A chromatin folding model that incorporates linker variability generates fibers resembling the native structures.

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 nudeosomes 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 nudeosome-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 structure. When the linker length between nucleosomes is aflowed to vary, as occurs in nature, fibers showing the types of irregulaity 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.The genome of most eukaryotes is complexed with proteins to form chromatin (1). Under low salt conditions in vitro, the complex assumes its simplest conformation and is seen as a beaded chain of 11-nm (diameter) nucleosomes (e.g., ref.2). As the ionic strength of the medium is raised, the nucleosomal chain condenses, eventually forming a compact fiber 30-40 nm in diameter (1-3). These compact fibers observed in isolated chromatin in vitro are presumed to be related to similar structures seen in thin sections of certain types of nuclei such as nucleated erythrocytes (e.g., refs. 4 and 5). X-ray scattering studies of whole cells and nuclei often show 30-to 45-nm reflections that have been interpreted as arising from the center-to-center spacing of compact chromatin fibers (6). These results suggest that the compact chromatin fiber constitutes a distinct level of chromatin organization, especially for transcriptionally inactive chromatin. In this context, the architecture of the fiber would implicitly define the substrate for the regulatory events that lead to chromatin unfolding, a prerequisite for transcription.Attempts to deduce the structure of compact chromatin fibers have resulted in a number of proposals that include both symmetrical and nonsymmetrical arrangements of nucleosomes (reviewed in ref. 7). There is evidence suggesting some degree of symmetry in fiber structure: an intermediate conformation between the nucleosome chain and the compact chromatin fiber is a "zig-zag ribbon" (2) that can display considerable regularity (8), and isolated fibers prepared for electron microscopy contain regions with a limited amount of internal order (2, 3, 9-11). All proposed model structuresThe publication costs of this article were defrayed in part by page charge payment. This article must ...

Evidence that DNA fragmentation in apoptosis is initiated and propagated by single-strand breaks

“…In this scenario, the Ca 2+ -dependent step could well be either the proteolytic step or be required for the structural alteration. Changes in linker DNA topology have recently been shown to induce profound changes in chromatin structure (Widom, 1992;Yao et al, 1993;Woodcock et al, 1993;Polach and Widom, 1995;Krajewski, 1995). Since neither VM26 nor camptothecin trigger the release of small fragments there is no evidence that either Topo I or Topo II are involved in linker DNA cleavage.…”

Alterations in the internucleosomal DNA helical twist in chromatin of human erythroleukemia cells in vivo influences the chromatin higher‐order folding

“…Woodcock et al [5] had recently theorized a range of chromatin architectures generated by continuous changes of the linker DNA length (and, therefore, the relative rotational angle) between consecutive nucleosomes. For all models a symmetrical assemblage was produced, ranging from the completely extended beads-on-a-string (relative rotational angle 180 °) to fibers with the most densely packed nucleosomes (rotational angle 252-288°).…”

“…How~ver, as yet we have no clear picture of how the chromatin ~nvironment changes in vivo to allow these central nuclear processes to occur. Significant advances in this area have come from the recent appreciation that chromatin fiber folding may be affected by variations in the linker DNA length between ,zonsecutive nucleosomes, giving rise to changes in the relative rotation angle as well as the distance between them [3][4][5].…”

Chromatin: A tunable spring at work inside chromosomes

“…The first step of their study is to relate the distribution of stresses along linker DNA to the "macroscopic" stresses (force and torque) applied to the fiber ends. This allows to compute analytically the elastic constants describing the linear response of the fiber from the knowledge of naked DNA elastic constants, and to investigate quantitatively how they vary with the relaxed fiber structure, itself controlled by the "microscopic" structural parameters, as linker length l, or equivalently its relaxed twist τ 0 , and entry/exit angle Φ of linker DNA on the nucleosome [10]. The results substantiate an effective continuous description of the 30-nm fiber as an extensible worm-like rope (EWLR) extending the classical worm-like chain model [14] to an extensible and twistable chain [15] [16] [17].…”

“…naked DNA connecting the nucleosomes). In Section II, we introduce a mechanical model of chromatin fiber, quite similar to the so-called two-angle model [10]; it incorporates microscopic data such as DNA structure and elastic properties [11] [12] as well as nucleosome cristallographic data [13] into an analytically tractable assembly. Its implementation gives the geometric properties of the chromatin fiber, presented in Section III with a special mention to symmetry properties and to the quantities relevant to the mechanics of the fiber.…”