Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.21.1 (DNase)
 7,655 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The chromatin core particle DNA conformation deduced in broad outline by Finch et al. [Finch, J. T., Lutter, L. C., Rhodes, D., Brown, R. S., Rushton, B., Levitt, M. & Klug, A. (1977) Nature 269, 29-36] can be described in detail using other available experimental results. Histone binding sites compatible with the pattern of pancreatic DNase I digestion (Simpson, R. T. & Whitlock, J. P., Jr. (1976) Cell 9, 347-353; Noll, M. (1977) J. Mol. Biol. 116, 49-71; Lutter, L. C. (1977) J. Mol. Biol. 117, 53-69] lend to core particle DNA pseudosymmetry characteristic of molecular point group D(3). DNA symmetry and pseudosymmetry, in turn, imply equivalence and quasi-equivalence properties of the histone packing arrangement that support the following deductions: (i) One and only one alpha(2)beta(2) histone tetramer, presumably (H3)(2)(H4)(2), can serve as a stable subassembly within the histone octamer. (ii) There is a unique, strand-specific way to assign DNA binding domains to the arginine-rich histones (H3 and H4). (iii) Histones H3 and H4 alone should suffice to impose a supercoiled structure on DNA, as is observed experimentally, because only the tetramer can mimic a screw dislocation and thereby complement the screw symmetry of the DNA supercoil. (iv) The two slightly lysine-rich histones H2A and H2B are probably responsible, each in a different way, for dividing the eukaryotic chromatin fiber into discrete subunits. (v) The proposed arrangement of four distinct proteins appears to be a minimum formal requirement for making nucleosomes; that is, for introducing regularly spaced supercoiled DNA folds without also allowing formation of an indefinitely long (and genetically inert) DNA superhelix.
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PMID:Histone packing in the nucleosome core particle of chromatin. 27 80

We have found that DNAase I digestion of yeast, HeLa and chicken erythrocyte nuclei produces a pattern of DNA fragments spaced 10 bases apart and extending to at least 300 bases. This "extended ladder" of DNA fragments is most clearly seen with yeast, and least clearly with chicken erythrocytes. The appearance of regular and discrete bands at sizes much larger than the repeat size shows that the core particles (140 bp of DNA + H2A, H2B, H3 H4) in at least some fraction of chromatin are spaced in a particular fashion, by discrete lengths of spacer DNA, and not randomly. Based on the abundance of small repeats in yeast and from experiments with nucleosome oligomers, we conclude that the extended ladder and nucleosomal phasing probably arise mainly from regions in the chromatin in which nucleosome cores are closely packed or closely spaced (140-160 bp X n). Contributions from less closely packed but still accurately phased nucleosomes, however, cannot be entirely excluded.
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PMID:On the occurrence of nucleosome phasing in chromatin. 33 21

Chicken erythrocyte inner histones (H2A, H2B, H3 and H4) were associated with the two complementary homopolymeric polydeoxyribonucleotides and the two alternating copolymeric polydeoxyribonucleotides. No evidence for formation of chromatin-like structures was obtained for the complexes with poly(dG) . poly(dC) or poly(dA) . poly(dT). Both poly (dGdC) . poly(dGdC) and poly(dAdT) . poly(dAdT) could be folded by histones to yield material digested by DNAase I to multiples of about 10 and by staphylococcal nuclease to 146 bp core particles. Due to the lack of sequence heterogeniety in the complex of histones with poly(dAdT) . poly(dAdT), core particles with remarkable fine structural detail are obtained. The internal organization of DNA in the AT-containing and GC-containing core particles appears not to be identical.
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PMID:Cromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence. 45 Jul

Core histones (H2A, H2B, H3, and H4) are reconstituted by salt gradient dialysis with DNA molecules ranging in length from 177 bp down to 50 bp. While reconstituted particles containing 125 bp are very similar to native particles, those particles containing a single piece of shorter DNA tend to aggregate. The aggregation depends on the ionic strength and DNA length. The DNA placement on the histone core is not random as determined by pancreatic DNase I digestions of particles containing 32P 5'-end-labeled DNA. Rather, it is found that all DNA molecules, up to 161 bp in length, reassociate with core histones in such a way as to produce defined patterns of DNase I cutting with respect to the 5' ends. Particles were made that contained two pieces of 65-bp DNA. These particles are very similar to native particles under most conditions but tended to dissociation results in the production of two half-nucleosomes (hemisones).
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PMID:Nucleosome reconstitution: effect of DNA length on nuclesome structure. 47 61

