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DNA methylation effects on tetra-nucleosome compaction and aggregation. Biophys J 2015; 107:1629-36. [PMID: 25296315 DOI: 10.1016/j.bpj.2014.05.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 05/27/2014] [Accepted: 05/30/2014] [Indexed: 12/19/2022] Open
Abstract
DNA CpG methylation has been associated with chromatin compaction and gene silencing. Whether DNA methylation directly contributes to chromatin compaction remains an open question. In this study, we used fluorescence fluctuation spectroscopy (FFS) to evaluate the compaction and aggregation of tetra-nucleosomes containing specific CpG patterns and methylation levels. The compactness of both unmethylated and methylated tetra-nucleosomes is dependent on DNA sequences. Specifically, methylation of the CpG sites located in the central dyad and the major grooves of DNA seem to have opposite effects on modulating the compactness of tetra-nucleosomes. The interactions among tetra-nucleosomes, however, seem to be enhanced because of DNA methylation independent of sequence contexts. Our finding can shed light on understanding the role of DNA methylation in determining nucleosome positioning pattern and chromatin compactness.
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Abstract
In this review, we attempt to summarize, in a critical manner, what is currently known about the processes of condensation and decondensation of chromatin fibers. We begin with a critical analysis of the possible mechanisms for condensation, considering both old and new evidence as to whether the linker DNA between nucleosomes bends or remains straight in the condensed structure. Concluding that the preponderance of evidence is for straight linkers, we ask what other fundamental process might allow condensation, and argue that there is evidence for linker histone-induced contraction of the internucleosome angle, as salt concentration is raised toward physiological levels. We also ask how certain specific regions of chromatin can become decondensed, even at physiological salt concentration, to allow transcription. We consider linker histone depletion and acetylation of the core histone tails, as possible mechanisms. On the basis of recent evidence, we suggest a unified model linking targeted acetylation of specific genomic regions to linker histone depletion, with unfolding of the condensed fiber as a consequence.
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Affiliation(s)
- K van Holde
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331-7305, USA
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Yao J, Lowary PT, Widom J. Direct detection of linker DNA bending in defined-length oligomers of chromatin. Proc Natl Acad Sci U S A 1990; 87:7603-7. [PMID: 2217191 PMCID: PMC54796 DOI: 10.1073/pnas.87.19.7603] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Linker DNA, which connects between nucleosomes in chromatin, is short and, therefore, may be essentially straight and inflexible. We have carried out hydrodynamic and electron microscopic studies of dinucleosomes--fragments of chromatin containing just two nucleosomes--to test the ability of linker DNA to bend. We find that ionic conditions that stabilize the folding of long chromatin cause linker DNA in dinucleosomes to bend, bringing the two nucleosomes into contact. The results uphold a key prediction of the solenoid model of chromosome folding and suggest a mechanism by which proteins that are separated along the DNA can interact by direct contact.
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Affiliation(s)
- J Yao
- Department of Chemistry, University of Illinois, Urbana-Champaign 61801
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Dorbic T, Wittig B. Isolation of oligonucleosomes from active chromatin using HMG17-specific monoclonal antibodies. Nucleic Acids Res 1986; 14:3363-76. [PMID: 3703677 PMCID: PMC339778 DOI: 10.1093/nar/14.8.3363] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We report the preparation of HMG17-containing oligonucleosomes from chicken embryos and from liver and oviduct of laying hens. Monoclonal antibodies against HMG17 were used for their isolation. An unusual size distribution with respect to their repeat number was observed. The oligonucleosomes of repeat number up to N6 were highly enriched for DNA of the vitellogenin II gene (liver) and for DNA of the ovalbumin and lysozyme genes (oviduct).
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H1 histone exchange is limited to particular regions of chromatin that differ in aggregation properties. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)35800-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Abstract
Nucleosomal subunits isolated from rabbit thymus nuclei in 0.04 M K2SO4-0.02 M Tris, pH 7.4 were devoid of histone H1, while whole chromatin prepared in the same buffer contained the full complement of histone H1. The question is asked why histone H1 dissociates from the subunits but not from the high molecular weight material. We propose that, at physiological salt concentrations, histone H1 is not bound to linker DNA as depicted in the current models; rather, alternate attachment sites, present only in the polymer, are involved.
