101
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Pehrson JR, Litwin S, Myers CB, Cohen LH. Pyrimidine dimer formation as a probe of nucleosome core and linker structure in situ. Methods 1999; 19:447-56. [PMID: 10579940 DOI: 10.1006/meth.1999.0881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The photoinduced dimerization of adjacent pyrimidines in DNA is influenced in predictable ways by DNA conformation. A method is described for determining patterns of pyrimidine dimer formation under conditions in which the chromatin is minimally perturbed. The relation of such patterns to the conformation of nucleosomal core DNA and linker DNA, as well as the interaction of histone H1 with nucleosomal DNA, is presented. Such data indicate that sharp bends in the path of DNA seen in crystals of isolated nucleosome core particles are also present in intact chromatin. They also indicate that most of the linker has very little curvature except for a small bend at its junction with the nucleosome core. The linker path inferred from such experiments supports models in which the chromatin fiber consists of a zigzag chain of nucleosomes.
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Affiliation(s)
- J R Pehrson
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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102
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Martino JA, Katritch V, Olson WK. Influence of nucleosome structure on the three-dimensional folding of idealized minichromosomes. Structure 1999; 7:1009-22. [PMID: 10467141 DOI: 10.1016/s0969-2126(99)80127-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
BACKGROUND The closed circular, multinucleosome-bound DNA comprising a minichromosome provides one of the best known examples of chromatin organization beyond the wrapping of the double helix around the core of histone proteins. This higher level of chain folding is governed by the topology of the constituent nucleosomes and the spatial disposition of the intervening protein-free DNA linkers. RESULTS By simplifying the protein-DNA assembly to an alternating sequence of virtual bonds, the organization of a string of nucleosomes on the minichromosome can be treated by analogy to conventional chemical depictions of macromolecular folding in terms of the bond lengths, valence angles, and torsions of the chain. If the nucleosomes are evenly spaced and the linkers are sufficiently short, regular minichromosome structures can be identified from analytical expressions that relate the lengths and angles formed by the virtual bonds spanning the nucleosome-linker repeating units to the pitch and radius of the organized quaternary structures that they produce. CONCLUSIONS The resulting models with 4-24 bound nucleosomes illustrate how a minichromosome can adopt the low-writhe folding motifs deduced from biochemical studies, and account for published images of the 30 nm chromatin fiber and the simian virus 40 (SV40) nucleohistone core. The marked sensitivity of global folding to the degree of protein-DNA interactions and the assumed nucleosomal shape suggest potential mechanisms for chromosome rearrangements upon histone modification.
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Affiliation(s)
- J A Martino
- Department of Chemistry, Rutgers, The State University of New Jersey, Piscataway 08854-8087, USA
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103
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Bednar J, Horowitz RA, Grigoryev SA, Carruthers LM, Hansen JC, Koster AJ, Woodcock CL. Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc Natl Acad Sci U S A 1998; 95:14173-8. [PMID: 9826673 PMCID: PMC24346 DOI: 10.1073/pnas.95.24.14173] [Citation(s) in RCA: 383] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/1998] [Accepted: 10/05/1998] [Indexed: 11/18/2022] Open
Abstract
The compaction level of arrays of nucleosomes may be understood in terms of the balance between the self-repulsion of DNA (principally linker DNA) and countering factors including the ionic strength and composition of the medium, the highly basic N termini of the core histones, and linker histones. However, the structural principles that come into play during the transition from a loose chain of nucleosomes to a compact 30-nm chromatin fiber have been difficult to establish, and the arrangement of nucleosomes and linker DNA in condensed chromatin fibers has never been fully resolved. Based on images of the solution conformation of native chromatin and fully defined chromatin arrays obtained by electron cryomicroscopy, we report a linker histone-dependent architectural motif beyond the level of the nucleosome core particle that takes the form of a stem-like organization of the entering and exiting linker DNA segments. DNA completes approximately 1.7 turns on the histone octamer in the presence and absence of linker histone. When linker histone is present, the two linker DNA segments become juxtaposed approximately 8 nm from the nucleosome center and remain apposed for 3-5 nm before diverging. We propose that this stem motif directs the arrangement of nucleosomes and linker DNA within the chromatin fiber, establishing a unique three-dimensional zigzag folding pattern that is conserved during compaction. Such an arrangement with peripherally arranged nucleosomes and internal linker DNA segments is fully consistent with observations in intact nuclei and also allows dramatic changes in compaction level to occur without a concomitant change in topology.
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Affiliation(s)
- J Bednar
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
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104
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Butler PJ, Thomas JO. Dinucleosomes show compaction by ionic strength, consistent with bending of linker DNA. J Mol Biol 1998; 281:401-7. [PMID: 9698556 DOI: 10.1006/jmbi.1998.1954] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleosome dimers from chicken erythrocytes show an ionic strength dependence of sedimentation coefficient similar to that of trimers, and indicative of a degree of compaction over a range of low ionic strengths. This is not easily reconciled with straight linkers but is consistent with bending or kinking of the linker DNA.
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Affiliation(s)
- P J Butler
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK
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105
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Widom J. Structure, dynamics, and function of chromatin in vitro. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1998; 27:285-327. [PMID: 9646870 DOI: 10.1146/annurev.biophys.27.1.285] [Citation(s) in RCA: 236] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The substrates for the essential biological processes of transcription, replication, recombination, DNA repair, and cell division are not naked DNA; rather, they are protein-DNA complexes known as chromatin, in one or another stage of a hierarchical series of compactions. These are exciting times for students of chromatin. New studies provide incontrovertible evidence linking chromatin structure to function. Exceptional progress has been made in studies of the structure of chromatin subunits. Surprising new dynamic properties have been discovered. And, much progress has been made in dissecting the functional roles of specific chromatin proteins and domains. This review focuses on in vitro studies of chromatin structure, dynamics, and function.
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Affiliation(s)
- J Widom
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, IL 60208, USA.
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106
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Bermúdez A, Bartolomé S, Daban JR. Partial denaturation of small chromatin fragments: direct evidence for the radial distribution of nucleosomes in folded chromatin fibers. J Cell Sci 1998; 111 ( Pt 12):1707-15. [PMID: 9601100 DOI: 10.1242/jcs.111.12.1707] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To examine the internal structure of chromatin fibers, we have developed procedures for partial denaturation of small chromatin fragments (8–30 nucleosomes) from chicken erythrocytes. Electron micrographs of samples prepared under conditions that cause nucleosome dissociation show rods and loops projecting from short compact fibers fixed by glutaraldehyde in 1.7 mM Mg2+. According to previous studies in our laboratory, these images correspond to the top view of partially denatured fibers. Our results indicate that rods and loops consist of extended duplex DNA of different lengths. DNA in loops is nicked, as demonstrated by experiments performed in the presence of high concentrations of ethidium bromide. Length measurements indicate that the radial projections of DNA are produced by unfolding of nucleosomal units. Loops are formed by DNA from denatured nucleosomes in internal positions of the fiber; DNA from denatured nucleosomes in terminal positions form rods. Our micrographs show clearly a radial distribution of DNA loops and rods projecting from fibers. Rods are orthogonal to the surface of the chromatin fragments. Considering that the high ionic strength used in this study (0.8-2.0 M NaCl) neutralizes the electrostatic repulsions between rods and fiber, this observation suggests that rods are extensions of nucleosomes radially organized inside the fiber. The position of the entry points of DNA loops into the fiber could be influenced by constraint on loops, but our results showing that the arc that separates these points in dinucleosome loops is relatively short suggest that consecutive nucleosomes are relatively close to each other in the folded fiber.
