are involved in DNA damage detection and repair. Altered telomere chromatin structure has been linked to defective DNA damage response (DDR), and eukaryotic cells have evolved DDR mechanisms utilizing proficient DNA repair and cell cycle checkpoints in order to maintain genomic stability. Recent studies suggest that chromatin modifying factors play a critical role in the maintenance of genomic stability. This review will summarize the role of DNA damage repair proteins specifically ataxia-telangiectasia mutated (ATM) and its effectors and the telomere complex in maintaining genome stability.
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Affiliation(s)
- S Misri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
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Zhai L, Joo HY, Wang H. In vitro and in vivo assays for studying histone ubiquitination and deubiquitination. Methods Mol Biol 2009; 523:295-309. [PMID: 19381930 DOI: 10.1007/978-1-59745-190-1_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Posttranslational histone modifications play important roles in regulating chromatin structure and function (Martin and Zhang, Nat Rev Mol Cell Biol 6:838-849, 2005; Jenuwein and Allis, Science 293:1074-1080, 2001). One example of such modifications is histone ubiquitination, which occurs predominately on H2A and H2B. Recent studies have highlighted important regulatory roles of H2A ubiquitination in Polycomb group proteins-mediated gene silencing (Wang et al., Nature 431:873-878, 2004; Joo et al., Nature 449:1068-1072, 2007) and H2B ubiquitination in transcription, H3 methylation, and DNA methylation (Zhang, Genes Dev 17:2733-2740, 2003; Sun and Allis, Nature 418:104-108, 2002; Sridhar et al., Nature 447:735-738, 2007). Here we describe methods for in vitro histone ubiquitination and deubiquitination assays. We also describe approaches to investigate the in vivo function of a putative histone ubiquitin ligase and deubiquitinase. These experimental procedures are largely based on our studies in mammalian cells. These methods should provide useful tools for studying this bulky histone modification.
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Affiliation(s)
- Ling Zhai
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
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Liu Z, Oh SM, Okada M, Liu X, Cheng D, Peng J, Brat DJ, Sun SY, Zhou W, Gu W, Ye K. Human BRE1 is an E3 ubiquitin ligase for Ebp1 tumor suppressor. Mol Biol Cell 2008; 20:757-68. [PMID: 19037095 DOI: 10.1091/mbc.e08-09-0983] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Human Bre1, an E3 ligase for H2B monoubiquitination, binds p53 and enhances activator-dependent transcription. Ebp1, an ErbB3 receptor-binding protein, inhibits cell proliferation and acts as a tumor suppressor. Here, we show that hBre1 acts as an E3 ubiquitin ligase for Ebp1 tumor suppressor and promotes its polyubiquitination and degradation. Ebp1 is polyubiquitinated in cancer cells, which is regulated by its phosphorylation. We identified hBre1 acting as an E3 ligase for Ebp1 and increasing its polyubiquitination. Depletion of hBre1 blocks Ebp1's polyubiquitination and elevates its protein level, preventing cancer proliferation. hBre1 binds Ebp1 and suppresses its repressive effect on E2F-1. Moreover, Ebp1 protein level is substantially diminished in human cancers. It is robustly phosphorylated and localized in the nucleus of primary gliomas, correlating with hBre1 subcellular residency. Thus, hBre1 inhibits Ebp1's tumor suppressive activity through mediating its polyubiquitination and degradation.
