101
|
Machha VR, Mikek CG, Wellman S, Lewis EA. Temperature and osmotic stress dependence of the thermodynamics for binding linker histone H1 0, Its carboxyl domain (H1 0-C) or globular domain (H1 0-G) to B-DNA. Biochem Biophys Rep 2017; 12:158-165. [PMID: 29090277 PMCID: PMC5645174 DOI: 10.1016/j.bbrep.2017.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/21/2017] [Accepted: 09/25/2017] [Indexed: 12/24/2022] Open
Abstract
Linker histones (H1) are the basic proteins in higher eukaryotes that are responsible for the final condensation of chromatin. In contrast to the nucleosome core histone proteins, the role of H1 in compacting DNA is not clearly understood. In this study ITC was used to measure the binding constant, enthalpy change, and binding site size for the interactions of H10, or its C-terminal (H10-C) and globular (H10-G) domains to highly polymerized calf-thymus DNA at temperatures from 288 K to 308 K. Heat capacity changes, ΔCp, for these same H10 binding interactions were estimated from the temperature dependence of the enthalpy changes. The enthalpy changes for binding H10, H10-C, or H10-G to CT-DNA are all endothermic at 298 K, becoming more exothermic as the temperature is increased. The ΔH for binding H10-G to CT-DNA is exothermic at temperatures above approximately 300 K. Osmotic stress experiments indicate that the binding of H10 is accompanied by the release of approximately 35 water molecules. We estimate from our naked DNA titration results that the binding of the H10 to the nucleosome places the H10 protein in close contact with approximately 41 DNA bp. The breakdown is that the H10 carboxyl terminus interacts with 28 bp of linker DNA on one side of the nucleosome, the H10 globular domain binds directly to 7 bp of core DNA, and shields another 6 linker DNA bases, 3 bp on either side of the nucleosome where the linker DNA exits the nucleosome core.
Collapse
Affiliation(s)
- V R Machha
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - C G Mikek
- Department of Chemistry, Mississippi State University, Mississippi, MS 39762, USA
| | - S Wellman
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, 2500 N. State Street, Jackson, MS 39216, USA
| | - E A Lewis
- Department of Chemistry, Mississippi State University, Mississippi, MS 39762, USA
| |
Collapse
|
102
|
Meyer RG, Ketchum CC, Meyer-Ficca ML. Heritable sperm chromatin epigenetics: a break to remember†. Biol Reprod 2017; 97:784-797. [DOI: 10.1093/biolre/iox137] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/31/2017] [Indexed: 02/07/2023] Open
|
103
|
Sivanandam M, Saravanan K, Kumaradhas P. Insights into intermolecular interactions, electrostatic properties and the stability of C646 in the binding pocket of p300 histone acetyltransferase enzyme: a combined molecular dynamics and charge density study. J Biomol Struct Dyn 2017; 36:3246-3264. [DOI: 10.1080/07391102.2017.1384761] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Magudeeswaran Sivanandam
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
| | - Kandasamy Saravanan
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
| | - Poomani Kumaradhas
- Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics, Periyar University, Salem 636 011, India
| |
Collapse
|
104
|
Rachdaoui N, Li L, Willard B, Kasumov T, Previs S, Sarkar D. Turnover of histones and histone variants in postnatal rat brain: effects of alcohol exposure. Clin Epigenetics 2017; 9:117. [PMID: 29075360 PMCID: PMC5654083 DOI: 10.1186/s13148-017-0416-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 10/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alcohol consumption during pregnancy is a significant public health problem and can result in a continuum of adverse outcomes to the fetus known as fetal alcohol spectrum disorders (FASD). Subjects with FASD show significant neurological deficits, ranging from microencephaly, neurobehavioral, and mental health problems to poor social adjustment and stress tolerance. Neurons are particularly sensitive to alcohol exposure. The neurotoxic action of alcohol, i.e., through ROS production, induces DNA damage and neuronal cell death by apoptosis. In addition, epigenetics, including DNA methylation, histone posttranslational modifications (PTMs), and non-coding RNA, play an important role in the neuropathology of FASD. However, little is known about the temporal dynamics and kinetics of histones and their PTMs in FASD. RESULTS We examined the effects of postnatal alcohol exposure (PAE), an animal model of human third-trimester equivalent, on the kinetics of various histone proteins in two distinct brain regions, the frontal cortex, and the hypothalamus, using in vivo 2H2O-labeling combined with mass spectrometry-based proteomics. We show that histones have long half-lives that are in the order of days. We also show that H3.3 and H2Az histone variants have faster turnovers than canonical histones and that acetylated histones, in general, have a faster turnover than unmodified and methylated histones. Our work is the first to show that PAE induces a differential reduction in turnover rates of histones in both brain regions studied. These alterations in histone turnover were associated with increased DNA damage and decreased cell proliferation in postnatal rat brain. CONCLUSION Alterations in histone turnover might interfere with histone deposition and chromatin stability, resulting in deregulated cell-specific gene expression and therefore contribute to the development of the neurological disorders associated with FASD. Using in vivo 2H2O-labeling and mass spectrometry-based proteomics might help in the understanding of histone turnover following alcohol exposure and could be of great importance in enabling researchers to identify novel targets and/or biomarkers for the prevention and management of fetal alcohol spectrum disorders.
Collapse
Affiliation(s)
- Nadia Rachdaoui
- Department of Animal Sciences, Rutgers Endocrine Research Program, Rutgers, the State University of New Jersey, 67 Poultry Farm Lane, New Brunswick, NJ 08901 USA
| | - Ling Li
- Department of Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106 USA
| | - Belinda Willard
- Department of Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106 USA
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272 USA
| | - Stephen Previs
- Cardiometabolic Disease, Merck & Co., Inc, Kenilworth, NJ USA
| | - Dipak Sarkar
- Department of Animal Sciences, Rutgers Endocrine Research Program, Rutgers, the State University of New Jersey, 67 Poultry Farm Lane, New Brunswick, NJ 08901 USA
| |
Collapse
|
105
|
Khuong MT, Fei J, Cruz-Becerra G, Kadonaga JT. A simple and versatile system for the ATP-dependent assembly of chromatin. J Biol Chem 2017; 292:19478-19490. [PMID: 28982979 DOI: 10.1074/jbc.m117.815365] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/26/2017] [Indexed: 12/17/2022] Open
Abstract
Chromatin is the natural form of DNA in the eukaryotic nucleus and is the substrate for diverse biological phenomena. The functional analysis of these processes ideally would be carried out with nucleosomal templates that are assembled with customized core histones, DNA sequences, and chromosomal proteins. Here we report a simple, reliable, and versatile method for the ATP-dependent assembly of evenly spaced nucleosome arrays. This minimal chromatin assembly system comprises the Drosophila nucleoplasmin-like protein (dNLP) histone chaperone, the imitation switch (ISWI) ATP-driven motor protein, core histones, template DNA, and ATP. The dNLP and ISWI components were synthesized in bacteria, and each protein could be purified in a single step by affinity chromatography. We show that the dNLP-ISWI system can be used with different DNA sequences, linear or circular DNA, bulk genomic DNA, recombinant or native Drosophila core histones, native human histones, the linker histone H1, the non-histone chromosomal protein HMGN2, and the core histone variants H3.3 and H2A.V. The dNLP-ISWI system should be accessible to a wide range of researchers and enable the assembly of customized chromatin with specifically desired DNA sequences, core histones, and other chromosomal proteins.
Collapse
Affiliation(s)
- Mai T Khuong
- From the Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Jia Fei
- From the Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - Grisel Cruz-Becerra
- From the Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| | - James T Kadonaga
- From the Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093
| |
Collapse
|
106
|
Bayona-Feliu A, Casas-Lamesa A, Reina O, Bernués J, Azorín F. Linker histone H1 prevents R-loop accumulation and genome instability in heterochromatin. Nat Commun 2017; 8:283. [PMID: 28819201 PMCID: PMC5561251 DOI: 10.1038/s41467-017-00338-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/22/2017] [Indexed: 12/01/2022] Open
Abstract
Linker histone H1 is an important structural component of chromatin that stabilizes the nucleosome and compacts the nucleofilament into higher-order structures. The biology of histone H1 remains, however, poorly understood. Here we show that Drosophila histone H1 (dH1) prevents genome instability as indicated by the increased γH2Av (H2AvS137P) content and the high incidence of DNA breaks and sister-chromatid exchanges observed in dH1-depleted cells. Increased γH2Av occurs preferentially at heterochromatic elements, which are upregulated upon dH1 depletion, and is due to the abnormal accumulation of DNA:RNA hybrids (R-loops). R-loops accumulation is readily detectable in G1-phase, whereas γH2Av increases mainly during DNA replication. These defects induce JNK-mediated apoptosis and are specific of dH1 depletion since they are not observed when heterochromatin silencing is relieved by HP1a depletion. Altogether, our results suggest that histone H1 prevents R-loops-induced DNA damage in heterochromatin and unveil its essential contribution to maintenance of genome stability.While structural importance of linker histone H1 in packaging eukaryotic genome into chromatin is well known, its biological function remains poorly understood. Here the authors reveal that Drosophila linker histone H1 prevents DNA:RNA hybrids accumulation and genome instability in heterochromatin.
Collapse
Affiliation(s)
- Aleix Bayona-Feliu
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
| | - Anna Casas-Lamesa
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Oscar Reina
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Jordi Bernués
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain.
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.
| | - Fernando Azorín
- Institute of Molecular Biology of Barcelona, IBMB, CSIC, Baldiri Reixac, 4, 08028, Barcelona, Spain.
- Institute for Research in Biomedicine, IRB Barcelona, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.
| |
Collapse
|
107
|
Histone Acetylation, Not Stoichiometry, Regulates Linker Histone Binding in Saccharomyces cerevisiae. Genetics 2017; 207:347-355. [PMID: 28739661 DOI: 10.1534/genetics.117.1132] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/12/2017] [Indexed: 12/27/2022] Open
Abstract
Linker histones play a fundamental role in shaping chromatin structure, but how their interaction with chromatin is regulated is not well understood. In this study, we used a combination of genetic and genomic approaches to explore the regulation of linker histone binding in the yeast, Saccharomyces cerevisiae We found that increased expression of Hho1, the yeast linker histone, resulted in a severe growth defect, despite only subtle changes in chromatin structure. Further, this growth defect was rescued by mutations that increase histone acetylation. Consistent with this, genome-wide analysis of linker histone occupancy revealed an inverse correlation with histone tail acetylation in both yeast and mouse embryonic stem cells. Collectively, these results suggest that histone acetylation negatively regulates linker histone binding in S. cerevisiae and other organisms and provide important insight into how chromatin structure is regulated and maintained to both facilitate and repress transcription.