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Affiliation(s)
- A Bermúdez
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències, Universitat Autònoma de Barcelona, Barcelona, Spain
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107
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Staynov DZ, Proykova YG. Quantitative analysis of DNase I digestion patterns of oligo- and polynucleosomes. J Mol Biol 1998; 279:59-71. [PMID: 9636700 DOI: 10.1006/jmbi.1998.1777] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNase I digestion of unlabelled chromatin has been used to determine the orientation of nucleosomes in the higher-order structure of chromatin. DNA digestion patterns were analysed quantitatively and compared with simulation curves that were generated with the experimentally obtained rate constants for cutting inside nucleosomes and the half-height widths of the bands. The rate constants for cutting at the linker DNA were varied to fit the experimental curves. By comparing the digestion profiles of polynucleosomes, oligonucleosomes and H1/H5-depleted oligonucleosomes we have been able to distinguish between protection caused by H1/H5 histones only and protection caused by the higher-order structure. By the nature of this method the area protected by H1/H5 histones appears symmetrical around the centre of the nucleosomal DNA on the dyad axis (position S[0]), but it can also be interpreted as a superposition of two separate protected areas that are symmetrical around position S[0]. Protection by the higher-order structure shows that the nucleosomes are oriented with their S[0] positions inside the 30 nm fibre and that there is a minimum number of nucleosomes required for this structure to be formed. We have also found that the linker DNA is cut in a continuous (non-periodical) way and that there are considerable amounts of nucleosomes at discrete distances of multiples of ten nucleotides (10a nt) as well as stretches of nucleosomes positioned either at random or at distances of (10a + 5)nt.
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Affiliation(s)
- D Z Staynov
- Department of Allergy and Respiratory Medicine, UMDS Guy's Hospital, University of London, UK
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108
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Prunell A. A topological approach to nucleosome structure and dynamics: the linking number paradox and other issues. Biophys J 1998; 74:2531-44. [PMID: 9591679 PMCID: PMC1299595 DOI: 10.1016/s0006-3495(98)77961-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The linking number paradox of DNA in chromatin (two negative crossings around the octamer, associated with a unit linking number reduction), which is 21 years old this year, has come of age. After stirring much debate in the past, the initially hypothetical explanation of the paradox by DNA overtwisting on the nucleosome surface is now presented as a hard fact in recent textbooks. The first part of this article presents a historical perspective of the problem and details the numerous attempts to measure DNA local periodicity, which in one remarkable example sowed the seeds for the discovery of DNA bending. The second part is devoted to the DNA minicircle system, which has been developed in the author's laboratory as an alternative to the local-periodicity-measurement approach. It offers a simple proposal: a unit linking number reduction associated with a single crossing. This conclusion is contrasted with the latest high-resolution crystallographic data of the nucleosome in the third part of the article, and the fourth part examines the available evidence supporting an extension of these results to nucleosomes in chromatin. The last part addresses another basic question pertaining to nucleosome dynamics, the conformational flexibility of the histone tetramer.
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Affiliation(s)
- A Prunell
- Institut Jacques Monod, Centre National de la Recherche Scientifique and Université Paris 7, France.
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109
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Affiliation(s)
- J R Daban
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències, Universitat Autònoma de Barcelona, Barcelona, Spain.
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110
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Maccioni E, Vergani L, Dembo A, Mascetti G, Nicolini C. X-ray small angle scattering study of chromatin as a function of fiber length. Mol Biol Rep 1998; 25:73-86. [PMID: 9540068 DOI: 10.1023/a:1006838708493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This work investigates the structure of native calf thymus chromatin as a function of fiber length and isolation procedures by using X-ray small angle scattering technique. Two methods of chromatin isolation have been compared in order to better understand the differences reported by various authors in terms of chromatin high order structure. In addition to these experimental results the effects of shearing have also been studied. In order to explain the differences among these chromatin preparations we built several models of chromatin fibers (represented as a chain of spherical subunits) assuming increasing level of condensation at increasing salt concentrations. For all these fiber models the corresponding theoretical X-ray scattering curves have been calculated and these results have been used to explain the influence of fiber length on the scattering profiles of chromatin. The comparison between experimental and theoretical curves confirms that the high molecular weight chromatin-DNA prepared by hypotonic swelling of nuclei (without enzymatic digestion) displays a partially folded structure even at low ionic strength, whereas the low molecular weight chromatin-DNA prepared by a brief nuclease digestion appears very weakly folded at the same ionic conditions.
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Affiliation(s)
- E Maccioni
- EL.B.A. Foundation, Marciana Marina, (LI), Italy
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111
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Woodcock CL, Horowitz RA. Electron microscopic imaging of chromatin with nucleosome resolution. Methods Cell Biol 1997; 53:167-86. [PMID: 9348509 DOI: 10.1016/s0091-679x(08)60879-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- C L Woodcock
- Department of Biology, University of Massachusetts, Amherst 01003, USA
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112
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Sewack GF, Hansen U. Nucleosome positioning and transcription-associated chromatin alterations on the human estrogen-responsive pS2 promoter. J Biol Chem 1997; 272:31118-29. [PMID: 9388265 DOI: 10.1074/jbc.272.49.31118] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The positioning of nucleosomes on a promoter is a significant determinant in its responsiveness to inducing signals. We have mapped the chromatin structure of the human, estrogen-responsive pS2 promoter at nucleotide level resolution within the context of its normal genomic location in human mammary epithelial cells. In vivo digestion by nucleases followed by ligation-mediated polymerase chain reaction analysis revealed two rotationally phased and translationally positioned nucleosomes within the promoter between nucleotide positions -450 and +7. The estrogen response elements at -400 and TATAA box at -35 are each located at the edge of a nucleosome. The two precisely positioned nucleosomes exist in both transformed and nontransformed human mammary epithelial cells, regardless of estrogen receptor status or transcriptional activity of the gene. However, two structural alterations correlate with the transcriptional potential of the promoter. In MCF-7 cells, in which the pS2 promoter is inducible, the chromatin exhibits an increased sensitivity to DNase I in a region of DNA adjacent to the TATAA box and an additional micrococcal nuclease-hypersensitive site in the linker DNA between the two positioned nucleosomes. We were also able to demonstrate that nucleotides -1100 to +10 of the pS2 promoter are sufficient to determine the positioning of these two nucleosomes. Our results establish the structural features of the chromatin covering the pS2 promoter as well as transcriptionally associated alterations, suggesting how the nucleosomal template influences transcriptional regulation by estrogen receptor.
