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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

To address the relationship between chromatin structure and histone gene expression, the nucleosomal organization of a cell cycle-dependent human H4 histone gene in a bovine papilloma virus (BPV) minichromosome was examined. The nucleosome repeat length of the human H4 histone gene, maintained as a stable episome in a C127 mouse cell line designated I-8, was compared with that of the chromosomal copy of the H4 gene in human (HeLa) cells. In both cell lines, the H4 histone gene is predominantly expressed during the S phase of the cell cycle. The nucleosome repeat length of total HeLa cell and C127 mouse cell chromatin was similarly examined. Nuclei were digested with micrococcal nuclease and the DNA was fractionated electrophoretically, transferred to nitrocellulose filters and hybridized with radiolabelled (32P) cloned DNA probes. The nucleosome repeat length of the H4 gene, as an episome in the C127 mouse cell (153 +/- 8) and as an integrated copy in a HeLa cell (163 +/- 10) was considerably shorter than total genomic host cell (C127) (190 +/- 5) or HeLa cell chromatin (183 +/- 7). Our results indicate that the episomal H4 histone gene is packaged as chromatin. Moreover, the shortened nucleosome repeat length of the H4 gene, both as an episome or integrated chromosome sequence, suggests that the repeat length is characteristic of the gene and may be functionally related to its cell cycle regulated expression.
Mol Cell Biochem 1987 Apr
PMID:Nucleosomal organization of a BPV minichromosome containing a human H4 histone gene. 303 7

We have analyzed micrococcal nuclease (MNase) DNA cleavage patterns at the sequence level by examining 2.3 X 10(3) base-pairs of data derived from the Drosophila melanogaster 44D larval cuticle locus. Within this region, MNase preferentially cleaved 140 sites. Clusters of these sites appear to generate the preferential MNase eukaryotic DNA cleavage sites seen on agarose gels at roughly 100 to 300 base-pair intervals. These clusters of preferential cleavage sites rarely occur within gene coding regions. The analysis revealed that duplex DNA sequences preferentially cleaved by MNase are generally determined by a single strand sequence: d(A-T)n, where n greater than or equal to 1, flanked by a 5' dC or dG. Cleavage of the other strand is generally staggered 5' by several nucleotides and occurs even if such sequences are absent on that strand. An empirical predictive DNA cleavage model derived from a statistical analysis of the sequence level data was applied to seven eukaryotic gene loci of known sequence. The predicted patterns were in good general agreement with the previously observed eukaryotic gene/spacer cleavage pattern. Statistical analysis also revealed that sites of predicted preferential DNA cleavage occur less frequently in protein coding regions than for randomized sequences of the same length and nucleotide content. Comparison of the MNase cleavage patterns to the sequence-dependent pattern of binding energies between duplex DNA strands indicates that MNase preferentially cleaves sequences with low helix stability.
J Mol Biol 1986 Aug 20
PMID:Micrococcal nuclease as a DNA structural probe: its recognition sequences, their genomic distribution and correlation with DNA structure determinants. 309 28

