Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

---

Query: EC:3.1.30.1 (S1 nuclease)
3,660 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The epidermal growth factor (EGF) receptor is the functional target of the mitogen EGF and the cellular homolog of the avian erythroblastosis virus erbB oncogene product. Regulation of expression of the proto-oncogene encoding the EGF receptor can be elucidated by studying the structure and function of the gene promoter outside the confines of the cell. Previously, we reported the isolation of the human EGF receptor gene promoter. The promoter is highly GC rich, contains no TATA or CAAT box, and has multiple transcription start sites. An S1 nuclease-sensitive site has now been found 80 to 110 base pairs (bp) upstream from the major in vivo transcription initiation site. Two sets of direct repeat sequences were found in this area; both conform to the motif TCCTCCTCC. When deletion mutations were made in this region of the promoter by using either Bal 31 exonuclease or S1 nuclease, we found that in vivo activity dropped three- to fivefold, on the basis of transient-transfection analysis. Examination of nuclear protein binding to normal and mutated promoter DNAs by gel retardation analysis and DNase I footprinting revealed that two specific factors bind to the direct repeat region but cannot bind to the S1 nuclease-mutated promoter. One of the specific factors is the transcription factor Sp1. The results suggest that these nuclear trans-acting factors interact with the S1 nuclease-sensitive region of the EGF receptor gene promoter and either directly or indirectly stimulate transcription.
...
PMID:Modulation of epidermal growth factor receptor proto-oncogene transcription by a promoter site sensitive to S1 nuclease. 284 30

Expression of the melR gene is required for melibiose-dependent stimulation of transcription initiation at the promoter of the melAB operon. Using the S1 nuclease method we have located the melR transcription start point. Transcription from the melR promoter is dependent on cAMP-CRP: specific nucleotide sequences downstream of bp -59 with respect to the melR transcription start are sufficient for full promoter activity. Nucleotide sequence homologies suggest that the cAMP-CRP binding site is located from bp -52 to -31, in exactly the same position as at the galP1 promoter. Using DNase I footprinting we show that cAMP-CRP and RNA polymerase together bind tightly to the melR promoter sequence, creating a strong footprint from bp -70 to +20. Alone, cAMP-CRP binding is hardly detectable, whereas RNA polymerase alone creates a weak footprint centred around the -10 hexamer sequence. When the melR gene is expressed from a cAMP-CRP-independent promoter, melibiose-dependent transcription from the melAB promoter becomes independent of cAMP-CRP, showing that the melR promoter is the primary site of control by cAMP-CRP in the mel regulon.
...
PMID:Transcription from the Escherichia coli melR promoter is dependent on the cyclic AMP receptor protein. 285 97

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.
...
PMID:Fine mapping of the chromatin structure of a cell cycle-regulated human H4 histone gene. 291 Aug 51

The human dihydrofolate reductase (DHFR) gene was found to be undermethylated only in its 5' promoter region; the remaining CCGG residues in the 30-kilobase (kb) DHFR gene were insensitive to digestion by HpaII. Each of 27 CpG residues that were part of an HpaII or HhaI cutting site within a 1.1-kb segment of the DHFR gene promoter region were found to be unmethylated. All 80 copies of the DHFR gene in methotrexate-resistant HeLa cell line exhibited this pattern of undermethylation of only the promoter region. This same region was shown to be DNase I hypersensitive in chromatin from normal cells and from those cells in which the DHFR gene was amplified. Again, all copies of the amplified gene exhibited DNase I hypersensitivity of the promoter region. The remainder of the 30-kb DHFR gene is both completely methylated and insensitive to DNase I digestion. Detailed mapping of the DNase I-hypersensitive region revealed four strong cutting sites within a 500-base pair segment immediately upstream from the DHFR coding sequence and a weak cutting site within intron I. Two of the strong DNase I cutting sites in chromatin were also sensitive to S1 nuclease nicking when this DNA fragment was part of supercoiled plasmid DNA. Promoter undermethylation and DNase I hypersensitivity, features previously shown for specialized and inducible genes, have now been shown to be characteristic of the constitutively expressed DHFR gene. That these features characterize all copies of the amplified DHFR gene in a methotrexate-resistant cell line suggest that all gene copies are transcriptionally active.
...
PMID:Only the promoter region of the constitutively expressed normal and amplified human dihydrofolate reductase gene is DNase I hypersensitive and undermethylated. 298 20

The regulatory region of the Escherichia coli cya gene was analyzed by using S1 nuclease mapping and in vitro transcription experiments. The cya gene was transcribed, both in vivo and in vitro, from one major promoter (P2) and two weak promoters (P1 and P1') that are located about 200 base pairs upstream of P2. The transcription from P2 was specifically inhibited by cAMP-CRP (cAMP receptor protein) in vitro. This regulatory mechanism was shown to be physiologically relevant through quantitative analyses of the cya mRNA in intact cells by S1 and dot blot assays. DNase I protection experiments revealed that cAMP-CRP binds to the cya DNA region between +11 and -20, in which a consensus CRP binding sequence is present. Moreover, it was found that cAMP-CRP alters the binding of RNA polymerase to the promoter region, thus inhibiting the transcription of the cya gene.
...
PMID:Transcription of the Escherichia coli adenylate cyclase gene is negatively regulated by cAMP-cAMP receptor protein. 298 47