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Affiliation(s)
- G F Sewack
- Department of Molecular Genetics, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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113
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Horowitz RA, Koster AJ, Walz J, Woodcock CL. Automated electron microscope tomography of frozen-hydrated chromatin: the irregular three-dimensional zigzag architecture persists in compact, isolated fibers. J Struct Biol 1997; 120:353-62. [PMID: 9441938 DOI: 10.1006/jsbi.1997.3921] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The potential of electron microscope tomography as a tool for obtaining three-dimensional (3D) information about large macromolecular assemblies is greatly extended by automation of data collection. With the implementation of automated control of tilting, focusing, and digital image recording described here, tilt series of frozen-hydrated specimens can be collected with the requisite low dose. Long chromatin fibers were prepared in 90 mM monovalent ions to maintain a fully compact conformation, and after vitrification were completely contained within the ice layer. Tilt series of this material were recorded at 5 degrees tilt increments between +60 degrees and -60 degrees, with a cumulative dose of approximately 35 e-/A2 for the series. This extremely low dose data was successfully aligned, then reconstructed by weighted backprojection. The underlying architecture of the fibers is an irregular 3D zigzag of interconnected nucleosomes, with the linker DNA between successive nucleosomes in a largely extended conformation. The visualization of this structural motif within long, frozen-hydrated chromatin fibers at relatively high salt extends our previous studies on small fragments at low ionic strength and is in agreement with the observation of this architecture in chromatin fibers in situ in sectioned nuclei.
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Affiliation(s)
- R A Horowitz
- Biology Department, University of Massachusetts at Amherst 01003, USA
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114
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Nicolini C, Carrara S, Mascetti G. High order DNA structure as inferred by optical fluorimetry and scanning calorimetry. Mol Biol Rep 1997; 24:235-46. [PMID: 9403866 DOI: 10.1023/a:1006861801216] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
New quantitative insights on the native high order chromatin-DNA structure existing within interphase nuclei are obtained by monitoring the effects of two common well-characterized fixatives, glutaraldehyde and ethanol/acetic acid mixture, at the level of the intranuclear DNA distribution and structures. Reproducible distinct levels of DNA fluorescence intensity and their intranuclear distribution are apparent in unfixed and fixed thymocytes by using DAPI and quantitative optical microscopy based on a charge coupled device. The fluorescent histograms correlated with the calorimetric thermograms on the very same thymocytes fixed and unfixed, establish an unequivocal baseline for the different levels of structural organization of the chromatin within the intact nucleus; namely their number, DNA packing ratio and fiber diameter. A systematic comparison among all the numerous models, being so far proposed for the quinternary and quaternary levels of DNA folding, to identifies the rope or ribbon-like and the chromonema as the ones that best fit with the in situ distribution.
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Affiliation(s)
- C Nicolini
- Institute of Biophysics, University of Genoa, Italy
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115
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Leforestier A, Livolant F. Liquid crystalline ordering of nucleosome core particles under macromolecular crowding conditions: evidence for a discotic columnar hexagonal phase. Biophys J 1997; 73:1771-6. [PMID: 9336172 PMCID: PMC1181077 DOI: 10.1016/s0006-3495(97)78207-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Macromolecular crowding conditions occurring inside the cell nucleus were reproduced experimentally with solutions of mononucleosome core particles to study their supramolecular organization. We report here that under these conditions, and over a large range of monovalent salt concentrations, mononucleosome core particles self-assemble to form a discotic liquid crystalline phase characterized in polarizing and freeze-fracture electron microscopy. Mononucleosomes are stacked on each other to form columns, which are themselves closely packed into an hexagonal array. The nucleosome concentration, estimated from the network parameters, falls in the range of values measured in cell nuclei. We suggest that these concentrated solutions, although their organization cannot be immediately compared to the organization of chromatin in vivo, may be used to investigate the nucleosome-nucleosome interactions. Furthermore, this approach may be complexified to take into account the complexity of the eucaryotic chromatin.
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Affiliation(s)
- A Leforestier
- Laboratoire de Physique des Solides, Université Paris-Sud, Orsay, France
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116
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Iwano M, Fukui K, Takaichi S, Isogai A. Globular and fibrous structure in barley chromosomes revealed by high-resolution scanning electron microscopy. Chromosome Res 1997; 5:341-9. [PMID: 9292240 DOI: 10.1023/b:chro.0000038766.53836.c3] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Barley chromosomes were prepared for high-resolution scanning electron microscopy using a combination of enzyme maceration, treatment in acetic acid and osmium impregnation using thiocarbohydrazide. Using this technique, the three-dimensional ultrastructure of interphase nuclei and mitotic chromosomes was examined. In Interphase, different levels of chromatin condensation were observed, consisting of fibrils 10 nm in diameter, 20- to 40-nm fibres and a higher order complex. In prophase, globular and strand-like structures composed of 20- to 40-nm fibres were dominant. As the cells progressed through the cell cycle and the chromatin condensed, globular and strand-like structures (chromomeres) were coiled and packed to form chromosomes. Chromomeres were observed as globular protuberances on the surface of metaphase chromosomes. These findings indicate that the chromomere is a fundamental substructure of the higher order architecture of the chromosome. In the centromeric region, there were no globular protuberances, but 20- to 40-nm fibres were folded compactly to form a higher level organization surrounding the chromosomal axia.
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Affiliation(s)
- M Iwano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Japan.
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117
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Abstract
Electron microscopy, with its ability to image DNA and nucleosomes, can provide a key visual link in the understanding of chromatin conformation. We discuss applications of EM to current chromatin research with emphasis on strategies that eliminate many of the potential problems associated with conventional EM preparative techniques. Cryo-electron microscopy (cryo-EM) of isolated chromatin, whereby samples are imaged "in solution" in thin vitrified films, is considered in detail, with emphasis on the recovery of three-dimensional information and on its application to linker DNA conformation and to salt-induced compaction. Factors that currently limit the technique, and the prospects of overcoming them, are also considered.
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Affiliation(s)
- C L Woodcock
- Department of Biology, University of Massachusetts, Amherst
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118
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Abstract
Our current level of understanding of chromatin structure was to a large extent achieved with the help of DNA-protein cross-linking. The versatile inventory of cross-linking techniques allows the identification of the contacts between DNA and proteins with a single nucleotide-single amino acid precision, to detect minor components of the complex nucleoprotein systems, to reveal the interactions of the flexible protein domains with DNA, and to assay for conformational changes in the nucleosomes.