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Affiliation(s)
- Zhixue Liu
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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Fingerman IM, Du HN, Briggs SD. Controlling histone methylation via trans-histone pathways. Epigenetics 2008; 3:237-42. [PMID: 18806472 DOI: 10.4161/epi.3.5.6869] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Geng F, Tansey WP. Polyubiquitylation of histone H2B. Mol Biol Cell 2008; 19:3616-24. [PMID: 18562693 PMCID: PMC2526708 DOI: 10.1091/mbc.e08-01-0050] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2008] [Revised: 05/06/2008] [Accepted: 06/05/2008] [Indexed: 12/28/2022] Open
Abstract
Covalent modification of histones by ubiquitylation is a prominent epigenetic mark that features in a variety of chromatin-based events such as histone methylation, gene silencing, and repair of DNA damage. The prototypical example of histone ubiquitylation is that of histone H2B in Saccharomyces cerevisiae. In this case, attachment of ubiquitin to lysine 123 (K123) of H2B is important for regulation of both active and transcriptionally silent genes and participates in trans to signal methylation of histone H3. It is generally assumed that H2B is monoubiquitylated at K123 and that it is this single ubiquitin moiety that influences H2B function. To determine whether this assumption is correct, we have re-examined the ubiquitylation status of endogenous H2B in yeast. We find that, contrary to expectations, H2B is extensively polyubiquitylated. Polyubiquitylation of H2B appears to occur within the context of chromatin and is not associated with H2B destruction. There are at least two distinct modes of H2B polyubiquitylation: one that occurs at K123 and depends on the Rad6-Bre1 ubiquitylation machinery and another that occurs on multiple lysine residues and is catalyzed by an uncharacterized ubiquitin ligase(s). Interestingly, these ubiquitylation events are under the influence of different combinations of ubiquitin-specific proteases, suggesting that they have distinct biological functions. These results raise the possibility that some of the biological effects of ubiquitylation of H2B are exerted via ubiquitin chains, rather than a single ubiquitin group.
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Affiliation(s)
- Fuqiang Geng
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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41
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Donati G, Gatta R, Dolfini D, Fossati A, Ceribelli M, Mantovani R. An NF-Y-dependent switch of positive and negative histone methyl marks on CCAAT promoters. PLoS One 2008; 3:e2066. [PMID: 18446193 PMCID: PMC2312324 DOI: 10.1371/journal.pone.0002066] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 03/11/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Histone tails have a plethora of different post-translational modifications, which are located differently in "open" and "closed" parts of genomes. H3K4me3/H3K79me2 and H4K20me3 are among the histone marks associated with the early establishment of active and inactive chromatin, respectively. One of the most widespread promoter elements is the CCAAT box, bound by the NF-Y trimer. Two of NF-Y subunits have an H2A-H2B-like structure. PRINCIPAL FINDINGS We established the causal relationship between NF-Y binding and positioning of methyl marks, by ChIP analysis of mouse and human cells infected with a dominant negative NF-YA: a parallel decrease in NF-Y binding, H3K4me3, H3K79me2 and transcription was observed in promoters that are dependent upon NF-Y. On the contrary, changes in the levels of H3K9-14ac were more subtle. Components of the H3K4 methylating MLL complex are not recruited in the absence of NF-Y. As for repressed promoters, NF-Y removal leads to a decrease in the H4K20me3 mark and deposition of H3K4me3. CONCLUSIONS Two relevant findings are reported: (i) NF-Y gains access to its genomic locations independently from the presence of methyl histone marks, either positive or negative; (ii) NF-Y binding has profound positive or negative consequences on the deposition of histone methyl marks. Therefore NF-Y is a fundamental switch at the heart of decision between gene activation and repression in CCAAT regulated genes.
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Affiliation(s)
- Giacomo Donati
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Milano, Italy
| | - Raffaella Gatta
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Milano, Italy
| | - Diletta Dolfini
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Milano, Italy
| | - Andrea Fossati
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Milano, Italy
| | - Michele Ceribelli
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università di Milano, Milano, Italy
- * E-mail:
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H3 K79 dimethylation marks developmental activation of the beta-globin gene but is reduced upon LCR-mediated high-level transcription. Blood 2008; 112:406-14. [PMID: 18441235 DOI: 10.1182/blood-2007-12-128983] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome-wide analyses of the relationship between H3 K79 dimethylation and transcription have revealed contradictory results. To clarify this relationship at a single locus, we analyzed expression and H3 K79 modification levels of wild-type (WT) and transcriptionally impaired beta-globin mutant genes during erythroid differentiation. Analysis of fractionated erythroid cells derived from WT/Delta locus control region (LCR) heterozygous mice reveals no significant H3 K79 dimethylation of the beta-globin gene on either allele prior to activation of transcription. Upon transcriptional activation, H3 K79 di-methylation is observed along both WT and DeltaLCR alleles, and both alleles are located in proximity to H3 K79 dimethylation nuclear foci. However, H3 K79 di-methylation is significantly increased along the DeltaLCR allele compared with the WT allele. In addition, analysis of a partial LCR deletion mutant reveals that H3 K79 dimethylation is inversely correlated with beta-globin gene expression levels. Thus, while our results support a link between H3 K79 dimethylation and gene expression, high levels of this mark are not essential for high level beta-globin gene transcription. We propose that H3 K79 dimethylation is destabilized on a highly transcribed template.