Collapse
|
108
|
Piñeiro-Hermida S, López IP, Alfaro-Arnedo E, Torrens R, Iñiguez M, Alvarez-Erviti L, Ruíz-Martínez C, Pichel JG. IGF1R deficiency attenuates acute inflammatory response in a bleomycin-induced lung injury mouse model. Sci Rep 2017; 7:4290. [PMID: 28655914 PMCID: PMC5487362 DOI: 10.1038/s41598-017-04561-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 05/17/2017] [Indexed: 01/13/2023] Open
Abstract
IGF1R (Insulin-like Growth Factor 1 Receptor) is a tyrosine kinase with pleiotropic cellular functions. IGF activity maintains human lung homeostasis and is implicated in pulmonary diseases such as cancer, ARDS, COPD, asthma and fibrosis. Here we report that lung transcriptome analysis in mice with a postnatally-induced Igf1r gene deletion showed differentially expressed genes with potentially protective roles related to epigenetics, redox and oxidative stress. After bleomycin-induced lung injury, IGF1R-deficient mice demonstrated improved survival within a week. Three days post injury, IGF1R-deficient lungs displayed changes in expression of IGF system-related genes and reduced vascular fragility and permeability. Mutant lungs presented reduced inflamed area, down-regulation of pro-inflammatory markers and up-regulation of resolution indicators. Decreased inflammatory cell presence in BALF was reflected in diminished lung infiltration mainly affecting neutrophils, also corroborated by reduced neutrophil numbers in bone marrow, as well as reduced lymphocyte and alveolar macrophage counts. Additionally, increased SFTPC expression together with hindered HIF1A expression and augmented levels of Gpx8 indicate that IGF1R deficiency protects against alveolar damage. These findings identify IGF1R as an important player in murine acute lung inflammation, suggesting that targeting IGF1R may counteract the inflammatory component of many lung diseases.
Collapse
Affiliation(s)
- Sergio Piñeiro-Hermida
- Lung Cancer and Respiratory Diseases Unit, Centro de Investigación Biomédica de La Rioja (CIBIR), Fundación Rioja Salud, Logroño, Spain
| | - Icíar P López
- Lung Cancer and Respiratory Diseases Unit, Centro de Investigación Biomédica de La Rioja (CIBIR), Fundación Rioja Salud, Logroño, Spain
| | - Elvira Alfaro-Arnedo
- Lung Cancer and Respiratory Diseases Unit, Centro de Investigación Biomédica de La Rioja (CIBIR), Fundación Rioja Salud, Logroño, Spain
| | - Raquel Torrens
- Lung Cancer and Respiratory Diseases Unit, Centro de Investigación Biomédica de La Rioja (CIBIR), Fundación Rioja Salud, Logroño, Spain
| | - María Iñiguez
- Genomics Core Facility, Centro de Investigación Biomédica de La Rioja (CIBIR), Fundación Rioja Salud, Logroño, Spain
| | - Lydia Alvarez-Erviti
- Molecular Neurobiology Unit, Centro de Investigación Biomédica de la Rioja (CIBIR), Fundación Rioja Salud, Logroño, Spain
| | | | - José G Pichel
- Lung Cancer and Respiratory Diseases Unit, Centro de Investigación Biomédica de La Rioja (CIBIR), Fundación Rioja Salud, Logroño, Spain.
| |
Collapse
|
109
|
Kowalski A, Knaga S. Evidence on the stability of histone H1.a polymorphic variants during selection in quail. Arch Anim Breed 2017. [DOI: 10.5194/aab-60-145-2017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The goal of this work was to check whether selection for quantitative traits may cause a change in the histone H1 allelic complement and whether it can therefore be considered a modulator of histone H1-dependent chromatin functioning. For this purpose, a fluctuation of histone H1.a polymorphic variants was analyzed among a non-selected (control) quail line and the line selected for a high cholesterol content in the egg yolk. The histone H1.a was found to be polymorphic due to its differential migration rate in the AU-PAGE (acetic acid–urea polyacrylamide gel electrophoresis). Based on this, two H1.a isoforms (H1.a1 and H1.a2) that form three phenotypes (a1, a2 and a1a2) were distinguished in the quail lines tested. A comparably expressed (p > 0. 05) and low relative variable (coefficient of variation, CV < 0. 25) histone H1.a phenotypes were in agreement with Hardy–Weinberg equilibrium (HWE) in both the non-selected (χ2 = 1. 29, p = 0. 25) and selected (χ2 = 1. 9, p = 0. 16) quail line. The similarity among quail lines was assessed based on the equal distribution of histone H1.a phenotypes (χ2 = 1. 63, p = 0. 44) and alleles (χ2 = 0. 018, p = 0. 89) frequency in both quail lines tested. This indicates that selection does not affect the histone H1.a polymorphic variants. The stability of histone H1.a during selection might suggest that likely chromatin processes coupled to the selected trait are not linked to the activity of histone H1.a.
Collapse
|
110
|
Wang Y, Jain N, Nagarajan M, Maharana S, Iyer KV, Talwar S, Shivashankar GV. Coupling between chromosome intermingling and gene regulation during cellular differentiation. Methods 2017; 123:66-75. [PMID: 28554525 DOI: 10.1016/j.ymeth.2017.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/04/2017] [Accepted: 05/24/2017] [Indexed: 11/19/2022] Open
Abstract
In this article, we summarize current findings for the emergence of biophysical properties such as nuclear stiffness, chromatin compaction, chromosome positioning, and chromosome intermingling during stem cell differentiation, which eventually correlated with the changes of gene expression profiles during cellular differentiation. An overview is first provided to link stem cell differentiation with alterations in nuclear architecture, chromatin compaction, along with nuclear and chromatin dynamics. Further, we highlight the recent biophysical and molecular approaches, imaging methods and computational developments in characterizing transcription-related chromosome organization especially chromosome intermingling and nano-scale chromosomal contacts. Finally, the article ends with an outlook towards the emergence of a functional roadmap in setting up chromosome positioning and intermingling in a cell type specific manner during cellular differentiation.
Collapse
Affiliation(s)
- Yejun Wang
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Nikhil Jain
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Mallika Nagarajan
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Shovamayee Maharana
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - K Venkatesan Iyer
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - Shefali Talwar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore
| | - G V Shivashankar
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, 117411 Singapore, Singapore; FIRC Institute for Molecular Oncology (IFOM), Milan 20139, Italy.
| |
Collapse
|
111
|
Vergara Z, Gutierrez C. Emerging roles of chromatin in the maintenance of genome organization and function in plants. Genome Biol 2017; 18:96. [PMID: 28535770 PMCID: PMC5440935 DOI: 10.1186/s13059-017-1236-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish boundaries between chromatin states and nuclear territories. Chromatin organization is crucial for genome replication, transcriptional silencing, and DNA repair and recombination. The replication machinery is relevant for the maintenance of chromatin states, influencing DNA replication origin specification and accessibility. Current studies reinforce the idea of intimate crosstalk between chromatin features and processes involving DNA transactions.
Collapse
Affiliation(s)
- Zaida Vergara
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain.
| |
Collapse
|
112
|
Liao R, Mizzen CA. Site-specific regulation of histone H1 phosphorylation in pluripotent cell differentiation. Epigenetics Chromatin 2017; 10:29. [PMID: 28539972 PMCID: PMC5440973 DOI: 10.1186/s13072-017-0135-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/11/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Structural variation among histone H1 variants confers distinct modes of chromatin binding that are important for differential regulation of chromatin condensation, gene expression and other processes. Changes in the expression and genomic distributions of H1 variants during cell differentiation appear to contribute to phenotypic differences between cell types, but few details are known about the roles of individual H1 variants and the significance of their disparate capacities for phosphorylation. In this study, we investigated the dynamics of interphase phosphorylation at specific sites in individual H1 variants during the differentiation of pluripotent NT2 and mouse embryonic stem cells and characterized the kinases involved in regulating specific H1 variant phosphorylations in NT2 and HeLa cells. RESULTS Here, we show that the global levels of phosphorylation at H1.5-Ser18 (pS18-H1.5), H1.2/H1.5-Ser173 (pS173-H1.2/5) and H1.4-Ser187 (pS187-H1.4) are regulated differentially during pluripotent cell differentiation. Enrichment of pS187-H1.4 near the transcription start site of pluripotency factor genes in pluripotent cells is markedly reduced upon differentiation, whereas pS187-H1.4 levels at housekeeping genes are largely unaltered. Selective inhibition of CDK7 or CDK9 rapidly diminishes pS187-H1.4 levels globally and its enrichment at housekeeping genes, and similar responses were observed following depletion of CDK9. These data suggest that H1.4-S187 is a bona fide substrate for CDK9, a notion that is further supported by the significant colocalization of CDK9 and pS187-H1.4 to gene promoters in reciprocal re-ChIP analyses. Moreover, treating cells with actinomycin D to inhibit transcription and trigger the release of active CDK9/P-TEFb from 7SK snRNA complexes induces the accumulation of pS187-H1.4 at promoters and gene bodies. Notably, the levels of pS187-H1.4 enrichment after actinomycin D treatment or cell differentiation reflect the extent of CDK9 recruitment at the same loci. Remarkably, the global levels of H1.5-S18 and H1.2/H1.5-S173 phosphorylation are not affected by these transcription inhibitor treatments, and selective inhibition of CDK2 does not affect the global levels of phosphorylation at H1.4-S187 or H1.5-S18. CONCLUSIONS Our data provide strong evidence that H1 variant interphase phosphorylation is dynamically regulated in a site-specific and gene-specific fashion during pluripotent cell differentiation, and that enrichment of pS187-H1.4 at genes is positively related to their transcription. H1.4-S187 is likely to be a direct target of CDK9 during interphase, suggesting the possibility that this particular phosphorylation may contribute to the release of paused RNA pol II. In contrast, the other H1 variant phosphorylations we investigated appear to be mediated by distinct kinases and further analyses are needed to determine their functional significance.
