Three-dimensional reconstruction of chromatin fibers

Lessons from tomographic studies of the mammalian Golgi

Basic structure studies of the biosynthetic machinery of the cell by electron microscopy (EM) have underpinned much of our fundamental knowledge in the areas of molecular cell biology and membrane traffic. Driven by our collective desire to understand how changes in the complex and dynamic structure of this enigmatic organelle relate to its pivotal roles in the cell, the comparatively high-resolution glimpses of the Golgi and other compartments of the secretory pathway offered to us through EM have helped to inspire the development and application of some of our most informative, complimentary (molecular, biochemical and genetic) approaches. Even so, no one has yet even come close to relating the basic molecular mechanisms of transport, through and from the Golgi, to its ultrastructure, to everybody's satisfaction. Over the past decade, EM tomography has afforded new insights into structure-function relationships of the Golgi and provoked a re-evaluation of older paradigms. By providing a set of tools for structurally dissecting cells at high-resolution in three-dimensions (3D), EM tomography has emerged as a method for studying molecular cell biology in situ. As we move rapidly toward the establishment of molecular atlases of organelles through advances in proteomics and genomics, tomographic studies of the Golgi offer the tantalizing possibility that one day, we will be able to map the spatio-temporal coordinates of Golgi-related proteins and lipids accurately in the context of 4D cellular space.

Effect of in vivo histone hyperacetylation on the state of chromatin fibers

We evaluated the contribution of in vivo histone acetylation to the folding of chromatin into its higher-order structures. We have compared high-order folding patterns of hyperacetylated vs. unmodified chromatin in living green monkey kidney cells (CV1 line) using intercalator chloroquine diphospate to induce alterations in the twist of internucleosomal linker DNA. We have shown that histone hyperacetylation induced by antibiotic Trichostatin A significantly alters intercalator-mediated chromatin folding pattern.

Modulation of the higher-order folding of chromatin by deletion of histone H3 and H4 terminal domains

The 'tails' of histones H3 and H4 were removed by light in situ trypsin digestion of the nuclei. The alterations in the higher-order folding of chromatin resulting from this treatment were monitored by ethidium bromide titration. We found that DNA-intercalation of ethidium bromide under these conditions exhibited a complex concentration effect that was dependent on the extent of chromatin folding. This most likely reflects the structural transitions of chromatin during its folding as a result of the changes in the nucleosome linker twist [Woodcock, Grigoryev, Horowitz and Whitaker (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 9021-9025]. These results strongly suggest that the H3 and H4 terminal domains play a very important role in chromatin folding. We discuss the molecular basis of this phenomenon and propose a novel generalized model for the higher-order folding of chromatin.

Order and disorder in 30 nm chromatin fibers

The tendency of DNA to form fibers upon condensation with counterions is reviewed. It is shown that chromatin fibers may acquire a relatively constant diameter of about 30 nm simply as an optimal size achieved upon neutralization of DNA, without requiring a repetitive internal structure. Thus the size of chromatin fibers would not be determined by any specific spatial interaction between DNA and histones. The driving force for the formation of fibers in chromatin would be similar to that found in proteins when they acquire a compact globular shape.

The application of the maximum entropy method to electron microscopic tomography

The maximum entropy method has been applied to single axis tilt electron microscopic tomography. Its application requires that the problem be correctly formulated and that the model for the noise in electron micrographs be developed. A suitable noise model was determined empirically. The maximum entropy method was applied to a reconstruction of a test object from projections to which noise had been added. These reconstructions were superior to those obtained by reciprocal space weighted back protection. The method was also robust towards the incorrect specification of the noise, the penalty being an increase in the time required for convergence rather than degradation of the quality of the reconstructed image. In the reconstruction of negatively stained chromatin fibres it was possible to obtain satisfactory images utilizing all the information in the projections, in contrast to conventional methods in which high resolution data are removed by the application of Fourier space filters.