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Abstract
Chromosomal genes modulate Ty retrotransposon movement in the genome of Saccharomyces cerevisiae. We have screened a collection of 4739 deletion mutants to identify those that increase Ty1 mobility (Ty1 restriction genes). Among the 91 identified mutants, 80% encode products involved in nuclear processes such as chromatin structure and function, DNA repair and recombination, and transcription. However, bioinformatic analyses encompassing additional Ty1 and Ty3 screens indicate that 264 unique genes involved in a variety of biological processes affect Ty mobility in yeast. Further characterization of 33 of the mutants identified here show that Ty1 RNA levels increase in 5 mutants and the rest affect mobility post-transcriptionally. RNA and cDNA levels remain unchanged in mutants defective in transcription elongation, including ckb2Delta and elf1Delta, suggesting that Ty1 integration may be more efficient in these strains. Insertion-site preference at the CAN1 locus requires Ty1 restriction genes involved in histone H2B ubiquitination by Paf complex subunit genes, as well as BRE1 and RAD6, histone H3 acetylation by RTT109 and ASF1, and transcription elongation by SPT5. Our results indicate that multiple pathways restrict Ty1 mobility and histone modifications may protect coding regions from insertional mutagenesis.
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44
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Zhou W, Zhu P, Wang J, Pascual G, Ohgi KA, Lozach J, Glass CK, Rosenfeld MG. Histone H2A monoubiquitination represses transcription by inhibiting RNA polymerase II transcriptional elongation. Mol Cell 2008; 29:69-80. [PMID: 18206970 DOI: 10.1016/j.molcel.2007.11.002] [Citation(s) in RCA: 287] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2007] [Revised: 09/01/2007] [Accepted: 11/05/2007] [Indexed: 11/27/2022]
Abstract
Solving the biological roles of covalent histone modifications, including monoubiquitination of histone H2A, and the molecular mechanisms by which these modifications regulate specific transcriptional programs remains a central question for all eukaryotes. Here we report that the N-CoR/HDAC1/3 complex specifically recruits a specific histone H2A ubiquitin ligase, 2A-HUB/hRUL138, to a subset of regulated gene promoters. 2A-HUB catalyzes monoubiquitination of H2A at lysine 119, functioning as a combinatoric component of the repression machinery required for specific gene regulation programs. Thus, 2A-HUB mediates a selective repression of a specific set of chemokine genes in macrophages, critically modulating migratory responses to TLR activation. H2A monoubiquitination acts to prevent FACT recruitment at the transcriptional promoter region, blocking RNA polymerase II release at the early stage of elongation. We suggest that distinct H2A ubiquitinases, each recruited based on interactions with different corepressor complexes, contribute to distinct transcriptional repression programs.
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Affiliation(s)
- Wenlai Zhou
- Howard Hughes Medical Institute, School of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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45
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Abstract
In the fission yeast Schizosaccharomyces pombe, the RNAi pathway plays an important role in the formation and maintenance of heterochromatin. Heterochromatin, or silent chromatin, is an epigenetically inherited attribute of eukaryotic chromosomes which is required for gene regulation, chromosome segregation and maintenance of genome stability. In S. pombe, heterochromatin forms on related repetitive DNA sequences at specific loci. These repetitive sequences, in concert with the RNAi machinery, are thought to attract several proteins including chromatin-modifying enzymes which act to promote heterochromatin formation. The purification of complexes participating in heterochromatin formation has allowed us to begin to analyse in detail the processes involved. In the future this will help us to understand how the RNAi machinery acts to induce the chromatin modifications which lead to heterochromatin assembly in fission yeast.