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Touchette NA, Cole RD. Differential scanning calorimetry of nuclei reveals the loss of major structural features in chromatin by brief nuclease treatment. Proc Natl Acad Sci U S A 1985; 82:2642-6. [PMID: 3857606 PMCID: PMC397620 DOI: 10.1073/pnas.82.9.2642] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Differential scanning calorimetry revealed that chromatin melts in four distinct transitions in intact HeLa nuclei at 60 degrees C, 76 degrees C, 88 degrees C, and 105 degrees C. Calorimetry of whole cells was characterized by the same four transitions along with another at 65 degrees C, which was probably RNA. Isolated chromatin, however, melted in only two transitions at 72 degrees C and 85 degrees C. Very brief digestion of HeLa nuclei with either micrococcal nuclease or DNase I resulted in the conversion of a structure that melted at 105 degrees C to one that melted at 88 degrees C. Further digestion with micrococcal nuclease to the level of the mononucleosome did not result in any further substantial changes in either enthalpy or melting temperatures. In contrast, further DNase I digestion that resulted in cleavage within the nucleosome produced a pronounced shift in melting temperatures to broad transitions at 62 degrees C and 78 degrees C.
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Perry M, Chalkley R. Histone acetylation increases the solubility of chromatin and occurs sequentially over most of the chromatin. A novel model for the biological role of histone acetylation. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34382-5] [Citation(s) in RCA: 113] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Wittig S, Wittig B. Site directed in-vitro assembly of nucleosomes. Nucleic Acids Res 1982; 10:3647-65. [PMID: 6287417 PMCID: PMC320741 DOI: 10.1093/nar/10.12.3647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
An in-vitro system is described allowing for the assembly of nucleosomes on preselected sites of a cloned tRNA gene. The system consists of a soluble nucleoprotein fraction, a histone source, and circular DNA containing a single stranded stretch (sssDNA). Nucleosomes assemble on the sssDNA, if the three components are incubated as a highly concentrated solution in the presence of the four deoxyribonucleotidetriphosphates and of ATP. The single stranded stretch is rendered double stranded during incubation. The middle axis of one assembled nucleosome always coincides roughly with the midpoint of the original single stranded DNA stretch.
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Marion C, Bezot P, Hesse-Bezot C, Roux B, Bernengo JC. Conformation of chromatin oligomers. A new argument for a change with the hexanucleosome. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 120:169-76. [PMID: 7308214 DOI: 10.1111/j.1432-1033.1981.tb05685.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Quasielastic laser light scattering measurements have been made on chromatin oligomers to obtain information on the transition in their electrooptical properties, previously observed for the hexameric structures [Marion, C. and Roux, B. (1978) Nucleic Acids Res. 5, 4431-4449]. Translational diffusion coefficients were determined for mononucleosomes to octanucleosomes containing histone H1 over a range of ionic strength. At high ionic strength, oligomers show a linear dependence of the logarithm of diffusion coefficient upon the logarithm of number of nucleosomes. At low ionic strength a change occurs between hexamer and heptamer. Our results agree well with the recent sedimentation data of Osipova et al. [Eur. J. Biochem. (1980) 113, 183-188] and of Butler and Thomas [J. Mol. Biol. (1980) 140, 505-529] showing a change in stability with hexamer. Various models for the arrangements of nucleosomes in the superstructure of chromatin are discussed. All calculations clearly indicate a conformational change with the hexanucleosome and the results suggest that, at low ionic strength, the chromatin adopts a loosely helical structure of 28-nm diameter and 22-nm pitch. These results are also consistent with a discontinuity every sixth nucleosome, corresponding to a turn of the helix. This discontinuity may explain the recent electric dichroism data of Lee et al. [Biochemistry (1981) 20, 1438-1445]. The hexanucleosome structure which we have previously suggested, with the faces of nucleosomes arranged radially to the helical axis has been recently confirmed by Mc Ghee et al. [Cell (1980) 22, 87-96]. With an increase of ionic strength, the helix becomes more regular and compact with a slightly reduced outer diameter and a decreased pitch, the dimensions resembling those proposed for solenoid models.
