Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.30.1 (S1 nuclease)
 3,660 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The chromatin structure and protein-DNA interactions of a cell cycle regulated human H3 histone gene have been examined at different levels of resolution. Using traditional Southern blot analysis we have investigated the accessibility of the H3 coding region and its flanking sequences to DNase I, S1 nuclease and restriction endonuclease digestion. Using the native genomic blotting method recently developed in our laboratory, two sites of protein-DNA interaction in the proximal 240 bp of the promoter region of this H3 gene were established. Further in vivo analysis of protein-DNA binding sites in intact cells by genomic sequencing revealed, with single nucleotide resolution, the guanine contacts and footprints of the proteins bound to the promoter. The relative locations of protein-DNA interactions in this H3 gene are similar to those identified in vivo and in vitro in a cell cycle dependent human H4 histone gene. The proteins complexed with the H3 histone gene promoter can be dissociated between 0.16 and 0.28 M NaCl. The protein-DNA contacts persist throughout the cell cycle and thus may have a functional relationship with the basal level of transcription of this H3 gene that occurs during and outside of S phase.
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PMID:In vivo protein binding sites and nuclease hypersensitivity in the promoter region of a cell cycle regulated human H3 histone gene. 253 85

We have used an oligonucleotide complementary to a sequence coding for the conserved central globular domain of H1s to screen a mouse genomic library for H1 genes. We then used a series of universal histone oligonucleotides to identify five different H1 genes which were linked to core histone genes. We characterized one of the H1 genes which was linked to an H2a, an H2b, an H3, and an H4 histone gene. This characterization involved: 1) sequencing of the coding region of the gene and several hundred base pairs of flanking region. 2) Comparison of this sequence to other H1 sequences from other organisms. This sequence analysis clearly showed that the gene coded for an H1 and identified H1 consensus sequences in the 5'- and 3'-flanking region. 3) Mapping of the 5'- and 3'-ends of the mRNA complementary to this gene by S1 nuclease analysis. 4) Identifying this gene and an adjacent H3 gene as being of the fully replication-dependent expression class, by measuring changes in the steady state levels of their mRNAs in the presence of hydroxyurea and during differentiation of murine erythroleukemia cells.
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PMID:Isolation and characterization of a mouse fully replication-dependent H1 gene within a genomic cluster of core histone genes. 282 17

We have examined the chromatin structure of the cell cycle regulated human H4 histone gene FO108A at various times during the cell cycle, by treating nuclei isolated from synchronized HeLa S3 cells with micrococcal nuclease. Purified DNA was fractionated electrophoretically, transferred to nitrocellulose, and hybridized to small (150-250 nucleotides) radiolabeled probes from various portions of the promoter and coding regions of the gene. Our results indicate the existence of a micrococcal nuclease sensitive region located between positions -60 and +90 base pairs (bp) from the start codon of the gene, which includes the TATA box. This nuclease-sensitive region persists at all the cell cycle times analyzed. Hybridization with a 250-bp probe containing only coding region sequences reveals a disrupted nucleosomal ladder during early S phase, when this H4 histone gene replicates and exhibits an enhanced level of transcription. By mid-S phase, the regular nucleosomal structure of the coding region is restored and persists during subsequent phases of the cell cycle. The disruption of a normal nucleosomal organization in the promoter and mRNA coding regions of this H4 histone gene is also supported by the sensitivity of these sequences to S1 nuclease.
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PMID:Persistence of a micrococcal nuclease sensitive region spanning the promoter-coding region junction of a cell cycle regulated human H4 histone gene throughout the cell cycle. 283 73

We have observed changes in the chromatin structure of a human histone gene promoter that may be functionally related to variations in transcription during the cell cycle. A detailed analysis of the chromatin structure of a cell cycle-dependent human H4 histone gene and its flanking sequences was performed using DNase I, S1 nuclease, and restriction endonucleases. This gene was previously shown to have a DNase I- and S1-sensitive site for which the boundaries varied with the cell cycle, and we have now precisely mapped these modifications. During S phase, the entire coding region of this gene and the 5'-flanking region up to approximately -600 base pairs are sensitive to both DNase I and S1, while during mitosis/G1, accessibility to these enzymes is greatly decreased in regions from -250 to -600 base pairs and downstream of +100 base pairs. DNase I- and S1-hypersensitive sites in the proximal promoter region (which contains two sites of protein-DNA interaction as well as sequence elements necessary for the correct initiation of transcription) are present throughout the cell cycle, as is an additional site sensitive to both DNase I and S1, located at -700 to -800 base pairs. Restriction enzyme analysis confirmed the general openness of the promoter region and relative insensitivity of the 3'-flanking region, while salt wash experiments indicated several discrete sites in the promoter that are candidates for regulatory interactions. The chromatin structure of the proximal promoter region of this H4 gene is different during early S phase when it is maximally transcribed, as indicated by the ability of a high salt wash to render this region inaccessible to the restriction enzyme MspI only at this time of the cell cycle.
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PMID:Fine mapping of the chromatin structure of a cell cycle-regulated human H4 histone gene. 291 Aug 51