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Affiliation(s)
- D Pruss
- Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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119
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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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120
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Bedoyan JK, Lejnine S, Makarov VL, Langmore JP. Condensation of rat telomere-specific nucleosomal arrays containing unusually short DNA repeats and histone H1. J Biol Chem 1996; 271:18485-93. [PMID: 8702494 DOI: 10.1074/jbc.271.31.18485] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Vertebrate telomeres contain arrays of nucleosomes with unusually short and regular repeat lengths (Makarov, V. L., Lejnine, S., Bedoyan, J., and Langmore, J. P.(1993) Cell 73, 775-787; Lejnine, S., Makarov, V., and Langmore, J. P. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 2393-2397). In order to better define the specific structural features of telomere chromatin, we examined the condensation and H1 content of telomere nucleoproteins from rat liver. Velocity sedimentation analysis shows that telomeric nucleosome arrays condense with increasing ionic strength and molecular weight in a manner comparable with that of bulk chromatin despite the very short repeat length. However, these condensed structures do not exhibit the approximately 100-base pair deoxyribonuclease II repeat characteristic of condensed bulk chromatin. Frictional coefficient calculations suggest that telomere-specific higher order structure is more compact than bulk chromatin. Nucleoprotein gel electrophoresis shows that telomeric dinucleosomes from soluble chromatin contain H1. Finally, direct isolation and analysis of telomere nucleoproteins from formaldehyde-cross-linked nuclei indicate the presence of core histone proteins and H1. These results are consistent with the view that a major fraction of the long telomeres of rat are organized as specialized nucleosome arrays with features similar but not identical to those of bulk chromatin.
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Affiliation(s)
- J K Bedoyan
- Graduate Program in Cellular and Molecular Biology, Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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121
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Labarbe R, Mignon S, Flock S, Houssier C. Diffusion-enhanced resonance energy transfer shows that linker-DNA accessibility decreases during salt-induced chromatin condensation. J Fluoresc 1996; 6:107-18. [DOI: 10.1007/bf00732050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/1995] [Accepted: 05/07/1996] [Indexed: 10/26/2022]
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122
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Zlatanova J, van Holde K. The linker histones and chromatin structure: new twists. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 52:217-59. [PMID: 8821262 DOI: 10.1016/s0079-6603(08)60968-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- J Zlatanova
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331, USA
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123
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Stein A. Signals in eukaryotic DNA promote and influence formation of nucleosome arrays. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 54:333-81. [PMID: 8768079 DOI: 10.1016/s0079-6603(08)60367-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- A Stein
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47906-1392, USA
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124
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Graziano V, Gerchman SE, Schneider DK, Ramakrishnan V. Neutron scattering studies on chromatin higher-order structure. BASIC LIFE SCIENCES 1996; 64:127-36. [PMID: 9031508 DOI: 10.1007/978-1-4615-5847-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have been engaged in studies of the structure and condensation of chromatin into the 30 nm filament using small-angle neutron scattering. We have also used deuterated histone H1 to determine its location in the chromatin 30 nm filament. Our studies indicate that chromatin condenses with increasing ionic strength to a limiting structure that has a mass per unit length of 6-7 nucleosomes/11 nm. They also show that the linker histone H1/H5 is located in the interior of the chromatin filament, in a position compatible with its binding to the inner face of the nucleosome. Analysis of the mass per unit length as a function of H5 stoichiometry suggests that 5-7 contiguous nucleosomes need to have H5 bound before a stable higher order structure can exist.
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Affiliation(s)
- V Graziano
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
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125
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Bartolomé S, Bermúdez A, Daban JR. Electrophoresis of chromatin on nondenaturing agarose gels containing Mg2+. Self-assembly of small chromatin fragments and folding of the 30-nm fiber. J Biol Chem 1995; 270:22514-21. [PMID: 7673242 DOI: 10.1074/jbc.270.38.22514] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We show that nondenaturing agarose gels can be used for the study of the structure and dynamic properties of native (uncross-linked) chromatin. In gels containing 1.7 mM Mg2+, chicken erythrocyte chromatin fragments having from about 6 to 50 nucleosomes produce well defined bands. These bands have an electrophoretic mobility that decreases only slightly with molecular weight. This surprising behavior is not observed in low ionic strength gels. Fragments with less than 6 nucleosomes and low content of histones H1-H5 give rise to broad bands in gels with Mg2+. In contrast, fragments containing only 3-4 nucleosomes but with the normal H1-H5 content are able to form associated structures with a mobility similar to that observed for high molecular weight chromatin. Electron microscopy results indicate that the associated fragments and the fragments of higher molecular weight show similar electrophoretic properties because they become very compact in the presence of Mg2+ and form cylindrical structures with a diameter of approximately 33 nm. Our results suggest that the interactions involved in the self-assembly of small fragments are the same that direct the folding of larger fragments; in both cases, the resulting compact chromatin structure is formed from a basic element containing 5-7 nucleosomes.
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Affiliation(s)
- S Bartolomé
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències, Universitat Autònoma de Barcelona, Bellaterra, Spain
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126
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Pehrson JR. Probing the Conformation of Nucleosome Linker DNA in Situ with Pyrimidine Dimer Formation. J Biol Chem 1995. [DOI: 10.1016/s0021-9258(18)90157-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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127
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Abstract
The predominant view of chromatin structure is that the beaded chain of nucleosomes is folded into a symmetrical helical fibre. Recently, however, direct evidence from cryoelectron microscopy and other imaging techniques confirms a non-symmetrical organization, consistent with modelling based on the heterogeneity of linker DNA lengths. This mode of chromatin folding is more compatible with the range of functional states in the living nucleus.
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Affiliation(s)
- C L Woodcock
- Dept of Biology and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003, USA
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128
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Fritzsche W, Schaper A, Jovin TM. Scanning force microscopy of chromatin fibers in air and in liquid. SCANNING 1995; 17:148-155. [PMID: 7795839 DOI: 10.1002/sca.4950170305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have adapted specimen preparation techniques of conventional electron microscopy for visualizing chromatin structures in the scanning force microscope (SFM) in air and in liquid. The beaded substructure of the nucleoprotein filament was obtained after hypotonic lysis of chicken erythrocytes and air drying, whereas supranucleosomal structures were preserved after treatment of cell nuclei with detergent. In the latter case, the nucleosomes were still distinct but appeared more condensed. A modified droplet diffusion-spreading technique of chromatin from Namalwa cells (a human B-lymphoid line) yielded a uniform filamentous morphology and similar fiber appearance. A reversible swelling of spread chromatin was observed upon exposure of air-dried samples to solutions differing in salt concentrations.