Collapse
Affiliation(s)
- Ruiqi Liao
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, B107 Chemistry and Life Sciences Building, MC-123 601 S. Goodwin Ave., Urbana, IL 61801 USA
| | - Craig A Mizzen
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, B107 Chemistry and Life Sciences Building, MC-123 601 S. Goodwin Ave., Urbana, IL 61801 USA.,Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801 USA
| |
Collapse
|
113
|
Kajitani K, Kato K, Nagata K. Histone H1 chaperone activity of TAF-I is regulated by its subtype-dependent intramolecular interaction. Genes Cells 2017; 22:334-347. [PMID: 28251751 DOI: 10.1111/gtc.12478] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 01/14/2017] [Indexed: 11/29/2022]
Abstract
Linker histone H1 is involved in the regulation of gene activity through the maintenance of higher-order chromatin structure. Previously, we have shown that template activating factor-I (TAF-I or protein SET) is involved in linker histone H1 dynamics as a histone H1 chaperone. In human and murine cells, two TAF-I subtypes exist, namely TAF-Iα and TAF-Iβ. TAF-I has a highly acidic amino acid cluster in its C-terminal region and forms homo- or heterodimers through its dimerization domain. Both dimer formation and the C-terminal region of TAF-I are essential for the histone chaperone activity. TAF-Iα exhibits less histone chaperone activity compared with TAF-Iβ even though TAF-Iα and β differ only in their N-terminal regions. However, it is unclear how subtype-specific TAF-I activities are regulated. Here, we have shown that the N-terminal region of TAF-Iα autoinhibits its histone chaperone activity via intramolecular interaction with its C-terminal region. When the interaction between the N- and C-terminal regions of TAF-Iα is disrupted, TAF-Iα shows a histone chaperone activity similar to that of TAF-Iβ. Taken together, these results provide mechanistic insights into the concept that fine tuning of TAF-I histone H1 chaperone activity relies on the subtype compositions of the TAF-I dimer.
Collapse
Affiliation(s)
- Kaori Kajitani
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.,University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Kohsuke Kato
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan.,University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| | - Kyosuke Nagata
- University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8575, Japan
| |
Collapse
|
114
|
Ponte I, Romero D, Yero D, Suau P, Roque A. Complex Evolutionary History of the Mammalian Histone H1.1-H1.5 Gene Family. Mol Biol Evol 2017; 34:545-558. [PMID: 28100789 PMCID: PMC5400378 DOI: 10.1093/molbev/msw241] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
H1 is involved in chromatin higher-order structure and gene regulation. H1 has a tripartite structure. The central domain is stably folded in solution, while the N- and C-terminal domains are intrinsically disordered. The terminal domains are encoded by DNA of low sequence complexity, and are thus prone to short insertions/deletions (indels). We have examined the evolution of the H1.1-H1.5 gene family from 27 mammalian species. Multiple sequence alignment has revealed a strong preferential conservation of the number and position of basic residues among paralogs, suggesting that overall H1 basicity is under a strong purifying selection. The presence of a conserved pattern of indels, ancestral to the splitting of mammalian orders, in the N- and C-terminal domains of the paralogs, suggests that slippage may have favored the rapid divergence of the subtypes and that purifying selection has maintained this pattern because it is associated with function. Evolutionary analyses have found evidences of positive selection events in H1.1, both before and after the radiation of mammalian orders. Positive selection ancestral to mammalian radiation involved changes at specific sites that may have contributed to the low relative affinity of H1.1 for chromatin. More recent episodes of positive selection were detected at codon positions encoding amino acids of the C-terminal domain of H1.1, which may modulate the folding of the CTD. The detection of putative recombination points in H1.1-H1.5 subtypes suggests that this process may has been involved in the acquisition of the tripartite H1 structure.
Collapse
Affiliation(s)
- Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Devani Romero
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Daniel Yero
- Instituto de Biotecnología y de Biomedicina (IBB) y Departamento de Genética y Microbiología, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| |
Collapse
|
115
|
Starkova TY, Polyanichko AM, Artamonova TO, Khodorkovskii MA, Kostyleva EI, Chikhirzhina EV, Tomilin AN. Post-translational modifications of linker histone H1 variants in mammals. Phys Biol 2017; 14:016005. [PMID: 28000612 DOI: 10.1088/1478-3975/aa551a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The covalent modifications of the linker histone H1 and the core histones are thought to play an important role in the control of chromatin functioning. Histone H1 variants from K562 cell line (hH1), mouse (mH1) and calf (cH1) thymi were studied by matrix-activated laser desorption/ionization fourier transform ion cyclotron resonance mass-spectroscopy (MALDI-FT-ICR-MS). The proteomics analysis revealed novel post-translational modifications of the histone H1, such as meK34-mH1.4, meK35-cH1.1, meK35-mH1.1, meK75-hH1.2, meK75-hH1.3, acK26-hH1.4, acK26-hH1.3 and acK17-hH1.1. The comparison of the hH1, mH1 and cH1 proteins has demonstrated that the types and positions of the post-translational modifications of the globular domains of the H1.2-H1.4 variants are very conservative. However, the post-translational modifications of the N- and C-terminal tails of H1.2, H1.3 and H1.4 are different. The differences of post-translational modifications in the N- and C-terminal tails of H1.2, H1.3 and H1.4 likely lead to the differences in DNA-H1 and H1-protein interactions.
Collapse
Affiliation(s)
- T Yu Starkova
- Institute of Cytology of the Russian Academy of Sciences, St Petersburg, Russia. Saint Petersburg State University, Saint Petersburg, Russia. Author to whom any correspondence should be addressed. The authors made equal contribution to preparation of the manuscript
| | | | | | | | | | | | | |
Collapse
|
116
|
Lyubitelev AV, Nikitin DV, Shaytan AK, Studitsky VM, Kirpichnikov MP. Structure and Functions of Linker Histones. BIOCHEMISTRY (MOSCOW) 2017; 81:213-23. [PMID: 27262190 DOI: 10.1134/s0006297916030032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Linker histones such as variants H1, H5, and other similar proteins play an important role in regulation of chromatin structure and dynamics. However, interactions of linker histones with DNA and proteins, as well as specific functions of their different variants, are poorly studied. This is because they acquire tertiary structure only when interacting with a nucleosome, and because of limitations of currently available methods. However, deeper investigation of linker histones and their interactions with other proteins will address a number of important questions - from structure of compacted chromatin to regulation of early embryogenesis. In this review, structures of histone H1 variants and its interaction with chromatin DNA are considered. A possible functional significance of different H1 variants, a role of these proteins in maintaining interphase chromatin structure, and interactions of linker histones with other cellular proteins are also discussed.
Collapse
Affiliation(s)
- A V Lyubitelev
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
| | | | | | | | | |
Collapse
|
117
|
Zhang P, Branson OE, Freitas MA, Parthun MR. Identification of replication-dependent and replication-independent linker histone complexes: Tpr specifically promotes replication-dependent linker histone stability. BMC BIOCHEMISTRY 2016; 17:18. [PMID: 27716023 PMCID: PMC5045598 DOI: 10.1186/s12858-016-0074-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 09/20/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND There are 11 variants of linker histone H1 in mammalian cells. Beyond their shared abilities to stabilize and condense chromatin, the H1 variants have been found to have non-redundant functions, the mechanisms of which are not fully understood. Like core histones, there are both replication-dependent and replication-independent linker histone variants. The histone chaperones and other factors that regulate linker histone dynamics in the cell are largely unknown. In particular, it is not known whether replication-dependent and replication-independent linker histones interact with distinct or common sets of proteins. To better understand linker histone dynamics and assembly, we used chromatography and mass spectrometry approaches to identify proteins that are associated with replication-dependent and replication-independent H1 variants. We then used a variety of in vivo analyses to validate the functional relevance of identified interactions. RESULTS We identified proteins that bind to all linker histone variants and proteins that are specific for only one class of variant. The factors identified include histone chaperones, transcriptional regulators, RNA binding proteins and ribosomal proteins. The nuclear pore complex protein Tpr, which was found to associate with only replication-dependent linker histones, specifically promoted their stability. CONCLUSION Replication-dependent and replication-independent linker histone variants can interact with both common and distinct sets of proteins. Some of these factors are likely to function as histone chaperones while others may suggest novel links between linker histones and RNA metabolism. The nuclear pore complex protein Tpr specifically interacts with histone H1.1 and H1.2 but not H1x and can regulate the stability of these replication-dependent linker histones.
Collapse
Affiliation(s)
- Pei Zhang
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210 USA
| | - Owen E. Branson
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210 USA
| | - Michael A. Freitas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210 USA
| | - Mark R. Parthun
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210 USA
| |
Collapse
|
118
|
Shen C, Li YJ, Yin QQ, Jiao WW, Li QJ, Xiao J, Sun L, Xu F, Li JQ, Qi H, Shen AD. Identification of differentially expressed transcripts targeted by the knockdown of endogenous IFITM3. Mol Med Rep 2016; 14:4367-4373. [PMID: 27667301 DOI: 10.3892/mmr.2016.5777] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 08/24/2016] [Indexed: 11/05/2022] Open
Abstract
Interferon inducible transmembrane protein 3 (IFITM3) is a double transmembrane protein. As a member of the IFITM family, IFITM3 can be upregulated by interferon (IFN) to be involved in various biological processes. In order to determine whether gene expression profiles can be altered by a lack of IFITM3, the present study used shRNAs lentivirus for knocking down the endogenous expression of IFITM3 in human HeLa cells and human whole genome microarrays to obtain gene expression profiles. A total of 1,011 downregulated transcripts and 615 upregulated transcripts were identified using the Agilent expression platform. The identified transcripts were involved in multiple pathways, including the complement pathways, and the antigen processing and presentation pathway. The present study identified the transcripts, which were affected by the downregulation of endogenous IFITM3 and the pathways they were involved in. These findings may lead to an improved understanding of the biological functions of IFITM3.