DNA sequences of the X-chromosome-linked hypoxanthine phosphoribosyltransferase (HPRT) and glucose 6-phosphate dehydrogenase (G6PD) genes have revealed the presence of clusters of CpG dinucleotides, raising the possibility that such clusters are involved in the control of expression of these genes, which are expressed in all tissues. Although CpG clusters are not exclusive features of the X chromosome, the analysis of X-linked genes provides the means to determine whether CpG clusters are control elements; one of the two homologous X loci in female mammals is not expressed, so that active and inactive versions of the gene can be compared. In fact, it has been shown that these CpG clusters are undermethylated when the gene is active and extensively methylated when the gene is inactive. In addition to hypomethylation, chromatin hypersensitivity to endonuclease digestion is a known hallmark of regulatory sequences in eukaryotic genes. We report here that the CpG clusters of the active hprt and g6pd genes are not only undermethylated, but also hypersensitive to MspI, DNase I and S1 nuclease, further supporting the suggestion that they are involved in the control of expression of these genes.
...
PMID:Clusters of CpG dinucleotides implicated by nuclease hypersensitivity as control elements of housekeeping genes. 298 78

The internal promoter of the Xenopus laevis oocyte-type 5S RNA gene is preferentially cleaved by S1 and Bal-31 nucleases in plasmid DNA. S1 nuclease sensitivity is largely dependent on supercoiling; however, Bal-31 cleaves within the 5S RNA gene in linear as well as in supercoiled DNA. The S1 nuclease-hypersensitive site is centered at position +48-52 of the gene at the 5' boundary of the promoter. A DNAase I-hypersensitive site is induced at this position upon binding of the transcription factor, TFIIIA, specific for the 5S RNA gene. The somatic-type 5S RNA gene promoter is not preferentially cleaved by S1 nuclease or Bal-31 nuclease in supercoiled DNA, nor does TFIIIA induce a DNase I site at position +50. This differential promoter response may be related to a 4-fold difference in TFIIIA affinity between the oocyte and somatic 5S RNA genes.
...
PMID:Torsional stress induces an S1 nuclease-hypersensitive site within the promoter of the Xenopus laevis oocyte-type 5S RNA gene. 298 60

The promoter region of the epidermal growth factor (EGF) receptor has been identified by in vitro transcription using EGF receptor genomic DNA fragments as template and by primer extension and nuclease S1 mapping using EGF receptor mRNA. Six transcriptional start sites were identified. DNA sequence analysis shows that the promoter region contains neither a "TATA box" nor a "CAAT box," has an extremely high G+C content (88%), and contains five CCGCCC repeats and four (TCC)TCCTCCTCC repeats. This promoter region is situated close to or within a DNase I-hypersensitive site in A431 human epidermoid carcinoma cells, which overproduce the EGF receptor. The EGF receptor gene promoter has some resemblance to the promoter of the hydroxymethylglutaryl-CoA reductase gene and the early promoter of simian virus 40. This similarity may offer a clue to the mechanism by which the receptor gene is regulated.
...
PMID:Characterization and sequence of the promoter region of the human epidermal growth factor receptor gene. 299 99

We have examined the nuclease sensitivity of the 5' flanking region of the rabbit beta 1 globin gene in bone marrow nuclei and in supercoiled plasmids. A DNase I hypersensitive site was found about 100 base-pairs 5' to the cap site in bone marrow nuclei. S1 nuclease can introduce a specific double-strand cut in the DNA in the same region. The presence of the nuclease-hypersensitive region correlates with the active transcription of gene beta 1 in bone marrow. Treatment with nuclease S1 of a supercoiled plasmid containing 1400 base-pairs of 5' flanking sequences as well as part of the beta 1 gene reveals a major double-strand cut 400 base-pairs 5' to the cap site. This cut maps within a stretch of repeating dinucleotides (C-T)12 and does not correspond to the in vivo site. Introduction of an RsaI fragment containing the nuclease S1-hypersensitive site into plasmid pBR322 shows that this fragment alone is sufficient to generate the hypersensitive site. Deletion of that RsaI fragment from the beta 1 plasmid reveals another site 1300 base-pairs upstream. Further deletion of this secondary site uncovers numerous other sites, none of which corresponds to the site in nuclei. Chromatin reconstitution with plasmids carrying the 5' flanking region of beta 1 and histones is capable of suppressing the in vitro nuclease-S1-hypersensitive site at --400 but is incapable of generating the in vivo site at --100. Fine analysis at the nucleotide level of the early events in the digestion with nuclease S1 shows that the enzyme attacks preferentially the sequence (G-A)12 on the message complementary strand. The region of DNA containing the supercoil-dependent S1 site adopts at least three different conformations that can be resolved electrophoretically. These different conformations are detected in linear restriction fragments and may represent non-B DNA or unusual B-form DNA.
...
PMID:DNase I and nuclease S1 sensitivity of the rabbit beta 1 globin gene in nuclei and in supercoiled plasmids. 299 30

A new and easy technique for accurately mapping DNase I- and S1 nuclease-hypersensitive sites is described. The technique is a modification of primer extension and S1 nuclease methods conventionally used to map RNA ends.
...
PMID:High-resolution mapping of S1- and DNase I-hypersensitive sites in chromatin. 299 71


<< Previous 1 2 3 4 5 6 7 8 9 10 Next >>

---