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Affiliation(s)
- W Fritzsche
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
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129
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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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130
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Leuba SH, Yang G, Robert C, Samori B, van Holde K, Zlatanova J, Bustamante C. Three-dimensional structure of extended chromatin fibers as revealed by tapping-mode scanning force microscopy. Proc Natl Acad Sci U S A 1994; 91:11621-5. [PMID: 7972114 PMCID: PMC45283 DOI: 10.1073/pnas.91.24.11621] [Citation(s) in RCA: 201] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Unfixed chicken erythrocyte chromatin fibers in very low salt have been imaged with a scanning force microscope operating in the tapping mode in air at ambient humidity. These images reveal a three-dimensional organization of the fibers. The planar "zig-zag" conformation is rare, and extended "beads-on-a-string" fibers are seen only in chromatin depleted of histones H1 and H5. Glutaraldehyde fixation reveals very similar structures. Fibers fixed in 10 mM salt appear somewhat more compacted. These results, when compared with modeling studies, suggest that chromatin fibers may exist as irregular three-dimensional arrays of nucleosomes even at low ionic strength.
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Affiliation(s)
- S H Leuba
- Department of Chemistry, University of Oregon, Eugene
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131
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Bartolomé S, Bermúdez A, Daban JR. Internal structure of the 30 nm chromatin fiber. J Cell Sci 1994; 107 ( Pt 11):2983-92. [PMID: 7698998 DOI: 10.1242/jcs.107.11.2983] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the presence of 1.7 mM Mg2+, the diameter of the circular structures produced by small chromatin fragments isolated from chicken erythrocytes remains essentially unchanged when the number of nucleosomes in these fragments increases from 10 to 36. In contrast, the results obtained in unidirectional shadowing experiments show that under the same conditions the height of the chromatin fragments increases with the number of nucleosomes. These observations indicate that the electron microscope images studied in this work correspond to a top view of small chromatin fragments. Rotary-shadowed chromatin fragments show three parts: (a) a contour with a heavy deposition of platinum; (b) an annular zone between the central region and the periphery; and (c) a central hole. The heterogeneous ring generated by the deposition of platinum in the periphery suggests that nucleosomes form a one-start helix (5-7 nucleosomes per turn) that apparently can be left- or right-handed. The annular region (thickness of about 11 nm) shows spokes probably due to flat faces and core DNA of radially oriented nucleosomes. The central hole (8-12 nm) is clearly seen in many images but it is not empty because some deformed fragments show coated material (probably linker DNA) that protrudes from this central depression. We have observed that these structural elements directly detected in short chromatin fragments are also present in long chromatin fibers. This allows us to conclude that these elements are basic structural components of the 30 nm chromatin fiber.
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Affiliation(s)
- S Bartolomé
- Departament de Bioquímica i Biologia Molecular, Facultat de Ciències, Universitat Autònoma de Barcelona, Spain
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132
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Woodcock CL. Chromatin fibers observed in situ in frozen hydrated sections. Native fiber diameter is not correlated with nucleosome repeat length. J Biophys Biochem Cytol 1994; 125:11-9. [PMID: 8138565 PMCID: PMC2120018 DOI: 10.1083/jcb.125.1.11] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Chromatin fibers have been observed and measured in frozen hydrated sections of three types of cell (chicken erythrocytes and sperm of Patiria miniata and Thyone briareus) representing an approximately 20-bp range of nucleosomal repeat lengths. For sperm of the starfish P. miniata, it was possible to obtain images of chromatin fibers from cells that were swimming in seawater up to the moment of cryo-immobilization, thus providing a record of the native morphology of the chromatin of these cells. Glutaraldehyde fixation produced no significant changes in the ultrastructure or diameter of chromatin fibers, and fiber diameters observed in cryosections were similar to those recorded after low temperature embedding in Lowicryl K11M. Chromatin fiber diameters measured from cryosections of the three types of nuclei were similar, a striking contrast to the situation for chromatin isolated from these cell types, where a strong positive correlation between diameter and nucleosomal repeat length has been established. The demonstration of chromatin fibers in unfixed whole cells establishes an unequivocal baseline for the study of native chromatin and chromosome architecture. The significant differences between chromatin fibers in nucleo and after isolation supports a previous observation (P. J. Giannasca, R. A. Horowitz, and C. L. Woodcock. 1993. J. Cell Sci. 105:551-561), and suggests that structural studies on isolated material should be interpreted with caution until the changes that accompany chromatin isolation are understood.
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Affiliation(s)
- C L Woodcock
- Biology Department, University of Massachusetts, Amherst 01003
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133
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Horowitz RA, Agard DA, Sedat JW, Woodcock CL. The three-dimensional architecture of chromatin in situ: electron tomography reveals fibers composed of a continuously variable zig-zag nucleosomal ribbon. J Cell Biol 1994; 125:1-10. [PMID: 8138564 PMCID: PMC2120010 DOI: 10.1083/jcb.125.1.1] [Citation(s) in RCA: 197] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The three dimensional (3D) structure of chromatin fibers in sections of nuclei has been determined using electron tomography. Low temperature embedding and nucleic acid-specific staining allowed individual nucleosomes to be clearly seen, and the tomographic data collection parameters provided a reconstruction resolution of 2.5 nm. Chromatin fibers have complex 3D trajectories, with smoothly bending regions interspersed with abrupt changes in direction, and U turns. Nucleosomes are located predominantly at the fiber periphery, and linker DNA tends to project toward the fiber interior. Within the fibers, a unifying structural motif is a two nucleosome-wide ribbon that is variably bent and twisted, and in which there is little face-to-face contact between nucleosomes. It is suggested that this asymmetric 3D zig-zag of nucleosomes and linker DNA represents a basic principle of chromatin folding that is determined by the properties of the nucleosome-linker unit. This concept of chromatin fiber architecture is contrasted with helical models in which specific nucleosome-nucleosome contacts play a major role in generating a symmetrical higher order structure. The transcriptional control implications of a more open and irregular chromatin structure are discussed.
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Affiliation(s)
- R A Horowitz
- Department of Biology, University of Massachusetts, Amherst 01003
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134
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Woodcock CL, Grigoryev SA, Horowitz RA, Whitaker N. A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. Proc Natl Acad Sci U S A 1993; 90:9021-5. [PMID: 8415647 PMCID: PMC47493 DOI: 10.1073/pnas.90.19.9021] [Citation(s) in RCA: 215] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The "30-nm" chromatin fibers, as observed in eukaryotic nuclei, are considered a discrete level in a hierarchy of DNA folding. At present, there is considerable debate as to how the nucleosomes and linker DNA are organized within chromatin fibers, and a number of models have been proposed, many of which are based on helical symmetry and imply specific contacts between nucleosomes. However, when observed in nuclei or after isolation, chromatin fibers show considerable structural irregularity. In the present study, chromatin folding is considered solely in terms of the known properties of the nucleosome-linker unit, taking into account the relative rotation between consecutive nucleosomes that results from the helical twist of DNA. Model building based on this premise, and with a constant length of linker DNA between consecutive nucleosomes, results in a family of fiber- and ribbon-like structures. When the linker length between nucleosomes is allowed to vary, as occurs in nature, fibers showing the types of irregularity observed in nuclei and in isolated chromatin are created. The potential application of the model in determining the three-dimensional organization of chromatin in which nucleosome positions are known is discussed.