The intact interphase genome of Drosophila melanogaster has been isolated by sucrose gradient centrifugation after gentle lysis of tissue culture cells in 0.9 M NaCl-0.4% nonidet P40. The non-viscous folded DNA sediments as a single broad 5000S peak in a complex with RNA (a fraction of the nuclear nascent RNA) and protein (all of the four intranuclesome histones: H2A, H2B, H3, and H4). The folded DNA is supercoiled and can be relaxed to slower sedimenting forms either by intercalating ethidium or by nicking with DNAase I. Incomplete DNAase treatment gives partially relaxed complexes, indicating that each nick relaxes only a stretch of DNA (defined as a supercoiled DNA loop) without affecting the superhelical content of the rest of the genome. The concentration of superhelices in the Drosophila folded DNA is the same as in the E. coli and SV40 closed circular DNAs-that is, about one negative turn every 200 base pairs (bp) in 0.15 M NaCl at 26 degrees C. The estimated average size of the supercoiled DNA loops, about 85,000 bp, equals the size of the larger Drosophila chromomeres. Ethidium intercalation in 0.9 M NaCl both removes the negative superhelical turns and dissociates the four histones from the DNA. The four histones are dissociated in equimolar concentrations, and the relative proportion of histones displaced from the DNA is a function of ethidium concentration. The histones are completely dissociated from the folded DNA at the ethidium concentration. The histones are completely dissociated from the folded DNA at the ethidium concentration which removes all of the negative superhelices. Thus the data strongly suggest that the rotation of the Watson Crick helix which accompanies ethidium intercalation causes the loss of nucleosomes from the DNA. The results are interpreted in terms of a model for the folded Drosophila genome which has the DNA constrained (by both protein-DNA and RNA- DNA interactions) into independent supercoiled loops containing on the average 400 nucleosomes per loop. Each nucleosome is composed of a histone core with the DNA wound around it in a 360 degrees left-handed toroidal supercoil; each nucleosome toroidal supercoil plus its relaxed internucleosome DNA contains, on the average, 200 bp.
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PMID:Isolation, characterization, and structure of the folded interphase genome of Drosophila melanogaster. 82 31

A DNA endonuclease complex which recognizes predominantly pyrimidine dimers in UVC irradiated DNA has been isolated from the chromatin of normal human and xeroderma pigmentosum, complementation group D (XPD) lymphoblastoid cells. The activity of the normal complex on UVC irradiated DNA was increased approximately 2.5 and 1.5 fold over activity on damaged naked DNA, when core (histones H2A, H2B, H3, H4) and total (core+histone H1) nucleosomal DNA, respectively, was used. In contrast, the XPD complex showed no increase in activity on UVC irradiated total and only a 1.4 fold increase on UVC irradiated core nucleosomal DNA, indicating that the XPD complex is defective in its ability to incise UVC irradiated nucleosomal DNA. The normal complex was able to correct this defect in the XPD complex at the nucleosomal level.
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PMID:Isolation of a DNA endonuclease complex in XPD cells which is defective in ability to incise nucleosomal DNA containing pyrimidine dimers. 147 50

Chromatin organization of the early histone gene repeat was studied at the early embryonic stages of the sea urchin S. purpuratus. Micrococcal nuclease digestion showed a highly irregular packaging of the whole repeat at the period of transcriptional activity, which was progressively replaced by more regular nucleosomal arrays upon developmentally programmed inactivation. No evidence for unique positioning of the nucleosomes was found. Regions upstream of each of the genes were hypersensitive to DNAase I digestion in the active state. These regions contained one (H2A and H2B), or two (H3 and H4) well-defined DNAase I cutting sites, or two poorly-defined sites (H1). They mapped within DNA sequences shown previously to be required for proper expression of the genes. Hypersensitivity continued in the hatching blastula, which have a conventional nucleosomal structure and a much reduced transcriptional activity. Hypersensitivity of these regions during morula and early blastula was not dependent on the torsional strain in chromatin, as it was not influenced by extensive gamma ray-induced nicking of the DNA in nuclei. By late blastula no hypersensitive regions were present.
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PMID:Chromatin structure of the developmentally regulated early histone genes of the sea urchin Strongylocentrotus purpuratus. 240 46

