Chromatin associated proteins

High mobility group (HMG) proteins are a family of small nonhistone chromatin-associated proteins which recognize structural distortions in DNA (11, 74, 75). Several NMR structures of HMG domains have been determined (76-78). High mobility group 1 (HMG1) box A... 

Histones and Chromatin-Associated Proteins as Targets for PARylation... 

Murnion ME, Adams RR, Callister DM, Allis CD, Earnshaw WC, Swedlow JR (2001) Chromatin-associated protein phosphatase 1 regulates aurora-B and histone H3 phosphorylation. J Biol Chem 276(28) 26656-26665... 

Goodwin, G.H., Sanders, C., and Johns, E.W. (1973) A new group of chromatin-associated proteins with a high content of acidic and basic amino acids. Eur. J. Biochem. 38, 14-19. 

Stoler, S., Keith, K.C., Curnick, K.E., and Fitzgerald-Hayes, M. (1995) A mutation in CSE4, an essential gene encoding a novel chromatin-associated protein in yeast, causes chromosome nondisjunction and cell cycle arrest at mitosis. Gene Dev. 9, 573-586. 

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. 

Inactive and active chromatin domains can be defined at the molecular level by the presence (or absence) of specific histone modifications (or combinations of modifications), by the degree of chromatin compaction and the presence of chromatin associated proteins. Several earlier studies focusing on specific genes or loci showed that active chromatin is generally more accessible and enriched in acetylated forms of histones H3, H4, H2A [5] and histone H3 methylated at lysine 4 (H3/K4) [6]. H3/K4 di- and tri-methylation and H 3 acetylation correlate globally with open chromatin [7]. 

Accordingly, some effort has been devoted to studying the effects of cisplatin on transcription. In vitro experiments with RNA polymerases demonstrated that productive elongation activity was prematurely terminated by the whole spectrum of cisplatin-DNA adducts, but not by the /ran.y-DDP 1,3-intrastrand adducts [150-152], Selective bypass of trans-DDP adducts was also demonstrated in XPA cells, suggesting that repair of the DNA lesions did not contribute to differential transcription inhibition by the platinum compounds [153], In vivo, hormone-induced chromatin remodeling and subsequent transcription from the MMTV promoter was specifically inhibited by cisplatin [154], In this case, platinum adducts seemed to cause a decrease in the DNA binding of one of the transcription factors, NF1. Several chromatin-associated proteins, such as the linker histone protein HI or... 

Histone tails can also be modified by methylatlon, phosphorylation, and monoubiquitination. These modifications influence chromatin structure by regulating the binding of histone tails to other less abundant chromatin-associated proteins. 

Mammalian poly (ADP-ribose) polymerase-1 (PARP-1) is a nuclear chromatin associated protein and belongs to a lai e family of enzymes that can synthesize large branched polymers of ADP-ribose units by using -nicotinamide adenine dinucleotide (NAD ) as substrate. A pathophysiological role for PARP-1 has been demonstrated in a number of diseases and animal models using PARP-1 knockout mice. 

We have previously described a method for subfraetionating isolated nuclei (Aris and Blobel, 1991), which stipulated the use of buffers lacking Mg and containing EDTA for the purpose of dissociating histones from chromatin digested with DNase I. In the method described herein, brief exposure to a low concentration of heparin in the presence of Mg is used to facilitate dissociation of histones and other chromatin-associated proteins. Heparin has been used previously for this purpose by Courvalin and co-workers (1982), as well as by Rout and Kilmartin (1990). A concentration of 1 mA/ Mg has been chosen because it approximates the intracellular value (see Loukin and Kung, 1995),... 

The presence of NaCl in buffers at concentrations of 50-300 m A/ was examined in order to ascertain if increased ionic strength may improve release of chromatin-associated proteins prior to the sucrose step gradient. Low salt concentrations (50-150 mM) did not improve histone release, and high salt concentrations (200-300 mM) reduced the yield of nucleoli and increased the amount of Noplp detected in upper step gradient fractions. 

To isolate chromatin-associated proteins following incubation of sperm nuclei in Xenopus egg extract, the mixture should first be diluted with buffer XN (Philpott and Leno, 1992 Leno et ai, 1996) and the nuclei pelleted by centrifugation at 3500 rpm for 10 min in an SW50.1 rotor (Beckman). The nuclei are then resuspended in buffer, recentrifuged under the same conditions, and finally... 

Fig. 2 Two-dimensional PAGE analysis of sperm-associated proteins on condensed chromatin and following chromatin decondensation in egg extract and purified nucleoplasmin. Sperm nuclei were incubated in either (A) buffer, (B) Xenopus egg HSS, or (C) purified egg nucleoplasmin for 10 min. The nuclei were then pelleted, washed, and the chromatin-associated proteins were extracted with acid and analyzed in the first dimension by Triton-acid-urea (TAU)-PACE (left to right) and in the second dimension by SDS-PAGE (top to bottom). The positions of the core histones are indicated as H2A, H2B. H3. and H4 and the sperm-specific basic proteins as X and Y. The arrowheads and arrow indicate the positions of the cleavage-stage linker histone. B4, and Xenopus HMG-2, respectively (Dimitrov et at., 1994). [Reproduced from Philpott and Leno (1992) Copyright Cell Press.]...

Since the discovery of poly(ADP-ribose) synthetase and its role in cellular NAD turnover there has been a great deal of speculation concerning the physiological function of this enzyme and the polymer it synthesizes. The observation that the poly(ADP-ribose) synthetase is responsible for modification of chromatin-associated proteins led to the suggestion of its involvement in regulation of nuclear metabolism. Correlations between synthesis of poly(ADP-ribose) and DNA repair, cellular differentiation, DNA synthesis, and cellular proliferation have been noted. In most of these instances, however, when one set of data... 

Murdoch GH, Rosenfeld MG, Evans RM (1982) Eukaryotic transcriptional regulation and chromatin-associated protein phosphorylation by cyclic AMP. Science 218 1315-1317... 

At present the events triggering and the mechanism controlling muscle differentiation are not well understood they may include changes in chromatin structure, gene amplification, and specific DNA and/or protein modification. One such modification, namely, poly(ADP-ribosyl)ation of nuclear proteins has recently attracted much attention and several studies have indicated that the enzyme poly(ADP-ribose) synthetase plays a role in cellular differentiation [6-9]. This enz)mie is a nuclear chromatin-associated protein which catalyzes covalent modification of both histone and nonhistone protein acceptors (for reviews see [10-13]). The synthetase is activated by DNA strand breaks and it has been suggested that DNA fragmentation and the consequent increase in poly(ADP-ribose) activity are obligatory events for chick muscle differentiation [6]. 

Poly(AIH -Ribose) Modified Proteins. Poly(ADP-ribose) appears to be involved as a modifier of chromatin-associated proteins in several cellular processes (reviewed in [12]). To determine the role of poly(ADP-ribose) in myogenesis we attempted to identify the acceptor proteins which undergo this modification, and to de e the specificity of such modification. 

Xie A, Hartlerode A, Stuck M et al (2007) Distinct roles of chromatin-associated proteins MDCl and 53BP1 in mammalian double-strand break repair. Mol Cell 28 1045-1057... 

It is clear that the regulation of gene expression is involved not only in long-term plant cell response to phytohormones, but also in short-term responses [21]. Trewavas [23] was the first to suggest that phosphorylation of chromatin-associated protein may mediate the hormonal regulation of transcription in plant cells. 

Using the chromatin-associated protein histone Hj as a substrate and partially purified protein kinases from different biological sources, the inhibitory potency of these alkaloids was measured in vitro (table 1). 

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