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Rouhiainen A, Zhao X, Vanttola P, Qian K, Kulesskiy E, Kuja-Panula J, Gransalke K, Grönholm M, Unni E, Meistrich M, Tian L, Auvinen P, Rauvala H. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. Sci Rep 2016; 6:32960. [PMID: 27608812 PMCID: PMC5036535 DOI: 10.1038/srep32960] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 08/18/2016] [Indexed: 12/21/2022] Open
Abstract
HMGB4 is a new member in the family of HMGB proteins that has been characterized in sperm cells, but little is known about its functions in somatic cells. Here we show that HMGB4 and the highly similar rat Transition Protein 4 (HMGB4L1) are expressed in neuronal cells. Both proteins had slow mobility in nucleus of living NIH-3T3 cells. They interacted with histones and their differential expression in transformed cells of the nervous system altered the post-translational modification statuses of histones in vitro. Overexpression of HMGB4 in HEK 293T cells made cells more susceptible to cell death induced by topoisomerase inhibitors in an oncology drug screening array and altered variant composition of histone H3. HMGB4 regulated over 800 genes in HEK 293T cells with a p-value ≤0.013 (n = 3) in a microarray analysis and displayed strongest association with adhesion and histone H2A –processes. In neuronal and transformed cells HMGB4 regulated the expression of an oligodendrocyte marker gene PPP1R14a and other neuronal differentiation marker genes. In conclusion, our data suggests that HMGB4 is a factor that regulates chromatin and expression of neuronal differentiation markers.
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Affiliation(s)
- Ari Rouhiainen
- Neuroscience center, University of Helsinki, Finland.,Department of Biosciences, University of Helsinki, Finland
| | - Xiang Zhao
- Neuroscience center, University of Helsinki, Finland.,Schools of Pharmacy and Medicine, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | | | - Kui Qian
- Institute of Biotechnology, University of Helsinki, Finland
| | - Evgeny Kulesskiy
- Neuroscience center, University of Helsinki, Finland.,Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland
| | | | | | | | - Emmanual Unni
- Department of Biochemistry, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marvin Meistrich
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Li Tian
- Neuroscience center, University of Helsinki, Finland.,Psychiatry Research Center, Beijing Hui Long Guan Hospital, Peking University, Beijing, China
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Finland
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Facilitated Dissociation of a Nucleoid Protein from the Bacterial Chromosome. J Bacteriol 2016; 198:1735-42. [PMID: 27044624 DOI: 10.1128/jb.00225-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/29/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Off-rates of proteins from the DNA double helix are widely considered to be dependent only on the interactions inside the initially bound protein-DNA complex and not on the concentration of nearby molecules. However, a number of recent single-DNA experiments have shown off-rates that depend on solution protein concentration, or "facilitated dissociation." Here, we demonstrate that this effect occurs for the major Escherichia coli nucleoid protein Fis on isolated bacterial chromosomes. We isolated E. coli nucleoids and showed that dissociation of green fluorescent protein (GFP)-Fis is controlled by solution Fis concentration and exhibits an "exchange" rate constant (kexch) of ≈10(4) M(-1) s(-1), comparable to the rate observed in single-DNA experiments. We also show that this effect is strongly salt dependent. Our results establish that facilitated dissociation can be observed in vitro on chromosomes assembled in vivo IMPORTANCE Bacteria are important model systems for the study of gene regulation and chromosome dynamics, both of which fundamentally depend on the kinetics of binding and unbinding of proteins to DNA. In experiments on isolated E. coli chromosomes, this study showed that the prolific transcription factor and chromosome packaging protein Fis displays a strong dependence of its off-rate from the bacterial chromosome on Fis concentration, similar to that observed in in vitro experiments. Therefore, the free cellular DNA-binding protein concentration can strongly affect lifetimes of proteins bound to the chromosome and must be taken into account in quantitative considerations of gene regulation. These results have particularly profound implications for transcription factors where DNA binding lifetimes can be a critical determinant of regulatory function.
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Scovell WM. High mobility group protein 1: A collaborator in nucleosome dynamics and estrogen-responsive gene expression. World J Biol Chem 2016; 7:206-222. [PMID: 27247709 PMCID: PMC4877529 DOI: 10.4331/wjbc.v7.i2.206] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 02/19/2016] [Accepted: 03/14/2016] [Indexed: 02/05/2023] Open
Abstract
High mobility group protein 1 (HMGB1) is a multifunctional protein that interacts with DNA and chromatin to influence the regulation of transcription, DNA replication and repair and recombination. We show that HMGB1 alters the structure and stability of the canonical nucleosome (N) in a nonenzymatic, adenosine triphosphate-independent manner. As a result, the canonical nucleosome is converted to two stable, physically distinct nucleosome conformers. Although estrogen receptor (ER) does not bind to its consensus estrogen response element within a nucleosome, HMGB1 restructures the nucleosome to facilitate strong ER binding. The isolated HMGB1-restructured nucleosomes (N’ and N’’) remain stable and exhibit a number of characteristics that are distinctly different from the canonical nucleosome. These findings complement previous studies that showed (1) HMGB1 stimulates in vivo transcriptional activation at estrogen response elements and (2) knock down of HMGB1 expression by siRNA precipitously reduced transcriptional activation. The findings indicate that a major facet of the mechanism of HMGB1 action involves a restructuring of aspects of the nucleosome that appear to relax structural constraints within the nucleosome. The findings are extended to reveal the differences between ER and the other steroid hormone receptors. A working proposal outlines mechanisms that highlight the multiple facets that HMGB1 may utilize in restructuring the nucleosome.
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54
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Zeng Z, Jiang J. Isolation and Proteomics Analysis of Barley Centromeric Chromatin Using PICh. J Proteome Res 2016; 15:1875-82. [DOI: 10.1021/acs.jproteome.6b00063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Zixian Zeng
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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Zhang J, Klufas D, Manalo K, Adjepong K, Davidson JO, Wassink G, Bennet L, Gunn AJ, Stopa EG, Liu K, Nishibori M, Stonestreet BS. HMGB1 Translocation After Ischemia in the Ovine Fetal Brain. J Neuropathol Exp Neurol 2016; 75:527-38. [PMID: 27151753 DOI: 10.1093/jnen/nlw030] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Inflammation contributes to the evolution of hypoxic-ischemic (HI) brain injury. High-mobility group box-1 (HMGB1) is a nuclear protein that is translocated from the nucleus and released after ischemia in adult rodents and thereby initiates inflammatory responses. However, there is very little information regarding the effects of HI on HMGB1 in immature brains. To investigate the effects of HI on HMGB1 in the term-equivalent fetal brain, ovine fetuses at 127 days gestation were studied after 30 minutes of carotid occlusion. Groups were sham-control and ischemia with 48 hours and ischemia with 72 hours of reperfusion. By immunohistochemistry, HMGB1 was found to be localized primarily in cell nuclei and partially in cytoplasmic compartments in the cerebral cortex of controls. Ischemia increased the area fraction of neuronal cells with cytoplasmic HMGB1 staining, and Western immunoblot revealed that cytosolic HMGB1 expression increased after ischemia (p < 0.05) and decreased in nuclei in ischemic versus the sham-control brains (p < 0.05). These data indicate that HMGB1 translocates from the nuclear to cytosolic compartments after ischemic brain injury in fetal sheep. This translocation may enable the action of HMGB1 as a proinflammatory cytokine that contributes to HI injury in the developing brain.
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Affiliation(s)
- Jiyong Zhang
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Daniel Klufas
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Karina Manalo
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Kwame Adjepong
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Joanne O Davidson
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Guido Wassink
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Laura Bennet
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Alistair J Gunn
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Edward G Stopa
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Keyue Liu
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Masahiro Nishibori
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN)
| | - Barbara S Stonestreet
- From the Department of Pediatrics, The Alpert Medical School of Brown University, Women & Infants Hospital of Rhode Island, Providence, Rhode Island (JZ, DK, KM, KA, BSS); Department of Physiology, University of Auckland, Auckland, New Zealand (JOD, GW, LB, AJG); Department of Pathology and Neurosurgery, The Alpert Medical School of Brown University, Rhode Island Hospital, Providence, Rhode Island (EGS); and Dentistry and Pharmaceutical Sciences, Graduate School of Medicine, Okayama University, Okayama, Japan (KL, MN).
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56
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Roque A, Ponte I, Suau P. Post-translational modifications of the intrinsically disordered terminal domains of histone H1: effects on secondary structure and chromatin dynamics. Chromosoma 2016; 126:83-91. [DOI: 10.1007/s00412-016-0591-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 01/14/2023]
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Panday A, Grove A. The high mobility group protein HMO1 functions as a linker histone in yeast. Epigenetics Chromatin 2016; 9:13. [PMID: 27030801 PMCID: PMC4812653 DOI: 10.1186/s13072-016-0062-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/16/2016] [Indexed: 12/18/2022] Open
Abstract
Background Eukaryotic chromatin consists of nucleosome core particles connected by linker DNA of variable length. Histone H1 associates with the linker DNA to stabilize the higher-order chromatin structure and to modulate the ability of regulatory factors to access their nucleosomal targets. In Saccharomyces cerevisiae, the protein with greatest sequence similarity to H1 is Hho1p. However, during vegetative growth, hho1∆ cells do not show any discernible cell growth defects or the changes in bulk chromatin structure that are characteristic of chromatin from multicellular eukaryotes in which H1 is depleted. In contrast, the yeast high mobility group (HMGB) protein HMO1 has been reported to compact chromatin, as evidenced by increased nuclease sensitivity in hmo1∆ cells. HMO1 has an unusual domain architecture compared to vertebrate HMGB proteins in that the HMG domains are followed by a lysine-rich extension instead of an acidic domain. We address here the hypothesis that HMO1 serves the role of H1 in terms of chromatin compaction and that this function requires the lysine-rich extension. Results We show here that HMO1 fulfills this function of a linker histone. For histone H1, chromatin compaction requires its basic C-terminal domain, and we find that the same pertains to HMO1, as deletion of its C-terminal lysine-rich extension renders chromatin nuclease sensitive. On rDNA, deletion of both HMO1 and Hho1p is required for significantly increased nuclease sensitivity. Expression of human histone H1 completely reverses the nuclease sensitivity characteristic of chromatin isolated from hmo1∆ cells. While chromatin remodeling events associated with repair of DNA double-strand breaks occur faster in the more dynamic chromatin environment created by the hmo1 deletion, expression of human histone H1 results in chromatin remodeling and double-strand break repair similar to that observed in wild-type cells. Conclusion Our data suggest that S. cerevisiae HMO1 protects linker DNA from nuclease digestion, a property also characteristic of mammalian linker histone H1. Notably, association with HMO1 creates a less dynamic chromatin environment that depends on its lysine-rich domain. That HMO1 has linker histone function has implications for investigations of chromatin structure and function as well as for evolution of proteins with roles in chromatin compaction.
