Crystal structures nucleosomes

Page 1171 (Figure 28 7) is adapted from crystallograpliic coordinates deposited with The Protein Data Bank PDB ID lAOl Luger A Mader W Richmond R K Sargent D F Richmond T J Crystal Structure of the Nucleosome Core Particle at 2 8 A Resolution Nature 1997 V 389 251... 

Fig. 3.18 Nucleosome core particle (NCP)-polyamide co-crystal structures (PDB codes 1M18 and 1M19). (Top) Partial structure, viewed down the superhelical axis. Base pairs 58-145 (shown in white) and associated proteins (H3, blue H4, green H2A, yellow H2B, red) are shown for each complex. Superhelix locations (SHLs) are labeled as each major...

Luger L et al Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 1997 398 251. 

A low-energy in vitro form of nucleosome packing was observed in nucleosome core particle crystals (Finch et al., 1977). Two variants of these crystals occurred, (a) Wavy columns of nucleosomes stacked one on top of each other with an axial repeat of 340 A were obtained upon crystallization of nucleosomes containing proteolytically cleaved histones (Finch et al., 1977). (b) Straight columns of closely packed nucleosomes, 110 A in diameter, were obtained upon crystallization of nucleosomes with intact histones (Finch and Klug, 1978). In both these structures histone-histone contacts between nucleosomes are implied. Similar face-to-face packing of nucleosomes in arcs and helical patterns was observed in the EM by Dubochet and Noll (1978). 

Grune T, Brzeski J, Eberharter A, Clapier CR, Corona DF, Becker PB, Muller CW (2003) Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWl. Mol Cell 12 449-460... 

Luger K, Mader, AW., Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389 251-260 Ma Y, Jacobs SB, Jackson-Grusby L, Mastrangelo MA, Torres-Betancourt JA, Jaenisch R, Rasmussen TP (2005) DNA CpG hypomethylation induces heterochromatin reorganization involving the histone variant macroH2A. J Cell Sci 118 1607-1616... 

Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403 41-45 Suto RK, Clarkson MJ, Tremethick DJ, Luger K (2000) Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Nature Struct. Biol. 7 1121-1124 Swaminathan J, Baxter EM, Corces VG (2005) The role of histone H2Av variant replacement and histone H4 acetylation in the establishment of Drosophila heterochromatin. Genes Dev 19 65-76... 

Fig. 1. The core particle, the DNA superhelix and H2B and H3 N-terminal tails, (a) Space-filling representation of the 2.8 A crystal structure of the 146 bp human a-satellite nucleosome core particle [22]. The dyad is in the plane of the paper and the superhelix axis slightly off that plane. Positive and negative numbers mark the superhelix locations (SHL) in the upper and lower gyres, respectively, and the dotted curve follows the path of the double helix axis, (b) Ribbon representation of the DNA superhelix slit along a line parallel to its axis, opened out and laid flat on the paper surface. SHL are also indicated, together with H2B and H3 tails passage points between the gyres. (From Fig. 5 in Ref [29].)...

In conclusion, nucleosome cleavage periodicity data, together with direct measurements of a defined nucleosome crystal structure, suggest that wrapped DNA may be overtwisted to different extents, but in no case do these overtwistings appear sufficient to explain the paradox ( 0.5 bp/turn overtwisting required, against 0.2 bp/turn observed at the most). 

Less is known about the interaction of the nucleosomes between themselves or with free DNA. The nucleosome-nucleosome interaction has recently been parameterized by using the surface charge density of the known crystal structure [39] in a point-charge model [51]. While in that work only electrostatic interactions were considered and the quantitative influence of the histone tails on the interaction potential still remains obscure, simulations based on this potential allowed to predict an ionic-strength dependent structural transition of a 50-nucleosome chromatin fragment that occurred at a salt concentration compatible with known experimental data (Ref. [65], see below). 

Suto, R.K., Edayathumangalam, R.S., White, C.L., Melander, C., Gottesfeld, J.M., Dervan, P.B., and huger, K. (2003) Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands. I. Mol. Biol. 326, 371-380. 

Except for histone H4, each of the other histone types are found in different isoforms and are called histone variants. The chapter by Pehrson (Chapter 8) will provide a more in-depth discussion of these forms. It is worth pointing out that with regard to transcription through nucleosomes, some of these variants are expressed in a replication-independent process and are found in active gene fractions that have been prepared using the nuclease-sensitive solubilization procedures described above. Of particular note are two minor histone variants, H2A.Z and H3.3. Both are expressed throughout the cell cycle and incorporated into the nucleosomes of active genes ([38,39], see reviews [46,47]). For example, both Tetrahymena, H2A.Z (termed Tetrahymena hvl) and an H3.3-like histone (hv2) are preferentially present in the active macronucleus and are expressed in the micronucleus just prior to the time when this nucleus becomes transcriptionally active [48,49]. Suto et al. [50] have determined the crystal structure of a nucleosome... 

Ramakrishnan, V., et al. (1993). Crystal structure of globular domain of histone H5 and its impUcations for nucleosome binding. Nature 362, 219-223. 

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