1
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Zhang S, Postnikov Y, Lobanov A, Furusawa T, Deng T, Bustin M. H3K27ac nucleosomes facilitate HMGN localization at regulatory sites to modulate chromatin binding of transcription factors. Commun Biol 2022; 5:159. [PMID: 35197580 PMCID: PMC8866397 DOI: 10.1038/s42003-022-03099-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 02/01/2022] [Indexed: 11/09/2022] Open
Abstract
Nucleosomes containing acetylated H3K27 are a major epigenetic mark of active chromatin and identify cell-type specific chromatin regulatory regions which serve as binding sites for transcription factors. Here we show that the ubiquitous nucleosome binding proteins HMGN1 and HMGN2 bind preferentially to H3K27ac nucleosomes at cell-type specific chromatin regulatory regions. HMGNs bind directly to the acetylated nucleosome; the H3K27ac residue and linker DNA facilitate the preferential binding of HMGNs to the modified nucleosomes. Loss of HMGNs increases the levels of H3K27me3 and the histone H1 occupancy at enhancers and promoters and alters the interaction of transcription factors with chromatin. These experiments indicate that the H3K27ac epigenetic mark enhances the interaction of architectural protein with chromatin regulatory sites and identify determinants that facilitate the localization of HMGN proteins at regulatory sites to modulate cell-type specific gene expression.
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Affiliation(s)
- Shaofei Zhang
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Yuri Postnikov
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Maryland, MD, USA
| | - Takashi Furusawa
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
| | - Tao Deng
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA
- Cell Translation Laboratory, NCATS, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD, 20850, USA
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, Maryland, USA.
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2
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Gould TJ, Tóth K, Mücke N, Langowski J, Hakusui AS, Olins AL, Olins DE. Defining the epichromatin epitope. Nucleus 2017; 8:625-640. [PMID: 28960120 DOI: 10.1080/19491034.2017.1380141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Epichromatin is identified by immunostaining fixed and permeabilized cells with particular bivalent anti-nucleosome antibodies (mAbs PL2-6 and 1H6). During interphase, epichromatin resides adjacent to the inner nuclear membrane; during mitosis, at the outer surface of mitotic chromosomes. By STED (stimulated emission depletion) microscopy, PL2-6 stained interphase epichromatin is ∼76 nm thick and quite uniform; mitotic epichromatin is more variable in thickness, exhibiting a "wrinkled" surface with an average thickness of ∼78 nm. Co-immunostaining with anti-Ki-67 demonstrates Ki-67 deposition between the PL2-6 "ridges" of mitotic epichromatin. Monovalent papain-derived Fab fragments of PL2-6 yield a strikingly different punctate "chromomeric" immunostaining pattern throughout interphase nuclei and along mitotic chromosome arms. Evidence from electrophoretic mobility shift assay (EMSA) and from analytical ultracentrifugation characterize the Fab/mononucleosome complex, supporting the concept that there are two binding sites per nucleosome. The peptide sequence of the Hv3 region (heavy chain variable region 3) of the PL2-6 antibody binding site strongly resembles other nucleosome acidic patch binding proteins (especially, LANA and CENPC), supporting that the nucleosome acidic patch is included within the epichromatin epitope. It is speculated that the interphase epichromatin epitope is "exposed" with favorable geometric arrangements for binding bivalent PL2-6 at the surface chromatin; whereas, the epitope is "hidden" within internal chromatin. Furthermore, it is suggested that the "exposed" nucleosome surface of mitotic epichromatin may play a role in post-mitotic nuclear envelope reformation.
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Affiliation(s)
- Travis J Gould
- a Department of Physics & Astronomy , Bates College , Lewiston , ME , USA
| | - Katalin Tóth
- b Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Norbert Mücke
- b Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jörg Langowski
- b Division of Biophysics of Macromolecules, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | | | - Ada L Olins
- c Department of Pharmaceutical Sciences , College of Pharmacy, University of New England , Portland , ME , USA
| | - Donald E Olins
- c Department of Pharmaceutical Sciences , College of Pharmacy, University of New England , Portland , ME , USA
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3
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Shimahara H, Hirano T, Ohya K, Matsuta S, Seeram SS, Tate SI. Nucleosome structural changes induced by binding of non-histone chromosomal proteins HMGN1 and HMGN2. FEBS Open Bio 2013; 3:184-91. [PMID: 23772392 PMCID: PMC3668530 DOI: 10.1016/j.fob.2013.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/18/2013] [Accepted: 03/20/2013] [Indexed: 01/07/2023] Open
Abstract
Interactions between the nucleosome and the non-histone chromosomal proteins (HMGN1 and HMGN2) were studied by circular dichroism (CD) spectroscopy to elucidate structural changes in the nucleosome induced by HMGN binding. Unlike previous studies that used a nucleosome extracted from living cells, in this study we utilized a nucleosome reconstituted from unmodified recombinant histones synthesized in Escherichia coli and a 189-bp synthetic DNA fragment harboring a nucleosome positioning sequence. This DNA fragment consists of 5′-TATAAACGCC-3′ repeats that has a high affinity to the histone octamer. A nucleosome containing a unique octamer-binding sequence at a specific location on the DNA was produced at sufficiently high yield for spectroscopic analysis. CD data have indicated that both HMGN1 and HMGN2 can increase the winding angle of the nucleosome DNA, but the extent of the structural changes induced by these proteins differs significantly. This suggests HMGN1 and HMGN2 would have different abilities to facilitate nucleosome remodeling. A nucleosome was reconstituted from recombinant histones and a synthetic DNA. Nucleosomes were produced at sufficiently high yield for spectroscopic analysis. A nucleosome with and without HMGN proteins was analyzed using CD spectroscopy. CD data indicate that HMGN proteins increase the winding angle of the nucleosome DNA. HMGN1 and HMGN2 may have different abilities to facilitate nucleosome remodeling.