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Affiliation(s)
- C L Woodcock
- Department of Biology, University of Massachusetts, Amherst 01003
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135
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Giannasca PJ, Horowitz RA, Woodcock CL. Transitions between in situ and isolated chromatin. J Cell Sci 1993; 105 ( Pt 2):551-61. [PMID: 8408284 DOI: 10.1242/jcs.105.2.551] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We show that the mechanism by which chromatin displaying higher-order structure is usually isolated from nuclei involves a transition to an extended nucleosomal arrangement. After being released from nuclei, chromatin must refold in order to produce the typical chromatin fibers observed in solution. For starfish sperm chromatin with a long nucleosome repeat (222 bp), isolated fibers are significantly wider than those in the nucleus, indicating that the refolding process does not regenerate the native higher-order structure. We also propose that for typical eukaryotic nuclei, the concept that the native state of the (inactive) bulk of the genome is a chromatin fiber with defined architecture be reconsidered.
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Affiliation(s)
- P J Giannasca
- Department of Biology, University of Massachusetts, Amherst 01003
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136
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Godde JS, Widom J. Chromatin structure of Schizosaccharomyces pombe. A nucleosome repeat length that is shorter than the chromatosomal DNA length. J Mol Biol 1992; 226:1009-25. [PMID: 1518041 DOI: 10.1016/0022-2836(92)91049-u] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have used new methods for chromatin isolation, together with conventional methods for measuring the nucleosome repeat length, to determine the repeat length of Schizosaccharomyces pombe chromatin. We obtain a result of 156(+/- 2) bp. Equivalent results are obtained using a psoralen crosslinking method for measuring the repeat length in viable spheroplasts. That result, together with other control experiments, rules out many possible artifacts. The measured value of 156(+/- 2) bp is smaller than the length of DNA found in the chromatosome. Thus, the chromatosome cannot be the fundamental unit of chromatin structure in all eukaryotes. The crossed linker model of chromatin higher order structure is incompatible with a nucleosome repeat length of 156 bp, and thus cannot apply to all eukaryotes. The solenoid model of higher order structure is compatible with this repeat length only if the solenoid is right-handed. We note two other properties of this chromatin. (1) Early in digestion, the DNA length of mononucleosomes from S. pombe and Aspergillus nidulans exceeds the nucleosome repeat length. (2) Many methods for isolating chromatin from S. pombe yield an apparent nucleosome repeat length of less than or equal to 140 bp; this result is found to be an artifactual consequence of nucleosome sliding.
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Affiliation(s)
- J S Godde
- Department of Biochemistry, University of Illinois, Urbana 61801
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137
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Fujiwara S. Interpretation of the X-ray scattering profiles of chromatin at various NaCl concentrations by a simple chain model. Biophys Chem 1992; 43:81-7. [PMID: 1633260 DOI: 10.1016/0301-4622(92)80044-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In order to interpret the change in the X-ray scattering profiles from rat thymus chromatin, extensive model calculation was carried out. Chromatin is modelled as a string of subunits (nucleosomes) in which disorder is introduced into the positions of adjacent subunits. Disposition parameters characterizing the arrangement of subunits were estimated for various states of chromatin, so that the main feature of the scattering profiles is described. The result indicated that the structure of chromatin changes, as the NaCl concentration increases, from the extended "beads-on-a string" structure to the condensed helical structure. The latter has an outer diameter of about 26 nm with 3-4 nucleosomes per turn. In the intermediate state, it has a loose helical structure. The estimation of disorder suggested that the arrangement of subunits is appreciably disordered even in the condensed helical filament at 50 mM NaCl. Our model for chromatin condensation seems to support models of the "crossed linker" type.
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Affiliation(s)
- S Fujiwara
- Department of Biophysical Engineering, Faculty of Engineering Science, Osaka University, Japan
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138
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Abstract
This review will consider solution studies of structure and interactions of DNA and DNA complexes using linear dichroism spectroscopy, with emphasis on the technique of orientation by flow. The theoretical and experimental background to be given may serve, in addition, as a general introduction into the state of the art of linear dichroism spectroscopy, particularly as it is applied to biophysical problems.
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Affiliation(s)
- B Norden
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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139
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140
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Lee MS, Garrard WT. Positive DNA supercoiling generates a chromatin conformation characteristic of highly active genes. Proc Natl Acad Sci U S A 1991; 88:9675-9. [PMID: 1946386 PMCID: PMC52781 DOI: 10.1073/pnas.88.21.9675] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
During transcription, positive DNA supercoils generated ahead of RNA polymerase could theoretically uncoil the negative DNA supercoils associated with nucleosomes and thereby decondense the chromatin fiber in preparation for RNA polymerase passage. Here we examine the effect of positive DNA supercoiling on the structure of yeast 2-microns minichromosomes. We utilized a conditional topoisomerase mutant expressing Escherichia coli topoisomerase I to convert the DNA supercoiling state from negative to positive in vivo. Minichromosomes containing positively supercoiled DNA exhibited a striking increase in DNase I sensitivity. They also displayed additional micrococcal nuclease cleavage sites but yielded nearly typical nucleosomal ladders after extensive digestion. Upon in vitro relaxation with eukaryotic topoisomerase I, the minichromosomes remained DNase I sensitive but were converted to negative DNA supercoiling with a slightly increased linking number compared to typical minichromosomes, thus indicating the presence of bound histones. Therefore, positive DNA supercoiling provides a mechanism for generating, but is not required for maintaining, a conformation in chromatin characteristic of highly transcribed genes.
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Affiliation(s)
- M S Lee
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235
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141
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Williams SP, Langmore JP. Small angle x-ray scattering of chromatin. Radius and mass per unit length depend on linker length. Biophys J 1991; 59:606-18. [PMID: 2049522 PMCID: PMC1281225 DOI: 10.1016/s0006-3495(91)82276-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Analyses of low angle x-ray scattering from chromatin, isolated by identical procedures but from different species, indicate that fiber diameter and number of nucleosomes per unit length increase with the amount of nucleosome linker DNA. Experiments were conducted at physiological ionic strength to obtain parameters reflecting the structure most likely present in living cells. Guinier analyses were performed on scattering from solutions of soluble chromatin from Necturus maculosus erythrocytes (linker length 48 bp), chicken erythrocytes (linker length 64 bp), and Thyone briareus sperm (linker length 87 bp). The results were extrapolated to infinite dilution to eliminate interparticle contributions to the scattering. Cross-sectional radii of gyration were found to be 10.9 +/- 0.5, 12.1 +/- 0.4, and 15.9 +/- 0.5 nm for Necturus, chicken, and Thyone chromatin, respectively, which are consistent with fiber diameters of 30.8, 34.2, and 45.0 nm. Mass per unit lengths were found to be 6.9 +/- 0.5, 8.3 +/- 0.6, and 11.8 +/- 1.4 nucleosomes per 10 nm for Necturus, chicken, and Thyone chromatin, respectively. The geometrical consequences of the experimental mass per unit lengths and radii of gyration are consistent with a conserved interaction among nucleosomes. Cross-linking agents were found to have little effect on fiber external geometry, but significant effect on internal structure. The absolute values of fiber diameter and mass per unit length, and their dependencies upon linker length agree with the predictions of the double-helical crossed-linker model. A compilation of all published x-ray scattering data from the last decade indicates that the relationship between chromatin structure and linker length is consistent with data obtained by other investigators.