The studies reported here demonstrate that ATP may be used in lieu of EDTA to inhibit nuclease digestion of DNA and chromatin. Because ATP is a milder chelator than EDTA and is a biochemical common to the cellular microenvironment in vivo, critical studies of cellular processes that require native structure to be maintained are more feasible without the presence of strong chelators. During the digestion of chromatin into its components by nuclease treatment, ATP assures the retention of nucleoprotein compaction, particularly for large to intermediate-sized oligosomes (2400bp-1000bp in length). ATP used at a concentration of 3.3 mM appears to be somewhat better than EDTA, 1.0 mM, for minimizing degradation of nuclease-treated chromatin. However, termination of nuclease digestion of chromatin and minimization of further degradation by the addition of ATP to a concentration of 1.0 mM was almost equivalent to the addition of EDTA to a concentration of 1.0 mM. Slightly more degradation was observed for the latter condition. In addition, ATP can be used to inhibit endogenous nuclease activity when specific restriction enzymes are needed. Standard low ionic strength DNP, deoxyribonucleoprotein, and DNA electrophoresis of proteinized and deproteinized chromatin oligomers, respectively, indicated that ATP effectively inhibits staphylococcal nuclease. Low ionic strength nucleoprotein electrophoresis to resolve staphylococcal nuclease-digested chromatin indicates that as little as 10(-4) M EDTA can promote structural unfolding resulting in changes in apparent mobilities for chromatin oligomers 250 and 600 bp in length. Comparative digestion of chromatin with staphylococcal nuclease followed by reaction termination by ATP or EDTA showed that this observation was not merely the result of degradation due to inefficiency of ATP enzyme inhibition.
Mol Cell Biochem 1987 Aug
PMID:ATP as an alternative inhibitor of bacterial and endogenous nucleases and its effect on native chromatin compaction. 311 82

The organization of chromatin in D. melanogaster ribosomal repeats with and without insertions was studied. We have shown earlier that upon digestion with micrococcal nuclease a "non-transcribed" intergenic spacer produces unusual chromatin particles containing DNA fragments 200-280 b.p. in length. These particles sediment like H1-containing nucleosomes, are stable only in the presence of polyamines, and are probably bound to some non-histone protein. The content of core histones and H1 in different regions of ribosomal genes has been studied by two-dimensional electrophoresis of chromatin particles and by "protein-image" hybridization. The content of histones and respectively the degree of chromatin condensation increase in the following order: the 1kb-long region surrounding the initiation site is practically free of histones less than the region of 240 b.p. repeats from the intergenic spacer, containing homologies with the ribosomal promotor less than coding region preceding the usual site of insertions less than coding region lying behind this site less than inactive type II ribosomal insertion. Therefore, the region of the beginning of transcription of most ribosomal genes is in an active conformation, even though at least 75% of the genes are repressed. Ribosomal insertions are in a compact, repressed form. We suggest that their inhibitory action on the transcription of corresponding genes at the molecular level is similar to the position effect of heterochromatic regions at the chromosomal level.
Mol Biol (Mosk)
PMID:[Gradient condensation of chromatin in ribosomal genes of Drosophila melanogaster]. 313 62

The arrangement of histones along nucleosomal DNA within particular active and inactive genome regions was analysed by using protein-DNA crosslinking methods combined with hybridization tests. Two-dimensional gel electrophoresis was employed to compare the nucleosome conformation and nucleosomal DNA size. The arrangement of histones along DNA and general compactness of nucleosomes were shown to be very similar in transcriptionally active and inactive genomic regions. On the other hand, nucleosomes within transcriptionally active chromatin are characterized by a somewhat larger size of nucleosomal DNA produced by micrococcal nuclease digestion and some peculiarity in electrophoretic mobility. It appears that changes in transcribed chromatin structure (such as an enhanced nuclease sensitivity) occur on the supranucleosomal level rather than in the nucleosomal core structure.
Mol Biol (Mosk)
PMID:[The structure of nucleosomal core particles located on the transcribed genome regions]. 314 77

It was revealed by means of nucleoprotein-celite-chromatography that DNA-protein interactions in the chromatin fraction sensitive to micrococcal nuclease and DNase II are weaker that in the resistant one. The micrococcal nuclease destroys the DNA-matrix bond resistant to salt-urea, while DNase II does not change the DNA-matrix integrity. Tightness of the DNA-protein interactions is weakened by the increasing chromatin fragmentation, but does not depend on the size of chromatin particles.
Mol Gen Mikrobiol Virusol 1988 Oct
PMID:[Stability of DNA-protein interactions in chromatin fractions with different sensitivity to nucleases]. 323 Dec 30