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Key Words
- CD
- CD, circular dichroism
- HMG, high mobility group
- HMGN
- HMGN1 HMGN2, non-histone chromosomal proteins
- IPTG, isopropyl-β-d-galactopyranoside
- LB, Luria–Bertani
- MNase, micrococcal nuclease
- NMR, nuclear magnetic resonance
- Nucleosome
- PCR, polymerase chain reaction
- RP-HPLC, reverse phase high performance liquid chromatography
- Reconstitution
- SDS–PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis
- Unmodified recombinant histones
- phH2A, phH2B, phH3, and phH4, vectors for the gene expression of all four recombinant human core histones H2A, H2B, H3, and H4, respectively
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Affiliation(s)
- Hideto Shimahara
- Corresponding author. Tel.: +81 761 51 1478; fax: +81 761 51 1455.
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4
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Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR. Proc Natl Acad Sci U S A 2011; 108:12283-8. [PMID: 21730181 DOI: 10.1073/pnas.1105848108] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromatin structure and function are regulated by numerous proteins through specific binding to nucleosomes. The structural basis of many of these interactions is unknown, as in the case of the high mobility group nucleosomal (HMGN) protein family that regulates various chromatin functions, including transcription. Here, we report the architecture of the HMGN2-nucleosome complex determined by a combination of methyl-transverse relaxation optimized nuclear magnetic resonance spectroscopy (methyl-TROSY) and mutational analysis. We found that HMGN2 binds to both the acidic patch in the H2A-H2B dimer and to nucleosomal DNA near the entry/exit point, "stapling" the histone core and the DNA. These results provide insight into how HMGNs regulate chromatin structure through interfering with the binding of linker histone H1 to the nucleosome as well as a structural basis of how phosphorylation induces dissociation of HMGNs from chromatin during mitosis. Importantly, our approach is generally applicable to the study of nucleosome-binding interactions in chromatin.
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5
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Genomic profiling of HMGN1 reveals an association with chromatin at regulatory regions. Mol Cell Biol 2010; 31:700-9. [PMID: 21173166 DOI: 10.1128/mcb.00740-10] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The interaction of architectural proteins such as the linker histone H1 and high-mobility-group (HMG) proteins with nucleosomes leads to changes in chromatin structure and histone modifications and alters the cellular transcription profile. The interaction of HMG proteins with chromatin is dynamic. However, it is not clear whether the proteins are constantly and randomly redistributed among all the nucleosomes or whether they preferentially associate with, and turn over at, specific regions in chromatin. To address this question, we examined the genome-wide distribution of the nucleosome binding protein HMGN1 and compared it to that of regulatory chromatin marks. We find that HMGN1 is not randomly distributed throughout the genome. Instead, the protein preferentially localizes to DNase I hypersensitive (HS) sites, promoters, functional enhancers, and transcription factor binding sites. Our results suggest that HMGN1 is part of the cellular machinery that modulates transcriptional fidelity by generating, maintaining, or preferentially interacting with specific sites in chromatin.
