Solenoid (DNA)

About: Solenoid (DNA) is a research topic. Over the lifetime, 817 publications have been published within this topic receiving 59658 citations.

Chromatin structure: a repeating unit of histones and DNA.

Abstract: ciations of the histones in chromatin but says nothing of details, such as whether the F2A1 and F3 pair, which occurs as an (F2Al)2(F3)2 tetramer in solution, also occurs as a tetramer in chromatin. The most direct evidence for an (F2Al)2(F3)2 tetramer in chromatin is that a complex formed from tetramers, F2A2-F2B oligomers, and DNA gives the same x-ray pattern as chromatin (Fig. 4, upper two traces). Tetramers and F2A2-F2B oligomers are both required to give the x-ray pattern (Fig. 4, lower two traces), but Fl is not-in keeping with previous observations (3, 23 ) that removing Fl from chromatin does not affect the x-ray pattern. Further implications of these results are discussed in the accompanying article (24). We are currently studying associations of the histones in chromatin by cross-linking. There are two difficulties that do not arise in experiments on the histones in solution: the amino side chains are involved in salt linkages with the phosphate groups of DNA and are thus less available for chemical modification; and the presence of five rather than two histones complicates identification of products from molecular weights. -Preliminary results do show less cross-linking of histones in chromatin than in solution, but crosslinked products up to pentamers are readily observed and call for further investigation.

Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin.

Abstract: We describe the results of a systematic study, using electron microscopy, of the effects of ionic strength on the morphology of chromatin and of H1-depleted chromatin. With increasing ionic strength, chromatin folds up progressively from a filament of nucleosomes at approximately 1 mM monovalent salt through some intermediate higher-order helical structures (Thoma, F., and T. Koller, 1977, Cell 12:101-107) with a fairly constant pitch but increasing numbers of nucleosomes per turn, until finally at 60 mM (or else in approximately 0.3 mM Mg++) a thick fiber of 250 A diameter is formed, corresponding to a structurally well-organized but not perfectly regular superhelix or solenoid of pitch approximately 110 A as described by Finch and Klug (1976, Proc. Natl. Acad. Sci. U.S.A. 73:1897-1901). The numbers of nucleosomes per turn of the helical structures agree well with those which can be calculated from the light-scattering data of Campbell et al. (1978, Nucleic Acids Res. 5:1571-1580). H1-depleted chromatin also condenses with increasing ionic strength but not so densely as chromatin and not into a definite structure with a well-defined fiber direction. At very low ionic strengths, nucleosomes are present in chromatin but not in H1-depleted chromatin which has the form of an unravelled filament. At somewhat higher ionic strengths (greater than 5 mM triethanolamine chloride), nucleosomes are visible in both types of specimen but the fine details are different. In chromatin containing H1, the DNA enters and leaves the nucleosome on the same side but in chromatin depleted of H1 the entrance and exit points are much more random and more or less on opposite sides of the nucleosome. We conclude that H1 stabilizes the nucleosome and is located in the region of the exit and entry points of the DNA. This result is correlated with biochemical and x-ray crystallographic results on the internal structure of the nucleosome core to give a picture of a nucleosome in which H1 is bound to the unique region on a complete two-turn, 166 base pair particle (Fig. 15). In the formation of higher-order structures, these regions on neighboring nucleosomes come closer together so that an H1 polymer may be formed in the center of the superhelical structures.

A genomic code for nucleosome positioning

Abstract: Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves. Eukaryotic genomes do not exist in vivo as naked DNA, but in complexes known as chromatin. Chromatin contains nucleosomes, short stretches of DNA tightly wrapped around a histone protein core, which exclude most DNA binding proteins and so act as repressors. A combined computational and experimental approach has been used to determine DNA sequence preferences of nucleosomes and to predict genome-wide nucleosome organization. The yeast genome encodes an intrinsic nucleosome organization that explains about half of the in vivo nucleosome positions. Highly conserved across eukaryotes, the code directs transcription factors to their binding sites and facilitates many other specific chromosome functions. An accompanying News and Views piece discusses the role of DNA sequence and other regulators in nucleosome positioning. The cover graphic represents a stretch of chromatin including several nucleosomes. A combined computational and experimental approach is used to determine the DNA sequence preferences of nucleosomes and predict genome-wide nucleosome organization. The yeast genome encodes an intrinsic nucleosome organization, which can explain about 50% of in vivo nucleosome positions.

The structure of DNA in the nucleosome core

Abstract: The 1.9-A-resolution crystal structure of the nucleosome core particle containing 147 DNA base pairs reveals the conformation of nucleosomal DNA with unprecedented accuracy. The DNA structure is remarkably different from that in oligonucleotides and non-histone protein-DNA complexes. The DNA base-pair-step geometry has, overall, twice the curvature necessary to accommodate the DNA superhelical path in the nucleosome. DNA segments bent into the minor groove are either kinked or alternately shifted. The unusual DNA conformational parameters induced by the binding of histone protein have implications for sequence-dependent protein recognition and nucleosome positioning and mobility. Comparison of the 147-base-pair structure with two 146-base-pair structures reveals alterations in DNA twist that are evidently common in bulk chromatin, and which are of probable importance for chromatin fibre formation and chromatin remodelling.

Structure of chromatin.

Abstract: STRUCTURE OF NUCLEOSOMES 940 Core and Linker 940 Arrangement of Histones 942 Path Followed by the DNA 944 Conformation of Histones 948