Collapse
Affiliation(s)
- Chen Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| | - Ying-Jia Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| | - Qing-Qin Yin
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| | - Wei-Wei Jiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| | - Qin-Jing Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| | - Jing Xiao
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| | - Lin Sun
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| | - Fang Xu
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| | - Jie-Qiong Li
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| | - Hui Qi
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| | - A-Dong Shen
- Key Laboratory of Major Diseases in Children, Ministry of Education, National Key Discipline of Pediatrics, National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing 100045, P.R. China
| |
Collapse
|
119
|
Segalés J, Perdiguero E, Muñoz-Cánoves P. Regulation of Muscle Stem Cell Functions: A Focus on the p38 MAPK Signaling Pathway. Front Cell Dev Biol 2016; 4:91. [PMID: 27626031 PMCID: PMC5003838 DOI: 10.3389/fcell.2016.00091] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/17/2016] [Indexed: 12/17/2022] Open
Abstract
Formation of skeletal muscle fibers (myogenesis) during development and after tissue injury in the adult constitutes an excellent paradigm to investigate the mechanisms whereby environmental cues control gene expression programs in muscle stem cells (satellite cells) by acting on transcriptional and epigenetic effectors. Here we will review the molecular mechanisms implicated in the transition of satellite cells throughout the distinct myogenic stages (i.e., activation from quiescence, proliferation, differentiation, and self-renewal). We will also discuss recent findings on the causes underlying satellite cell functional decline with aging. In particular, our review will focus on the epigenetic changes underlying fate decisions and on how the p38 MAPK signaling pathway integrates the environmental signals at the chromatin to build up satellite cell adaptive responses during the process of muscle regeneration, and how these responses are altered in aging. A better comprehension of the signaling pathways connecting external and intrinsic factors will illuminate the path for improving muscle regeneration in the aged.
Collapse
Affiliation(s)
- Jessica Segalés
- Cell Biology Group, Department of Experimental and Health Sciences, CIBER on Neurodegenerative diseases (CIBERNED), Pompeu Fabra University Barcelona, Spain
| | - Eusebio Perdiguero
- Cell Biology Group, Department of Experimental and Health Sciences, CIBER on Neurodegenerative diseases (CIBERNED), Pompeu Fabra University Barcelona, Spain
| | - Pura Muñoz-Cánoves
- Cell Biology Group, Department of Experimental and Health Sciences, CIBER on Neurodegenerative diseases (CIBERNED), Pompeu Fabra UniversityBarcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA)Barcelona, Spain; Tissue Regeneration Laboratory, Centro Nacional de Investigaciones CardiovascularesMadrid, Spain
| |
Collapse
|
120
|
Kowalski A, Pałyga J. Modulation of chromatin function through linker histone H1 variants. Biol Cell 2016; 108:339-356. [PMID: 27412812 DOI: 10.1111/boc.201600007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 07/08/2016] [Accepted: 07/08/2016] [Indexed: 12/30/2022]
Abstract
In this review, the structural aspects of linker H1 histones are presented as a background for characterization of the factors influencing their function in animal and human chromatin. The action of H1 histone variants is largely determined by dynamic alterations of their intrinsically disordered tail domains, posttranslational modifications and allelic diversification. The interdependent effects of these factors can establish dynamic histone H1 states that may affect the organization and function of chromatin regions.
Collapse
Affiliation(s)
- Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
| | - Jan Pałyga
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, 25-406 Kielce, Poland
| |
Collapse
|
121
|
Kowalski A. Nuclear and nucleolar activity of linker histone variant H1.0. Cell Mol Biol Lett 2016; 21:15. [PMID: 28536618 PMCID: PMC5414669 DOI: 10.1186/s11658-016-0014-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/28/2016] [Indexed: 12/31/2022] Open
Abstract
Histone H1.0 belongs to the class of linker histones (H1), although it is substantially distinct from other histone H1 family members. The differences can be observed in the chromosomal location and organization of the histone H1.0 encoding gene, as well as in the length and composition of its amino acid chain. Whereas somatic (H1.1-H1.5) histone H1 variants are synthesized in the cell cycle S-phase, histone H1.0 is synthesized throughout the cell cycle. By replacing somatic H1 variants during cell maturation, histone H1.0 is gradually deposited in low dividing cells and achieves the highest level of expression in the terminally differentiated cells. Compared to other differentiation-specific H1 histone (H5) characteristic for unique tissue and organisms, the distribution of histone H1.0 remains non-specific. Classic investigations emphasize that histone H1.0 is engaged in the organization of nuclear chromatin accounting for formation and maintenance of its nucleosomal and higher-order structure, and thus influences gene expression. However, the recent data confirmed histone H1.0 peculiar localization in the nucleolus and unexpectedly revealed its potential for regulation of nucleolar, RNA-dependent, activity via interaction with other proteins. According to such findings, histone H1.0 participates in the formation of gene-coded information through its control at both transcriptional and translational levels. In order to reappraise the biological significance of histone H1.0, both aspects of its activity are presented in this review.
Collapse
Affiliation(s)
- Andrzej Kowalski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, Świętokrzyska 15, 25-406 Kielce, Poland
| |
Collapse
|
122
|
Muller S, Radic M. Citrullinated Autoantigens: From Diagnostic Markers to Pathogenetic Mechanisms. Clin Rev Allergy Immunol 2016; 49:232-9. [PMID: 25355199 DOI: 10.1007/s12016-014-8459-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The conversion of an arginine residue in a protein to a citrulline residue, a reaction carried out by enzymes called peptidylarginine deiminases (PADs), is rather subtle. One of the terminal imide groups in arginine is replaced by oxygen in citrulline, thus resulting in the loss of positive charge and the gain of 1 dalton. This post-translational modification by PAD enzymes is conserved in vertebrates and affects specific substrates during development and in various mature cell lineages. Citrullination offers a unique perspective on autoimmunity because PAD activity is stringently regulated, yet autoantibodies to citrullinated proteins predictably arise. Autoantigens recognized by anti-citrullinated protein antibodies (ACPA) include extracellular proteins such as filaggrin, collagen II, fibrinogen, and calreticulin; membrane-associated proteins such as myelin basic protein; cytoplasmic proteins such as vimentin and enolase; and even nuclear proteins such as histones. Some ACPA are remarkably effective as diagnostics in autoimmune disorders, most notably rheumatoid arthritis (RA). Several ACPA can be observed before other clinical RA manifestations are apparent. In patients with RA, ACPA may attain a sensitivity that exceeds 70 % and specificity that approaches 96-98 %. The biological context that may account for the induction of ACPA emerges from studies of the cellular response of the innate immune system to acute or chronic stimuli. In response to infections or inflammation, neutrophil granulocytes activate PAD, citrullinate multiple autoantigens, and expel chromatin from the cell. The externalized chromatin is called a neutrophil extracellular "trap" (NET). Citrullination of core and linker histones occurs prior to the release of chromatin from neutrophils, thus implicating the regulation of citrullinated chromatin release in the development of autoreactivity. The citrullination of extracellular autoantigens likely follows the release of NETs and associated PADs. Autoantibodies to citrullinated histones arise in RA, systemic lupus erythematosus, and Felty's syndrome patients. The citrullination of linker histone H1 may play a key role in NET release because the H1 histone regulates the entry and exit of DNA from the nucleosome. Juxtaposition of citrullinated histones with infectious pathogens and complement and immune complexes may compromise tolerance of nuclear autoantigens and promote autoimmunity.
Collapse
Affiliation(s)
- Sylviane Muller
- Immunopathology and Therapeutic Chemistry/Laboratory of Excellence MEDALIS, CNRS, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | - Marko Radic
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA.
| |
Collapse
|
123
|
Yu S, Yang F, Shen WH. Genome maintenance in the context of 4D chromatin condensation. Cell Mol Life Sci 2016; 73:3137-50. [PMID: 27098512 PMCID: PMC4956502 DOI: 10.1007/s00018-016-2221-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/07/2016] [Indexed: 12/20/2022]
Abstract
The eukaryotic genome is packaged in the three-dimensional nuclear space by forming loops, domains, and compartments in a hierarchical manner. However, when duplicated genomes prepare for segregation, mitotic cells eliminate topologically associating domains and abandon the compartmentalized structure. Alongside chromatin architecture reorganization during the transition from interphase to mitosis, cells halt most DNA-templated processes such as transcription and repair. The intrinsically condensed chromatin serves as a sophisticated signaling module subjected to selective relaxation for programmed genomic activities. To understand the elaborate genome-epigenome interplay during cell cycle progression, the steady three-dimensional genome requires a time scale to form a dynamic four-dimensional and a more comprehensive portrait. In this review, we will dissect the functions of critical chromatin architectural components in constructing and maintaining an orderly packaged chromatin environment. We will also highlight the importance of the spatially and temporally conscious orchestration of chromatin remodeling to ensure high-fidelity genetic transmission.
Collapse
Affiliation(s)
- Sonia Yu
- Department of Radiation Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY, 10065, USA
| | - Fan Yang
- Department of Radiation Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY, 10065, USA
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Wen H Shen
- Department of Radiation Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY, 10065, USA.
| |
Collapse
|
124
|
Cutter AR, Hayes JJ. Linker histones: novel insights into structure-specific recognition of the nucleosome. Biochem Cell Biol 2016; 95:171-178. [PMID: 28177778 DOI: 10.1139/bcb-2016-0097] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Linker histones (H1s) are a primary component of metazoan chromatin, fulfilling numerous functions, both in vitro and in vivo, including stabilizing the wrapping of DNA around the nucleosome, promoting folding and assembly of higher order chromatin structures, influencing nucleosome spacing on DNA, and regulating specific gene expression. However, many molecular details of how H1 binds to nucleosomes and recognizes unique structural features on the nucleosome surface remain undefined. Numerous, confounding studies are complicated not only by experimental limitations, but the use of different linker histone isoforms and nucleosome constructions. This review summarizes the decades of research that has resulted in several models of H1 association with nucleosomes, with a focus on recent advances that suggest multiple modes of H1 interaction in chromatin, while highlighting the remaining questions.