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6
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Ong MS, Vasudevan D, Davey CA. Divalent metal- and high mobility group N protein-dependent nucleosome stability and conformation. J Nucleic Acids 2010; 2010:143890. [PMID: 21188164 PMCID: PMC3005839 DOI: 10.4061/2010/143890] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 09/29/2010] [Indexed: 11/21/2022] Open
Abstract
High mobility group N proteins (HMGNs) bind specifically to the nucleosome core and act as chromatin unfolding and activating factors. Using an all-Xenopus system, we found that HMGN1 and HMGN2 binding to nucleosomes results in distinct ion-dependent conformation and stability. HMGN2 association with nucleosome core particle or nucleosomal array in the presence of divalent metal triggers a reversible transition to a species with much reduced electrophoretic mobility, consistent with a less compact state of the nucleosome. Residues outside of the nucleosome binding domain are required for the activity, which is also displayed by an HMGN1 truncation product lacking part of the regulatory domain. In addition, thermal denaturation assays show that the presence of 1 mM Mg2+> or Ca2+ gives a reduction in nucleosome core terminus stability, which is further substantially diminished by the binding of HMGN2 or truncated HMGN1. Our findings emphasize the importance of divalent metals in nucleosome dynamics and suggest that the differential biological activities of HMGNs in chromatin activation may involve different conformational alterations and modulation of nucleosome core stability.
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Affiliation(s)
- Michelle S Ong
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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7
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Biochemical analyses of nuclear receptor-dependent transcription with chromatin templates. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 87:137-92. [PMID: 20374704 DOI: 10.1016/s1877-1173(09)87005-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Chromatin, the physiological template for transcription, plays important roles in gene regulation by nuclear receptors (NRs). It can (1) restrict the binding of NRs or the transcriptional machinery to their genomic targets, (2) serve as a target of regulatory posttranslational modifications by NR coregulator proteins with histone-directed enzymatic activities, and (3) function as a binding scaffold for a variety of transcription-related proteins. The advent of in vitro or "cell-free" systems that accurately recapitulate ligand-dependent transcription by NRs with chromatin templates has allowed detailed analyses of these processes. Biochemical studies have advanced our understanding of the mechanisms of gene regulation, including the role of ligands, coregulators, and nucleosome remodeling. In addition, they have provided new insights about the dynamics of NR-mediated transcription. This chapter reviews the current methodologies for assembling, transcribing, and analyzing chromatin in vitro, as well as the new information that has been gained from these studies.
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8
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Rattner BP, Yusufzai T, Kadonaga JT. HMGN proteins act in opposition to ATP-dependent chromatin remodeling factors to restrict nucleosome mobility. Mol Cell 2009; 34:620-6. [PMID: 19524541 DOI: 10.1016/j.molcel.2009.04.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 04/03/2009] [Accepted: 04/10/2009] [Indexed: 12/20/2022]
Abstract
The high-mobility group N (HMGN) proteins are abundant nonhistone chromosomal proteins that bind specifically to nucleosomes at two high-affinity sites. Here we report that purified recombinant human HMGN1 (HMG14) and HMGN2 (HMG17) potently repress ATP-dependent chromatin remodeling by four different molecular motor proteins. In contrast, mutant HMGN proteins with double Ser-to-Glu mutations in their nucleosome-binding domains are unable to inhibit chromatin remodeling. The HMGN-mediated repression of chromatin remodeling is reversible and dynamic. With the ACF chromatin remodeling factor, HMGN2 does not directly inhibit the ATPase activity but rather appears to reduce the affinity of the factor to chromatin. These findings suggest that HMGN proteins serve as a counterbalance to the action of the many ATP-dependent chromatin remodeling activities in the nucleus.
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Affiliation(s)
- Barbara P Rattner
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0347, USA
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9
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Hill DA, Peterson CL, Imbalzano AN. Effects of HMGN1 on chromatin structure and SWI/SNF-mediated chromatin remodeling. J Biol Chem 2005; 280:41777-83. [PMID: 16253989 DOI: 10.1074/jbc.m509637200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The dynamic modulation of chromatin structure is determined by many factors, including enzymes that modify the core histone proteins, enzymes that remodel the structure of chromatin, and factors that bind to genomic DNA to affect its structure. Previous work indicates that the nucleosome binding family of high mobility group proteins (HMGN) facilitates the formation of a chromatin structure that is more conducive for transcription. SWI/SNF complexes are ATP-dependent chromatin remodeling enzymes that alter nucleosome structure to facilitate the binding of various regulatory proteins to chromatin. Here we examine the structural consequences of reconstituting chromatin with HMGN1 and the resulting effects on hSWI/SNF function. We demonstrate that HMGN1 decreases the sedimentation velocity of nucleosomal arrays in low ionic strength buffers but has little effect on the structure of more highly folded arrays. We further demonstrate that HMGN1 does not affect SWI/SNF-dependent chromatin remodeling on either mononucleosomes or nucleosomal arrays, indicating that SWI/SNF functions independently of HMGN1.
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Affiliation(s)
- David A Hill
- Department of Cell Biology at the University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA.