The influence of nucleosomes on the activity of two chromatin-associated apurinic/apyrimidinic (AP) DNA endonuclease activities, pIs 9.2 and 9.8, from normal and xeroderma pigmentosum, complementation group A (XPA), lymphoblastoid cells was examined. These AP endonuclease activities were studied on non-nucleosomal and nucleosomal plasmid pWT830/pBR322 DNA which had been reconstituted with core (H2A, H2B, H3, H4) or total (core plus H1) histones from normal or XPA cells. Both nucleosomal and non-nucleosomal DNA was rendered partially AP by alkylation with 12.5 mM methyl methanesulfonate, followed by heating it at 70 degrees C, to produce approximately three AP sites per DNA molecule. The activities of both normal lymphoblastoid AP endonuclease activities on nucleosomal AP DNA, reconstituted with core histones, was approximately 2.5 times greater than that on non-nucleosomal AP DNA. When histone H1 was added to the system, this increase was reduced. XPA AP endonuclease activities, on the other hand, did not show any increase in activity on nucleosomal AP DNA reconstituted with core histones. These differences between normal and XPA endonuclease activities on AP nucleosomal DNA were the same regardless of whether histones from normal or XPA cells were used in the reconstituted system.
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PMID:Enhancement of two apurinic/apyrimidinic endonuclease activities from normal but not xeroderma pigmentosum lymphoblastoid cells by nucleosome structure. 242 53

The beta-globin and histone H5 genes are transcriptionally active in immature chicken erythrocytes and potentially active in mature erythrocytes. In both immature and mature erythrocytes, the majority of these erythroid-specific gene sequences are located in two chromatin fractions: the low-salt-insoluble residual nuclear material and the 0.15 M-NaCl-soluble oligo- and poly-nucleosomes. These salt-soluble chromatin fragments are enriched in hyperacetylated species of H4 and H2B, ubiquitinated and polyubiquitinated species of H2A and H2B and are depleted of linker histones H1 and H5. The competent, transcriptionally inactive embryonic epsilon-globin gene, which is part of the DNAase I-sensitive beta-globin domain, is highly enriched in the 0.15 M-NaCl-soluble polynucleosome fraction but not in the insoluble nuclear material. The repressed vitellogenin gene shows no enrichment in either of these fractions. These results suggest that only those genes that are expressed or have the potential for expression are enriched in the low-salt-insoluble nuclear material of immature or mature erythrocytes. The enrichment of active genes in the low-salt-insoluble residual nuclear material of immature erythrocytes is not dependent on on-going transcription, the presence of RNA or changes in the amount of acetylated histone species. Our results are consistent with the hypothesis that active and potentially active genes are insoluble because of the presence of preinitiation transcription complexes.
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PMID:Chromatin structure of erythroid-specific genes of immature and mature chicken erythrocytes. 260 93

Poly(ADP-ribosyl)ation of nuclear proteins was several-fold higher in the pachytene spermatocytes than in the premeiotic germ cells of the rat. Among the histones of the pachytene nucleus, histone subtypes H2A, H1 and H3 were poly(ADP-ribosyl)ated. Based on the immunoaffinity fractionation procedure of Malik, Miwa, Sugimara & Smulson [(1983) Proc. Natl. Acad. Sci. U.S.A. 80, 2554-2558] we have fractionated DNAase-II-solubilized chromatin into poly(ADP-ribosyl)ated chromatin (PAC) and non-poly(ADP-ribosyl)ated chromatin (non-PAC) domains on an anti-[poly(ADP-ribose)] IgG affinity matrix. Approx. 2.5% of the pachytene chromatin represented the PAC domains. A significant amount of [alpha-32P]dATP-labelled pachytene chromatin (labelled in vitro) was bound to the affinity matrix. The DNA of pachytene PAC domains had internal strand breaks, significant length of gaps and ligatable ends, namely 5'-phosphoryl and 3'-hydroxyl termini. On the other hand, the PAC domains from 18 h regenerating liver had very few gaps, if any. The presence of gaps in the pachytene PAC DNA was also evident from thermal denaturation studies. Although many of the polypeptides were common to the PAC domains of both pachytene and regenerating liver, the DNA sequences associated with these domains were quite different. A 20 kDa protein and the testis-specific histone H1t were selectively enriched in the pachytene PAC domains. The pachytene PAC domains also contained approx. 10% of the messenger coding sequences present in the DNAase-II-solubilized chromatin. The pachytene PAC domains, therefore, may represent highly enriched DNA-repair domains of the pachytene nucleus.
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PMID:Characterization of poly(ADP-ribosyl)ated domains of rat pachytene chromatin. 280 42


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