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Affiliation(s)
- Arvind Panday
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA
| | - Anne Grove
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 USA
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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.
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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
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Weber DJ, Allette YM, Wilkes DS, White FA. The HMGB1-RAGE Inflammatory Pathway: Implications for Brain Injury-Induced Pulmonary Dysfunction. Antioxid Redox Signal 2015; 23:1316-28. [PMID: 25751601 PMCID: PMC4685484 DOI: 10.1089/ars.2015.6299] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
SIGNIFICANCE Deceased patients who have suffered severe traumatic brain injury (TBI) are the largest source of organs for lung transplantation. However, due to severely compromised pulmonary lung function, only one-third of these patients are eligible organ donors, with far fewer capable of donating lungs (∼ 20%). As a result of this organ scarcity, understanding and controlling the pulmonary pathophysiology of potential donors are key to improving the health and long-term success of transplanted lungs. RECENT ADVANCES Although the exact mechanism by which TBI produces pulmonary pathophysiology remains unclear, it may be related to the release of damage-associated molecular patterns (DAMPs) from the injured tissue. These heterogeneous, endogenous host molecules can be rapidly released from damaged or dying cells and mediate sterile inflammation following trauma. In this review, we highlight the interaction of the DAMP, high-mobility group box protein 1 (HMGB1) with the receptor for advanced glycation end-products (RAGE), and toll-like receptor 4 (TLR4). CRITICAL ISSUES Recently published studies are reviewed, implicating the release of HMGB1 as producing marked changes in pulmonary inflammation and physiology following trauma, followed by an overview of the experimental evidence demonstrating the benefits of blocking the HMGB1-RAGE axis. FUTURE DIRECTIONS Targeting the HMGB1 signaling axis may increase the number of lungs available for transplantation and improve long-term benefits for organ recipient patient outcomes.
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Affiliation(s)
- Daniel J Weber
- 1 Center for Immunobiology, Indiana University School of Medicine , Indianapolis, Indiana.,2 Department of Surgery, Indiana University School of Medicine , Indianapolis, Indiana
| | - Yohance M Allette
- 3 Department of Anatomy and Cell Biology, Indiana University School of Medicine , Indianapolis, Indiana
| | - David S Wilkes
- 1 Center for Immunobiology, Indiana University School of Medicine , Indianapolis, Indiana.,4 Department of Medicine, Microbiology and Immunology, Indiana University School of Medicine , Indianapolis, Indiana
| | - Fletcher A White
- 1 Center for Immunobiology, Indiana University School of Medicine , Indianapolis, Indiana.,5 Department of Anesthesia, Indiana University School of Medicine , Indianapolis, Indiana
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HMGB1 Promotes Hepatitis C Virus Replication by Interaction with Stem-Loop 4 in the Viral 5' Untranslated Region. J Virol 2015; 90:2332-44. [PMID: 26656705 DOI: 10.1128/jvi.02795-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/04/2015] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED High-mobility group box 1 (HMGB1) protein is a highly conserved nuclear protein involved in multiple human diseases, including infectious diseases, immune disorders, metabolic disorders, and cancer. HMGB1 is comprised of two tandem HMG boxes (the A box and the B box) containing DNA-binding domains and an acidic C-terminal peptide. It has been reported that HMGB1 enhances viral replication by binding to viral proteins. However, its role in hepatitis C virus (HCV) replication is unknown. Here, we show that HMGB1 promoted HCV replication but had no effect on HCV translation. RNA immunoprecipitation experiments indicated that the positive strand, not the negative strand, of HCV RNA interacted with HMGB1. HCV infection triggered HMGB1 protein translocation from the nucleus to the cytoplasm, in which it interacted with the HCV genome. Moreover, the A box of HMGB1 is the pivotal domain to interact with stem-loop 4 (SL4) of the HCV 5' untranslated region. Deletion of the HMGB1 A box abrogated the enhancement of HCV replication by HMGB1. Our data suggested that HMGB1 serves as a proviral factor of HCV to facilitate viral replication in hepatocytes by interaction with the HCV genome. IMPORTANCE Hepatitis C virus (HCV) is a major global health threat, affecting more than 170 million people infection worldwide. These patients are at high risk of developing severe liver diseases such as chronic hepatitis, cirrhosis, and hepatocellular carcinoma. Currently, no vaccine is available. Many host factors may be implicated in the pathogenesis of HCV-related diseases. In this study, we found a novel HCV RNA-binding protein, HMGB1, that promotes HCV RNA replication. Moreover, SL4 in the 5' untranslated region of the HCV genome is the key region for HMGB1 binding, and the A box of HMGB1 protein is the functional domain to interact with HCV RNA and enhance viral replication. HMGB1 appears to play an important role in HCV-related diseases, and further investigation is warranted to elucidate the specific actions of HMGB1 in HCV pathogenesis.
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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.
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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.
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Rutowicz K, Puzio M, Halibart-Puzio J, Lirski M, Kotliński M, Kroteń MA, Knizewski L, Lange B, Muszewska A, Śniegowska-Świerk K, Kościelniak J, Iwanicka-Nowicka R, Buza K, Janowiak F, Żmuda K, Jõesaar I, Laskowska-Kaszub K, Fogtman A, Kollist H, Zielenkiewicz P, Tiuryn J, Siedlecki P, Swiezewski S, Ginalski K, Koblowska M, Archacki R, Wilczynski B, Rapacz M, Jerzmanowski A. A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis. PLANT PHYSIOLOGY 2015; 169:2080-101. [PMID: 26351307 PMCID: PMC4634048 DOI: 10.1104/pp.15.00493] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/07/2015] [Indexed: 05/18/2023]
Abstract
Linker (H1) histones play critical roles in chromatin compaction in higher eukaryotes. They are also the most variable of the histones, with numerous nonallelic variants cooccurring in the same cell. Plants contain a distinct subclass of minor H1 variants that are induced by drought and abscisic acid and have been implicated in mediating adaptive responses to stress. However, how these variants facilitate adaptation remains poorly understood. Here, we show that the single Arabidopsis (Arabidopsis thaliana) stress-inducible variant H1.3 occurs in plants in two separate and most likely autonomous pools: a constitutive guard cell-specific pool and a facultative environmentally controlled pool localized in other tissues. Physiological and transcriptomic analyses of h1.3 null mutants demonstrate that H1.3 is required for both proper stomatal functioning under normal growth conditions and adaptive developmental responses to combined light and water deficiency. Using fluorescence recovery after photobleaching analysis, we show that H1.3 has superfast chromatin dynamics, and in contrast to the main Arabidopsis H1 variants H1.1 and H1.2, it has no stable bound fraction. The results of global occupancy studies demonstrate that, while H1.3 has the same overall binding properties as the main H1 variants, including predominant heterochromatin localization, it differs from them in its preferences for chromatin regions with epigenetic signatures of active and repressed transcription. We also show that H1.3 is required for a substantial part of DNA methylation associated with environmental stress, suggesting that the likely mechanism underlying H1.3 function may be the facilitation of chromatin accessibility by direct competition with the main H1 variants.
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Affiliation(s)
- Kinga Rutowicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Marcin Puzio
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Joanna Halibart-Puzio
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Maciej Kotliński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Magdalena A Kroteń
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Lukasz Knizewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Bartosz Lange
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Katarzyna Śniegowska-Świerk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Janusz Kościelniak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Roksana Iwanicka-Nowicka
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Krisztián Buza
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Franciszek Janowiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Katarzyna Żmuda
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Indrek Jõesaar
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Katarzyna Laskowska-Kaszub
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Hannes Kollist
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Jerzy Tiuryn
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Paweł Siedlecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Szymon Swiezewski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Krzysztof Ginalski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Marta Koblowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Rafał Archacki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Bartek Wilczynski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Marcin Rapacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
| | - Andrzej Jerzmanowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland (K.R., J.H.-P., M.L., M.Kot., A.M., R.I.-N., A.F., P.Z., P.S., S.S., M.Kob., A.J.);Laboratory of Systems Biology, University of Warsaw, 02-106 Warsaw, Poland (M.P., M.Kot., B.L., R.I.-N., K.L.-K., P.S., M.Kob., R.A., A.J.);Institute of Plant Physiology, University of Rzeszów, 36-100 Kolbuszowa, Poland (J.H.-P.);College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, 02-089 Warsaw, Poland (M.A.K.);Laboratory of Bioinformatics and Systems Biology, Center of New Technologies (L.K., A.M., K.G.), and Institute of Informatics (K.B., J.T., B.W.), University of Warsaw, 02-097 Warsaw, Poland;Department of Plant Physiology, University of Agriculture in Cracow, 30-239 Cracow, Poland (K.Ś.-Ś., J.K., K.Ż., M.R.);Institute of Plant Physiology, Polish Academy of Sciences, 30-239 Cracow, Poland (F.J.); andInstitute of Technology, University of Tartu, 50411 Tartu, Tartumaa, Estonia (I.J., H.K.)
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63
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Flickinger R. AT-rich repetitive DNA sequences, transcription frequency and germ layer determination. Mech Dev 2015; 138 Pt 3:227-32. [PMID: 26506258 DOI: 10.1016/j.mod.2015.10.004] [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] [Received: 07/27/2015] [Revised: 10/19/2015] [Accepted: 10/21/2015] [Indexed: 01/30/2023]
Abstract
Non-coding sequences of frog embryo endoderm poly (A+) nuclear RNA are AU-enriched, as compared to those of ectoderm and mesoderm. Endoderm blastomeres contain much less H1 histone than is present in ectoderm and mesoderm. H1 histone preferentially binds AT-rich DNA sequences to repress their transcription. The AT-enrichment of non-coding DNA sequences transcribed into poly (A+) nuclear RNA, as well as the low amount of H1 histone, may contribute to the higher transcription frequency of mRNA of endoderm, as compared to that of ectoderm and mesoderm. A greater accumulation of H1 histone in presumptive mesoderm and ectoderm may prevent transcription of endoderm specifying genes in mesoderm and ectoderm. Experimental upregulation of various transcription factors (TFs) can redirect germ layer fate. Most of these TFs bind AT-rich consensus sequences in DNA, suggesting that H1 histone and TFs active during germ layer determination are binding similar sequences.
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Affiliation(s)
- Reed Flickinger
- Emeritus Department, Biological Sciences State University of New York at Buffalo, Buffalo, N.Y. 14260, USA.