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10
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Affiliation(s)
- Katherine L West
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA
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11
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The role of HMGN proteins in chromatin function. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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12
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Birger Y, Ito Y, West KL, Landsman D, Bustin M. HMGN4, a newly discovered nucleosome-binding protein encoded by an intronless gene. DNA Cell Biol 2001; 20:257-64. [PMID: 11410162 DOI: 10.1089/104454901750232454] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We describe a newly discovered nuclear protein, HMGN4, that is closely related to the canonical HMGN2 nucleosome-binding protein. The protein is encoded by an intronless gene, which, in humans, is located in the hereditary hemochromatosis [correction of hemachromatosis] region at position 6p21.3. A single approximately 2-kb HMGN4 mRNA was found to be expressed, in variable amounts, in all human tissues tested; however, the HMGN4 transcript was significantly less abundant than that of HMGN2. The HMGN4 protein could be detected in HeLa cells by Western analysis with an antibody elicited against a unique region of the protein. Transfection of HeLa cells with a plasmid expressing HMGN4-GFP indicated that the protein localizes to the nucleus. Our results expand the multiplicity of the HMGN protein family and increase the known cellular repertoire of nucleosome-binding proteins.
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Affiliation(s)
- Y Birger
- Protein Section, Laboratory of Metabolism, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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13
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Reeves R, Nissen MS. Purification and assays for high mobility group HMG-I(Y) protein function. Methods Enzymol 1999; 304:155-88. [PMID: 10372360 DOI: 10.1016/s0076-6879(99)04011-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
MESH Headings
- Animals
- Base Sequence
- Cell Fractionation/methods
- Cell Nucleus/chemistry
- Cell Nucleus/ultrastructure
- Centrifugation/methods
- Chromatin/chemistry
- Chromatin/ultrastructure
- Chromatography, High Pressure Liquid/methods
- Chromatography, Ion Exchange/methods
- DNA Footprinting/methods
- DNA, Superhelical/chemistry
- DNA, Superhelical/isolation & purification
- DNA, Superhelical/metabolism
- Deoxyribonuclease I
- HMGA1a Protein
- HeLa Cells
- High Mobility Group Proteins/analysis
- High Mobility Group Proteins/isolation & purification
- High Mobility Group Proteins/metabolism
- Humans
- Indicators and Reagents
- Interleukin-4/genetics
- Leukemia, Erythroblastic, Acute/metabolism
- Leukemia, Erythroblastic, Acute/pathology
- Mice
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Neoplasm Proteins/isolation & purification
- Plasmids
- Receptors, Interleukin-2/genetics
- Recombinant Proteins/analysis
- Recombinant Proteins/isolation & purification
- Recombinant Proteins/metabolism
- Transcription Factors/analysis
- Transcription Factors/isolation & purification
- Transcription Factors/metabolism
- Transfection
- Tumor Cells, Cultured
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Affiliation(s)
- R Reeves
- Department of Biochemistry/Biophysics, Washington State University, Pullman 99164-4660, USA
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14
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Postnikov YV, Bustin M. Reconstitution of high mobility group 14/17 proteins into nucleosomes and chromatin. Methods Enzymol 1999; 304:133-55. [PMID: 10372359 DOI: 10.1016/s0076-6879(99)04010-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- Y V Postnikov
- Protein Section, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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15
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Bustin M, Reeves R. High-mobility-group chromosomal proteins: architectural components that facilitate chromatin function. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 54:35-100. [PMID: 8768072 DOI: 10.1016/s0079-6603(08)60360-8] [Citation(s) in RCA: 568] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- M Bustin
- Laboratory of Molecular Carcinogenesis, National Cancer Institute, National Institute of Health, Bethesda, Maryland 20892, USA
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16
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Paranjape SM, Krumm A, Kadonaga JT. HMG17 is a chromatin-specific transcriptional coactivator that increases the efficiency of transcription initiation. Genes Dev 1995; 9:1978-91. [PMID: 7649479 DOI: 10.1101/gad.9.16.1978] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have examined the effect of HMG17 on transcription by RNA polymerase II by the assembly and analysis of HMG17-containing chromatin templates consisting of regularly spaced nucleosomal arrays. Structural analysis of the chromatin indicated that HMG17 is incorporated into chromatin in a physiological manner with the full complement of core histones. The transcriptional studies revealed that HMG17 stimulates transcription in conjunction with the sequence-specific activator GAL4-VP16. This effect was observed with chromatin, but not with non-nucleosomal templates, and required the presence of HMG17 during chromatin assembly. The incorporation of HMG17 into chromatin resulted in a 7- to 40-fold stimulation of GAL4-VP16-activated transcription to levels that were comparable to those observed with histone-free DNA templates. In contrast, transcription from HMG17-containing chromatin was not detectable in the absence of GAL4-VP16 or with a GAL4 derivative [GAL4(1-147)] lacking the VP16 activation domain. Finally, the incorporation of HMG17 into chromatin was found to increase the efficiency of transcription initiation, but not the extent of transcriptional elongation. Thus, HMG17 is a chromatin-specific transcriptional coactivator that increases the efficiency of initiation of transcription by RNA polymerase II.