Collapse
Affiliation(s)
- Amber R Cutter
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jeffrey J Hayes
- Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.,Department of Biochemistry & Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| |
Collapse
|
125
|
Staneva D, Georgieva M, Miloshev G. Kluyveromyces lactis genome harbours a functional linker histone encoding gene. FEMS Yeast Res 2016; 16:fow034. [PMID: 27189369 DOI: 10.1093/femsyr/fow034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2016] [Indexed: 11/14/2022] Open
Abstract
Linker histones are essential components of chromatin in eukaryotes. Through interactions with linker DNA and nucleosomes they facilitate folding and maintenance of higher-order chromatin structures and thus delicately modulate gene activity. The necessity of linker histones in lower eukaryotes appears controversial and dubious. Genomic data have shown that Schizosaccharomyces pombe does not possess genes encoding linker histones while Kluyveromyces lactis has been reported to have a pseudogene. Regarding this controversy, we have provided the first direct experimental evidence for the existence of a functional linker histone gene, KlLH1, in K. lactis genome. Sequencing of KlLH1 from both genomic DNA and copy DNA confirmed the presence of an intact open reading frame. Transcription and splicing of the KlLH1 sequence as well as translation of its mRNA have been studied. In silico analysis revealed homology of KlLH1p to the histone H1/H5 protein family with predicted three domain structure characteristic for the linker histones of higher eukaryotes. This strongly proves that the yeast K. lactis does indeed possess a functional linker histone gene thus entailing the evolutionary preservation and significance of linker histones. The nucleotide sequences of KlLH1 are deposited in the GenBank under accession numbers KT826576, KT826577 and KT826578.
Collapse
Affiliation(s)
- Dessislava Staneva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - Milena Georgieva
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| | - George Miloshev
- Laboratory of Yeast Molecular Genetics, Institute of Molecular Biology, Bulgarian Academy of Sciences, 'Acad. Roumen Tsanev', Sofia 1113, Bulgaria
| |
Collapse
|
126
|
Kavi H, Emelyanov AV, Fyodorov DV, Skoultchi AI. Independent Biological and Biochemical Functions for Individual Structural Domains of Drosophila Linker Histone H1. J Biol Chem 2016; 291:15143-55. [PMID: 27226620 DOI: 10.1074/jbc.m116.730705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Indexed: 12/20/2022] Open
Abstract
Linker histone H1 is among the most abundant components of chromatin. H1 has profound effects on chromosome architecture. H1 also helps to tether DNA- and histone-modifying enzymes to chromatin. Metazoan linker histones have a conserved tripartite structure comprising N-terminal, globular, and long, unstructured C-terminal domains. Here we utilize truncated Drosophila H1 polypeptides in vitro and H1 mutant transgenes in vivo to interrogate the roles of these domains in multiple biochemical and biological activities of H1. We demonstrate that the globular domain and the proximal part of the C-terminal domain are essential for H1 deposition into chromosomes and for the stability of H1-chromatin binding. The two domains are also essential for fly viability and the establishment of a normal polytene chromosome structure. Additionally, through interaction with the heterochromatin-specific histone H3 Lys-9 methyltransferase Su(var)3-9, the H1 C-terminal domain makes important contributions to formation and H3K9 methylation of heterochromatin as well as silencing of transposons in heterochromatin. Surprisingly, the N-terminal domain does not appear to be required for any of these functions. However, it is involved in the formation of a single chromocenter in polytene chromosomes. In summary, we have discovered that linker histone H1, similar to core histones, exerts its multiple biological functions through independent, biochemically separable activities of its individual structural domains.
Collapse
Affiliation(s)
- Harsh Kavi
- From the Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Alexander V Emelyanov
- From the Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Dmitry V Fyodorov
- From the Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Arthur I Skoultchi
- From the Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| |
Collapse
|
127
|
Abstract
H1T is a linker histone H1 variant that is highly expressed at the primary spermatocyte stage through to the early spermatid stage of spermatogenesis. While the functions of the somatic types of H1 have been extensively investigated, the intracellular role of H1T is unclear. H1 variants specifically expressed in germ cells show low amino acid sequence homology to somatic H1s, which suggests that the functions or target loci of germ cell-specific H1T differ from those of somatic H1s. Here, we describe the target loci and function of H1T. H1T was expressed not only in the testis but also in tumor cell lines, mouse embryonic stem cells (mESCs), and some normal somatic cells. To elucidate the intracellular localization and target loci of H1T, fluorescent immunostaining and ChIP-seq were performed in tumor cells and mESCs. We found that H1T accumulated in nucleoli and predominantly targeted rDNA repeats, which differ from somatic H1 targets. Furthermore, by nuclease sensitivity assay and RT-qPCR, we showed that H1T repressed rDNA transcription by condensing chromatin structure. Imaging analysis indicated that H1T expression affected nucleolar formation. We concluded that H1T plays a role in rDNA transcription, by distinctively targeting rDNA repeats.
Collapse
Affiliation(s)
- Ruiko Tani
- a Department of Animal Resource Sciences/Veterinary Medical Sciences , The University of Tokyo , Bunkyo-ku, Tokyo , Japan
| | - Koji Hayakawa
- a Department of Animal Resource Sciences/Veterinary Medical Sciences , The University of Tokyo , Bunkyo-ku, Tokyo , Japan
| | - Satoshi Tanaka
- a Department of Animal Resource Sciences/Veterinary Medical Sciences , The University of Tokyo , Bunkyo-ku, Tokyo , Japan
| | - Kunio Shiota
- a Department of Animal Resource Sciences/Veterinary Medical Sciences , The University of Tokyo , Bunkyo-ku, Tokyo , Japan
| |
Collapse
|
128
|
Turinetto V, Giachino C. Histone variants as emerging regulators of embryonic stem cell identity. Epigenetics 2016; 10:563-73. [PMID: 26114724 DOI: 10.1080/15592294.2015.1053682] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Dynamic regulation of chromatin structure is an important mechanism for balancing the pluripotency and cell fate decision in embryonic stem cells (ESCs). Indeed ESCs are characterized by unusual chromatin packaging, and a wide variety of chromatin regulators have been implicated in control of pluripotency and differentiation. Genome-wide maps of epigenetic factors have revealed a unique epigenetic signature in pluripotent ESCs and have contributed models to explain their plasticity. In addition to the well known epigenetic regulation through DNA methylation, histone posttranslational modifications, chromatin remodeling, and non-coding RNA, histone variants are emerging as important regulators of ESC identity. In this review, we summarize and discuss the recent progress that has highlighted the central role of histone variants in ESC pluripotency and ESC fate, focusing, in particular, on H1 variants, H2A variants H2A.X, H2A.Z and macroH2A and H3 variant H3.3.
Collapse
Affiliation(s)
- Valentina Turinetto
- a Department of Clinical and Biological Sciences; University of Turin ; Orbassano , Turin , Italy
| | | |
Collapse
|
129
|
Kalashnikova AA, Rogge RA, Hansen JC. Linker histone H1 and protein-protein interactions. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:455-61. [PMID: 26455956 PMCID: PMC4775371 DOI: 10.1016/j.bbagrm.2015.10.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 09/21/2015] [Accepted: 10/05/2015] [Indexed: 01/11/2023]
Abstract
Linker histones H1 are ubiquitous chromatin proteins that play important roles in chromatin compaction, transcription regulation, nucleosome spacing and chromosome spacing. H1 function in DNA and chromatin structure stabilization is well studied and established. The current paradigm of linker histone mode of function considers all other cellular roles of linker histones to be a consequence from H1 chromatin compaction and repression. Here we review the multiple processes regulated by linker histones and the emerging importance of protein interactions in H1 functioning. We propose a new paradigm which explains the multi functionality of linker histones through linker histones protein interactions as a way to directly regulate recruitment of proteins to chromatin.
Collapse
Affiliation(s)
- Anna A Kalashnikova
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Ryan A Rogge
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA.
| |
Collapse
|
130
|
Millán-Ariño L, Izquierdo-Bouldstridge A, Jordan A. Specificities and genomic distribution of somatic mammalian histone H1 subtypes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:510-9. [DOI: 10.1016/j.bbagrm.2015.10.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 11/15/2022]
|
131
|
Yang H, Yang N, Wang T. Proteomic analysis reveals the differential histone programs between male germline cells and vegetative cells in Lilium davidii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:660-674. [PMID: 26846354 DOI: 10.1111/tpj.13133] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/12/2016] [Accepted: 01/25/2016] [Indexed: 06/05/2023]
Abstract
In flowering plants, male germline fate is determined after asymmetric division of the haploid microspore. Daughter cells have distinct fates: the generative cell (GC) undergoes further mitosis to generate sperm cells (SCs), and the vegetative cell (VC) terminally differentiates. However, our understanding of the mechanisms underlying germline development remains limited. Histone variants and modifications define chromatin states, and contribute to establishing and maintaining cell identities by affecting gene expression. Here, we constructed a lily protein database, then extracted and detailed histone entries into a comprehensive lily histone database. We isolated large amounts of nuclei from VCs, GCs and SCs from lily, and profiled histone variants of all five histone families in all three cell types using proteomics approaches. We revealed 92 identities representing 32 histone variants: six for H1, 11 for H2A, eight for H2B, five for H3 and two for H4. Nine variants, including five H1, two H2B, one H3 and one H4 variant, specifically accumulated in GCs and SCs. We also detected H3 modification patterns in the three cell types. GCs and SCs had almost identical histone profiles and similar H3 modification patterns, which were significantly different from those of VCs. Our study also revealed the presence of multiple isoforms, and differential expression patterns between isoforms of a variant. The results suggest that differential histone programs between the germline and companion VCs may be established following the asymmetric division, and are important for identity establishment and differentiation of the male germline as well as the VC.
