Histone in nucleosomes

Fig. 10.2. FSPIM analysis of the interaction between maize transcriptional coactivators—GCN5 and ADA2—fused to CFP and YFP. GCN5 is a histone acetyltransferase that, in conjunction with adaptor protein ADA2, modulates transcription in diverse eukaryotes by affecting the acetylation status of the core histones in nucleosomes [63]. CFP- and YFP-tagged proteins, expressed in protoplasts, were excited by the 458 nm and the 514 nm laser lines sequentially. CFP fluorescence was selectively detected by an FIFT 458 dichroic mirror and BP 470-500 band pass emission filter while YFP fluorescence was selectively detected by using an HFT 514 dichroic mirror and...

Fig. 1. Core histone modifications. Human histone N-terminal and in some cases C-terminal amino acid sequences are shown. The modifications include methylation (M), acetylation (Ac), phosphorylation (P), ubiquitination (U), and ADP ribosylation (step ladder). The sites of trypsin digestion of histones in nucleosomes are indicated (T).

Another factor that affects the binding of DNA to histones in nucleosome cores is the sequence of the... 

The rate of formation of cisplatin-DNA adducts was found to be independent of superhelicity [59] and appears to be unaffected by the presence of histones in nucleosomes [29] and in chromatin [77], Therefore, isolated DNA in aqueous solution appears to be a relevant model for kinetic and mechanistic studies of cellular DNA-platination. It was early checked that the cisplatin-DNA adducts were stable for a least three days at 37 °C after their formation [78], There are now a few cases reported of unstable platinum adducts (vide supra) i) monoadducts with the diazapyrenium ligand [52], ii) a cisplatin intrastrand GG chelate rearranging into a GG interstrand crosslink [63], iii) cisplatin GG interstrand diadducts, slowly rearranging into intrastrand ones [65], tv) transplatin intrastrand GNG diadducts rearranging into interstrand crosslinks (J.-M. Malinge and M. Leng, Part 3). 

Another approach to regulating the activity of transcription factors is to modify the chromatin state and therefore the accessibility of the promoter and TF binding sites (78, 79). Chromatin states are modulated partially by posttranslational modifications of the histones in nucleosomes, which have significant effects on transcription levels (14, 80). These modifications include phosphorylation, methylation, acetylation, and ubiquitination (80, 81). An early indication of the importance of these covalent modifications on transcription emerged from the observation... 

The process of replication in eukaryotes is similar to that in prokaryotes. Differences in the processes are related mainly to the vastly larger amount of DNA in eukaryotic cells (over 1,000 times the amount in E. coli) and the association of eukaryotic DNA with histones in nucleosomes. Enzymes with DNA polymerase, primase, ligase, helicase, and topoisomerase activity are all present in eukaryotes, although these enzymes differ in some respects from those of prokaryotes. 

DNA Is Involved In several biological functions requiring substantial changes In conformation. For example, the Intrinsically stiff DNA molecule Is wrapped fairly tightly about histones In nucleosomes, and this entire complex must be partially unraveled during replication and transcription. The ability of DNA to assume several different conformational forms In response to Its solid and solution environments has been evident for some time. Recent applications of spectroscopic methods sensitive to molecular dynamics have Indicated that double stranded DNA can also undergo rapid local motions of significant amplitude. 

Heterogeneous reaction (Section 6 1) A reaction involving two or more substances present in different phases Hydro genation of alkenes is a heterogeneous reaction that takes place on the surface of an insoluble metal catalyst Heterolytic cleavage (Section 4 16) Dissociation of a two electron covalent bond in such a way that both electrons are retained by one of the initially bonded atoms Hexose (Section 25 4) A carbohydrate with six carbon atoms High density lipoprotein (HDL) (Section 26 11) A protein that carries cholesterol from the tissues to the liver where it is metabolized HDL is often called good cholesterol Histones (Section 28 9) Proteins that are associated with DNA in nucleosomes... 

Histones (Section 28.9) Proteins that are associated with DNA in nucleosomes. 

Histones are small, basic proteins required to condense DNA into chromatin. They have been first described and named in 1884 by Albrecht Kossel. There are five main histones HI, H2A, H2B, H3 andH4. An octamer of core histones H2A, H2B, H3 andH4 is located inside a nucleosome, the central building block of chromatin, with about 150 base pairs of DNA wrapped around. The basic nature of histones, mediated by the high content of lysine and arginine residues, allows a direct interaction with the acidic phosphate back bone of DNA. The fifth histone HI is located outside at the junction between nucleosomes and is referred to as the linker histone. Besides the main histones, so-called histone variants are known, which replace core histones in certain locations like centromers. 

Cocco, L., Martelli, A., Billi, A., Matteucci, A., Vitale, M., Neri, L., and Manzoli, F. (1986) Changes in nucleosome structure and histone H3 accessibility. Iodoacetamidofluorescein labeling after treatment with phosphatidylserine vesicles. Exp. Cell Res. 166, 465 174. 

Furthermore, it was found that stimulated human neutrophils are able to produce 5-chloro-2 -deoxycytidine and that the myeloperoxidase system generates just the same levels of 5-chlorocytosine in DNA and RNA in vitro (Reaction (4), Figure 28.3). It is possible that myeloperoxidase-generated chlorinated products may modify nuclear acids of pathogens and nuclear acids in host cells during inflammation. Hawkins et al. [48] suggested that DNA oxidation may be initiated by protein chloramines formed in the reaction of HOCl with histones in the nucleosome. 

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.