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Vicent GP, Wright RHG, Beato M. Linker histones in hormonal gene regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:520-5. [PMID: 26518266 DOI: 10.1016/j.bbagrm.2015.10.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 12/20/2022]
Abstract
In the present review, we summarize advances in our knowledge on the role of the histone H1 family of proteins in breast cancer cells, focusing on their response to progestins. Histone H1 plays a dual role in gene regulation by hormones, both as a structural component of chromatin and as a dynamic modulator of transcription. It contributes to hormonal regulation of the MMTV promoter by stabilizing a homogeneous nucleosome positioning, which reduces basal transcription whereas at the same time promoting progesterone receptor binding and nucleosome remodeling. These combined effects enhance hormone dependent gene transcription, which eventually requires H1 phosphorylation and displacement. Various isoforms of histone H1 have specific functions in differentiated breast cancer cells and compact nucleosomal arrays to different extents in vitro. Genome-wide studies show that histone H1 has a key role in chromatin dynamics of hormone regulated genes. A complex sequence of enzymatic events, including phosphorylation by CDK2, PARylation by PARP1 and the ATP-dependent activity of NURF, are required for H1 displacement and gene de-repression, as a prerequisite for further nucleosome remodeling. Similarly, during hormone-dependent gene repression a dedicated enzymatic mechanism controls H1 deposition at promoters by a complex containing HP1γ, LSD1 and BRG1, the ATPase of the BAF complex. Thus, a broader vision of the histone code should include histone H1, as the linker histone variants actively participate in the regulation of the chromatin structure. How modifications of the core histones tails affect H1 modifications and vice versa is one of the many questions that remains to be addressed to provide a more comprehensive view of the histone cross-talk mechanisms.
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Affiliation(s)
- G P Vicent
- Centre de Regulació Genòmica (CRG), Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, E-08003, Barcelona, Spain
| | - R H G Wright
- Centre de Regulació Genòmica (CRG), Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, E-08003, Barcelona, Spain
| | - M Beato
- Centre de Regulació Genòmica (CRG), Spain; Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, E-08003, Barcelona, Spain
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65
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Functional interplay between histone H1 and HMG proteins in chromatin. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:462-7. [PMID: 26455954 DOI: 10.1016/j.bbagrm.2015.10.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/02/2015] [Accepted: 10/05/2015] [Indexed: 11/22/2022]
Abstract
The dynamic interaction of nucleosome binding proteins with their chromatin targets is an important element in regulating the structure and function of chromatin. Histone H1 variants and High Mobility Group (HMG) proteins are ubiquitously expressed in all vertebrate cells, bind dynamically to chromatin, and are known to affect chromatin condensation and the ability of regulatory factors to access their genomic binding sites. Here, we review the studies that focus on the interactions between H1 and HMGs and highlight the functional consequences of the interplay between these architectural chromatin binding proteins. H1 and HMG proteins are mobile molecules that bind to nucleosomes as members of a dynamic protein network. All HMGs compete with H1 for chromatin binding sites, in a dose dependent fashion, but each HMG family has specific effects on the interaction of H1 with chromatin. The interplay between H1 and HMGs affects chromatin organization and plays a role in epigenetic regulation.
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Flanagan TW, Brown DT. Molecular dynamics of histone H1. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:468-75. [PMID: 26454113 DOI: 10.1016/j.bbagrm.2015.10.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/17/2015] [Accepted: 10/05/2015] [Indexed: 12/28/2022]
Abstract
The H1 or linker histones bind dynamically to chromatin in living cells via a process that involves transient association with the nucleosome near the DNA entry/exit site followed by dissociation, translocation to a new location, and rebinding. The mean residency time of H1 on any given nucleosome is about a minute, which is much shorter than that of most core histones but considerably longer than that of most other chromatin-binding proteins, including transcription factors. Here we review recent advances in understanding the kinetic pathway of H1 binding and how it relates to linker histone structure and function. We also describe potential mechanisms by which the dynamic binding of H1 might contribute directly to the regulation of gene expression and discuss several situations for which there is experimental evidence to support these mechanisms. Finally, we review the evidence for the participation of linker histone chaperones in mediating H1 exchange.
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Affiliation(s)
- Thomas W Flanagan
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA
| | - David T Brown
- Department of Biochemistry, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS 39216, USA.
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Reeves R. High mobility group (HMG) proteins: Modulators of chromatin structure and DNA repair in mammalian cells. DNA Repair (Amst) 2015; 36:122-136. [PMID: 26411874 DOI: 10.1016/j.dnarep.2015.09.015] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
It has been almost a decade since the last review appeared comparing and contrasting the influences that the different families of High Mobility Group proteins (HMGA, HMGB and HMGN) have on the various DNA repair pathways in mammalian cells. During that time considerable progress has been made in our understanding of how these non-histone proteins modulate the efficiency of DNA repair by all of the major cellular pathways: nucleotide excision repair, base excision repair, double-stand break repair and mismatch repair. Although there are often similar and over-lapping biological activities shared by all HMG proteins, members of each of the different families appear to have a somewhat 'individualistic' impact on various DNA repair pathways. This review will focus on what is currently known about the roles that different HMG proteins play in DNA repair processes and discuss possible future research areas in this rapidly evolving field.
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Affiliation(s)
- Raymond Reeves
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-4660, USA.
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Sánchez-Giraldo R, Acosta-Reyes FJ, Malarkey CS, Saperas N, Churchill MEA, Campos JL. Two high-mobility group box domains act together to underwind and kink DNA. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1423-32. [PMID: 26143914 PMCID: PMC4498601 DOI: 10.1107/s1399004715007452] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/15/2015] [Indexed: 01/22/2023]
Abstract
High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A is thought to be responsible for the majority of HMGB1-DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.
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Affiliation(s)
- R. Sánchez-Giraldo
- Departament d’Enginyeria Quimica, Universitat Politecnica de Catalunya, 08028 Barcelona, Spain
| | - F. J. Acosta-Reyes
- Departament d’Enginyeria Quimica, Universitat Politecnica de Catalunya, 08028 Barcelona, Spain
| | - C. S. Malarkey
- Department of Pharmacology and the Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - N. Saperas
- Departament d’Enginyeria Quimica, Universitat Politecnica de Catalunya, 08028 Barcelona, Spain
| | - M. E. A. Churchill
- Department of Pharmacology and the Program in Structural Biology and Biochemistry, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - J. L. Campos
- Departament d’Enginyeria Quimica, Universitat Politecnica de Catalunya, 08028 Barcelona, Spain
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Abstract
The extent to which DNA repair machinery facilitates gene activation remains poorly appreciated. A new study published in Cell Research reports a novel function of H2AX, a substrate of ATM and known DNA damage marker, in transcriptional initiation.
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Singh I, Ozturk N, Cordero J, Mehta A, Hasan D, Cosentino C, Sebastian C, Krüger M, Looso M, Carraro G, Bellusci S, Seeger W, Braun T, Mostoslavsky R, Barreto G. High mobility group protein-mediated transcription requires DNA damage marker γ-H2AX. Cell Res 2015; 25:837-50. [PMID: 26045162 DOI: 10.1038/cr.2015.67] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 04/27/2015] [Accepted: 05/04/2015] [Indexed: 12/13/2022] Open
Abstract
The eukaryotic genome is organized into chromatins, the physiological template for DNA-dependent processes including replication, recombination, repair, and transcription. Chromatin-mediated transcription regulation involves DNA methylation, chromatin remodeling, and histone modifications. However, chromatin also contains non-histone chromatin-associated proteins, of which the high-mobility group (HMG) proteins are the most abundant. Although it is known that HMG proteins induce structural changes of chromatin, the processes underlying transcription regulation by HMG proteins are poorly understood. Here we decipher the molecular mechanism of transcription regulation mediated by the HMG AT-hook 2 protein (HMGA2). We combined proteomic, ChIP-seq, and transcriptome data to show that HMGA2-induced transcription requires phosphorylation of the histone variant H2AX at S139 (H2AXS139ph; γ-H2AX) mediated by the protein kinase ataxia telangiectasia mutated (ATM). Furthermore, we demonstrate the biological relevance of this mechanism within the context of TGFβ1 signaling. The interplay between HMGA2, ATM, and H2AX is a novel mechanism of transcription initiation. Our results link H2AXS139ph to transcription, assigning a new function for this DNA damage marker. Controlled chromatin opening during transcription may involve intermediates with DNA breaks that may require mechanisms that ensure the integrity of the genome.
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Affiliation(s)
- Indrabahadur Singh
- LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany
| | - Nihan Ozturk
- LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany
| | - Julio Cordero
- LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany
| | - Aditi Mehta
- LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany
| | - Diya Hasan
- LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany
| | - Claudia Cosentino
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02118, USA
| | - Carlos Sebastian
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02118, USA
| | - Marcus Krüger
- Division of Biomolecular Mass Spectrometry, Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany
| | - Mario Looso
- Group of Bioinformatics, Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany
| | - Gianni Carraro
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Saverio Bellusci
- 1] Chair for Lung Matrix Remodeling, Excellence Cluster Cardio Pulmonary System, University Justus Liebig, 35932 Giessen, Germany [2] Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russian Federation [3] Member of the Universities of Giessen and Marburg Lung Center (UGMLC) and the German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL)
| | - Werner Seeger
- 1] Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany [2] Member of the Universities of Giessen and Marburg Lung Center (UGMLC) and the German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL)
| | - Thomas Braun
- 1] Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany [2] Member of the Universities of Giessen and Marburg Lung Center (UGMLC) and the German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL)
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02118, USA
| | - Guillermo Barreto
- 1] LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany [2] Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russian Federation [3] Member of the Universities of Giessen and Marburg Lung Center (UGMLC) and the German Center of Lung Research (Deutsches Zentrum für Lungenforschung, DZL)
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Garfinkel BP, Melamed-Book N, Anuka E, Bustin M, Orly J. HP1BP3 is a novel histone H1 related protein with essential roles in viability and growth. Nucleic Acids Res 2015; 43:2074-90. [PMID: 25662603 PMCID: PMC4344522 DOI: 10.1093/nar/gkv089] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 12/28/2022] Open
Abstract
The dynamic architecture of chromatin is vital for proper cellular function, and is maintained by the concerted action of numerous nuclear proteins, including that of the linker histone H1 variants, the most abundant family of nucleosome-binding proteins. Here we show that the nuclear protein HP1BP3 is widely expressed in most vertebrate tissues and is evolutionarily and structurally related to the H1 family. HP1BP3 contains three globular domains and a highly positively charged C-terminal domain, resembling similar domains in H1. Fluorescence recovery after photobleaching (FRAP) studies indicate that like H1, binding of HP1BP3 to chromatin depends on both its C and N terminal regions and is affected by the cell cycle and post translational modifications. HP1BP3 contains functional motifs not found in H1 histones, including an acidic stretch and a consensus HP1-binding motif. Transcriptional profiling of HeLa cells lacking HP1BP3 showed altered expression of 383 genes, suggesting a role for HP1BP3 in modulation of gene expression. Significantly, Hp1bp3(-/-) mice present a dramatic phenotype with 60% of pups dying within 24 h of birth and the surviving animals exhibiting a lifelong 20% growth retardation. We suggest that HP1BP3 is a ubiquitous histone H1 like nuclear protein with distinct and non-redundant functions necessary for survival and growth.