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Affiliation(s)
- Sharon A White
- Welcome Trust Centre for Cell Biology, Institute of Cell Biology, The University of Edinburgh, Edinburgh, EH9 3JR Scotland, UK.
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Bardag-Gorce F, Oliva J, Villegas J, Fraley S, Amidi F, Li J, Dedes J, French B, French SW. Epigenetic mechanisms regulate Mallory Denk body formation in the livers of drug-primed mice. Exp Mol Pathol 2008; 84:113-21. [PMID: 18281034 DOI: 10.1016/j.yexmp.2007.12.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Accepted: 12/19/2007] [Indexed: 11/16/2022]
Abstract
The mechanism of Mallory Denk body formation is still not fully understood, but growing evidence implicates epigenetic mechanisms in MDB formation. In a previous study the epigenetic memory of MDB formation remained intact for at least 4 months after withdrawal from the DDC diet. In the present study, mice were fed a diet containing DDC or a diet containing DDC and S-adenosylmethionine (SAMe) to investigate the epigenetic memory of MDB formation. DDC feeding caused an increase in histone 3 acetylation, a decrease in histone 3 trimethylation, and an increase in histone ubiquitinylation. The addition of SAMe to the DDC diet prevented the DDC induced decrease of H3K4 and H3K9 trimethylation and the increase in histone ubiquitinylation. Changes in histone modifying enzymes (HATs and HDACs), were also found in the liver nuclear extracts of the DDC/SAMe fed mice. Data mining of microarray analysis confirmed that gene expression changed with DDC refeeding, particularly the SAMe metabolizing enzymes, Mat2a, AMD, AHCY and Mthfr. SAMe supplementation prevented the decrease of AHCY and GNMT, and prevented the increase in Mthfr, which provides a mechanism to explain how DDC inhibits methylation of histones. The results indicate that SAMe prevented the epigenetic cellular memory involved in the MDB formation.
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Affiliation(s)
- Fawzia Bardag-Gorce
- Department of Pathology, Harbor-UCLA Medical Center, 1000 W. Carson St., Torrance, CA 90509, USA
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47
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Ke Q, Ellen TP, Costa M. Nickel compounds induce histone ubiquitination by inhibiting histone deubiquitinating enzyme activity. Toxicol Appl Pharmacol 2007; 228:190-9. [PMID: 18279901 DOI: 10.1016/j.taap.2007.12.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 12/06/2007] [Accepted: 12/07/2007] [Indexed: 10/22/2022]
Abstract
Nickel (Ni) compounds are known carcinogens but underlying mechanisms are not clear. Epigenetic changes are likely to play an important role in nickel ion carcinogenesis. Previous studies have shown epigenetic effects of nickel ions, including the loss of histone acetylation and a pronounced increase in dimethylated H3K9 in nickel-exposed cells. In this study, we demonstrated that both water-soluble and insoluble nickel compounds induce histone ubiquitination (uH2A and uH2B) in a variety of cell lines. Investigations of the mechanism by which nickel increases histone ubiquitination in cells reveal that nickel does not affect cellular levels of the substrates of this modification, i.e., ubiquitin, histones, and other non-histone ubiquitinated proteins. In vitro ubiquitination and deubiquitination assays have been developed to further investigate possible effects of nickel on enzymes responsible for histone ubiquitination. Results from the in vitro assays demonstrate that the presence of nickel did not affect the levels of ubiquitinated histones in the ubiquitinating assay. Instead, the addition of nickel significantly prevents loss of uH2A and uH2B in the deubiquitinating assay, suggesting that nickel-induced histone ubiquitination is the result of inhibition of (a) putative deubiquitinating enzyme(s). Additional supporting evidence comes from the comparison of the response to nickel ions with a known deubiquitinating enzyme inhibitor, iodoacetamide (IAA). This study is the first to demonstrate such effects of nickel ions on histone ubiquitination. It also sheds light on the possible mechanisms involved in altering the steady state of this modification. The study provides further evidence that supports the notion that nickel ions alter epigenetic homeostasis in cells, which may lead to altered programs of gene expression and carcinogenesis.
