Published online 17 August 2007 Nucleic Acids Research, 2007, Vol. 35, No. 16 e106 doi:10.1093/nar/gkm560 Choreography for nucleosomes: the conformational freedom of the nucleosomal filament and its limitations Mogens Engelhardt* Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark Received May 3, 2007; Revised July 7, 2007; Accepted July 9, 2007 ABSTRACT Eukaryotic DNA is organized into nucleosomes by coiling around core particles of histones, forming a nucleosomal filament. The significance for the conformation of the filament of the DNA entry/exit angle (a) at the nucleosome, the angle of rotation (b) of nucleosomes around their interconnecting DNA (linker DNA) and the length of the linker DNA, has been studied by means of wire models with straight linkers. It is shown that variations in a and b endow the filament with an outstanding conformational freedom when a is increased beyond 60–90u, owing to the ability of the filament to change between forward right-handed and backward left-handed coiling. A wealth of different helical and looped conformations are formed in response to repeated b sequences, and helical conformations are shown to be able to contract to a high density and to associate pairwise into different types of double fibers. Filaments with random b sequences are characterized by relatively stable loop clusters connected by segments of higher flexibility. Displacement of core particles along the DNA in such fibers, combined with limited twisting of the linkers, can generate the b sequence necessary for compaction into a regular helix, thus providing a model for heterochromatinization. INTRODUCTION DNA in the cell nucleus is organized in nucleosomes by repetitive coiling 1.8 times around core particles consist- ing of two copies of each of four diﬀerent core histones (H2A, H2B, H3 and H4). In higher eukaryotes a ﬁfth histone, H1, is bound to the majority of the nucleosomes, bridging the DNA at the entry and exit of its coiling around the core particle. On average, one nucleosome is present for every 160–240 bp of DNA [the nucleosomal repeat length (NRL)]. The structure of the nucleosome is known in detail (1), and several models have been proposed for folding of the nucleosomal ﬁlaments into ﬁbers with a diameter of 30 nm (2), which have been observed by electron microscopy. These models are based on experimental evidence obtained by a number of diﬀerent techniques, using nuclear preparations, isolated chromatin and reconstituted oligonucleosomes. One of the main diﬀerences between the models is whether the DNA, which connects the nucleosomes (linker DNA), is straight or bent. Studies of chromatin in isolated nuclei have provided evidence for an organization of the ﬁlament into globular assemblies of nucleosomes (supranucleosomes or superbeads) (3) as well as for interdigitation of 30 nm ﬁbers (4,5). Supranucleosomes have been proposed to be caused by dislocations in a cross-linker helical structure (6), but no models have been developed to explain the geometry of double ﬁbers. The conformational freedom of the nucleosomal ﬁlament, i.e. the number of diﬀerent conformations it can attain, is limited by collisions between the nucleo- somes, and is in ﬁrst instance determined by the basic geometry of the ﬁlament, which is therefore of importance for the structure and function of the chromatin in the cell. One function concerns its role in transcription and trans- criptional regulation, in which its dynamic nature (7) and structural plasticity (8) must play an important role. Another function concerns the putative architectural role of the chromatin in the nucleus, of which not so much is known. A long-standing question is to which extent the chromatin is a self-organizing polymer and to which extent it is being organized by other structures in the nucleus (9,10). It is not known whether the basic geometry of the ﬁlament by itself makes possible the formation of stable ﬁber associations. Provided that the linker DNA is straight—and there is evidence to suggest that this is so in the cell (11)— conformational variations of the ﬁlament are mainly determined by two angles: the change in direction of the *To whom correspondence should be addressed. Tel: +45 35327768; Fax: +45 35327732; Email: engelhardt@imbg.ku.dk 2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.