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Affiliation(s)
- Benjamin P Garfinkel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Naomi Melamed-Book
- Bio-Imaging Unit, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eli Anuka
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Yu KR, Shin JH, Kim JJ, Koog MG, Lee JY, Choi SW, Kim HS, Seo Y, Lee S, Shin TH, Jee MK, Kim DW, Jung SJ, Shin S, Han DW, Kang KS. Rapid and Efficient Direct Conversion of Human Adult Somatic Cells into Neural Stem Cells by HMGA2/let-7b. Cell Rep 2015; 10:441-452. [PMID: 25600877 DOI: 10.1016/j.celrep.2014.12.038] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 10/13/2014] [Accepted: 12/16/2014] [Indexed: 12/13/2022] Open
Abstract
A recent study has suggested that fibroblasts can be converted into mouse-induced neural stem cells (miNSCs) through the expression of defined factors. However, successful generation of human iNSCs (hiNSCs) has proven challenging to achieve. Here, using microRNA (miRNA) expression profile analyses, we showed that let-7 microRNA has critical roles for the formation of PAX6/NESTIN-positive colonies from human adult fibroblasts and the proliferation and self-renewal of hiNSCs. HMGA2, a let-7-targeting gene, enables induction of hiNSCs that displayed morphological/molecular features and in vitro/in vivo differentiation potential similar to H9-derived NSCs. Interestingly, HMGA2 facilitated the efficient conversion of senescent somatic cells or blood CD34+ cells into hiNSCs through an interaction with SOX2, whereas other combinations or SOX2 alone showed a limited conversion ability. Taken together, these findings suggest that HMGA2/let-7 facilitates direct reprogramming toward hiNSCs in minimal conditions and maintains hiNSC self-renewal, providing a strategy for the clinical treatment of neurological diseases.
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Affiliation(s)
- Kyung-Rok Yu
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - Ji-Hee Shin
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - Jae-Jun Kim
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - Myung Guen Koog
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - Jin Young Lee
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - Soon Won Choi
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - Hyung-Sik Kim
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - Yoojin Seo
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - SeungHee Lee
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; Institute for Stem Cell and Regenerative Medicine in Kang Stem Biotech, Biotechnology Incubating Center, Seoul National University, Seoul 151-742, Korea
| | - Tae-Hoon Shin
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - Min Ki Jee
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea
| | - Dong-Wook Kim
- Department of Physiology and Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul 120-752, Korea
| | - Sung Jun Jung
- Department of Physiology, School of Medicine, Hanyang University, Seoul 133-791, Korea
| | - Sue Shin
- Department of Laboratory Medicine, SMG-SNU Boramae Medical Center, Seoul National University College of Medicine, Seoul 156-707, Korea; Seoul Metropolitan Public Cord Blood Bank, Allcord, Seoul 156-707, Korea
| | - Dong Wook Han
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 143-701, Korea
| | - Kyung-Sun Kang
- Adult Stem Cell Research Center, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 151-742, Korea.
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73
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Su B, Shi B, Tang Y, Guo Z, Yu X, He X, Li X, Gao X, Zhou L. HMGN5 knockdown sensitizes prostate cancer cells to ionizing radiation. Prostate 2015; 75:33-44. [PMID: 25307178 DOI: 10.1002/pros.22888] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/05/2014] [Indexed: 12/14/2022]
Abstract
BACKGROUND High Mobility Group N (HMGN) proteins are a family of chromatin structural proteins that specifically bind to nucleosome core particles. HMGN5 is a novel and characteristic member of the HMGN protein family. We have previously found that HMGN5 is upregulated in prostate cancer and its downregulation had been demonstrated to induce apoptosis and G2-M cell cycle arrest. METHODS The radiosensitization effect of HMGN5 knockdown on PC3 and DU145 cells was assessed using clonogenic assay, flow cytometry, and comet assay. The DNA double-strand break (DSB) repair kinetics of HMGN5 knockdown and control cells after radiation exposure was evaluated using immunocytofluorescence. The mitochondrial reactive oxygen species (ROS) levels were estimated using Dihydrorhodamine 123 (DHR 123) probes. Expression of mitochondrial antioxidant MnSOD was measured by real-time PCR and Western blot. The expression of antiapoptotic proteins Bcl-2 and Bcl-xL as well as cleavage of caspase-3, caspase-9, and PARP were also measured using Western blot. RESULTS HMGN5 knockdown cells exhibit decreased clonogenic survival and increased apoptosis rate in response to 2-8 Gy ionizing radiation (IR). Loss of HMGN5 does not affect the DSB repair kinetics after radiation exposure. HMGN5 knockdown cells demonstrated increased mitochondrial ROS level and suppressed induction of MnSOD upon radiation compared with control cells upon radiation. Further, MnSOD knockdown resulted in inhibited cell viability as well as increased mitochondrial ROS level and apoptosis upon radiation in PC3 and DU145 cells. Finally, HMGN5 knockdown cells showed significantly decreased levels of antiapoptotic proteins Bcl-2 and Bcl-xL as well as increased cleavage of caspase-3, caspase-9, and PARP compared with control cells after radiation. CONCLUSIONS HMGN5 knockdown sensitizes prostate cancer cells to ionizing radiation, and the radiosensitization effect may be partially mediated through suppressed induction of MnSOD and enhanced activation of apoptosis pathway in response to IR.
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Affiliation(s)
- Boxing Su
- Department of Urology, Peking University First Hospital and the Institute of Urology, Peking University, Beijing, China; National Urological Cancer Center, Beijing, China
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74
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Liu J, Wang H, Ma F, Xu D, Chang Y, Zhang J, Wang J, Zhao M, Lin C, Huang C, Qian H, Zhan Q. MTA1 regulates higher-order chromatin structure and histone H1-chromatin interaction in-vivo. Mol Oncol 2015; 9:218-35. [PMID: 25205035 PMCID: PMC5528677 DOI: 10.1016/j.molonc.2014.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/04/2014] [Accepted: 08/18/2014] [Indexed: 11/27/2022] Open
Abstract
In the current study, for the first time, we found that metastasis-associated gene 1 (MTA1) was a higher-order chromatin structure organizer that decondenses the interphase chromatin and mitotic chromosomes. MTA1 interacts dynamically with nucleosomes during the cell cycle progression, prominently contributing to the mitotic chromatin/chromosome structure transitions at both prophase and telophase. We showed that the decondensation of interphase chromatin by MTA1 was independent of Mi-2 chromatin remodeling activity. H1 was reported to stabilize the compact higher-order chromatin structure through its interaction with DNA. Our data showed that MTA1 caused a reduced H1-chromatin interaction in-vivo. Moreover, the dynamic MTA1-chromatin interaction in the cell cycle contributed to the periodical H1-chromatin interaction, which in turn modulated chromatin/chromosome transitions. Although MTA1 drove a global decondensation of chromatin structure, it changed the expression of only a small proportion of genes. After MTA1 overexpression, the up-regulated genes were distributed in clusters along with down-regulated genes on chromosomes at parallel frequencies.
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Affiliation(s)
- Jian Liu
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China; Medical Research Center, Beijing ChaoYang Hospital, Capital Medical University, Beijing 100020, China
| | - Haijuan Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Fei Ma
- Department of Medical Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, State Key Laboratory of Molecular Oncology, Beijing 100021, China
| | - Dongkui Xu
- Department of Abdominal Surgery, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, State Key Laboratory of Molecular Oncology, Beijing 100021, China
| | - Yanan Chang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Jinlong Zhang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Jia Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Mei Zhao
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Chen Lin
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China
| | - Changzhi Huang
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
| | - Qimin Zhan
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100021, China.
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75
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Flickinger RA. Possible role of H1 histone in replication timing. Dev Growth Differ 2014; 57:1-9. [PMID: 25495214 DOI: 10.1111/dgd.12190] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 01/02/2023]
Abstract
AT-rich repetitive DNA sequences become late replicating during cell differentiation. Replication timing is not correlated with LINE density in human cells (Ryba et al. 2010). However, short and properly spaced runs of oligo dA or dT present in nuclear matrix attachment regions (MARs) of the genome are good candidates for elements of AT-rich repetitive late replicating DNA. MAR attachment to the nuclear matrix is negatively regulated by chromatin binding of H1 histone, but this is counteracted by H1 phosphorylation, high mobility group proteins or, indirectly, core histone acetylation. Fewer MAR attachments correlates positively with longer average DNA loop size, longer replicons and an increase of late replicating DNA.
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Affiliation(s)
- Reed A Flickinger
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, 14260, New York, USA
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76
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Klement K, Goodarzi AA. DNA double strand break responses and chromatin alterations within the aging cell. Exp Cell Res 2014; 329:42-52. [PMID: 25218945 DOI: 10.1016/j.yexcr.2014.09.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/28/2014] [Accepted: 09/01/2014] [Indexed: 12/23/2022]
Abstract
Cellular senescence is a state of permanent replicative arrest that allows cells to stay viable and metabolically active but resistant to apoptotic and mitogenic stimuli. Specific, validated markers can identify senescent cells, including senescence-associated β galactosidase activity, chromatin alterations, cell morphology changes, activated p16- and p53-dependent signaling and permanent cell cycle arrest. Senescence is a natural consequence of DNA replication-associated telomere erosion, but can also be induced prematurely by telomere-independent events such as failure to repair DNA double strand breaks. Here, we review the molecular pathways of senescence onset, focussing on the changes in chromatin organization that are associated with cellular senescence, particularly senescence-associated heterochromatin foci formation. We also discuss the altered dynamics of the DNA double strand break response within the context of aging cells. Appreciating how, mechanistically, cellular senescence is induced, and how changes to chromatin organization and DNA repair contributes to this, is fundamental to our understanding of the normal and premature human aging processes associated with loss of organ and tissue function in humans.