Three-dimensional reconstruction of single particles from random and nonrandom tilt series

To overcome the radiation damage-induced limitations to the resolution of three-dimensional reconstructions from electron microscopic tilt series, novel reconstruction schemes have been developed that require only a single exposure of the specimen. The tilt series collected with these methods have random projection directions. First, three-dimensional reconstruction techniques are described that are applicable to data obtained from tilt series with regular tilt geometry, followed by the extensions of these techniques to permit analysis of projection series with randomly spaced tilts. The main emphasis is placed on the weighted back-projection methods, which have recently been extended so as to be applicable to random tilt series. Besides a description of the algorithms, the complete procedure for a three-dimensional reconstruction from a single-exposure, random conical tilt series is explained, including the determination of the azimuthal angles, the alignment scheme for conical tilt series, the dependence of the achievable resolution on the number of projections for regular conical and single-axis geometries, and the method to calculate the actual resolution of two-dimensional image averages and of three-dimensional reconstructions using the phase residual and Fourier ring correlation criteria. Examples are given of biological specimens to which these three-dimensional reconstruction methods have been applied.

Chromatin structures: dissecting their mixed patterns in nuclease digests

Four separate features could be distinguished in Fe-DNAase-1 digestions of human lymphoblast nuclei: a di-nucleosomal (2N) repeat, a mono-nucleosomal (1N) repeat, a component of "random" DNA, and triple splitting of major peaks. The random component is major, is unlikely to be completely artifactual, and is what would be expected from the face to face layering model of Subirana et. al., (1). The 2N pattern appeared to be associated with compact, metaphase-type chromatin, whereas the 1N pattern was associated with more exposed chromatin. These two modes are explained in terms of orderly back-to-back folding of zig-zag nucleofilaments, and face-to-face folding respectively. Hybridization studies indicated that the centromeric classes of repetitive DNA had the same digestion spectra as the major interspersed classes of repetitive DNA, and DNA enriched in transcriptionally active sequences. It is suggested that current coil models are all inadequate explanations of higher order chromatin packing.

Tomographic three-dimensional reconstruction of cilia ultrastructure from thick sections

We have applied a computer-based tomographic technique to reconstruct the three-dimensional ultrastructure of newt lung cilia. Epon-embedded samples were cut into 0.25-micron-thick sections that were imaged at 1 MV with a high-voltage electron microscope. For the reconstruction shown, a tilt series of 53 micrographs was taken at tilt angles between -54 degrees and +50 degrees. The reconstruction was accomplished from these projections using a weighted back-projection algorithm. The 12-nm resolution of the reconstruction was sufficient to resolve the outer doublet and central pair microtubules, dynein arms, radial spokes, and central sheath structures. The reconstruction can be viewed from various angles and with appropriate parts cut away to reveal structural features of interest. The sense of depth in these views can be enhanced by stereo viewing of shaded surface images. From this reconstruction, we determined that newt lung cilia contain the more common triplet grouping of radial spokes.

The layered organization of nucleosomes in 30 nm chromatin fibers

We have used electron microscopy and established methods of three-dimensional reconstruction to obtain structural information on the 30 nm chromatin fibers from sea cucumber sperm and chicken erythrocytes. The fibers show a longitudinal periodicity of 10-11 nm. We have interpreted this periodicity as due to a grouping of nucleosomes into disks, each disk containing about 5-6 nucleosomes. These disks are closely stacked to form the chromatin fiber. We have built a detailed model for four fibers and we have determined the approximate coordinates of all the nucleosomes in them. The average distance found between neighboring nucleosomes has a value close to 11 nm. They may be connected either as a regularly distorted helix or as a layered zigzag. The second model appears more appropriate, since in the constrictions of the fibers the nucleosomes can only be connected as a zigzag.

A triple helix model for the structure of chromatin fiber

A model of chromatin fiber structure is presented in which a repeating unit of a trinucleosome forms a 3-dimensional zigzag. Twisting and compression of the zigzag result in a triple helix structure. The model is built mainly on the flow linear dichroism data showing that nucleosomal disc faces are tilted relative to the fiber axis, the orientation of nucleosomes does not change upon folding and unfolding of chromatin, and the orientation of nucleosomes is maintained by the globular domain of histone H1.

Representation of three-dimensionally reconstructed objects in electron microscopy by surfaces of equal density

A surface representation algorithm has been developed to visualize the results of three-dimensional reconstructions from projections in electron microscopy. It produces an easily recognizable image of the reconstructed particle and facilitates comprehension of the three-dimensional structure. Thus building of physical models can be avoided in many cases. If such a model is needed the algorithm can be used to establish the correct particle boundary in advance. Some further effort has been made to represent long fibres and visualize inner structures of objects, which are obscured by outer high-density regions. Shading may be used to enhance the depth perception from single views.