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Affiliation(s)
- S P Williams
- Department of Biological Sciences, University of Michigan, Ann Arbor 48109-2099
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142
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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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143
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Athey BD, Smith MF, Rankert DA, Williams SP, Langmore JP. The diameters of frozen-hydrated chromatin fibers increase with DNA linker length: evidence in support of variable diameter models for chromatin. J Cell Biol 1990; 111:795-806. [PMID: 2391364 PMCID: PMC2116296 DOI: 10.1083/jcb.111.3.795] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The diameters of chromatin fibers from Thyone briareus (sea cucumber) sperm (DNA linker length, n = 87 bp) and Necturus maculosus (mudpuppy) erythrocytes (n = 48 bp) were investigated. Soluble fibers were frozen into vitrified aqueous solutions of physiological ionic strength (124 mM), imaged by cryo-EM, and measured interactively using quantitative computer image-processing techniques. Frozen-hydrated Thyone and Necturus fibers had significantly different mean diameters of 43.5 nm (SD = 4.2 nm; SEM = 0.61 nm) and 32.0 nm (SD = 3.0 nm; SEM = 0.36 nm), respectively. Evaluation of previously published EM data shows that the diameters of chromatin from a large number of sources are proportional to linker length. In addition, the inherent variability in fiber diameter suggests a relationship between fiber structure and the heterogeneity of linker length. The cryo-EM data were in quantitative agreement with space-filling double-helical crossed-linker models of Thyone and Necturus chromatin. The data, however, do not support solenoid or twisted-ribbon models for chromatin that specify a constant 30 nm diameter. To reconcile the concept of solenoidal packing with the data, we propose a variable-diameter solid-solenoid model with a fiber diameter that increases with linker length. In principle, each of the variable diameter models for chromatin can be reconciled with local variations in linker length.
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Affiliation(s)
- B D Athey
- Biophysics Research Division, University of Michigan, Ann Arbor 48109-2099
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144
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Selvin PR, Scalettar BA, Langmore JP, Axelrod D, Klein MP, Hearst JE. A polarized photobleaching study of chromatin reorientation in intact nuclei. J Mol Biol 1990; 214:911-22. [PMID: 2388274 DOI: 10.1016/0022-2836(90)90345-m] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Polarized fluorescence recovery after photobleaching (pFRAP) was used to monitor the effects that condensation, i.e. compaction and aggregation, have on the (microseconds and ms) internal dynamics of chromatin in intact nuclei. When divalent cations were present with physiological (approximately 90 mM) monovalent salt the chromatin was found to exist in a compact and aggregated state which was characterized by rotational immobilization over timescales that range from 10 microseconds to 40 milliseconds. This immobilization is attributed to suppression of internal dynamics by intermolecular interactions. When the divalent cations were removed, the compact fibers no longer aggregated and were free to reorient with a characteristic decay time of about 1.2 milliseconds. It is shown that this millisecond relaxation could represent rigid rotation of topologically independent structural domains. Dilution of the monovalent salt induced a gradual change in the structural state of the chromatin that was manifest as a dramatic increase in internal flexibility. At the lowest salt concentration studied (11 mM-monovalent salt) the chromatin reorients in fewer than ten microseconds. These changes in flexibility are continuous with salt concentration, indicating that there are no well-defined endpoints to structural transitions and that the microsecond-millisecond internal dynamics of chromatin are a sensitive measure of structure. Measurements made on nuclei from cells that are either transcriptionally quiescent or active indicate that the dynamics mirrors biological activity.
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Affiliation(s)
- P R Selvin
- Chemical Biodynamics Division, Lawrence Berkeley Laboratory, Berkley, CA 94720
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145
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Osipova TN, Karpova EV, Vorob'ev VI. Chromatin higher-order structure: two-start double superhelix formed by zig-zag shaped nucleosome chain with folded linker DNA. J Biomol Struct Dyn 1990; 8:11-22. [PMID: 2275789 DOI: 10.1080/07391102.1990.10507786] [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: 12/31/2022]
Abstract
Hydrodynamic properties of chromatins differing in linker DNA length and in transcriptional activity have been studied by the method of sedimentation velocity. Oligonucleosomes of different chain length were isolated from chromatins of pigeon brain cortical neurones, rat thymus and sea urchin sperm characterized by nucleosome DNA repeat length of 165, 198 and 248 base pairs respectively. The hydrodynamic behaviour of oligonucleosomes in the dependence on the number of nucleosomes in the chain and on the ionic strength has been analysed on the basis of cylinder model. The data obtained allows one to calculate the main structural parameters of the oligonucleosomal chain: its mass per unit length, the hydrodynamic diameter of the chain, the length of the chain per nucleosome and DNA packing ratio. It is shown that hydrodynamic behaviour of nucleosome oligomers from all types of chromatins investigated at low ionic strength can be well described by the model of three-dimensional zig-zag chain with similar diameter and length of the chain per nucleosome, DNA packing ratio growing with the increase of linker DNA length. It can be achieved by unfolding the short linker DNA in neurone chromatin and by coiling the long linker DNA of sea urchin sperm chromatin into a loop. With the increase of ionic strength zig-zag shaped nucleosomal chain is condensed into a two-start double superhelix with closely arranged nucleosomes and linker DNA loops packed inside the superhelix. The suggested model is in good agreement with available experimental data and overcomes a number of difficulties which arise for the solenoid model and other models of the 30-nm chromatin fibril.