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Affiliation(s)
- Karolin Klement
- Southern Alberta Cancer Research Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
| | - Aaron A Goodarzi
- Southern Alberta Cancer Research Institute, Departments of Biochemistry & Molecular Biology and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1.
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77
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PTEN interacts with histone H1 and controls chromatin condensation. Cell Rep 2014; 8:2003-2014. [PMID: 25199838 DOI: 10.1016/j.celrep.2014.08.008] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 07/05/2014] [Accepted: 08/05/2014] [Indexed: 01/16/2023] Open
Abstract
Chromatin organization and dynamics are integral to global gene transcription. Histone modification influences chromatin status and gene expression. PTEN plays multiple roles in tumor suppression, development, and metabolism. Here, we report on the interplay of PTEN, histone H1, and chromatin. We show that loss of PTEN leads to dissociation of histone H1 from chromatin and decondensation of chromatin. PTEN deletion also results in elevation of histone H4 acetylation at lysine 16, an epigenetic marker for chromatin activation. We found that PTEN and histone H1 physically interact through their C-terminal domains. Disruption of the PTEN C terminus promotes the chromatin association of MOF acetyltransferase and induces H4K16 acetylation. Hyperacetylation of H4K16 impairs the association of PTEN with histone H1, which constitutes regulatory feedback that may reduce chromatin stability. Our results demonstrate that PTEN controls chromatin condensation, thus influencing gene expression. We propose that PTEN regulates global gene transcription profiling through histones and chromatin remodeling.
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78
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Kadota S, Nagata K. Silencing of IFN-stimulated gene transcription is regulated by histone H1 and its chaperone TAF-I. Nucleic Acids Res 2014; 42:7642-53. [PMID: 24878923 PMCID: PMC4081089 DOI: 10.1093/nar/gku485] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Chromatin structure and its alteration play critical roles in the regulation of transcription. However, the transcriptional silencing mechanism with regard to the chromatin structure at an unstimulated state of the interferon (IFN)-stimulated gene (ISG) remains unclear. Here we investigated the role of template activating factor-I (TAF-I, also known as SET) in ISG transcription. Knockdown (KD) of TAF-I increased ISG transcript and simultaneously reduced the histone H1 level on the ISG promoters during the early stages of transcription after IFN stimulation from the unstimulated state. The transcription factor levels on the ISG promoters were increased in TAF-I KD cells only during the early stages of transcription. Furthermore, histone H1 KD also increased ISG transcript. TAF-I and histone H1 double KD did not show the additive effect in ISG transcription, suggesting that TAF-I and histone H1 may act on the same regulatory pathway to control ISG transcription. In addition, TAF-I KD and histone H1 KD affected the chromatin structure near the ISG promoters. On the basis of these findings, we propose that TAF-I and its target histone H1 are key regulators of the chromatin structure at the ISG promoter to maintain the silent state of ISG transcription.
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Affiliation(s)
- Shinichi Kadota
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Kyosuke Nagata
- Department of Infection Biology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
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79
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Chromatin maintenance and dynamics in senescence: a spotlight on SAHF formation and the epigenome of senescent cells. Chromosoma 2014; 123:423-36. [PMID: 24861957 DOI: 10.1007/s00412-014-0469-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 01/28/2023]
Abstract
Senescence is a stable proliferation arrest characterized by profound changes in cellular morphology and metabolism as well as by extensive chromatin reorganization in the nucleus. One particular hallmark of chromatin changes during senescence is the formation of punctate DNA foci in DAPI-stained senescent cells that have been called senescence-associated heterochromatin foci (SAHF). While many advances have been made concerning our understanding of the effectors of senescence, how chromatin is reorganized and maintained in senescent cells has remained largely elusive. Because chromatin structure is inherently dynamic, senescent cells face the challenge of developing chromatin maintenance mechanisms in the absence of DNA replication in order to maintain the senescent phenotype. Here, we summarize and review recent findings shedding light on SAHF composition and formation via spatial repositioning of chromatin, with a specific focus on the role of lamin B1 for this process. In addition, we discuss the physiological implication of SAHF formation, the role of histone variants, and histone chaperones during senescence and also elaborate on the more general changes observed in the epigenome of the senescent cells.
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80
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Bernas T, Brutkowski W, Zarębski M, Dobrucki J. Spatial heterogeneity of dynamics of H1 linker histone. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2014; 43:287-300. [PMID: 24830851 PMCID: PMC4053610 DOI: 10.1007/s00249-014-0962-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 04/10/2014] [Accepted: 04/25/2014] [Indexed: 02/04/2023]
Abstract
Linker histone H1 participates in maintaining higher order chromatin structures. It is a dynamic protein that binds to DNA and exchanges rapidly with a mobile pool. Therefore, the dynamics of H1 were probed in the nuclei of intact, live cells, using an array of microscopy techniques: fluorescence recovery after photobleaching (FRAP), raster image correlation spectroscopy (RICS), fluorescence correlation spectroscopy (FCS), pair correlation functions (pCF) and fluorescence anisotropy. Combination of these techniques yielded information on H1 dynamics at small (1–100 μs: FCS, RICS, anisotropy), moderate (1–100 ms: FCS, RICS, pCF) and large (1–100 s: pCF and FRAP) time scales. These results indicate that the global movement of H1 in nuclei (at distances >1 µm) occurs at the time scale of seconds and is determined by processes other than diffusion. Moreover, a fraction of H1, which remains immobile at the time scale of tenths of seconds, is detectable. However, local (at distances <0.7 µm) H1 dynamics comprises a process occurring at a short (~3 ms) time scale and multiple processes occurring at longer (10–2,500 ms) scales. The former (fast) process (corresponding probably to H1 diffusion) is more pronounced in the nuclear regions characterized by low H1 concentration, but the latter (slow, attributable to H1 binding) in the regions of high H1 concentration. Furthermore, some regions in nuclei (possibly containing dense chromatin) may constitute barriers that impair or block movement of H1 histones within short (<1 µm) distances.
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Affiliation(s)
- T Bernas
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland,
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81
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Ozturk N, Singh I, Mehta A, Braun T, Barreto G. HMGA proteins as modulators of chromatin structure during transcriptional activation. Front Cell Dev Biol 2014; 2:5. [PMID: 25364713 PMCID: PMC4207033 DOI: 10.3389/fcell.2014.00005] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 02/07/2014] [Indexed: 01/12/2023] Open
Abstract
High mobility group (HMG) proteins are the most abundant non-histone chromatin associated proteins. HMG proteins bind to DNA and nucleosome and alter the structure of chromatin locally and globally. Accessibility to DNA within chromatin is a central factor that affects DNA-dependent nuclear processes, such as transcription, replication, recombination, and repair. HMG proteins associate with different multi-protein complexes to regulate these processes by mediating accessibility to DNA. HMG proteins can be subdivided into three families: HMGA, HMGB, and HMGN. In this review, we will focus on recent advances in understanding the function of HMGA family members, specifically their role in gene transcription regulation during development and cancer.
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Affiliation(s)
- Nihan Ozturk
- LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research Bad Nauheim, Germany
| | - Indrabahadur Singh
- LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research Bad Nauheim, Germany
| | - Aditi Mehta
- LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research Bad Nauheim, Germany
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research Bad Nauheim, Germany
| | - Guillermo Barreto
- LOEWE Research Group Lung Cancer Epigenetic, Max-Planck-Institute for Heart and Lung Research Bad Nauheim, Germany
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82
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Polanská E, Pospíšilová Š, Štros M. Binding of histone H1 to DNA is differentially modulated by redox state of HMGB1. PLoS One 2014; 9:e89070. [PMID: 24551219 PMCID: PMC3923860 DOI: 10.1371/journal.pone.0089070] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 01/13/2014] [Indexed: 12/05/2022] Open
Abstract
HMGB1 is an architectural protein in chromatin, acting also as a signaling molecule outside the cell. Recent reports from several laboratories provided evidence that a number of both the intracellular and extracellular functions of HMGB1 may depend on redox-sensitive cysteine residues of the protein. In this study we demonstrate that redox state of HMGB1 can significantly modulate the ability of the protein to bind and bend DNA, as well as to promote DNA end-joining. We also report a high affinity binding of histone H1 to hemicatenated DNA loops and DNA minicircles. Finally, we show that reduced HMGB1 can readily displace histone H1 from DNA, while oxidized HMGB1 has limited capacity for H1 displacement. Our results suggested a novel mechanism for the HMGB1-mediated modulation of histone H1 binding to DNA. Possible biological consequences of linker histones H1 replacement by HMGB1 for the functioning of chromatin are discussed.
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Affiliation(s)
- Eva Polanská
- Laboratory of Analysis of Chromosomal Proteins, Institute of Biophysics, Academy of Science of the Czech Republic, Brno, Czech Republic
| | - Šárka Pospíšilová
- Central European Institute of Technology (CEITEC) – Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Štros
- Laboratory of Analysis of Chromosomal Proteins, Institute of Biophysics, Academy of Science of the Czech Republic, Brno, Czech Republic
- Central European Institute of Technology (CEITEC) – Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- * E-mail:
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83
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Nalabothula N, McVicker G, Maiorano J, Martin R, Pritchard JK, Fondufe-Mittendorf YN. The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. BMC Genomics 2014; 15:92. [PMID: 24484546 PMCID: PMC3928079 DOI: 10.1186/1471-2164-15-92] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 01/30/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. While these proteins are almost certainly important for gene regulation they have been studied far less than the core histone proteins. RESULTS Here we describe the genomic distributions and functional roles of two chromatin architectural proteins: histone H1 and the high mobility group protein HMGD1 in Drosophila S2 cells. Using ChIP-seq, biochemical and gene specific approaches, we find that HMGD1 binds to highly accessible regulatory chromatin and active promoters. In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks. We find that the ratio of HMGD1 to H1 binding is a better predictor of gene activity than either protein by itself, which suggests that reciprocal binding between these proteins is important for gene regulation. Using knockdown experiments, we show that HMGD1 and H1 affect the occupancy of the other protein, change nucleosome repeat length and modulate gene expression. CONCLUSION Collectively, our data suggest that dynamic and mutually exclusive binding of H1 and HMGD1 to nucleosomes and their linker sequences may control the fluid chromatin structure that is required for transcriptional regulation. This study provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation.