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Affiliation(s)
- S M Paranjape
- Department of Biology, University of California, San Diego, La Jolla 92093-0347, USA
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17
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Reeves R, Nissen M. Interaction of high mobility group-I (Y) nonhistone proteins with nucleosome core particles. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(19)36903-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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18
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Lehn DA, Bustin M. Evolutionarily conserved motifs and protein binding elements in the 5' region of the chromosomal protein HMG-14 gene. DNA Cell Biol 1993; 12:753-61. [PMID: 8397832 DOI: 10.1089/dna.1993.12.753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Although the structure of several genes coding for chromosomal proteins HMG-14 and HMG-17 has been determined, the mechanisms regulating the expression of these genes has not yet been examined. Toward this goal, we have cloned and sequenced a fragment containing the first three exons and 956 bp upstream from the start of translation of the functional mouse HMG-14 gene. Comparison of this sequence to the known sequence of the human HMG-14 gene revealed the presence of five distinct blocks of high sequence identity flanking the start of transcription and the CAAT box. DNase I and mobility-shift analysis identified a DNA region, downstream from the start of transcription, which may be important for the formation of a stable protein-DNA complex. Affinity chromatography on columns containing oligonucleotides corresponding to this sequence indicates that this region is a protein binding site.
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Affiliation(s)
- D A Lehn
- Protein Section, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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19
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Crippa MP, Alfonso PJ, Bustin M. Nucleosome core binding region of chromosomal protein HMG-17 acts as an independent functional domain. J Mol Biol 1992; 228:442-9. [PMID: 1453455 DOI: 10.1016/0022-2836(92)90833-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chromosomal proteins HMG-14 and HMG-17 have a modular structure. Here we examine whether the putative nucleosome-binding domain in these proteins can function as an independent module. Mobility shift assays with recombinant HMG-17 indicate that synthetic molecules can be used to analyze the interaction of this protein with the nucleosome core. Peptides corresponding to various regions of the protein have been synthesized and their interaction with nucleosome cores analyzed by mobility shift, thermal denaturation and DNase I digestion. A 30 amino acid long peptide, corresponding to the putative nucleosome-binding domain of HMG-17, specifically shifts the mobility of cores as compared to free DNA, elevates the tm of both the premelt and main melt of the cores and protects from DNase I digestion the same nucleosomal DNA sites as the intact protein. The binding of both the peptide and the intact protein is lost upon digestion of the histone tails by trypsin. The nucleosomal binding sites of the peptide appear identical to those of the intact protein. Thus, a region of the protein can acts as an independent functional domain. This supports the notion that HMG-14 and HMG-17 are modular proteins. This finding is relevant to the understanding of the function and evolution of HMG-14/-17, the only nucleosome core particle binding proteins known to date.
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Affiliation(s)
- M P Crippa
- Laboratory of Molecular Carcinogenesis National Cancer Institute, National Institutes of Health Bethesda, MD 20892
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20
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Brawley JV, Martinson HG. HMG proteins 14 and 17 become cross-linked to the globular domain of histone H3 near the nucleosome core particle dyad. Biochemistry 1992; 31:364-70. [PMID: 1731893 DOI: 10.1021/bi00117a008] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
HMG proteins were derivatized with the photoactivatable cross-linker N-succinimidyl 3-((4-azidophenyl)dithio)propionate and then allowed to associate with nucleosome core particles. Following photolysis, peptide mapping of the principal dimeric adducts was carried out. Cross-linking occurred primarily from a central location in the HMGs to a central location in H3. The positions of these cross-links, considered along with other data from the literature, show that HMG proteins 14 and 17 make important contacts to H3 near the front face of the nucleosome. This raises the possibility that HMGs 14 and 17 participate in the reported conformational transition which exposes the H3 sulfhydryls of active nucleosomes.
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Affiliation(s)
- J V Brawley
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90024
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21
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Sheflin LG, Fucile NW, Spaulding SW. HMG 14 and protamine enhance ligation of linear DNA to form linear multimers: phosphorylation of HMG 14 at Ser 20 specifically inhibits intermolecular DNA ligation. Biochem Biophys Res Commun 1991; 174:660-6. [PMID: 1847050 DOI: 10.1016/0006-291x(91)91468-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
HMG 14 and protamine can be used to enhance intermolecular ligation of low concentrations of linear DNA. Adding HMG 14 (50 moles per mole DNA) caused 50% of blunt-ended DNA to form predominantly dimers, and all cohesive-ended DNA to form multimers (greater than 6-mer) in response to T4 ligase. Protamine was maximally effective at 40:1, producing mostly dimers and trimers. Adding higher concentrations of HMG 14 did not affect the ligation pattern of cohesive-ended DNA, while higher concentrations of protamine inhibit the formation of multimers. Phosphorylation of HMG 14 at Ser 20 by Ca(++)-phospholipid dependent protein kinase abolished the ability of HMG 14 to stimulate intermolecular ligation, but did not substantially interfere with intramolecular ligation, or the binding of HMG 14 to linear or circular DNA as assessed by gel mobility. Thus Ser 20, which is located in the amino terminal DNA-binding domain of HMG 14, appears to modulate DNA-DNA interactions.