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Osipova TN, Pospelov VA, Svetlikova SB, Vorob'ev VI. The role of histone H1 in compaction of nucleosomes. Sedimentation behaviour of oligonucleosomes in solution. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 113:183-8. [PMID: 7460945 DOI: 10.1111/j.1432-1033.1980.tb06153.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The dependence of sedimentation coefficients of oligonucleosomes on the number of nucleosomes in the chain in solutions of different ionic strength has been studied for oligonucleosomes both containing and lacking histone H1. The analysis of these dependencies has shown that oligonucleosomes with H1 at low concentration (I = 0.01 mol/l) may be described by the model of a short cylinder with an average length of the chain per nucleosome l0 = 11 nm where the neighbouring nucleosomes are in close contact. Oligonucleosomes without H1 at I = 0.01 mol/l can be described by the model of a worm-like chain with l0 = 27 nm. This suggests that when H1 is removed the linker DNA unfolds completely. In 0.15 M NaCl the oligonucleosome chain without H1 folds up to a compact configuration typical of oligonucleosomes with H1 at I = 0.01 mol/l. Thus, the linker DNA, with charges being screened, may fold due to interactions with core histones. Oligonucleosomes with H1 in 0.15 M NaCl form a supercoiled structure, whose stable conformation is accounted for by cooperative interactions of no less than five nucleosomes.
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Jump DB, Butt TR, Smulson M. Reconstitution of HeLa cell poly(adenosine diphosphate ribose) polymerase with purified oligonucleosomal chromatin. Biochemistry 1980; 19:1031-7. [PMID: 6243957 DOI: 10.1021/bi00546a031] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Tsaneva I. Comparative study on the thermal denaturation of different nucleosome preparations. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1980; 11:211-6. [PMID: 7389979 DOI: 10.1016/0020-711x(80)90222-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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Abstract
DNA (760 bp) isolated from nucleosome tetramers of staphylococcal nuclease-digested chicken embryo chromatin was highly enriched for tRNA genes and subsequently cloned in E. coli chi 1776. The location of genes coding for chicken embryo tRNALys, tRNAPhe and tRNAiMet within the cloned nucleosome tetramer DNA was determined using restriction endonucleases for which single cleavage sites could be predicted from the respective tRNA base sequence. All our tRNA genes reside nonrandomly at four locations on nucleosome tetramer DNA. The spacing between the tRNA gene locations is approximately 190 bp, similar to the DNA repeat length of chicken embryo chromatin. The four tRNA gene locations were also defined in noncloned nucleosome tetramer DNA highly enriched for tRNA genes. The majority of genes coding for tRNALys, tRNAPhe and tRNAiMet, respectively, are located in equal proportion 40-45, 230, 420 and 610 bp distant from the 5' end of the tRNA-identical strand. Thus the tRNA structural gene sequences all appear to begin about 20 bp "inside" the nucleosome core. As observed with nucleosomal DNA not enriched for tRNA genes, the phase relationship between tRNA genes and nucleosome location is maintained over a distance of 4-6 subsequent nucleosomes. A cloned molecule of nucleosomal DNA containing both a tRNALys gene and a tRNAiMet gene in the same polarity reveals that a phase adjustment might be necessary for the nucleosomes between these two tRNA genes in chicken embryo chromatin.
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Wittig B, Wittig S. Stabilization of R loop structures by photochemical crosslinking with 4,5',8-trimethylpsoralen: application to gene enrichment and molecular cloning. Biochem Biophys Res Commun 1979; 91:554-62. [PMID: 518654 DOI: 10.1016/0006-291x(79)91558-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Fulmer AW, Fasman GD. Ionic strength-dependent conformational transitions of chromatin. Circular dichroism and thermal denaturation studies. Biopolymers 1979; 18:2875-91. [PMID: 508905 DOI: 10.1002/bip.1979.360181115] [Citation(s) in RCA: 42] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Wittig B, Wittig S. The enrichment of chicken embryo tRNA genes in nucleosomal DNA by reversed phase chromatography. FEBS Lett 1979; 105:254-8. [PMID: 573700 DOI: 10.1016/0014-5793(79)80623-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Wittig B, Wittig S, Grunz H. Cloning of chicken embryo tRNA genes using single stranded nucleosomal DNA highly enriched for tRNA complementary sequences. Nucleic Acids Res 1979; 6:3759-84. [PMID: 493122 PMCID: PMC327976 DOI: 10.1093/nar/6.12.3759] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
DNA from chicken embryo nucleosome tetramers (about 760 base pairs in size) was enriched for tRNA genes by RPC-5 chromatography. The enriched DNA was hybridized with chicken embryo total tRNA and the hybridized DNA isolated utilizing a) avidinbiotin interaction, b) diazobenzyloxymethyl paper, and c) high temperature RPC-5 chromatography. The obtained single stranded DNA highly enriched for tRNA complementary sequences was hybridized with total DNA from nucleosome monomers (140--190 base pairs in size) and the excess of non hybridized monomer nucleosome DNA removed by Sepharose 4B chromatography. The hybrid molecules obtained were made fully double stranded by incubation with E. coli DNA polymerase I, DNA ligase, and exonuclease III. DNA was inserted into plasmid pBR322 by G-C joining procedure and the recombinant DNA used to transform the E. coli strain chi 1776. More than 70% of the transformants obtained hybridize to chicken embryo total tRNA.