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84
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Ciappio ED, Krausz KW, Rochman M, Furusawa T, Bonzo JA, Tessarollo L, Gonzalez FJ, Bustin M. Metabolomics reveals a role for the chromatin-binding protein HMGN5 in glutathione metabolism. PLoS One 2014; 9:e84583. [PMID: 24392144 PMCID: PMC3879345 DOI: 10.1371/journal.pone.0084583] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/18/2013] [Indexed: 11/26/2022] Open
Abstract
High mobility group nucleosome-binding protein 5 (HMGN5) is a chromatin architectural protein that binds specifically to nucleosomes and reduces the compaction of the chromatin fiber. The protein is present in most vertebrate tissues however the physiological function of this protein is unknown. To examine the function of HMGN5 in vivo, mice lacking the nucleosome-binding domain of HMGN5 were generated and characterized. Serological analysis revealed that compared to wild-type littermates (Hmgn5+/Y), mice with a targeted mutation in the HMGN5 gene (Hmgn5tm1/Y), had elevated serum albumin, non-HDL cholesterol, triglycerides, and alanine transaminase, suggesting mild hepatic abnormalities. Metabolomics analysis of liver extracts and urine revealed clear differences in metabolites between Hmgn5tm1/Y and their Hmgn5+/Y littermates. Hmgn5tm1/Y mice had a significant increase in hepatic glutathione levels and decreased urinary concentrations of betaine, phenylacetylglycine, and creatine, all of which are metabolically related to the glutathione precursor glycine. Microarray and qPCR analysis revealed that expression of two genes affecting glutathione metabolism, glutathione peroxidase 6 (Gpx6) and hexokinase 1 (Hk1), was significantly decreased in Hmgn5tm1/Y mouse liver tissue. Analysis of chromatin structure by DNase I digestion revealed alterations in the chromatin structure of these genes in the livers of Hmgn5tm1/Y mice. Thus, functional loss of HMGN5 leads to changes in transcription of Gpx6 and Hk1 that alter glutathione metabolism.
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Affiliation(s)
- Eric D. Ciappio
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kristopher W. Krausz
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mark Rochman
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Takashi Furusawa
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jessica A. Bonzo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Lino Tessarollo
- Neural Development Section, Mouse Cancer Genetics Program, National Cancer Institute, Frederick, Maryland, United States of America
| | - Frank J. Gonzalez
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Bustin
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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85
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Li X, Venugopalan SR, Cao H, Pinho FO, Paine ML, Snead ML, Semina EV, Amendt BA. A model for the molecular underpinnings of tooth defects in Axenfeld-Rieger syndrome. Hum Mol Genet 2014; 23:194-208. [PMID: 23975681 PMCID: PMC3857954 DOI: 10.1093/hmg/ddt411] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 08/19/2013] [Indexed: 12/18/2022] Open
Abstract
Patients with Axenfeld-Rieger Syndrome (ARS) present various dental abnormalities, including hypodontia, and enamel hypoplasia. ARS is genetically associated with mutations in the PITX2 gene, which encodes one of the earliest transcription factors to initiate tooth development. Thus, Pitx2 has long been considered as an upstream regulator of the transcriptional hierarchy in early tooth development. However, because Pitx2 is also a major regulator of later stages of tooth development, especially during amelogenesis, it is unclear how mutant forms cause ARS dental anomalies. In this report, we outline the transcriptional mechanism that is defective in ARS. We demonstrate that during normal tooth development Pitx2 activates Amelogenin (Amel) expression, whose product is required for enamel formation, and that this regulation is perturbed by missense PITX2 mutations found in ARS patients. We further show that Pitx2-mediated Amel activation is controlled by chromatin-associated factor Hmgn2, and that Hmgn2 prevents Pitx2 from efficiently binding to and activating the Amel promoter. Consistent with a physiological significance to this interaction, we show that K14-Hmgn2 transgenic mice display a severe loss of Amel expression on the labial side of the lower incisors, as well as enamel hypoplasia-consistent with the human ARS phenotype. Collectively, these findings define transcriptional mechanisms involved in normal tooth development and shed light on the molecular underpinnings of the enamel defect observed in ARS patients who carry PITX2 mutations. Moreover, our findings validate the etiology of the enamel defect in a novel mouse model of ARS.
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Affiliation(s)
- Xiao Li
- Department of Anatomy and Cell Biology and Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52244, USA
| | - Shankar R. Venugopalan
- Department of Anatomy and Cell Biology and Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52244, USA
| | - Huojun Cao
- Department of Anatomy and Cell Biology and Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52244, USA
| | - Flavia O. Pinho
- Department of Anatomy and Cell Biology and Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52244, USA
| | - Michael L. Paine
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA and
| | - Malcolm L. Snead
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA and
| | - Elena V. Semina
- Division of Developmental Biology, Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Brad A. Amendt
- Department of Anatomy and Cell Biology and Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52244, USA
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86
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McKinnon PJ. Maintaining genome stability in the nervous system. Nat Neurosci 2013; 16:1523-9. [PMID: 24165679 PMCID: PMC4112580 DOI: 10.1038/nn.3537] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 09/11/2013] [Indexed: 01/09/2023]
Abstract
Active maintenance of genome stability is a prerequisite for the development and function of the nervous system. The high replication index during neurogenesis and the long life of mature neurons highlight the need for efficient cellular programs to safeguard genetic fidelity. Multiple DNA damage response pathways ensure that replication stress and other types of DNA lesions, such as oxidative damage, do not affect neural homeostasis. Numerous human neurologic syndromes result from defective DNA damage signaling and compromised genome integrity. These syndromes can involve different neuropathology, which highlights the diverse maintenance roles that are required for genome stability in the nervous system. Understanding how DNA damage signaling pathways promote neural development and preserve homeostasis is essential for understanding fundamental brain function.
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Affiliation(s)
- Peter J. McKinnon
- Department of Genetics, St Jude Children’s Research Hospital, Memphis TN, USA
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87
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Watson M, Stott K, Fischl H, Cato L, Thomas JO. Characterization of the interaction between HMGB1 and H3-a possible means of positioning HMGB1 in chromatin. Nucleic Acids Res 2013; 42:848-59. [PMID: 24157840 PMCID: PMC3902940 DOI: 10.1093/nar/gkt950] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
High mobility group protein B1 (HMGB1) binds to the internucleosomal linker DNA in chromatin and abuts the nucleosome. Bending and untwisting of the linker DNA results in transmission of strain to the nucleosome core, disrupting histone/DNA contacts. An interaction between H3 and HMGB1 has been reported. Here we confirm and characterize the interaction of HMGB1 with H3, which lies close to the DNA entry/exit points around the nucleosome dyad, and may be responsible for positioning of HMGB1 on the linker DNA. We show that the interaction is between the N-terminal unstructured tail of H3 and the C-terminal unstructured acidic tail of HMGB1, which are presumably displaced from DNA and the HMG boxes, respectively, in the HMGB1-nucleosome complex. We have characterized the interaction by nuclear magnetic resonance spectroscopy and show that it is extensive for both peptides, and appears not to result in the acquisition of significant secondary structure by either partner.
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Affiliation(s)
| | | | | | | | - Jean O. Thomas
- *To whom correspondence should be addressed. Tel: +44 1223 333670; Fax: +44 1223 766002;
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88
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Verma SC, Cai Q, Kreider E, Lu J, Robertson ES. Comprehensive analysis of LANA interacting proteins essential for viral genome tethering and persistence. PLoS One 2013; 8:e74662. [PMID: 24040311 PMCID: PMC3770571 DOI: 10.1371/journal.pone.0074662] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2013] [Accepted: 08/05/2013] [Indexed: 12/12/2022] Open
Abstract
Kaposi’s sarcoma associated herpesvirus is tightly linked to multiple human malignancies including Kaposi’s sarcoma (KS), Primary Effusion Lymphoma (PEL) and Multicentric Castleman’s Disease (MCD). KSHV like other herpesviruses establishes life-long latency in the infected host by persisting as chromatin and tethering to host chromatin through the virally encoded protein Latency Associated Nuclear Antigen (LANA). LANA, a multifunctional protein, is capable of binding to a large number of cellular proteins responsible for transcriptional regulation of various cellular and viral pathways involved in blocking cell death and promoting cell proliferation. This leads to enhanced cell division and replication of the viral genome, which segregates faithfully in the dividing tumor cells. The mechanism of genome segregation is well known and the binding of LANA to nucleosomal proteins, throughout the cell cycle, suggests that these interactions play an important role in efficient segregation. Various biochemical methods have identified a large number of LANA binding proteins, including histone H2A/H2B, histone H1, MeCP2, DEK, CENP-F, NuMA, Bub1, HP-1, and Brd4. These nucleosomal proteins may have various functions in tethering of the viral genome during specific phases of the viral life cycle. Therefore, we performed a comprehensive analysis of their interaction with LANA using a number of different assays. We show that LANA binds to core nucleosomal histones and also associates with other host chromatin proteins including histone H1 and high mobility group proteins (HMGs). We used various biochemical assays including co-immunoprecipitation and in-vivo localization by split GFP and fluorescence resonance energy transfer (FRET) to demonstrate their association.
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Affiliation(s)
- Subhash C. Verma
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, Nevada, United States of America
- * E-mail: (ESR); (SCV)
| | - Qiliang Cai
- MOE& MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine of Fudan University, Shanghai, China
| | - Edward Kreider
- Department of Microbiology and Tumor Virology Program of the Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jie Lu
- Department of Microbiology and Tumor Virology Program of the Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Erle S. Robertson
- Department of Microbiology and Tumor Virology Program of the Abramson Comprehensive Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (ESR); (SCV)
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Li G, Tang D, Lotze MT. Ménage à Trois in stress: DAMPs, redox and autophagy. Semin Cancer Biol 2013; 23:380-90. [PMID: 23994764 DOI: 10.1016/j.semcancer.2013.08.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/08/2013] [Accepted: 08/20/2013] [Indexed: 12/30/2022]
Abstract
Cells have evolved rather sophisticated mechanisms to deal with stress positively and efficiently. Accumulation of reactive oxygen species (ROS), release of damage-associated molecular pattern molecule (DAMPs), and autophagy induction, are three inter-related processes occurring during most if not all cellular adaptations to stress. They influence each other reciprocally, initiating individual pathways, mediating and/or inducing effector mechanisms and modifying cellular function. High-mobility group box 1 (HMGB1), is a prototypic DAMP molecule, with various roles depending on its compartmental localization (nuclear, cytosolic, extracellular), well-defined but rather promiscuous binding partners, and the redox status within or without the cell. Typically, HMGB1 serves as a redox sensor, where redox modification also defines its translocation, release and activity, illustrative of the coordinate and multiply determined paths involved in the response to cell stress. Since DAMPs, redox and autophagy are essential and multifaceted in their roles in host defense, inflammation, and homeostasis, understanding how they interact and coordinate various signaling pathways to adjust to the stressful environment is important in the development of various potential therapeutic strategies, including application to patients with cancer.
