Acetylated histones chromatin

Chromatin is composed of nucleosomes, where each comprise 147 base pairs of DNA wrapped around an octamer oftwo copies of each histone H2A, H2B, H3, and H4. Nucleosomes are folded into higher-order structures that are stabilized by linker histones. Chromatin structure can be altered by enzymes that posttranslationally modify histones (e.g., through phosphorylation, acetylation, methylation, or ubiquitination) or by ATP-driven chromatin-remodeling complexes that alter nucleosome position and/or composition. 

Grunstein M Histone acetylation in chromatin structure and transcription. Nature 1997 389 349. 

Figure 3. (a) Scheme of transcription, (b) Histone chaperone nucleophosmin/NPMl enhance acetylation dependent chromatin transcription NPMl stimulates chromatin transcription in a dose dependent manner. Lane 1,without activator lanes 2-6, with the activator Gal-VP16 (50 ng) lanes 3-6, with p300 (25 ng) lanes 4-6, with acetyl CoA (1.5 pM) lane 5, 1 pmol, lane 6, 10 pmols of full length NPMl... 

In summary what have we learned in 25 years In some areas, surprisingly little— for example, we cannot say that we really understand the condensed chromatin fiber structure much better than we did in 1978. Although the significance of the great majority of histone variants remains unknown, replacement histones appear now to be involved in major chromosomal functions. There are areas in which we have accrued incredible amounts of detailed information yet still do not quite know what to do with it. Histone acetylation is a prime example. Allfrey et al. [56] could predict its role in a general sense in 1964. We now know a whole rogue s gallery of acetylases and deacetylases plus the specific histone sites for many. Nevertheless, authorities in the field must still write in 2000, The mechanisms by which histone acetylation affects chromatin structure and transcription is not yet clear [58]. 

Fig. 4. Nucleosome relaxation, and influence of histone N-terminal tails. Example of nucleosomes on 356 bp ALk= —2.9 topoisomer from the pBR DNA minicircle series [28]. (a) Mononucleosomes (Mo) were reconstituted with control (Control) or acetylated (Acetyl) histones, incubated at 37 °C in Tris buffer [T 50 mM Tris-HCl (pH 7.5), 0.1 mM EDTA, 50 mM KCl, 5 mM MgC, and 0.5 mM dithiothreitol] or phosphate buffer [P same as Tris buffer with 50 mM potassium phosphate (pH 7.5) instead of 50 mM Tris-HCl] in the absence (Topo I —) or presence (Topo I +) of topoisomerase I, and electrophoresed in a native polyacrylamide gel at room temperature. Note the splitting of nucleosome relaxation products in two bands. TE starting chromatin in TE buffer, (b) Gel slices (brackets) were cut out, and eluted DNAs were electrophoresed in a chloroquine-containing native polyacrylamide gel, together with control naked topoisomers (C1-C4). Lanes were numbered as in the (a) gel. Autoradiograms are shown, (c) Radioactivity profiles of lanes 2 and 5 in the (b) gel. Topoisomers are indicated by their ALk values. (Adapted from Fig. 2 in Ref. [28].)...

Lutter, L.C., Judis, L., and Paretti, R.F. (1992) Effects of histone acetylation on chromatin topology in vivo. Mol. Cell. Biol. 12, 5004-5014. 

The association between a histone tail modification and a particular functional state of chromatin, came with the demonstration that transcriptionally active chromatin fractions were enriched in acetylated histones, firstly by biochemical co-fractionationation ([8,9] and references therein) and then by Chromatin ImmunoPrecipitation, ChIP [10]. Subsequently, regions of transcriptionally silent constitutive and facultative heterochromatin, were shown, by immunofluorescence microscopy, to be under-acetylated [11,12]. This supported the idea that acetylation of the histone tails, with the associated loss of positive charge and reduction in DNA-binding constant, somehow caused chromatin to become more open (or less condensed ) and thereby more conducive to transcription. While this is likely to be an important contributory factor, it has now become clear that the... 

It has been known for some time that certain bromodomains, sequence elements found in many chromatin associated proteins and most HATs [79], bind preferentially to acetylated peptides in in vitro binding assays, leading to speculation that acetylated histone tails could form targets for the binding of bromodomain-containing proteins in vivo [80,81]. Recent experiments provide direct evidence for this. 

Isolated di- and trinucleosomes Hyper-acetylated CE chromatin fibers isolated in the presences of the histone deacetylase inhibitor sodium butyrate... 

Shogren-Knaak, M., Ishii, H., Sun, J.M., Pazin, M.J., Davie, J.R. and Peterson, C.L. (2006) Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science, 311,... 

Histone deacetylases (HDAGs) catalyze the removal of acetyl groups from the Ne atom of histone lysines in a nucleosomal context, ensuring the reversibility of histone acetylation. Histone deacetylation is often associated vdth transcriptional repression and silencing since it promotes chromatin higher order structures and the recruitment of silencers [34]. As other enzymes involved in chromatin... 

Davie, J.R. and Candido, E.P. (1978) Acetylated histone H4 is preferentially associated with template-active chromatin. Proceedings of the National Academy of Sciences of the United States of America,... 

Immunoprecipitation can be used to study protein-DNA interactions (Kuo and Allis 1999). For instance, the basic chromatin immunoprecipitation technique is remarkably versatile and has now been used in a wide range of cell types, including budding yeast, fly, and human cells. This technique has been successfully employed to map the boundaries of specifically modified (e.g., acetylated) histones along target... 

Apart from DNA methylation studies, the second aspect of epigenetic misregulation involves disruption of histone acetylation and chromatin structure. Functional disruption of some HATs genes (such as the CBP and p300) is detected in some cancers, most notably, acute pro-myelocytic leukemia (51). This has lead to the hope that HD AC inhibitors will be useful for the treatment of this disease and a number of inhibitors are currently being assessed in clinical trials (see below). 

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