Collapse
Affiliation(s)
- Hao Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| |
Collapse
|
132
|
Flanagan TW, Files JK, Casano KR, George EM, Brown DT. Photobleaching studies reveal that a single amino acid polymorphism is responsible for the differential binding affinities of linker histone subtypes H1.1 and H1.5. Biol Open 2016; 5:372-80. [PMID: 26912777 PMCID: PMC4810752 DOI: 10.1242/bio.016733] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Mammals express six major somatic linker histone subtypes, all of which display dynamic binding to chromatin, characterized by transient binding at a given location followed by rapid translocation to a new site. Using photobleaching techniques, we systematically measured the exchange rate of all six mouse H1 subtypes to determine their relative chromatin-binding affinity. Two subtypes, H1.1 and H1.2, display binding affinities that are significantly lower than all other subtypes. Using in vitro mutagenesis, the differences in chromatin-binding affinities between H1.1 (lower binding affinity) and H1.5 (higher binding affinity) were mapped to a single amino acid polymorphism near the junction of the globular and C-terminal domains. Overexpression of H1.5 in density arrested fibroblasts did not affect cell cycle progression after release. By contrast, overexpression of H1.1 resulted in a more rapid progression through G1/S relative to control cells. These results provide structural insights into the proposed functional significance of linker histone heterogeneity. Summary: Mouse linker histone subtypes H1.1 and H1.5 bind to chromatin with different affinities due to a single amino acid polymorphism. Overexpression of H1.1 in fibroblasts accelerates cell cycle progression.
Collapse
Affiliation(s)
- Thomas W Flanagan
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jacob K Files
- Clinton High School, Clinton, MS 39056, USA Spring Hill College, Mobile, AL 36608, USA
| | | | - Eric M George
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA Department of Physiology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - David T Brown
- Department of Biochemistry, University of Mississippi Medical Center, Jackson, MS 39216, USA
| |
Collapse
|
133
|
Kunworarath N, Rangkadilok N, Suriyo T, Thiantanawat A, Satayavivad J. Longan (Dimocarpus longan Lour.) inhibits lipopolysaccharide-stimulated nitric oxide production in macrophages by suppressing NF-κB and AP-1 signaling pathways. JOURNAL OF ETHNOPHARMACOLOGY 2016; 179:156-61. [PMID: 26721218 DOI: 10.1016/j.jep.2015.12.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/27/2015] [Accepted: 12/21/2015] [Indexed: 05/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Flower, seed, and fruit of longan (Dimocarpus longan Lour.) have been used in the Traditional Chinese Medicine (TCM) serving as a common herb in relief of swelling which can be applied in cases of inflammatory diseases. However, the scientific evidence related to their effects on inflammation especially the possible cellular and molecular mechanisms of longan need to be clarified. AIM OF THE STUDY To evaluate the anti-inflammatory effect of the various parts of longan including flower, seed, and pulp. The mechanisms and molecular targets involved in their effects were also investigated. MATERIALS AND METHODS Different longan extracts were analyzed for their bioactive compounds and evaluated for anti-inflammation. Corilagin, ellagic acid, and gallic acid were detected using HPLC-DAD. In vitro anti-inflammatory effect of longan extracts and their polysaccharides were examined by analyzing nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages. Expression of the proteins that involved in NO production was detected by Western blot. RESULTS Flower extract contained the highest amounts of total phenolics, total flavonoids, proanthocyanidins, corilagin and ellagic acid when compared to seed and pulp extracts. The extracts of different longan parts inhibited LPS-induced NO production with different potency. The highest potency for the inhibition of NO production was shown with flower extract follow by seed and pulp (IC50=128.2, 1127.4, and 1260.2μgmL(-1), respectively). The mechanisms of this anti-NO production were associated with their NO scavenging effect and their decreasing the expression and catalytic activity of an inducible nitric oxide synthase (iNOS). Moreover, these longan extracts suppressed LPS-induced degradation of IκBα and activation of NF-κB, activator protein-1 (AP-1), Akt, and mitogen activated protein kinases (MAPKs). CONCLUSION These results suggest that the longan extracts possess anti-inflammatory property. Therefore, longan could provide potential dietary supplement for the treatment of inflammatory-related diseases.
Collapse
Affiliation(s)
- Nongluk Kunworarath
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand
| | - Nuchanart Rangkadilok
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Environmental Toxicology Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Education, Bangkok 10400, Thailand
| | - Tawit Suriyo
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok 10210, Thailand
| | - Apinya Thiantanawat
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Applied Biological Sciences Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Education, Bangkok 10400, Thailand
| | - Jutamaad Satayavivad
- Laboratory of Pharmacology, Chulabhorn Research Institute, Bangkok 10210, Thailand; Environmental Toxicology Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand; Center of Excellence on Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Education, Bangkok 10400, Thailand.
| |
Collapse
|
134
|
de Abreu da Silva IC, Carneiro VC, Vicentino ARR, Aguilera EA, Mohana-Borges R, Thiengo S, Fernandez MA, Fantappié MR. The distinct C-terminal acidic domains of HMGB proteins are functionally relevant in Schistosoma mansoni. Int J Parasitol 2016; 46:253-62. [PMID: 26820302 DOI: 10.1016/j.ijpara.2015.12.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Revised: 12/08/2015] [Accepted: 12/10/2015] [Indexed: 11/17/2022]
Abstract
The Schistosoma mansoni High Mobility Group Box (HMGB) proteins SmHMGB1, SmHMGB2 and SmHMGB3 share highly conserved HMG box DNA binding domains but have significantly different C-terminal acidic tails. Here, we used three full-length and tailless forms of the S. mansoni HMGB proteins to examine the functional roles of their acidic tails. DNA binding assays revealed that the different lengths of the acidic tails among the three SmHMGB proteins significantly and distinctively influenced their DNA transactions. Spectroscopic analyses indicated that the longest acidic tail of SmHMGB3 contributes to the structural stabilisation of this protein. Using immunohistochemical analysis, we showed distinct patterns of SmHMGB1, SmHMGB2 and SmHMGB3 expression in different tissues of adult worms. RNA interference approaches indicated a role for SmHMGB2 and SmHMGB3 in the reproductive system of female worms, whereas for SmHMGB1 no clear phenotype was observed. Schistosome HMGB proteins can be phosphorylated, acetylated and methylated. Importantly, the acetylation and methylation of schistosome HMGBs were greatly enhanced upon removal of the acidic tail. These data support the notion that the C-terminal acidic tails dictate the differences in the structure, expression and function of schistosome HMGB proteins.
Collapse
Affiliation(s)
- Isabel Caetano de Abreu da Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Brazil
| | - Vitor Coutinho Carneiro
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Brazil
| | - Amanda Roberta Revoredo Vicentino
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Brazil
| | | | - Ronaldo Mohana-Borges
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Brazil
| | - Silvana Thiengo
- Laboratório de Malacologia, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Brazil
| | | | - Marcelo Rosado Fantappié
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Universidade Federal do Rio de Janeiro, Brazil.
| |
Collapse
|
135
|
Machida S, Hayashida R, Takaku M, Fukuto A, Sun J, Kinomura A, Tashiro S, Kurumizaka H. Relaxed Chromatin Formation and Weak Suppression of Homologous Pairing by the Testis-Specific Linker Histone H1T. Biochemistry 2016; 55:637-46. [DOI: 10.1021/acs.biochem.5b01126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shinichi Machida
- Laboratory
of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Ryota Hayashida
- Laboratory
of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Motoki Takaku
- Laboratory
of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Atsuhiko Fukuto
- Department
of Cellular Biology, Research Institute for Radiation Biology and
Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Jiying Sun
- Department
of Cellular Biology, Research Institute for Radiation Biology and
Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Aiko Kinomura
- Department
of Cellular Biology, Research Institute for Radiation Biology and
Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Satoshi Tashiro
- Department
of Cellular Biology, Research Institute for Radiation Biology and
Medicine, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Hitoshi Kurumizaka
- Laboratory
of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
- Institute
for Medical-oriented Structural Biology, Waseda University, 2-2
Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| |
Collapse
|
136
|
Stützer A, Liokatis S, Kiesel A, Schwarzer D, Sprangers R, Söding J, Selenko P, Fischle W. Modulations of DNA Contacts by Linker Histones and Post-translational Modifications Determine the Mobility and Modifiability of Nucleosomal H3 Tails. Mol Cell 2016; 61:247-59. [PMID: 26778125 DOI: 10.1016/j.molcel.2015.12.015] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 09/23/2015] [Accepted: 12/03/2015] [Indexed: 10/22/2022]
Abstract
Post-translational histone modifications and linker histone incorporation regulate chromatin structure and genome activity. How these systems interface on a molecular level is unclear. Using biochemistry and NMR spectroscopy, we deduced mechanistic insights into the modification behavior of N-terminal histone H3 tails in different nucleosomal contexts. We find that linker histones generally inhibit modifications of different H3 sites and reduce H3 tail dynamics in nucleosomes. These effects are caused by modulations of electrostatic interactions of H3 tails with linker DNA and largely depend on the C-terminal domains of linker histones. In agreement, linker histone occupancy and H3 tail modifications segregate on a genome-wide level. Charge-modulating modifications such as phosphorylation and acetylation weaken transient H3 tail-linker DNA interactions, increase H3 tail dynamics, and, concomitantly, enhance general modifiability. We propose that alterations of H3 tail-linker DNA interactions by linker histones and charge-modulating modifications execute basal control mechanisms of chromatin function.
Collapse
Affiliation(s)
- Alexandra Stützer
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stamatios Liokatis
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Rössle Strasse 10, 13125 Berlin, Germany
| | - Anja Kiesel
- Research Group of Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Dirk Schwarzer
- Department of Chemical Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Rössle Strasse 10, 13125 Berlin, Germany
| | - Remco Sprangers
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Johannes Söding
- Research Group of Computational Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Gene Center and Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Philipp Selenko
- Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Rössle Strasse 10, 13125 Berlin, Germany.
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| |
Collapse
|
137
|
Hollar D. Epigenetic Significance of Chromatin Organization During Cellular Aging and Organismal Lifespan. EPIGENETICS, THE ENVIRONMENT, AND CHILDREN’S HEALTH ACROSS LIFESPANS 2016. [PMCID: PMC7153164 DOI: 10.1007/978-3-319-25325-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David Hollar
- Pfeiffer University, Morrisville, North Carolina USA
| |
Collapse
|
138
|
A dual affinity-tag strategy for the expression and purification of human linker histone H1.4 in Escherichia coli. Protein Expr Purif 2015; 120:160-8. [PMID: 26739785 DOI: 10.1016/j.pep.2015.12.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 12/24/2015] [Indexed: 11/22/2022]
Abstract
Linker histones are an abundant and critical component of the eukaryotic chromatin landscape. They play key roles in regulating the higher order structure of chromatin and many genetic processes. Higher eukaryotes possess a number of different linker histone subtypes and new data are consistently emerging that indicate these subtypes are functionally distinct. We were interested in studying one of the most abundant human linker histone subtypes, H1.4. We have produced recombinant full-length H1.4 in Escherichia coli. An N-terminal Glutathione-S-Transferase tag was used to promote soluble expression and was combined with a C-terminal hexahistidine tag to facilitate a simple non-denaturing two-step affinity chromatography procedure that results in highly pure full-length H1.4. The purified H1.4 was shown to be functional via in vitro chromatin assembly experiments and remains active after extended storage at -80 °C.