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Affiliation(s)
- T N Osipova
- Institute of Cytology, Academy of Sciences of the USSR, Leningrad
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146
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Bavykin SG, Usachenko SI, Zalensky AO, Mirzabekov AD. Structure of nucleosomes and organization of internucleosomal DNA in chromatin. J Mol Biol 1990; 212:495-511. [PMID: 2325131 DOI: 10.1016/0022-2836(90)90328-j] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have compared the mononucleosomal pattern produced by micrococcal nuclease digestion of condensed and unfolded chromatin and chromatin in nuclei from various sources with the repeat length varying from 165 to 240 base-pairs (bp). Upon digestion of isolated H1-containing chromatin of every tested type in a low ionic strength solution (unfolded chromatin), a standard series of mononucleosomes (MN) was formed: the core particle, MN145, and H1-containing, MN165, MN175, MN185, MN195, MN205 and MN215 (the indexes give an approximate length of the nucleosomal DNA that differs in these particles by an integral number of 10 bp). In addition to the pattern of unfolded chromatin, digestion of whole nuclei or condensed chromatin (high ionic strength of Ca2+) gave rise to nuclei-specific, H1-lacking MN155. Digestion of H1-lacking chromatin produced only MN145, MN155 and MN165 particles, indicating that the histone octamer can organize up to 165 bp of nucleosomal DNA. Although digestion of isolated sea urchin sperm chromatin (repeat length of about 240 bp) at a low ionic strength gave a typical "unfolded chromatin pattern", digests of spermal nuclei contained primarily MN145, MN155, MN235 and MN245 particles. A linear arrangement of histones along DNA (primary organization) of the core particle was found to be preserved in the mononucleosomes, with the spacer DNA length from 10 to 90 bp on one (in MN155) or both sides of core DNA being a multiple of about 10 bp. In MN235, the core particle occupies preferentially a central position with the length of the spacer DNA on both sides of the core DNA being usually about 30 + 60 or 40 + 50 bp. Histone H1 is localized at the ends of these particles, i.e. close to the centre of the spacer DNA. The finding that globular part of histones H3 and sea urchin sperm H2B can covalently bind to spacer DNA suggests their involvement in the organization of chromatin superstructure. Our data indicate that decondensation of chromatin is accompanied by rearrangement of histone H1 on the spacer DNA sites adjacent to the core particle and thus support a solenoid model for the chromatin superstructure in nuclei in which the core DNA together with the spacer DNA form a continuous superhelix.
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Affiliation(s)
- S G Bavykin
- Institute of Molecular Biology, USSR Academy of Sciences, Moscow
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147
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Reich Z, Ittah Y, Weinberger S, Minsky A. Chiral and structural discrimination in binding of polypeptides with condensed nucleic acid structures. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39402-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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148
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Horowitz RA, Giannasca PJ, Woodcock CL. Ultrastructural preservation of nuclei and chromatin: improvement with low-temperature methods. J Microsc 1990; 157:205-24. [PMID: 2313684 DOI: 10.1111/j.1365-2818.1990.tb02959.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ultrastructure of chromatin has been examined in nuclei prepared by a variety of low-temperature methods. Embedding glutaraldehyde (GA)-fixed nuclei in Lowicryl K4M or K11M following dehydration by the progressive lowering of temperature (PLT) method, or in K11M following spray freezing and freeze substitution (FS), produces chromatin fibres that have, in situ, a diameter close to the in vivo state, and show internal structural details consistent with patterns of nucleosome packing previously observed only in preparations of isolated fibres. This is a temperature-dependent effect; fibres conventionally dehydrated and embedded in Lowicryl at 0 degrees C or in conventional epoxy resin at 60 degrees C have lower and less uniform diameters, and lack internal structural details. Of the techniques used, spray freezing followed by FS resulted in the most notable improvement over conventional methods. Inclusion of GA during FS of rapidly frozen, unfixed nuclei in methanol does not result in cross-linking of nuclear proteins. In acetone, however, cross-linking by GA occurs at -45 degrees C, or at lower temperatures if the water content of the acetone-based FS media is kept deliberately high. Substitution regimes employing GA alone or in combination with uranyl acetate and/or osmium tetroxide do not result in fibre morphologies comparable to either prefixed or unfixed nuclei substituted in additive-free substitution media. Whole fibroblasts show excellent preservation of nuclei and the nuclear/cytoplasmic interface after spray freezing followed by FS and low-temperature embedding.
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Affiliation(s)
- R A Horowitz
- Department of Zoology, University of Massachusetts, Amherst 01003
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149
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Smith MF, Athey BD, Williams SP, Langmore JP. Radial density distribution of chromatin: evidence that chromatin fibers have solid centers. J Cell Biol 1990; 110:245-54. [PMID: 2298806 PMCID: PMC2116005 DOI: 10.1083/jcb.110.2.245] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Fiber diameter, radial distribution of density, and radius of gyration were determined from scanning transmission electron microscopy (STEM) of unstained, frozen-dried chromatin fibers. Chromatin fibers isolated under physiological conditions (ionic strength, 124 mM) from Thyone briareus sperm (DNA linker length, n = 87 bp) and Necturus maculosus erythrocytes (n = 48 bp) were analyzed by objective image-processing techniques. The mean outer diameters were determined to be 38.0 nm (SD = 3.7 nm; SEM = 0.36 nm) and 31.2 nm (SD = 3.6 nm; SEM = 0.32 nm) for Thyone and Necturus, respectively. These data are inconsistent with the twisted-ribbon and solenoid models, which predict constant diameters of approximately 30 nm, independent of DNA linker length. Calculated radial density distributions of chromatin exhibited relatively uniform density with no central hole, although the 4-nm hole in tobacco mosaic virus (TMV) from the same micrographs was visualized clearly. The existence of density at the center of chromatin fibers is in strong disagreement with the hollow-solenoid and hollow-twisted-ribbon models, which predict central holes of 16 and 9 nm for chromatin of 38 and 31 nm diameter, respectively. The cross-sectional radii of gyration were calculated from the radial density distributions and found to be 13.6 nm for Thyone and 11.1 nm for Necturus, in good agreement with x-ray and neutron scattering. The STEM data do not support the solenoid or twisted-ribbon models for chromatin fiber structure. They do, however, support the double-helical crossed-linker models, which exhibit a strong dependence of fiber diameter upon DNA linker length and have linker DNA at the center.
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Affiliation(s)
- M F Smith
- Department of Biological Sciences, University of Michigan, Ann Arbor 48109
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150
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Mirzabekov AD, Pruss DV, Ebralidse KK. Chromatin superstructure-dependent crosslinking with DNA of the histone H5 residues Thr1, His25 and His62. J Mol Biol 1990; 211:479-91. [PMID: 2106584 DOI: 10.1016/0022-2836(90)90366-t] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The points of histone H5 interactions with DNA within nucleosomes and chromatin at different levels of compaction are delineated by identification of H5 amino acid residues that can be covalently bound to DNA. Three major crosslinkable points of H5 are His25, His62 (both within the globular part of the molecule), and N-terminal Thr1. His25 interacts with the terminal regions of nucleosomal DNA; His62 appears to bind more distal segments of the linker DNA. The His25-DNA crosslink predominates in the isolated mononucleosomes and persists throughout the chromatin condensation states studied, from extended oligonucleosomal chains to nuclei. His62 is the strongest crosslinking site in nuclei; in oligonucleosomes, the predominance of the His62-DNA crosslink requires the number of nucleosomes in the chain to be above some critical value. The Thr1-DNA crosslink is generated only in decondensed poly- or oligonucleosomes, but not in mononucleosomes. Thus, underlying the higher-order folding transitions of the nucleosomal chain is the restructuring of H5-DNA interactions.
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Affiliation(s)
- A D Mirzabekov
- W. A. Engelhardt Institute of Molecular Biology, Academy of Sciences of the U.S.S.R., Moscow
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