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Brown FL, Musich PR, Maio JJ. The repetitive sequence structure of component alpha DNA and its relationship to the nucleosomes of the African green monkey. J Mol Biol 1979; 131:777-99. [PMID: 117111 DOI: 10.1016/0022-2836(79)90201-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Strätling WH. Role of histone H1 in the conformation of oligonucleosomes as a function of ionic strength. Biochemistry 1979; 18:596-603. [PMID: 420802 DOI: 10.1021/bi00571a008] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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25
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Weischet WO, Allen JR, Riedel G, Van Holde KE. The effects of salt concentration and H-1 depletion on the digestion of calf thymus chromatin by micrococcal nuclease. Nucleic Acids Res 1979; 6:1843-62. [PMID: 450715 PMCID: PMC327815 DOI: 10.1093/nar/6.5.1843] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We have removed histone H1 specifically from calf thymus nuclei by low pH treatment, and studied the digestion of such nuclei in comparison with undepleted nuclei. By a number of criteria the nuclei do not appear damaged. The DNA repeat-length in nuclear chromatin is found to be the same (192 +/- 4 bp) in the presence or absence of H1. These experiments demonstrate that the core histone complex of H2A, H2B, H3, and H4 can itself protect DNA sequences as long as 168 bp from nuclease. Our interpretation is that this represents an important structural element in chromatin, carrying two full turns of superhelical DNA. Depending on conditions of digestion this 168 bp fragment may be metastable and is normally rapidly converted by exonucleolytic trimming to the well-known "core-particle" containing 145 bp. Larger stable DNA fragments observed indigestion of H-1 depleted nuclei appear to arise from oligomers assembled from 168 bp cores in close contact exhibiting trimming of 0-20 bp at the ends. Electrophorograms of undepleted nuclear digests reveal oligomer bands in several size classes, each corresponding to one or more combinations of 168 bp particles, H1-protected spacers of about 20 bp length, and particles with ends trimmed to varying degrees.
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Wittig B, Wittig S. Purification of class A, B, and C DNA-dependent RNA polymerases from chicken embryos. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 520:598-611. [PMID: 718915 DOI: 10.1016/0005-2787(78)90145-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Crude nuclei were isolated from trunks of 13-day-old chicken embryos under conditions which prevent leakage of RNA polymerases from nuclei. RNA polymerases were solubilized by subsequent incubation in alkaline buffer and sonication at high salt concentration. Purification of RNA polymerases A, B, and C was achieved by conventional column chromatographic procedures. RNA polymerase B was freed from an UTP:polynucleotidyl exotransferase by chromatography on a tRNA-Sepharose column. Purified RNA polymerase A contained six putative subunits with molecular weights 190 000 (A1), 117 000 (A2), 57 000 (A3), 50 000 (A4), 25 000 (A5), 19 000 (A6); RNA polymerase B contained eight putative subunits with molecular weights 98 000 (B2'), 86 000 (B2''), 155 000 (B3), 44 000 (B4), 31 000 (B5), 28 000 (B6), 26 000 (B7), 19 000 (B8); RNA polymerase C contained nine putative subunits with molecular weights 170 000 (C1), 117 000 (C2), 84 000 (C3), 60 000 (C4), 49 000 (C5), 36 000 (C6), 33 000 (C7), 22 000 (C8), 19 000 (C9).
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Abstract
The 3' terminus of tRNA was enzymatically elongated by an oligo(A) tail. A fragment of DNA polymerase I (E. coli) was used in the presence of manganese to phase and synthesize a cleavable primer at the oligo(A)-tRNA template. When the threedimensional structure of oligo(A)-tRNA is being unfolded under conditions where the primer is still hybridized at the oligo(A) tail, the DNA polymerase I fragment transcribes oligo(A)-tRNA into DNA. Reverse transcription is slowed down and its fidelity suspended by the 1-methyladenine in oligo(A)-tRNAPhe(yeast). The reaction is stopped by the highly modified Y-base present in this template. Approximately full length transcripts can be obtained from oligo(A)-tRNA3Gly(E.coli). The transcription products were characterized by sequence analysis.
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