The histone octamer is the histone unit of the nucleosome. As discussed in Section II, it has been shown that at high salt concentration (7 > 2 M) the core histones can assemble on their own, in the absence of DNA, to form histone octamers (this assembly occurs with both acid- and salt-extracted histones). Furthermore, the secondary and tertiary structures of core histones at high salt concentration are similar to the structures they have in the intact nucleosome. The basic units of the assembly of the four core histones are histone dimers which are obtained at low salt concentration. Upon increase in salt concentration, tetramers, hexamers, and octamers are obtained. The cross-linking pattern of histones in high salt concentration is similar to that in chromatin, again supporting the idea that the assembly of core histones at high salt concentration is similar to that in chromatin. 

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). 

In arrays of closely packed nucleosomes composed of all four core histones, strands of H2A-H2B dimers could be incorporated in the grooves between the two H3-H4 strands, producing a four-stranded polymer. Alternatively, they could bind to the H3-H4 double-stranded fiber to give an octamer of the histones per nucleosome. This latter model is supported by the photochemical cross-linking of histones to DNA which have shown that within the nucleosome core the four core histones are not equivalently positioned with respect to... 

There is good agreement between the overall dimensions of the histone octamer found by Klug et al. and data obtained from other types of histone fibers discussed here. Similarity of cross-linking data of histone octamer fibers, octamer free in solution, and octamer in nucleosomes makes the extrapolation from the octamer model in the fibers to the octameric core of nucleosome valid (Klug et al., 1980). This further substantiates the idea that histones are part of an assembly system, and therefore the histone core of the nucleosome can be regarded as a truncated histone fiber (see Section IV). 

Hizume K, Yoshimura SH, Maruyama H, Kim J, Wada H, Takeyasu K (2002) Chromatin reconstitution development of a salt-dialysis method monitored by nano-technology. Arch Histol Cytol 65 405 13 Hizume K, Yoshimura SH, Takeyasu K (2004) Atomic force microscopy demonstrates a critical role of DNA superhelicity in nucleosome dynamics. Cell Biochem Biophys 40 249—262 Hizume K, Yoshimura SH, Takeyasu K (2005) Linker histone HI per se can induce three-dimensional folding of chromatin fiber. Biochemistry 44 12978-12989 Hofmann WA, de Lanerolle P (2006) Nuclear actin to polymerize or not to polymerize. J Cell Biol 172 495-496... 

Foltz DR, Jansen LE, Black BE, Bailey AO, Yates JR, Cleveland DW (2006) The human CENP-A centromeric nucleosome-associated complex. Nat Cell Biol 8 458 69 Foresta C, Zorzi M, Rossato M, Varotto A (1992) Sperm nuclear instability and staining with aniline blue abnormal persistence of histones in spermatozoa in infertile men. Int J Androl 15 330-337 Fukagawa T, Nogami M, Yoshikawa M, Ikeno M, Okazaki T, Takami Y, Nakayama T, Oshimura M (2004) Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nat Cell Biol 6 784-791... 

Yoda K, Ando S, Morishita S, Houmura K, Hashimoto K, Takeyasu K, Okazaki T (2000) Human centromere protein A (CENP-A) can replace histone H3 in nucleosome reconstitution in vitro. Proc Natl Acad Sci U S A 97 7266-7271... 

Woodcock CL, Skoultchi AI, Fan Y (2006) Role of linker histone in chromatin structure and function HI stoichiometry and nucleosome repeat length. Chromosome Res 14 17-25 Wu WH, Alami S, Luk E, Wu CH, Sen S, Mizuguchi G, Wei D, Wu C (2005) Swc2 is a widely conserved H2AZ-binding module essential for ATP-dependent histone exchange. Nat Struct Mol Biol 12 1064-1071... 

Figure 1. Different histone chaperones in the key histone metabolic pathways Functions of histone chaperones range from the storage of newly synthesized histones in the cytoplasm, its transfer into the nucleus and in histone assembly into nucleosomes. Apart from diis die histone chaperones are also involved in histone exchange, maintenance of heterochromatin and in the regulation of chromatin structure during transcription. (See Colour Plate 10.)...

Ito T (2003) Nucleosome assembly and remodehng. Curr Top Microbiol Immunol 274 1-22 Ito T, Tyler JK, Kadonaga JT (1997) Chromatin assembly factors a dual function in nucleosome formation and mobilization Genes Cells 2(10) 593-600 Ivanovska I, Khandan T, Ito T, Orr-Weaver TL (2005) A histone code in meiosis the histone kinase, NHK-1, is required for proper chromosomal architecture in Drosophila oocytes. Genes Dev 19(21) 2571-2582... 

Based on the biochemical studies, HLMTases can be classified into two categories. One type of the enzymes preferentially methylates histones in a nucleosomal context. This category includes the H3K27 HLMTase EZH2 (EED-EZH2 complex)... 

The phenylselenocysteine has also been used successfully to chemically append analogues of methyl- or acetyl-lysine, important histone modifications that can contribute to chromatin structure and accessibility of transcriptional machinery in eukaryotes. By introducing phenylselenocysteine into the Xenopus histone H3, both acetyl-lysine and mono-, di-, and trimethyl-lysine analogues were appended to the purified unnatural amino acid-containing FI 3 protein (Figure 10). " Additionally, the H3 protein with a modification mimicking acetylation of lysine 9 can be deactylated by a histone deacetylation complex and is also a substrate for phosphorylation by Aurora B kinase. Such purified and chemically labeled histones are likely functional in nucleosomes, and preparation of specifically modified histones for comprehensive analysis of chromatin structure and accessibility is particularly suited to this chemical labeling technique. 

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