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22
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Immunochemical analysis of the exposure of high mobility group protein 14 and 17 surfaces in chromatin. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)30469-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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23
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Abstract
Neutron scattering has been used to study the interaction of HMG14 with chromatin. Chromatin depleted of H1/H5 was reconstituted separately with histones H1 and H5, and complexed with HMG14. We have also studied the conformation of complexes formed by the binding of HMG14 to nucleosome dimers without linker DNA. Our data on the binding of HMG14 to linkerless nucleosome dimers argue against a significant change in the exit and entry angles of nucleosomal core DNA. Data on the condensation of chromatin into a higher-order structure suggest that there is no dramatic difference between the roles of H1 and H5 in their influence on HMG14 complex formation. However, there is a decrease of about 25% in the mass per unit length of chromatin fibers on HMG14 binding, which is not accompanied by a change in the fiber repeat distance. This is evidence that there are fewer nucleosomes per repeat in HMG14 containing chromatin fibers than in normal chromatin. Alteration of chromatin structure in this manner may be part of the role of HMG14 in actively transcribed chromatin.
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Affiliation(s)
- V Graziano
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973
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24
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Structural and transcriptional properties of different nucleosomal particles containing high mobility group proteins 14 and 17 (HMG 14/17). J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39061-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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25
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Prasad S, Thakur MK. Effects of spermine and sodium butyrate on the in vitro phosphorylation of HMG non-histone proteins of the liver of young and old rats. Arch Gerontol Geriatr 1990; 10:231-8. [PMID: 15374498 DOI: 10.1016/0167-4943(90)90024-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/1989] [Revised: 03/10/1990] [Accepted: 03/20/1990] [Indexed: 10/27/2022]
Abstract
The in vitro phosphorylation of high mobility group (HMG) proteins and its modulation by spermine and sodium butyrate were studied in the liver of young (15 week) and old (138 week) male rats. Except HMG 1 which remained unchanged, the phosphorylation of other proteins (HMG 2, 14 and 17) decreased drastically in old age. Spermine stimulated the phosphorylation of HMG 1 and 17 in young but HMG 1, 2 and 14 in old rats. The incorporation of (32)P into total HMG proteins was enhanced by butyrate in the liver of both ages. However, the degree of stimulation was higher in young rats. Particularly, the HMG 1 and 17 of young and HMG 2 and 17 of old rats showed increased phosphorylation. Furthermore, butyrate also inhibited the phosphorylation of HMG 2 in young and HMG 1 and 14 in old rats. Such alteration in the phosphorylation of major HMG proteins modulates their interaction with DNA and other components of chromatin. This may account for changes in the higher order organization of chromatin and expression of genes during aging.
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Affiliation(s)
- S Prasad
- Biochemistry and Molecular Biology Laboratory, Centre of Advanced Study in Zoology, Banaras Hindu University, Varanasi 221 005, India
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26
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Mosevitsky MI, Novitskaya VA, Iogannsen MG, Zabezhinsky MA. Tissue specificity of nucleo-cytoplasmic distribution of HMG1 and HMG2 proteins and their probable functions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1989; 185:303-10. [PMID: 2583185 DOI: 10.1111/j.1432-1033.1989.tb15116.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The levels and distribution between nucleus and cytoplasm of HMG1 and HMG2 proteins have been investigated in different tissues of mammals. In lymphoid tissues and testis high amounts of these proteins are present in both nuclei and cytoplasm, while in the hepatic tissues and brain they accumulate in cytoplasm, mainly in the cytosol. In particular, very low amounts, if any, of HMG1 and 2 are present in the nuclei active for DNA replication (rat regenerating liver and primary hepatoma) or transcription (adult liver and brain). Therefore, it appears that HMG1 and 2 are not necessary for these processes. On the other hand, nuclear (chromosomal) HMG1 and 2 are characteristic for the tissues containing undifferentiated cells: lymphoid tissues, testis, neonatal liver. These proteins are bound to the chromatin regions solubilized early by sonication or DNase action. Comparison of the data obtained for different tissues shows an inverse correlation between the amounts of chromosomal HMG1 and 2, on the one hand, and of histone H1(0), on the other hand. These results suggest that chromosomal HMG1 and 2 take part in the processes that occur during cell differentiation, while histone H1(0) is induced to preserve differentiated cells from dedifferentiation.
