Histone analysis

Histone Deacetylases (HDACs) catalyze the removal of the acetyl groups from lysines (see Fig. 1). Together with the HATs they are responsible for maintaining the level of histone acetylation throughout the genome. The family of HDAC proteins has been divided into four classes based on phylogenetic analysis and sequence comparison. HDACs of the classes I and II share the same Zn2+-based reaction and are evolutionary related. Class IV HDACs also possess a Zn2+-based reaction... 

Gregoretti IV, Lee YM, Goodson HV (2004) Molecular evolution of the histone deacetylase family functional implications of phylogenetic analysis. J Mol Biol 338 17-31... 

Wilson JR, Jing C, Walker PA, Martin SR, Howell SA, Blackburn GM, Gamblin SJ, Xiao B (2002) Crystal structure and functional analysis of the histone methyltransferase set7/9. Cell 111 105-115... 

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...

Murphy, F.R., Jorgensen, F.D., and Cantor, C.R. (1982) Kinetics of histone endocytosis in Chinese hamster cells. A flow cytofluorometric analysis./. Biol. Chem. 257, 1895. 

In this connection, it must also be borne in mind that the deoxyribonucleic acids subjected to analysis have probably not been homogeneous. Deoxyribonucleic acids have been fractionated by making use of their different solubilities in normal saline,186 by extracting thymus nucleo-his-tone with sodium chloride solutions of increasing concentration,187 by ion-exchange,187 and also by adsorption of the polynucleotide onto histone immobilized on a kieselguhr support.123 It is possible, however, that these are artefacts, since it has been shown that deoxyribonucleic acid fractions extracted from calf-thymus nucleohistone may or may not vary in composition according to the previous treatment of the material.188... 

The purpose of this article is to correlate the rather unique structural aspects of the five histone molecules—the differences among them as well as their similarities—with their biological function. Such an analysis is best approached, we believe, via a study of the many protein-protein (Section II) and protein-DNA (Section III) interactions in which the histones participate. Emphasis will be placed on the four core histones H2A, H2B, H3, and H4 HI will be discussed briefly, mainly in relation to its interaction with DNA. In no sense is the bibliography meant to be exhaustive. 

Palmer DK, O Day K, Margolis RL (1989) Biochemical analysis of CENP-A, a centromeric protein with histone-like properties. Prog Clin Biol Res 318 61-72... 

Notwithstanding the importance of in-depth analysis of the structural features of the association of the anti-gene transcription inhibitors with DNA, it is clear that structural studies on the association of these compounds with chromatin and its components like nucleosome and HI histone under different conditions are essential... 

Tillinghast GW, Partee J, Albert P, Kelley JM, Burtow KH, Kelly K (2003) Analysis of genetic stabiUty at the EP300 and CREBBP loci in a panel of cancer cell Unes. Genes Chromosomes. Cancer 37 121—131 Timmermann S, Lehrrnann H, Polesskaya A, Harel-Bellan A (2001) Histone acetylation and disease. 

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. 

In 1978, not only were all the major classes of histone recognized, but also sequences for the major variants of each had been determined. For example, all four core histones for calf had been sequenced (see Ref. [1], Chapter 4). The existence of certain minor variant forms had been established by electrophoretic analysis as early as 1966 [46]. However, the conclusive evidence for non-allelic variants... 

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