Acetylated histones

In addition protein domains have been identified which bind to modified histone tails. The so-called bromodomains bind to acetylated histone tail, but have little or no affinity to unmodified tails. Further known binding domains include chromodomains and SANT domains which possess preferential binding to methylated and unmodified tails. 

Histone Acetylation Histone Deacetylases Histone Methylation Histone Phosphorylation Histone Tails Hrv... 

H2A Barr body-deficient (Bbd) is an evolutionary relatively young histone variant sharing only about 48% amino acid sequence similarity to H2A. This histone variant appears to be specific for mammals (Chadwick and Willard 2001). As indicated by the name, the transcriptionally inactive and highly condensed X chromosome in female mammals (also known as Barr body ) is depleted for H2A , while this variant is detectable in autosomes and the active sex chromosomes. This observation suggested that H2A is linked to transcriptionally active euchromatin. H2A cofractionates in sedimentation centrifugation with hyper-acetylated histone H4, further corroborating that it associates with transcriptionally active euchromatin. 

Kanno T, Kanno Y, Siegel RM, Jang MK, Lenardo MJ, Ozato K (2004) Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. Mol Cell 13 33-43... 

Thyroid Hormone Receptor (TR) can bind to the LTR in vivo independently of its ligand and regulates promoter activity. ChIP assays with anti-acetylated-histone antibodies revealed that unliganded TR reduce the local histone acetylation levels at the HIV-1 LTR, while thyroid hormone treatment reverses this induction (Hsia and Shi, 2002). Accordingly, unliganded TR recruits co repressors and at least one HDAC (Hsia and Shi, 2002). 

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].)...

Fig. 5, Nucleosome relaxation data on the two DNA minicircle series, (a)-(c) Nucleosomes were reconstituted with control (Control) or acetylated histones (Acetylated) on ALk = —2.4 to —3.3 topoisomers of pBR 351-366 bp eleven DNA minicircles series or 5S 349-363 bp ten DNA minicircles series, and relaxed in Tris (Tris) or phosphate buffer (phosphate), as described in legend to Fig. 4(a). Topoisomer relative amounts in the equilibrium distributions (see examples in Fig. 4(c)) were plotted as functions of their ALk, calculated from Eq. (4) using h = QA94 ( 0.003) and 10.47s ( 0.003) bp/turn for pBR DNA in Tris and phosphate buffers [28], respectively, and 0 = 10.538 ( 0.006) bp/turn for 5S DNA in Tris buffer [29]. Smooth curves were calculated as described in the text. [Drawn from data in Ref [28] (Acetylated/phosphate) and adapted from Fig. 3 in Ref [29] (Control/Tris).]...

In a supplementary pathway, links between histone H3 Lys4 methylation and the upregulation of RNA synthesis have also been made. This discrete modification colocalizes with acetylated histone residues and is enriched in the transcriptionally active macronucleus of Tetrahymena [194]. Histone methylation at H3 Lys4 has been recently attributed to the novel HMT SET9, which contains the conserved SET catalytic domain, and noticeably lacks the juxtaposed pre- and post-SET... 

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. 

Spencer, V.A. and Davie, J.R. (2001) Dynamically acetylated histone associated with transcriptionally active and competent genes in the avian adult beta-globin gene domain. J. Biol. Chem. 276, 34810-34815. 

Covault, J. and Chalkley, R. (1980) The identification of distinct populations of acetylated histones. J. Biol. Chem. 255, 9110-9116. 

The co-repressor KAP-1 functionally links the DNA-binding Kruppel-associated box zinc finger proteins to the NURD complex by recruiting the Mi-2a subunit. [251]. This interaction requires a tandem PHD/bromodomain motif in which the individual domains appear to act together as a functional unit. The nature of any possible acetylated lysine targets of the bromodomain remains unclear but it is not excluded that this domain could bind to an acetylated lysine in Mi-2a rather than to an acetylated histone tail. 

---