A rapid affinity labeling procedure with enhanced specificity was developed to identify DNA-binding proteins. 32P was first introduced at unique phosphodiester bonds within the DNA recognition sequence. UV light-dependent cross-linking of pyrimidines to amino acid residues in direct contact at the binding site, followed by micrococcal nuclease digestion, resulted in the transfer of 32P to only those specific protein(s) which recognized the binding sequence. This method was applied to the detection and characterization of proteins that bound to the upstream promoter sequence (-50 to -66) of the human adenovirus type 2 major late promoter. We detected two distinct proteins with molecular weights of 45,000 and 116,000 that interacted with this promoter element. The two proteins differed significantly in their chromatographic and cross-linking behaviors.
Mol Cell Biol 1988 Jan
PMID:DNA affinity labeling of adenovirus type 2 upstream promoter sequence-binding factors identifies two distinct proteins. 333 54

We have mapped the DNase I- and micrococcal nuclease-hypersensitive sites present in the 5' end of the human apolipoprotein B (apo-B) gene in nuclei from cells expressing or not expressing the gene. Four DNase I-hypersensitive sites were found in nuclei from liver-derived HepG2 cells and intestine-derived CaCo-2 cells, which express the apo-B gene, but not in HeLa cells, which do not. These sites are located near positions -120, -440, -700, and +760 base pairs relative to the transcriptional start site. Undifferentiated CaCo-2 cells exhibited another site, near position -540. Six micrococcal nuclease-hypersensitive sites were found in nuclei from HepG2 and CaCo-2 cells, but not in HeLa cells or free DNA. These sites are located near positions -120, -390, -530, -700, -850, and +210. HepG2 cells exhibited another site, near position +460. Comparison of the DNA sequence of the 5' flanking regions of the human and mouse apo-B genes revealed a high degree of evolutionary conservation of short stretches of sequences in the immediate vicinity of each of the DNase I- and most of the micrococcal nuclease-hypersensitive sites.
Mol Cell Biol 1988 Jan
PMID:DNase I- and micrococcal nuclease-hypersensitive sites in the human apolipoprotein B gene are tissue specific. 333 67

By means of selective micrococcal nuclease digestion chromatin from early stages of the sea urchin St. droebachiensis embryogenesis was divided into fractions differing by their transcriptional activity. The electrophoretic analysis of histones at the gastrula stage showed that the transcriptionally active chromatin fraction was enriched with early variants of histone H2A and H1. On the stage of pluteus, when primary cell differentiation is completed, the amount of total histone H1 in this fraction was significantly decreased, however it was enriched in an early alpha variant. It was shown that after mild micrococcal nuclease digestion mononucleosomes, which were mostly derived from active chromatin, were significantly enriched with in vivo labeled early histone variants.
Mol Biol (Mosk)
PMID:[Nucleosomes of active chromatin from sea urchin embryo cells are rich in early histone variants]. 337 87

We have compared mononucleosomes that were obtained by hydrolysis of chromatin micrococcal nuclease from a number of sources with the length of a nucleosomal repeat 185--245 b. p. long. For hydrolysis of chromatin isolated from nuclei, a series of nucleosomes was formed: MN145 (core particle), MN165, MN175...MN205, MN215, the lengths of their DNAs differing (by approximately 10.n b.p. where n = 1, 2, 3...) by a factor of 10. A feature of hydrolysis of chromatin in nuclei was the appearance of an additional H1-depleted MN155 particle. It is suggested that upon isolation of chromatin from nuclei, its partial decompactization takes place. This decompactization changes the character of nuclease splitting and seems to be connected with rearrangement of histone H1. These observations demonstrate that besides core particles MN145 and chromatosomes MN165, the major particles of digest of nuclei appear to be MN155, and for isolated chromatin--MN175. Unlike this standard picture, mainly MN145, MN155, MN235 and MN245 are formed upon hydrolysis of sea urchin sperm nuclei.
Mol Biol (Mosk)
PMID:[Structure of nucleosomes and organization of inter-nucleosomal DNA in chromatin]. 339 53


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