Collapse
|
139
|
Geeven G, Zhu Y, Kim BJ, Bartholdy BA, Yang SM, Macfarlan TS, Gifford WD, Pfaff SL, Verstegen MJAM, Pinto H, Vermunt MW, Creyghton MP, Wijchers PJ, Stamatoyannopoulos JA, Skoultchi AI, de Laat W. Local compartment changes and regulatory landscape alterations in histone H1-depleted cells. Genome Biol 2015; 16:289. [PMID: 26700097 PMCID: PMC4699363 DOI: 10.1186/s13059-015-0857-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 12/09/2015] [Indexed: 12/27/2022] Open
Abstract
Background Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticipated to play a role in higher-order genome structure. Here we have used a combination of genome-wide approaches including DNA methylation, histone modification and DNase I hypersensitivity profiling as well as Hi-C to investigate the impact of reduced cellular levels of histone H1 in embryonic stem cells on chromatin folding and function. Results We find that depletion of histone H1 changes the epigenetic signature of thousands of potential regulatory sites across the genome. Many of them show cooperative loss or gain of multiple chromatin marks. Epigenetic alterations cluster to gene-dense topologically associating domains (TADs) that already showed a high density of corresponding chromatin features. Genome organization at the three-dimensional level is largely intact, but we find changes in the structural segmentation of chromosomes specifically for the epigenetically most modified TADs. Conclusions Our data show that cells require normal histone H1 levels to expose their proper regulatory landscape. Reducing the levels of histone H1 results in massive epigenetic changes and altered topological organization particularly at the most active chromosomal domains. Changes in TAD configuration coincide with epigenetic landscape changes but not with transcriptional output changes, supporting the emerging concept that transcriptional control and nuclear positioning of TADs are not causally related but independently controlled by the locally associated trans-acting factors. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0857-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Geert Geeven
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
| | - Yun Zhu
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
| | - Byung Ju Kim
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
| | - Seung-Min Yang
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
| | - Todd S Macfarlan
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, 20892, USA.
| | - Wesley D Gifford
- Gene Expression Laboratory and the Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines, La Jolla, CA, 92037, USA.
| | - Samuel L Pfaff
- Gene Expression Laboratory and the Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines, La Jolla, CA, 92037, USA.
| | - Marjon J A M Verstegen
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
| | - Hugo Pinto
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Marit W Vermunt
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
| | - Menno P Creyghton
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
| | - Patrick J Wijchers
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
| | - John A Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA. .,Department of Medicine, Division of Oncology, University of Washington, Seattle, WA, 98195, USA.
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
| | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584, CT, Utrecht, The Netherlands.
| |
Collapse
|
140
|
Pan C, Fan Y. Role of H1 linker histones in mammalian development and stem cell differentiation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:496-509. [PMID: 26689747 DOI: 10.1016/j.bbagrm.2015.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/09/2015] [Accepted: 12/09/2015] [Indexed: 12/19/2022]
Abstract
H1 linker histones are key chromatin architectural proteins facilitating the formation of higher order chromatin structures. The H1 family constitutes the most heterogeneous group of histone proteins, with eleven non-allelic H1 variants in mammals. H1 variants differ in their biochemical properties and exhibit significant sequence divergence from one another, yet most of them are highly conserved during evolution from mouse to human. H1 variants are differentially regulated during development and their cellular compositions undergo dramatic changes in embryogenesis, gametogenesis, tissue maturation and cellular differentiation. As a group, H1 histones are essential for mouse development and proper stem cell differentiation. Here we summarize our current knowledge on the expression and functions of H1 variants in mammalian development and stem cell differentiation. Their diversity, sequence conservation, complex expression and distinct functions suggest that H1s mediate chromatin reprogramming and contribute to the large variations and complexity of chromatin structure and gene expression in the mammalian genome.
Collapse
Affiliation(s)
- Chenyi Pan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Yuhong Fan
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA; The Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| |
Collapse
|
141
|
Linker histone H1 and H3K56 acetylation are antagonistic regulators of nucleosome dynamics. Nat Commun 2015; 6:10152. [PMID: 26648124 PMCID: PMC4682114 DOI: 10.1038/ncomms10152] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 11/08/2015] [Indexed: 11/17/2022] Open
Abstract
H1 linker histones are highly abundant proteins that compact nucleosomes and chromatin to regulate DNA accessibility and transcription. However, the mechanisms that target H1 regulation to specific regions of eukaryotic genomes are unknown. Here we report fluorescence measurements of human H1 regulation of nucleosome dynamics and transcription factor (TF) binding within nucleosomes. H1 does not block TF binding, instead it suppresses nucleosome unwrapping to reduce DNA accessibility within H1-bound nucleosomes. We then investigated H1 regulation by H3K56 and H3K122 acetylation, two transcriptional activating histone post translational modifications (PTMs). Only H3K56 acetylation, which increases nucleosome unwrapping, abolishes H1.0 reduction of TF binding. These findings show that nucleosomes remain dynamic, while H1 is bound and H1 dissociation is not required for TF binding within the nucleosome. Furthermore, our H3K56 acetylation measurements suggest that a single-histone PTM can define regions of the genome that are not regulated by H1. The linker histone H1 is highly abundant and regulates DNA accessibility by compacting chromatin. Here the authors analyze transcription factor binding to nucleosomes and show that histone H1 suppresses unwrapping but does not directly block the binding of transcription factors.
Collapse
|
142
|
Patil H, Wilks C, Gonzalez RW, Dhanireddy S, Conrad-Webb H, Bergel M. Mitotic Activation of a Novel Histone Deacetylase 3-Linker Histone H1.3 Protein Complex by Protein Kinase CK2. J Biol Chem 2015; 291:3158-72. [PMID: 26663086 PMCID: PMC4751364 DOI: 10.1074/jbc.m115.643874] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Indexed: 11/06/2022] Open
Abstract
Histone deacetylase 3 (HDAC3) and linker histone H1 are involved in both chromatin compaction and the regulation of mitotic progression. However, the mechanisms by which HDAC3 and H1 regulate mitosis and the factors controlling HDAC3 and H1 activity during mitosis are unclear. Furthermore, as of now, no association between class I, II, or IV (non-sirtuin) HDACs and linker histones has been reported. Here we describe a novel HDAC3-H1.3 complex containing silencing mediator of retinoic acid and thyroid hormone receptor (SMRT) and nuclear receptor corepressor 1 (N-CoR) that accumulated in synchronized HeLa cells in late G2 phase and mitosis. Nonetheless, the deacetylation activity by HDAC3 in the complex was evident only in mitotic complexes. HDAC3 associated with H1.3 was highly phosphorylated on Ser-424 only during mitosis. Isolation of inactive HDAC3-H1.3 complexes from late G2 phase cells, and phosphorylation of HDAC3 in the complexes at serine 424 by protein kinase CK2 (also known as casein kinase 2) activated the HDAC3 in vitro. In vivo, CK2α and CK2α' double knockdown cells demonstrated a significant decrease in HDAC3 Ser-424 phosphorylation during mitosis. HDAC3 and H1.3 co-localized in between the chromosomes, with polar microtubules and spindle poles during metaphase through telophase, and partially co-localized with chromatin during prophase and interphase. H1 has been reported previously to associate with microtubules and, therefore, could potentially function in targeting HDAC3 to the microtubules. We suggest that phosphorylation of HDAC3 in the complex by CK2 during mitosis activates the complex for a dual role: compaction of the mitotic chromatin and regulation of polar microtubules dynamic instability.
Collapse
Affiliation(s)
- Hemangi Patil
- From the Department of Biology, Texas Woman's University, Denton, Texas 76204
| | - Carrie Wilks
- From the Department of Biology, Texas Woman's University, Denton, Texas 76204
| | - Rhiannon W Gonzalez
- From the Department of Biology, Texas Woman's University, Denton, Texas 76204
| | - Sudheer Dhanireddy
- From the Department of Biology, Texas Woman's University, Denton, Texas 76204
| | - Heather Conrad-Webb
- From the Department of Biology, Texas Woman's University, Denton, Texas 76204
| | - Michael Bergel
- From the Department of Biology, Texas Woman's University, Denton, Texas 76204
| |
Collapse
|
143
|
Liao R, Mizzen CA. Interphase H1 phosphorylation: Regulation and functions in chromatin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:476-85. [PMID: 26657617 DOI: 10.1016/j.bbagrm.2015.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/25/2022]
Abstract
Many metazoan cell types differentially express multiple non-allelic amino acid sequence variants of histone H1. Although early work revealed that H1 variants, collectively, are phosphorylated during interphase and mitosis, differences between individual H1 variants in the sites they possess for mitotic and interphase phosphorylation have been elucidated only relatively recently. Here, we review current knowledge on the regulation and function of interphase H1 phosphorylation, with a particular emphasis on how differences in interphase phosphorylation among the H1 variants of mammalian cells may enable them to have differential effects on transcription and other chromatin processes.
