Histones nucleosome core particle

SADP or sulfo-SADP also have been used to study the phenylalanine-methionine-arginine-phenylalanine-amide-activated sodium channel (Coscoy et al., 1998), various apolipoprotein E isoforms (Mann et al., 1995), the high-affinity phenylalkylamine Ca2+ antagonist binding protein from guinea pig (Moebius et al., 1994), the interaction of non-histone proteins with nucleosome core particles (Reeves and Nissen, 1993), and the interactions among cytochromes P-450 in the endoplasmic reticulum (Alston et al., 1991). See Chapter 28 for methods of using photoreactive heterobifunctional crosslinkers to study protein interactions. 

The nucleosome is composed of 200 base pairs of DNA and an octamer of the histones H2A, H2B, H3, and H4 as well as histone HI (Komberg, 1974, 1977). Nucleosomes can be obtained by mild digestion of chromatin with micrococcal nuclease (Noll, 1974a Axel, 1975), followed by fractionation on a sucrose gradient. Further digestion of the nucleosomes results in the formation of nucleosome core particles composed of 145 base pairs of DNA and an octamer of the histones H2A, H2B, H3, and H4 (Rill and Van Holde, 1973 Sollner-Webb and Felsenfeld, 1975 Axel, 1975 Bakayev et al., 1975 Whitlock and Simpson, 1976 Noll and Komberg, 1977). The DNA piece thus excised is called linker DNA which serves as a link... 

The histone octamer of nucleosome core particles was cross-linked by dimethylsuberimidate and isolated from the DNA by precipitation in 3 M NaCl (0.05 M sodium phosphate buffer, pH 7.0). The cross-linked octamer, dissolved at low ionic strength, was reconstituted by mixing with DNA at 1.0 M NaCl (pH 8.0 Tris buffer) and dialyzed against 0.6 M NaCl in the same buffer. The reconstituted particle had properties similar to those of the cross-linked core particle. It sedi-... 

Fig. 5. Schematic model of the nucleosome, with histone HI shown as stabilizing the fold of the DNA molecule around the core histones [based on results of Sperling and Sperling (1978)]. The nucleosome dimensions are derived from X-ray (Finch et al., 1977) and neutron (Baldwin et al., 1975 Pardon et al., 1977 Suauet al., 1977) scattering experiments. The histone core dimensions are derived from electron microscopic and X-ray studies (Sperling and Amos, 1977 Wachtel and Sperling, 1979 Sperling and Wachtel, 1979). The regions of the DNA molecule indicated by dashed lines indicate those base pairs which are not present in nucleosome core particles.

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). 

Simon RH, Eelsenfeld G (1979) A new procedure for purifying histone pairs H2A + H2B and H3 + H4 from chromatin using hydroxylapatite. Nucleic Acids Res 6 689-696 Simpson RT (1978) Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones. Biochemistry 17 5524-5531 Simpson RT, Stafford DW (1983) Structural features of a phased nucleosome core particle. Proc Natl Acad Sci U S A 80 51-55... 

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... 

The genetic information of eukaryotic cells is propagated in the form of chromosomal DNA. Besides the nucleic acid component, chromosomes contain architectural proteins as stoichiometric components, which are involved in the protective compaction of the fragile DNA double strands. Together, the DNA and proteins form a nucleoprotein structure called chromatin. The fundamental repeating unit of chromatin is the nucleosome core particle. It consists of about 147 base pairs of DNA wrapped around a histone octamer of a (H3/H4)2 tetramer and two (H2A-H2B) heterodimers. One molecule of the linker histone HI (or H5) binds the linker DNA region between two nucleosome core particles (Bates and Thomas 1981). 

Nucleosomes core particles containing H2A only have 118 base pairs of DNA incorporated compared to the canonical nucleosomes protecting about 147 base pairs from micrococcal nuclease (Bao et al. 2004). These nucleosomes are more flexible in structure and might facilitate passage of RNA polymerase II. However, the function of this histone variant in mammalian cells is not fully understood. As... 

The genome of the eukaryotic cell is packaged in a topologically complex, fibrous superstructure known as chromatin. The nucleosome core particle is the fundamental building block of chromatin and contains 146 bp of DNA wrapped in roughly two super helical turns around an octamer of four core histones (H3, H2B, H2A and H4) resulting in a beads on a string structure. This 10 nm structure further folds and... 

Chopped core particle means nucleosome core particle with the N-terminal tails of core histones removed by tryptic digestion. 

The idea that chromatin possessed some kind of repetitive particulate structure, rather than existing as a uniform, histone-coated DNA supercoil, emerged from a number of laboratories in the early 1970s (see Refs. [2-6]). At any event, by 1978, the basic concept of the nucleosomal core particle, as currently envisioned, was well established. The histone octamer, involving strong H3 H4 and H2A H2B... 

The nucleosome is the fundamental repeating structural unit of chromatin. It is composed of two molecules of the core histones H2A, H2B, H3, H4, approximately two superhelical turns of double-stranded DNA, and linker histone HI (H5). In addition to biochemical studies, the existence of the nucleosome was established in electron micrographs (Fig. la) [1,2], and the name nucleosome, coined to incorporate the concept of the spherical nu-bodies [3]. Micrococcal nuclease limit digestion of chromatin established the nucleosome core particle (NCP) as the portion of the nucleosome containing only the core histones surrounded by 1.75 superhelical turns of double-stranded DNA [4,5]. 

The crystallization and structural determination of the histone octamer was first reported in 1984 [34], However, the overall dimensions of the 3.3 A structure [15] did not appear to fit within the known X-ray structures of the nucleosome core particle [12,13], In an elegant analysis [16], re-examination of the original phasing of the histone octamer data revealed misplacement of the heavy atom site by 2.7 A. The structure was resolved, after which it was possible to build molecular models of the individual histones into the 3.1 A resolution electron density map of the histone core of the nucleosome [17]. Figure 2 shows the first atomic resolution model of the core histone octamer. Several additional publications followed in which the histone octamer structure formed the basis for constructing models of the NCP [17-21],... 

Norton, V.G., Imai, B.S., Yau, P., and Bradbury, E.M. (1989) Histone acetylation reduces nucleosome core particle linking number change. Cell 57, 449-457. 

The nucleosome core particle is a relatively stable and homogenous structure that is easily prepared, and as such has formed the basis for numerous studies into chromatin structure and function. However, several recent studies have suggested that what is true for the nucleosome core may not always be true for nucleosome arrays, nor even for nucleosomes containing linker DNA. For example, the core histone tails preferentially interact with linker DNA when is it present, whereas they are constrained to bind intranucleosomal DNA in core particles [46 8]. Consequently, the activities of proteins that require access to the tails or the DNA may be affected, and it has been shown that both DNA ligase and P/CAF are less active on nucleosome core particles than other chromatin substrates [49,50]. Similar concerns apply to the interaction of HMGN proteins with nucleosome core particles, and results from studies of these complexes must be considered in the wider context of how these proteins may interact with nucleosome arrays. 

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