Cultured mammalian cells were transfected with a recombinant human H4 histone gene. S1 nuclease mapping of cellular RNAs from transfected cells revealed: (i) correct initiation of transcription at the cap site, with some transcripts originating from other sites in the 5' flanking region of this H4 gene; (ii) cis-linkage of an SV-40 transcriptional enhancer element upstream of the H4 5'-flanking region resulted in about a 50-fold increase in the level of correctly initiated H4 mRNA and (iii) in a heterologous murine system stability of human H4 mRNAs was apparently sensitive to inhibition of DNA-synthesis by hydroxyurea. Our results suggest that certain sequences required for the initiation of a human H4 histone gene transcript reside within the 210 nucleotides immediately upstream from the cap site and that the level of expression is influenced by the introduction of an enhancer element.
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PMID:Enhancer-facilitated expression of a human H4 histone gene. 298 8

Using S1 nuclease protection assays, we have examined the representation of cell cycle-dependent H4 histone RNAs in the nuclear matrix and nonmatrix nuclear fractions of human cells. Cytoplasmic and nuclear fractions were prepared from exponentially growing HeLa S3 cells by double detergent (sodium deoxycholate and NP40) lysis. The nuclear matrix and nonmatrix nuclear fractions were then prepared by digestion of nuclei with RNase-free DNase I and subsequent high-salt [0.4 M (NH4)2SO4] extraction. Subcellular fractions were characterized by 1) DNA, RNA, and protein composition; 2) electrophoretic analysis of the proteins in each fraction; 3) the representation of 45S ribosomal RNA precursors and processed 18S and 28S ribosomal RNAs; and 4) the presence of mitochondrial RNAs. In contrast to ribosomal and messenger RNA precursors, which are largely associated with the nuclear matrix, the human H4 histone RNAs in the nucleus were found predominantly in the nonmatrix nuclear fraction. The presence of H4 histone RNA in the nonmatrix nuclear fraction appeared to be coupled to DNA replication, since inhibition of DNA synthesis by hydroxyurea resulted in a loss of histone RNA from the nucleus. Our results suggest either that the association of histone RNAs with the nuclear matrix is very transient or that posttranscriptional modifications of the rapidly processed histone gene transcripts do not involve the nuclear matrix.
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PMID:Localization of human histone gene transcripts predominantly in the nonmatrix nuclear fraction. 301 90

We have examined the metabolism of human H4 histone mRNA in the nucleus and cytoplasm of HeLa S3 cells following inhibition of DNA synthesis to address the extent to which histone mRNA stability in these cellular compartments is coupled to DNA replication. The nuclear and cytoplasmic levels of histone mRNAs encoded by the pF0108A human H4 histone gene were determined by S1 nuclease analysis using a 32P-labeled probe that could distinguish pF0108A transcripts from those of other members of the H4 histone multigene family. Hydroxyurea treatment resulted within 15 min in a 75% reduction in the level of histone H4 mRNA in the nucleus, which corresponds to the 85% decrease observed for H4 histone mRNA in the cytoplasm. The kinetics of nuclear and cytoplasmic H4 mRNA turnover following hydroxyurea treatment were also similar. Northern blot analysis using a 32P-labeled mitochondrial cytochrome b probe indicated that the association of cytoplasmic RNA with the nuclear fraction was less than 0.5%. Treatment of cells with a protein synthesis inhibitor resulted in a 1.3-fold increase in nuclear H4 histone mRNA levels and a 1.5-fold increase of H4 mRNA in the cytoplasm after 45 min. Together, these results indicate that nuclear and cytoplasmic H4 histone mRNAs respond similarly to metabolic perturbations that influence message stability and that mechanisms operative in the turnover of histone mRNAs in the nucleus and cytoplasm may be similar.
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PMID:Coordinate turnover of nuclear and cytoplasmic histone messenger RNA following inhibition of DNA replication in HeLa S3 cells. 303 71

The human H1 histone gene FNC16 resides in a 2.7-kb EcoRI fragment present in a histone gene cluster that also contains one copy of each of the core (H2A, H2B, H3, and H4) histone genes. The cap site for FNC16 H1 mRNA is located 58 nucleotides upstream of the ATG translational start codon, and S1 nuclease protection analysis clearly distinguishes between correctly initiated FNC16 transcripts and transcripts from other nonidentical H1 histone genes. We have observed, using S1 analysis, that the FNC16 H1 histone gene is expressed in a replication-dependent manner in HeLa cells and is expressed in proliferating, but down-regulated in differentiated, HL60 cells. Similar results were found in HeLa S3 and HL60 cells for the cell cycle-dependent human H4 histone gene FO108. Nuclear extracts derived from HeLa S3 cells are capable of directing FNC16 H1 histone gene transcription in vitro. This finding is consistent with previous work that established at least two sites for protein-DNA interaction in vitro in the proximal promoter region of this gene. We have observed a difference in the extent to which the FNC16 H1 histone gene is expressed in HeLa S3 and proliferating HL60 cells, which suggests that this H1 gene is differentially regulated in various cell types. Although results reported for a potentially identical human H1 histone gene designated Hh8C (LaBella, F., Zhong, R., and Heintz, N. (1988) J. Biol. Chem. 263, 2115-2118) support differential regulation of human H1 genes in various cell types, their observations that the Hh8C gene is not expressed in HeLa cells and that the restriction patterns differ indicate that FNC16 and Hh8C are different H1 genes.
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PMID:The human H1 histone gene FNC16 is functionally expressed in proliferating HeLa S3 cells and is down-regulated during terminal differentiation in HL60 cells. 318 72