Collapse
Affiliation(s)
- Ruiqi Liao
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA
| | - Craig A Mizzen
- Department of Cell and Developmental Biology, University of Illinois at Urbana Champaign, USA; Institute for Genomic Biology, University of Illinois at Urbana Champaign, USA.
| |
Collapse
|
144
|
Abstract
Base Excision Repair (BER) is a conserved, intracellular DNA repair system that recognizes and removes chemically modified bases to insure genomic integrity and prevent mutagenesis. Aberrant BER has been tightly linked with a broad spectrum of human pathologies, such as several types of cancer, neurological degeneration, developmental abnormalities, immune dysfunction and aging. In the cell, BER must recognize and remove DNA lesions from the tightly condensed, protein-coated chromatin. Because chromatin is necessarily refractory to DNA metabolic processes, like transcription and replication, the compaction of the genomic material is also inhibitory to the repair systems necessary for its upkeep. Multiple ATP-dependent chromatin remodelling (ACR) complexes play essential roles in modulating the protein-DNA interactions within chromatin, regulating transcription and promoting activities of some DNA repair systems, including double-strand break repair and nucleotide excision repair. However, it remains unclear how BER operates in the context of chromatin, and if the chromatin remodelling processes that govern transcription and replication also actively regulate the efficiency of BER. In this review we highlight the emerging role of ACR in regulation of BER.
Collapse
Affiliation(s)
- John M Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA.
| | - Wioletta Czaja
- Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
| |
Collapse
|
145
|
Kim JM, Kim K, Punj V, Liang G, Ulmer TS, Lu W, An W. Linker histone H1.2 establishes chromatin compaction and gene silencing through recognition of H3K27me3. Sci Rep 2015; 5:16714. [PMID: 26581166 PMCID: PMC4652225 DOI: 10.1038/srep16714] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/19/2015] [Indexed: 12/21/2022] Open
Abstract
Linker histone H1 is a protein component of chromatin and has been linked to higher-order chromatin compaction and global gene silencing. However, a growing body of evidence suggests that H1 plays a gene-specific role, regulating a relatively small number of genes. Here we show that H1.2, one of the H1 subtypes, is overexpressed in cancer cells and contributes to gene silencing. H1.2 gets recruited to distinct chromatin regions in a manner dependent on EZH2-mediated H3K27me3, and inhibits transcription of multiple growth suppressive genes via modulation of chromatin architecture. The C-terminal tail of H1.2 is critical for the observed effects, because mutations of three H1.2-specific amino acids in this domain abrogate the ability of H1.2 to bind H3K27me3 nucleosomes and inactivate target genes. Collectively, these results provide a molecular explanation for H1.2 functions in the regulation of chromatin folding and indicate that H3K27me3 is a key mechanism governing the recruitment and activity of H1.2 at target loci.
Collapse
Affiliation(s)
- Jin-Man Kim
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Kyunghwan Kim
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.,Department of Biology, College of Natural Sciences, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea
| | - Vasu Punj
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA.,Department of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tobias S Ulmer
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Wange Lu
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, CA 90033, USA
| | - Woojin An
- Department of Biochemistry and Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| |
Collapse
|
146
|
Gaume X, Torres-Padilla ME. Regulation of Reprogramming and Cellular Plasticity through Histone Exchange and Histone Variant Incorporation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:165-175. [PMID: 26582788 DOI: 10.1101/sqb.2015.80.027458] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Early embryonic cells are totipotent and can generate a complete organism including embryonic and extraembryonic tissues. After division, cells lose their potency as they move toward a pluripotent state characterized by decreased cellular plasticity. During this transition, drastic changes in transcriptional programs occur in parallel with global chromatin reorganization. The epigenetic mechanisms governing the changes in chromatin signatures during the transitions of cellular plasticity states are starting to be understood. Among these mechanisms, recent studies highlight the importance of histone variant incorporation and/or eviction from chromatin in the regulation of the chromatin state that is linked to cellular potential. In this review, we discuss the role of histone variants during in vivo and in vitro reprogramming events. These results sustain the hypothesis that histone variants and histone exchange are key actors in the establishment of cellular plasticity programs.
Collapse
Affiliation(s)
- Xavier Gaume
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, U de S, F-67404 Illkirch, CU de Strasbourg, France
| | - Maria-Elena Torres-Padilla
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, U de S, F-67404 Illkirch, CU de Strasbourg, France
| |
Collapse
|
147
|
NPM1 histone chaperone is upregulated in glioblastoma to promote cell survival and maintain nucleolar shape. Sci Rep 2015; 5:16495. [PMID: 26559910 PMCID: PMC4642306 DOI: 10.1038/srep16495] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 10/14/2015] [Indexed: 01/08/2023] Open
Abstract
Glioblastoma (grade IV glioma) is the most common and aggressive adult brain tumor. A better understanding of the biology of glioblastoma cells is crucial to identify molecular targets stimulating cell death. NPM1 (nucleophosmin) is a multifunctional chaperone that plays an important role in cancer development. Herein, NPM1 was analyzed by immunohistochemistry in human astrocytic gliomas. NPM1 was detected in all tumors but with a significantly higher staining intensity in grade IV than in low grade tumors. Depletion of NPM1 had only modest effects on the viability of U251MG, U1242MG, and U343MGa Cl2:6 glioma cells, despite alterations in nucleolar morphology. Glioma cell cultures depleted of NPM1 exposed to micromolar levels of actinomycin D were more prone to cell death (apoptosis) compared to cultures retaining NPM1. We had previously found that NPM1 binds to linker histone H1.5. Here we could show that silencing of H1.5 triggered glioma cell apoptosis as evidenced by a marked increase in both the numbers of cleaved caspase-3+ cells and in the amounts of cleaved PARP. Enforced expression of NPM1 suppressed apoptosis in H1.5 depleted glioma cells. Although our studies would suggest little effectiveness of targeting NPM1 alone there could be potential using it as a combination treatment.
Collapse
|
148
|
Yu ZC, Huang YF, Shieh SY. Requirement for human Mps1/TTK in oxidative DNA damage repair and cell survival through MDM2 phosphorylation. Nucleic Acids Res 2015; 44:1133-50. [PMID: 26531827 PMCID: PMC4756815 DOI: 10.1093/nar/gkv1173] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/21/2015] [Indexed: 01/25/2023] Open
Abstract
Human Mps1 (hMps1) is a protein kinase essential for mitotic checkpoints and the DNA damage response. Here, we present new evidence that hMps1 also participates in the repair of oxidative DNA lesions and cell survival through the MDM2-H2B axis. In response to oxidative stress, hMps1 phosphorylates MDM2, which in turn promotes histone H2B ubiquitination and chromatin decompaction. These events facilitate oxidative DNA damage repair and ATR-CHK1, but not ATM-CHK2 signaling. Depletion of hMps1 or MDM2 compromised H2B ubiquitination, DNA repair and cell survival. The impairment could be rescued by re-expression of WT but not the phospho-deficient MDM2 mutant, supporting the involvement of hMps1-dependent MDM2 phosphorylation in the oxidative stress response. In line with these findings, localization of RPA and base excision repair proteins to damage foci also requires MDM2 and hMps1. Significantly, like MDM2, hMps1 is upregulated in human sarcoma, suggesting high hMps1 and MDM2 expression may be beneficial for tumors constantly challenged by an oxidative micro-environment. Our study therefore identified an hMps1-MDM2-H2B signaling axis that likely plays a relevant role in tumor progression.
Collapse
Affiliation(s)
- Zheng-Cheng Yu
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, No 1, Sec. 1, Jen-Ai Road, Taipei 100, Taiwan Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Road, Taipei 115, Taiwan
| | - Yi-Fu Huang
- Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Road, Taipei 115, Taiwan
| | - Sheau-Yann Shieh
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, No 1, Sec. 1, Jen-Ai Road, Taipei 100, Taiwan Institute of Biomedical Sciences, Academia Sinica, 128 Sec. 2, Academia Road, Taipei 115, Taiwan
| |
Collapse
|
149
|
Gandhi D, Tarale P, Naoghare PK, Bafana A, Krishnamurthi K, Arrigo P, Saravanadevi S. An integrated genomic and proteomic approach to identify signatures of endosulfan exposure in hepatocellular carcinoma cells. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2015; 125:8-16. [PMID: 26615145 DOI: 10.1016/j.pestbp.2015.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/16/2015] [Accepted: 06/19/2015] [Indexed: 06/05/2023]
Abstract
Present study reports the identification of genomic and proteomic signatures of endosulfan exposure in hepatocellular carcinoma cells (HepG2). HepG2 cells were exposed to sublethal concentration (15μM) of endosulfan for 24h. DNA microarray and MALDI-TOF-MS analyses revealed that endosulfan induced significant alterations in the expression level of genes and proteins involved in multiple cellular pathways (apoptosis, transcription, immune/inflammatory response, carbohydrate metabolism, etc.). Furthermore, downregulation of PHLDA gene, upregulation of ACIN1 protein and caspase-3 activation in exposed cells indicated that endosulfan can trigger apoptotic cascade in hepatocellular carcinoma cells. In total 135 transcripts and 19 proteins were differentially expressed. This study presents an integrated approach to identify the alteration of biological/cellular pathways in HepG2 cells upon endosulfan exposure.
Collapse
Affiliation(s)
- Deepa Gandhi
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Prashant Tarale
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Pravin K Naoghare
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Amit Bafana
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | - Kannan Krishnamurthi
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
| | | | - Sivanesan Saravanadevi
- Environmental Health Division, CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.
| |
Collapse
|
150
|
The Role of Extracellular Vesicles: An Epigenetic View of the Cancer Microenvironment. BIOMED RESEARCH INTERNATIONAL 2015; 2015:649161. [PMID: 26582468 PMCID: PMC4637039 DOI: 10.1155/2015/649161] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/14/2015] [Accepted: 07/21/2015] [Indexed: 01/16/2023]
Abstract
Exosomes, microvesicles, and other extracellular vesicles are released by many cell types, including cancer cells and cancer-related immune cells. Extracellular vesicles can directly or indirectly facilitate the transfer of bioinformation to recipient cells or to the extracellular environment. In cancer, exosomes have been implicated in tumor initiation, proliferation, and metastasis. Extracellular vesicles can transmit proteins and nucleic acids that participate in DNA methylation, histone modification, and posttranscriptional regulation of RNA. Factors transmitted by extracellular vesicles reflect the donor cell status, and extracellular vesicles derived from tumor cells may be also responsible for altering expression of tumor promoting and tumor suppressing genes in recipient cells. Thus, circulating extracellular vesicles may act as biomarkers of cancer, and detection of these biomarkers may be applied to diagnosis or assessment of prognosis in patients with cancer.
Collapse
|