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Affiliation(s)
- Guanqiao Li
- Department of Surgery, University of Pittsburgh School of Medicine and the University of Pittsburgh Cancer Institute, United States; Department of Immunology, University of Pittsburgh School of Medicine and the University of Pittsburgh Cancer Institute, United States; Tsinghua University, School of Medicine, Beijing, China
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Cirillo P, Giallauria F, Palma VD, Maresca F, Ziviello F, Bevilacqua M, Vigorito C, Trimarco B. Cardiovascular Disease and High-Mobility Group Box 1—Is a New Inflammatory Killer in Town? Angiology 2013; 64:343-355. [DOI: 10.1177/0003319712458032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
High-mobility group box 1 (HMGB-1) is a nuclear protein physiologically involved in the maintaining of DNA structure in the nucleus. When tissue damage occurs, necrotic cells as well as inflammatory cells, once activated, release this protein in circulating blood, where it seems to exert a direct proinflammatory action. Thus, HMGB-1 might be involved in the pathophysiology of several diseases, including cardiovascular disease. However, the experimental evidence has not yet clarified its cardiovascular role which is still debated. Specifically, it is still not completely resolved whether HMGB-1 plays a protective or detrimental role on cardiovascular function. In this review, we consider the role of HMGB-1 in pathological conditions and comment on the role of this protein in the cardiovascular disease.
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Affiliation(s)
- Plinio Cirillo
- Department of Clinical Medicine, Cardiovascular and Immunological Science, University of Naples “Federico II,” Naples, Italy
| | - Francesco Giallauria
- Department of Clinical Medicine, Cardiovascular and Immunological Science, University of Naples “Federico II,” Naples, Italy
| | - Vito Di Palma
- Department of Clinical Medicine, Cardiovascular and Immunological Science, University of Naples “Federico II,” Naples, Italy
| | - Fabio Maresca
- Department of Clinical Medicine, Cardiovascular and Immunological Science, University of Naples “Federico II,” Naples, Italy
| | - Francesca Ziviello
- Department of Clinical Medicine, Cardiovascular and Immunological Science, University of Naples “Federico II,” Naples, Italy
| | - Michele Bevilacqua
- Department of Clinical Medicine, Cardiovascular and Immunological Science, University of Naples “Federico II,” Naples, Italy
| | - Carlo Vigorito
- Department of Clinical Medicine, Cardiovascular and Immunological Science, University of Naples “Federico II,” Naples, Italy
| | - Bruno Trimarco
- Department of Clinical Medicine, Cardiovascular and Immunological Science, University of Naples “Federico II,” Naples, Italy
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91
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Mukherjee RM, Shravanti GV, Jakkampudi A, Kota R, Jangala AL, Reddy PB, Rao PN, Gupta R, Reddy DN. Reduced Expression of DNA Damage Repair Genes High Mobility Group Box1 and Poly(ADP-ribose) Polymerase1 in Inactive Carriers of Hepatitis B Virus Infection-A Possible Stage of Viral Integration. J Clin Exp Hepatol 2013; 3:89-95. [PMID: 25755481 PMCID: PMC3940113 DOI: 10.1016/j.jceh.2013.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 04/25/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND High mobility group box1 (HMGB1) and poly(ADP-ribose) polymerase1 (PARP1) proteins repair cellular DNA damage. Reduced expression of the corresponding genes can lead to an impaired DNA damage repair mechanism. Intracellular replication of hepatitis B virus (HBV) in such conditions can favor the integration of viral DNA into host genome leading to the development of hepatocellular carcinoma (HCC). OBJECTIVE This study was performed to assess the expression of HMGB1 and PARP1 mRNAs in conjunction with the estimation of HBV replication intermediate pregenomic RNA (PgRNA) in various phases of HBV infection. MATERIALS Eighty eight patients and 26 voluntary blood donors as controls were included in the study. Patients were grouped in to acute (AHB; n = 15), inactive carriers (IC; n = 36), cirrhosis (Cirr; n = 25) and hepatocellular carcinoma (HCC; n = 12). Serum HBV DNA was quantified by real time polymerase chain reaction (PCR) assay. Expression of HMGB1, PARP1 and PgRNA were evaluated using peripheral blood mononuclear cells (PBMCs) derived RNA by reverse transcription PCR (RT-PCR) and densitometry. RESULTS Significant reduction of HMGB1 and PARP1 gene expressions (P < 0.05) were observed in patients than controls with more explicit decline of PARP1 (P = 0.0002). Both genes were significantly downregulated (P < 0.001) in ICs than controls. In ICs, HMGB1 was significantly lowered than cirrhosis (P = 0.002) and HCC (P = 0.0006) while PARP1 declined significantly (P = 0.04) than HCC. Level of PgRNA was comparable in all the disease categories. CONCLUSION In conclusion, our findings indicate impaired DNA damage repair mechanisms in HBV infected cells of ICs. This, along with low viral load but higher level of PgRNA in this group is suggestive of the diversion of HBV replication pathway that might facilitate viral DNA integration in to host genome. Intrusion of HBV PgRNA reverse transcription in early stage of infection might appear advantageous to thwart the development of HCC.
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Key Words
- ADP, adenosine diphosphate
- AHB, acute hepatitis B
- ALT, alanine transferase
- AST, aspartate transferase
- BER, base excision repair
- CHB, chronic HBV
- CIRRH, cirrhosis
- CP, Child–Pugh
- DEPC, diethyl pyrocarbonate
- DTT, dithiothreitol
- ELISA, enzyme-linked immunosorbent assay
- HAV, hepatitis A virus
- HBV, hepatitis B virus
- HBX, hepatitis B virus X protein
- HBeAg, hepatitis B virus e antigen
- HBsAg, hepatitis B virus surface antigen
- HCC, hepatocellular carcinoma
- HDV, hepatitis delta virus
- HEV, hepatitis E virus
- HIV, human immunodeficiency virus
- HMGB1, high mobility group box1
- IC, inactive carriers
- IgG, immunoglobulin G
- IgM, immunoglobulin M
- MuLV-H, moloney murine leukemia virus Rnase H
- NER, nucleotide excision repair
- PARP1, poly(ADP-ribose) polymerase1
- PBMCs, peripheral blood mononuclear cells
- PCR, polymerase chain reaction
- PgRNA, pregenomic RNA
- RT-PCR, reverse transcription PCR
- SD, standard deviation
- UISs, unique integration sites
- cccDNA, covalently closed circular DNA
- dNTPs, deoxynucleoside triphosphates
- dsDNA, double stranded HBV DNA
- gene expression
- hepatitis B virus
- high mobility group box1
- poly(ADP-ribose) polymerase1
- pregenomic RNA
- rcDNA, relaxed circular DNA
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Affiliation(s)
- Rathindra M. Mukherjee
- Asian Health Care Foundation, Institute of Basic and Translational Research, 6-3-661, Somajiguda, Hyderabad 500082, India
- Address for correspondence: Dr. R.M. Mukherjee, Institute of Basic and Translational Research, Asian Health Care Foundation, 6-3-661, Somajiguda, Hyderabad 500082, India. Tel.: +91 40 23378888x742; fax: +91 40 23324255.
| | | | - Aparna Jakkampudi
- Asian Health Care Foundation, Institute of Basic and Translational Research, 6-3-661, Somajiguda, Hyderabad 500082, India
| | - Ramya Kota
- Asian Health Care Foundation, Institute of Basic and Translational Research, 6-3-661, Somajiguda, Hyderabad 500082, India
| | - Asha L. Jangala
- Asian Health Care Foundation, Institute of Basic and Translational Research, 6-3-661, Somajiguda, Hyderabad 500082, India
| | - Panyala B. Reddy
- Asian Health Care Foundation, Institute of Basic and Translational Research, 6-3-661, Somajiguda, Hyderabad 500082, India
| | - Padaki N. Rao
- Asian Institute of Gastroenterology, Somajiguda, Hyderabad, India
| | - Rajesh Gupta
- Asian Institute of Gastroenterology, Somajiguda, Hyderabad, India
| | - Duvvuru N. Reddy
- Asian Institute of Gastroenterology, Somajiguda, Hyderabad, India
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92
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Kugler JE, Horsch M, Huang D, Furusawa T, Rochman M, Garrett L, Becker L, Bohla A, Hölter SM, Prehn C, Rathkolb B, Racz I, Aguilar-Pimentel JA, Adler T, Adamski J, Beckers J, Busch DH, Eickelberg O, Klopstock T, Ollert M, Stöger T, Wolf E, Wurst W, Yildirim AÖ, Zimmer A, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Garfinkel B, Orly J, Ovcharenko I, Bustin M. High mobility group N proteins modulate the fidelity of the cellular transcriptional profile in a tissue- and variant-specific manner. J Biol Chem 2013; 288:16690-16703. [PMID: 23620591 DOI: 10.1074/jbc.m113.463315] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nuclei of most vertebrate cells contain members of the high mobility group N (HMGN) protein family, which bind specifically to nucleosome core particles and affect chromatin structure and function, including transcription. Here, we study the biological role of this protein family by systematic analysis of phenotypes and tissue transcription profiles in mice lacking functional HMGN variants. Phenotypic analysis of Hmgn1(tm1/tm1), Hmgn3(tm1/tm1), and Hmgn5(tm1/tm1) mice and their wild type littermates with a battery of standardized tests uncovered variant-specific abnormalities. Gene expression analysis of four different tissues in each of the Hmgn(tm1/tm1) lines reveals very little overlap between genes affected by specific variants in different tissues. Pathway analysis reveals that loss of an HMGN variant subtly affects expression of numerous genes in specific biological processes. We conclude that within the biological framework of an entire organism, HMGNs modulate the fidelity of the cellular transcriptional profile in a tissue- and HMGN variant-specific manner.