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Affiliation(s)
- Qingdong Ke
- Department of Environmental Medicine, New York University School of Medicine, 650 First Avenue, New York, NY 10016, USA
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48
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Zhu P, Zhou W, Wang J, Puc J, Ohgi KA, Erdjument-Bromage H, Tempst P, Glass CK, Rosenfeld MG. A histone H2A deubiquitinase complex coordinating histone acetylation and H1 dissociation in transcriptional regulation. Mol Cell 2007; 27:609-21. [PMID: 17707232 PMCID: PMC2709280 DOI: 10.1016/j.molcel.2007.07.024] [Citation(s) in RCA: 222] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Revised: 06/20/2007] [Accepted: 07/31/2007] [Indexed: 10/22/2022]
Abstract
Deciphering the epigenetic "code" remains a central issue in transcriptional regulation. Here, we report the identification of a JAMM/MPN(+) domain-containing histone H2A deubiquitinase (2A-DUB, or KIAA1915/MYSM1) specific for monoubiquitinated H2A (uH2A) that has permitted delineation of a strategy for specific regulatory pathways of gene activation. 2A-DUB regulates transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF in a coregulatory protein complex, with its deubiquitinase activity modulated by the status of acetylation of nucleosomal histones. Consistent with this mechanistic role, 2A-DUB participates in transcriptional regulation events in androgen receptor-dependent gene activation, and the levels of uH2A are dramatically decreased in prostate tumors, serving as a cancer-related mark. We suggest that H2A ubiquitination represents a widely used mechanism for many regulatory transcriptional programs and predict that various H2A ubiquitin ligases/deubiquitinases will be identified for specific cohorts of regulated transcription units.
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Affiliation(s)
- Ping Zhu
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Wenlai Zhou
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jianxun Wang
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Janusz Puc
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Kenneth A. Ohgi
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Hediye Erdjument-Bromage
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Paul Tempst
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
| | - Christopher K. Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Michael G. Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
- To whom correspondence should be addressed: M. G. Rosenfeld, Phone: 858-534-5858, Fax: 858-534-8180, E-mail:
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49
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Laribee RN, Fuchs SM, Strahl BD. H2B ubiquitylation in transcriptional control: a FACT-finding mission. Genes Dev 2007; 21:737-43. [PMID: 17403775 DOI: 10.1101/gad.1541507] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- R Nicholas Laribee
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599, USA
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50
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Hildmann C, Riester D, Schwienhorst A. Histone deacetylases—an important class of cellular regulators with a variety of functions. Appl Microbiol Biotechnol 2007; 75:487-97. [PMID: 17377789 DOI: 10.1007/s00253-007-0911-2] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 02/26/2007] [Accepted: 02/26/2007] [Indexed: 12/25/2022]
Abstract
The elucidation of mechanisms of chromatin remodeling, particular transcriptional activation, and repression by histone acetylation and deacetylation has shed light on the role of histone deacetylases (HDAC) as a new kind of therapeutic target for human cancer treatment. HDACs, in general, act as components of large corepressor complexes that prevent the transcription of several tumor suppression genes. In addition, they appear to be also involved in the deacetylation of nonhistone proteins. This paper reviews the most recent insights into the diverse biological roles of HDACs as well as the evolution of this important protein family.
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Affiliation(s)
- Christian Hildmann
- Department of Molecular Genetics and Preparative Molecular Biology, Institute for Microbiology and Genetics, Grisebachstr. 8, 37077, Göttingen, Germany
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