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Affiliation(s)
- M I Mosevitsky
- Leningrad Nuclear Physics Institute, Academy of Sciences of the USSR, Gatchina
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27
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Huang SY, Garrard WT. Electrophoretic analyses of nucleosomes and other protein-DNA complexes. Methods Enzymol 1989; 170:116-42. [PMID: 2770536 DOI: 10.1016/0076-6879(89)70044-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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28
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Aragay AM, Diaz P, Daban JR. Association of nucleosome core particle DNA with different histone oligomers. Transfer of histones between DNA-(H2A,H2B) and DNA-(H3,H4) complexes. J Mol Biol 1988; 204:141-54. [PMID: 3216389 DOI: 10.1016/0022-2836(88)90605-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In non-denaturing low ionic strength gels, the titration of core DNA with H2A,H2B produces five well-defined bands. Quantitative densitometry and cross-linking experiments indicate that these bands are due to the successive binding of H2A,H2B dimers to core DNA. Only two bands are obtained with DNA-(H3,H4) samples. The slower of these bands is broad and presumably corresponds to two complexes containing one and two H3,H4 tetramers, respectively. In gels of higher ionic strength, DNA-(H2A,H2B) samples produce an ill-defined band, suggesting that the lifetime of the complexes containing H2A,H2B is relatively short. However, the low intensity of the free DNA band observed in these gels indicates that most of the DNA is associated with H2A,H2B. In agreement with this, our results obtained using different techniques (sedimentation, cross-linking, trypsin and nuclease digestions, and thermal denaturation) demonstrate that the association of H2A,H2B with core DNA occurs in free solution in both the absence and presence of NaCl (0.1 to 0.2 M). The low mobilities of DNA-(H2A,H2B) complexes, together with sedimentation and DNase I digestion results, indicate that the DNA in these complexes is not folded into the compact structure found in the core particle. Furthermore, non-denaturing gels have been used to study the dynamic properties of DNA-(H2A,H2B) and DNA-(H3,H4) complexes in 0.2 M-NaCl. Our results show that: (1) H2A,H2B and H3,H4 can associate, respectively, with DNA-(H3,H4) and DNA-(H2A,H2B) to produce complexes containing the four core histones; (2) DNA-(H2A,H2B) and DNA-(H3,H4) are able to transfer histones to free core DNA; (3) an exchange of histone pairs takes place between DNA-(H2A,H2B) and DNA-(H3,H4) and produces complexes with the same histone composition as that of the normal nucleosome core particle; and (4) although both histone pairs can exchange, histones H2A,H2B show a higher tendency than H3,H4 to migrate from one incomplete core particle to another. The complexes produced in these reactions have the same compact structure as reconstituted core particles containing the four core histones. Our kinetic results are consistent with a reaction mechanism in which the transfer of histones involves direct contacts between the reacting complexes. The possible participation of these spontaneous reactions on the mechanism of nucleosome assembly is discussed.
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Affiliation(s)
- A M Aragay
- Departament de Bioquímica i Biologia Molecular Facultat de Ciències, Universitat Autònoma de Barcelona, Spain
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29
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Stros M, Kleinwächter V. Thermal denaturation and fluorescence study of nucleosomes containing non-histone chromosomal protein HMG2. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 910:163-70. [PMID: 3676320 DOI: 10.1016/0167-4781(87)90069-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Interaction of calf thymus non-histone chromosomal protein HMG2 with H1,H5-depleted nucleosomes from chicken erythrocytes was studied by means of thermal denaturation and an N-(3-pyrene)maleimide fluorescence probe. Under low ionic conditions (2 mM Tris buffer plus EDTA) addition of 1-2 molecules of HMG2 per nucleosome markedly stabilized the segment of the linker DNA against thermal denaturation. Under approximately physiological ionic conditions (0.1 M NaCl) addition of two HMG2 molecules per nucleosome, labeled by N-(3-pyrene)maleimide at the sulfhydryl groups of Cys-110 of histones H3, resulted in a decrease of the pyrene excimer fluorescence corresponding to the slight movement of the sulfhydryl groups of the two histone H3 molecules apart.
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Affiliation(s)
- M Stros
- Institute of Biophysics, Czechoslovak Academy of Sciences, Brno
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30
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Espel E, Bernués J, Pérez-Pons JA, Querol E. Binding of HMG14 non-histone protein to histones H2A, H2B, H1 and DNA in reconstituted chromatin. Biochem Biophys Res Commun 1985; 132:1031-7. [PMID: 4074344 DOI: 10.1016/0006-291x(85)91910-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The interaction between calf thymus HMG14 and rat liver chromatin components has been studied via reconstitution and chemical cross-linking. Selective labeling of HMG14 with photoactivable reversible heterobifunctional reagents has allowed a clear identification of the histones interacting with it (histones H2A, H2B and H1). These results are not dependent on whether the chromatin samples used were bulk chromatin, mononucleosomes, or core particles (for H2A and H2B). In addition to histone proteins, DNA also seems to be involved in HMG14 attachment to nucleosome.