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Affiliation(s)
- Jamie E Kugler
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Marion Horsch
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Di Huang
- Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Mark Rochman
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Lillian Garrett
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alexander Bohla
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Cornelia Prehn
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Birgit Rathkolb
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ildikó Racz
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Juan Antonio Aguilar-Pimentel
- Center of Allergy and Environment, Technische Universität München, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Dermatology and Allergy, Biederstein, Technische Universität München and Clinical Research Division of Molecular and Clinical Allergotoxicology, Technische Universität München, Munich, Germany
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Institute of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, München, Germany
| | - Jerzy Adamski
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85350 Freising-Weihenstephan, Germany
| | - Johannes Beckers
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Dirk H Busch
- Institute of Medical Microbiology, Immunology, and Hygiene, Technische Universität München, München, Germany
| | - Oliver Eickelberg
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institut, Ludwig-Maximilians-Universität München, Munich, Germany; German Center for Vertigo and Balance Disorders, Technische Universität München, Munich, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen-German Center for Neurodegenerative Diseases, Site Munich, Munich, Germany
| | - Markus Ollert
- Department of Dermatology and Allergy, Biederstein, Technische Universität München and Clinical Research Division of Molecular and Clinical Allergotoxicology, Technische Universität München, Munich, Germany
| | - Tobias Stöger
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Eckhard Wolf
- Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Wolfgang Wurst
- German Mouse Clinic, Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen-German Center for Neurodegenerative Diseases, Site Munich, Munich, Germany; Max Planck Institute of Psychiatry, Munich, Germany; Developmental Genetics, Technische Universität München c/o Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ali Önder Yildirim
- German Mouse Clinic, Comprehensive Pneumology Center, Institute of Lung Biology and Disease, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Lung Research, Munich, Germany
| | - Andreas Zimmer
- Institute of Molecular Psychiatry, University of Bonn, Bonn, Germany
| | - Valérie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany; Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany; German Center for Vertigo and Balance Disorders, Technische Universität München, Munich, Germany; German Center for Diabetes Research, Neuherberg, Germany
| | - Benny Garfinkel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Joseph Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ivan Ovcharenko
- Computational Biology Branch, NCBI, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20892
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892.
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Narayanan MS, Rudenko G. TDP1 is an HMG chromatin protein facilitating RNA polymerase I transcription in African trypanosomes. Nucleic Acids Res 2013; 41:2981-92. [PMID: 23361461 PMCID: PMC3597664 DOI: 10.1093/nar/gks1469] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Unusually for a eukaryote, Trypanosoma brucei transcribes its variant surface glycoprotein (VSG) gene expression sites (ESs) in a monoallelic fashion using RNA polymerase I (Pol I). It is still unclear how ES transcription is controlled in T. brucei. Here, we show that the TDP1 architectural chromatin protein is an essential high mobility group box (HMGB) protein facilitating Pol I transcription in T. brucei. TDP1 is specifically enriched at the active compared with silent VSG ES and immediately downstream of ribosomal DNA promoters and is abundant in the nucleolus and the expression site body subnuclear compartments. Distribution of TDP1 at Pol I-transcribed loci is inversely correlated with histones. Depletion of TDP1 results in up to 40–90% reduction in VSG and rRNA transcripts and a concomitant increase in histones H3, H2A and H1 at these Pol I transcription units. TDP1 shares features with the Saccharomyces cerevisiae HMGB protein Hmo1, but it is the first architectural chromatin protein facilitating Pol I-mediated transcription of both protein coding genes as well as rRNA. These results show that TDP1 has a mutually exclusive relationship with histones on actively transcribed Pol I transcription units, providing insight into how Pol I transcription is controlled.
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Affiliation(s)
- Mani Shankar Narayanan
- Division of Cell and Molecular Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
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94
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Coppotelli G, Mughal N, Callegari S, Sompallae R, Caja L, Luijsterburg MS, Dantuma NP, Moustakas A, Masucci MG. The Epstein-Barr virus nuclear antigen-1 reprograms transcription by mimicry of high mobility group A proteins. Nucleic Acids Res 2013; 41:2950-62. [PMID: 23358825 PMCID: PMC3597695 DOI: 10.1093/nar/gkt032] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Viral proteins reprogram their host cells by hijacking regulatory components of protein networks. Here we describe a novel property of the Epstein-Barr virus (EBV) nuclear antigen-1 (EBNA1) that may underlie the capacity of the virus to promote a global remodeling of chromatin architecture and cellular transcription. We found that the expression of EBNA1 in transfected human and mouse cells is associated with decreased prevalence of heterochromatin foci, enhanced accessibility of cellular DNA to micrococcal nuclease digestion and decreased average length of nucleosome repeats, suggesting de-protection of the nucleosome linker regions. This is a direct effect of EBNA1 because targeting the viral protein to heterochromatin promotes large-scale chromatin decondensation with slow kinetics and independent of the recruitment of adenosine triphosphate-dependent chromatin remodelers. The remodeling function is mediated by a bipartite Gly-Arg rich domain of EBNA1 that resembles the AT-hook of High Mobility Group A (HMGA) architectural transcription factors. Similar to HMGAs, EBNA1 is highly mobile in interphase nuclei and promotes the mobility of linker histone H1, which counteracts chromatin condensation and alters the transcription of numerous cellular genes. Thus, by regulating chromatin compaction, EBNA1 may reset cellular transcription during infection and prime the infected cells for malignant transformation.
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Affiliation(s)
- Giuseppe Coppotelli
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
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95
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The Gly-Ala repeat modulates the interaction of Epstein-Barr virus nuclear antigen-1 with cellular chromatin. Biochem Biophys Res Commun 2013; 431:706-11. [PMID: 23348225 DOI: 10.1016/j.bbrc.2013.01.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 01/12/2013] [Indexed: 11/24/2022]
Abstract
The Epstein-Barr virus (EBV) nuclear antigen-1 (EBNA1) plays a pivotal role in EBV infection by anchoring the viral episome to cellular DNA, which regulates replication and partitioning in dividing cells. Here, we have used fluorescence recovery after photobleaching (FRAP) and fluorescence loss in photobleaching (FLIP) techniques to study the interaction of EBNA1 with cellular chromatin in interphase and mitosis. This analysis revealed that while EBNA1 is highly mobile in both conditions, mobility is significantly reduced in mitosis when an immobile fraction is also detected. The N-terminal chromatin-targeting module of EBNA1 includes two Gly-Arg rich domains (GR1 and GR2) separated by a Gly-Ala repeat (GAr) of variable length. Using a set of deletion mutants and GFP-fusion reporters, we found that the GR domains cooperatively determine the mobility of EBNA1, whereas mobility is increased by the interposed GAr in a length-dependent manner. These findings highlight a previously unrecognized property of the interaction of EBNA1 with cellular chromatin that may fine-tune its function in the maintenance of viral latency.
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96
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Kishi Y, Fujii Y, Hirabayashi Y, Gotoh Y. HMGA regulates the global chromatin state and neurogenic potential in neocortical precursor cells. Nat Neurosci 2012; 15:1127-33. [PMID: 22797695 DOI: 10.1038/nn.3165] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/20/2012] [Indexed: 12/13/2022]
Abstract
Neural precursor cells (NPCs) in the mouse neocortex generate various neuronal and glial cell types in a developmental stage–dependent manner. Most NPCs lose their neurogenic potential during development, although the underlying mechanisms of this process are not fully understood. We found that the chromatin of mouse NPCs gradually becomes more condensed and less dynamic on a global scale during neocortical development. Furthermore, we found high mobility group A (HMGA) proteins to be essential for the open chromatin state of NPCs at early developmental stages. Knockdown of HMGA proteins in early-stage NPCs reduced their neurogenic potential. Conversely, overexpression of HMGA proteins conferred neurogenic potential on late-stage NPCs, an effect that was antagonized by coexpression of a histone H1 mutant that inhibits chromatin opening. Thus, HMGA proteins contribute to the neurogenic potential of NPCs in the early stages of neocortical development, possibly through induction of an open chromatin state.
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Affiliation(s)
- Yusuke Kishi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
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97
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Rowell JP, Simpson KL, Stott K, Watson M, Thomas JO. HMGB1-facilitated p53 DNA binding occurs via HMG-Box/p53 transactivation domain interaction, regulated by the acidic tail. Structure 2012; 20:2014-24. [PMID: 23063560 DOI: 10.1016/j.str.2012.09.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2012] [Revised: 08/10/2012] [Accepted: 09/07/2012] [Indexed: 01/13/2023]
Abstract
Facilitated binding of p53 to DNA by high mobility group B1 (HMGB1) may involve interaction between the N-terminal region of p53 and the high mobility group (HMG) boxes, as well as HMG-induced bending of the DNA. Intramolecular shielding of the boxes by the HMGB1 acidic tail results in an unstable complex with p53 until the tail is truncated to half its length, at which point the A box, proposed to be the preferred binding site for p53(1-93), is exposed, leaving the B box to bind and bend DNA. The A box interacts with residues 38-61 (TAD2) of the p53 transactivation domain. Residues 19-26 (TAD1) bind weakly, but only in the context of p53(1-93) and not as a free TAD1 peptide. We have solved the structure of the A-box/p53(1-93) complex by nuclear magnetic resonance spectroscopy. The incipient amphipathic helix in TAD2 recognizes the concave DNA-binding face of the A box and may be acting as a single-stranded DNA mimic.
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Affiliation(s)
- John P Rowell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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98
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Schubert T, Pusch MC, Diermeier S, Benes V, Kremmer E, Imhof A, Längst G. Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin. Mol Cell 2012; 48:434-44. [PMID: 23022379 DOI: 10.1016/j.molcel.2012.08.021] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 07/02/2012] [Accepted: 08/07/2012] [Indexed: 12/13/2022]
Abstract
Packaging of DNA into nucleosomes and the formation of higher-order chromatin structures determine DNA accessibility and activity of genome domains. We identified an RNA-dependent mechanism maintaining the open chromatin structure within euchromatic regions in Drosophila cells. The mechanism of reversible chromatin opening, reconstituted in vitro, depends on the Drosophila decondensation factor 31 (Df31) that specifically binds to RNA and localizes to euchromatic regions. Df31 is capable to tether a heterogeneous pool of short, single-stranded RNAs to chromatin. This class of chromatin-associated RNA (caRNA) is stably linked to chromatin and is largely composed of snoRNAs, which are preferentially bound by Df31. We suggest that the Df31-mediated linkage of snoRNAs and chromatin, forms a RNA-chromatin network resulting in the establishment of open chromatin domains. Analysis of caRNAs in human cells also reveals a strong enrichment of snoRNAs, implying a conserved role for these molecules in higher-order structures of chromatin.
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Affiliation(s)
- Thomas Schubert
- Institut für Biochemie III, Universität Regensburg, Universitätsstrasse 31. 93053 Regensburg, Germany
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99
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Antosch M, Mortensen SA, Grasser KD. Plant proteins containing high mobility group box DNA-binding domains modulate different nuclear processes. PLANT PHYSIOLOGY 2012; 159:875-83. [PMID: 22585776 PMCID: PMC3387713 DOI: 10.1104/pp.112.198283] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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100
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Öberg C, Izzo A, Schneider R, Wrange Ö, Belikov S. Linker Histone Subtypes Differ in Their Effect on Nucleosomal Spacing In Vivo. J Mol Biol 2012; 419:183-97. [DOI: 10.1016/j.jmb.2012.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/17/2012] [Accepted: 03/12/2012] [Indexed: 10/28/2022]
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