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31
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32
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Abstract
Active genes are known to have an altered chromatin structure that is preferentially sensitive to digestion with DNAase I. We find that when chicken red blood cells are incubated in media containing the topoisomerase II inhibitor novobiocin, the preferential DNAase I sensitivity of the active beta-globin genes is reversed in vivo with as little as 20 min of drug treatment. Control experiments suggest that inhibition of a topoisomerase II is responsible for this alteration in active gene conformation. Reversal of DNAase I sensitivity can also be induced in vitro by partial cleavage of the nuclear DNA with staphylococcal nuclease. We propose that the altered structure around active genes is maintained by continuous DNA supercoiling and that in the absence of this superhelical tension active chromatin reverts to a less DNAase I-sensitive ground state.
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33
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Abstract
Eukaryotic chromatin has a dynamic, complex hierarchical structure. Active gene transcription takes place on only a small proportion of it at a time. While many workers have tried to characterize active chromatin, we are still far from understanding all the biochemical, morphological and compositional features that distinguish it from inactive nuclear material. Active genes are apparently packaged in an altered nucleosome structure and are associated with domains of chromatin that are less condensed or more open than inactive domains. Active genes are more sensitive to nuclease digestions and probably contain specific nonhistone proteins which may establish and/or maintain the active state. Variant or modified histones as well as altered configurations or modifications of the DNA itself may likewise be involved. Practically nothing is known about the mechanisms that control these nuclear characteristics. However, controlled accessibility to regions of chromatin and specific sequences of DNA may be one of the primary regulatory mechanisms by which higher cells establish potentially active chromatin domains. Another control mechanism may be compartmentalization of active chromatin to certain regions within the nucleus, perhaps to the nuclear matrix. Topological constraints and DNA supercoiling may influence the active regions of chromatin and be involved in eukaryotic genomic functions. Further, the chromatin structure of various DNA regulatory sequences, such as promoters, terminators and enhancers, appears to partially regulate transcriptional activity.
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34
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Sasi R, Fasman GD. The effect of a high mobility group protein (HMG 17) on the structure of acetylated and control core HeLa cell chromatin. BIOCHIMICA ET BIOPHYSICA ACTA 1984; 782:55-66. [PMID: 6232953 DOI: 10.1016/0167-4781(84)90106-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The effect of binding a high mobility group protein (HMG 17) on the stability and conformation of acetylated and control HeLa high molecular weight core chromatin (stripped of H1 and non-histone chromosomal proteins) was studied by circular dichroism and thermal-denaturation measurements. Previously it had been shown that conformational differences exist between native whole chromatin derived from butyrate-treated (acetylated) and control HeLa cells and that these conformational differences disappear by removing H1 and non-histone chromosomal proteins ( Reczek , P.R., Weissman , D., Huvos , P.E. and Fasman, G.D. (1982) Biochemistry 21, 993-1002). The circular dichroism spectra and the thermal denaturation profiles of control and acetylated core chromatin were found to be similar. The circular dichroism properties of HMG 17 reconstituted highly acetylated and control core chromatin indicated the same alteration of chromatin structure at low ionic strength (1 mM sodium phosphate/0.25 mM EDTA, pH 7.0). The magnitudes of the decrease in ellipticity were proportional to the amount of HMG 17 bound and were found to be the same for both the acetylated and control core chromatin. Thermal denaturation profiles confirmed this change in structure induced by HMG 17 on control and highly acetylated core chromatin. The thermal denaturation profiles, which were resolved into three component transitions, exhibited a shifting of hyperchromicity from the lower melting transitions to the higher melting transitions, with a concomitant rise in Tm, on HMG 17 binding to both control and acetylated chromatin. The natures of the interactions of HMG 17 at higher ionic strength (50 mM NaCl/0.25 mM EDTA/1 mM sodium phosphate, pH 7.0) with acetylated and control core chromatin were slightly different, as measured by circular dichroism; however, a decrease in ellipticity was observed for both samples upon binding of HMG 17. These observations suggest that acetylation coupled with HMG 17 binding to core chromatin does not loosen chromatin structure. HMG 17 binding to control and acetylated core chromatin produces an overall stabilization and compaction of chromatin structure.
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35
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Kelner DN, McCarty KS. Porcine liver nuclear histone acetyltransferase. Partial purification and basic properties. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)43109-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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