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

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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)

A block to elongation of transcription has been shown to occur within the first exon of the human and murine c-myc genes. The extent of this block was found to vary with the physiological state of cells, indicating that modulation of the transcriptional block can serve to control the expression of this gene. To determine which sequences are required in cis for the transcriptional block, we generated a series of constructs containing various portions of murine c-myc 5'-flanking and exon 1 sequences. We established populations of HeLa and CV-1 cells stably transfected with these constructs. The transcription start sites were determined by S1 nuclease mapping analysis, and the extent of transcriptional block was measured by nuclear run-on transcription assays. Our results demonstrate that at least two cis-acting elements are necessary for the transcriptional block. A 3' element was found to be located in the region where transcription stopped and showed features reminiscent of some termination sites found in procaryotes. A 5' element was positioned between the P1 and P2 (C. Asselin, A. Nepveu, and K. B. Marcu, Oncogene 4:549-558, 1989). Removal of the more 3' binding site abolished the transcriptional block.
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PMID:A cis-acting element in the promoter region of the murine c-myc gene is necessary for transcriptional block. 268 59

We have isolated a 12 kb clone from the murine genome which we show by DNA transfection studies to contain an entire functional L-myc gene and the transcriptional promoter sequences necessary for its expression. We have also isolated a 3.1 kb cDNA sequence from a murine brain cDNA library which corresponds to most of the L-myc mRNA. We have identified the L-myc coding region within the genomic clone by a combination of S1 nuclease analyses. Northern blotting analyses and comparative nucleotide sequence analyses with the cDNA clone. The L-myc gene appears to be organized similarly to the other well-characterized myc-family genes, c-myc and N-myc. The predicted amino acid coding sequence of the L-myc gene indicates that the L-myc protein is significantly smaller than c- and N-myc, but is highly related. In particular, comparison of the N- and c-myc protein sequences reveals seven relatively conserved regions interspersed among non-conserved regions; the L-myc gene retains five of these conserved regions but lacks two others. In addition, a portion of one highly conserved region is encoded within a different region of the L-myc gene but, due to changes in the size of L-myc exons relative to those of N- and c-myc, maintains its overall position in the peptide backbone with respect to other conserved regions. We discuss these findings in the context of potential functional domains and the possibility of overlapping and distinct activities of myc-family proteins.
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PMID:Structure and expression of the murine L-myc gene. 282 24

Chicken syncytial virus, a member of the reticuloendotheliosis virus family, induces B-cell lymphomas in chickens that arise by transcriptional activation of the chicken c-myc gene. In vitro transcription studies on cloned tumor DNA containing a deleted chicken syncytial virus provirus integrated upstream from, and in the same transcriptional orientation as, the chicken c-myc coding region were utilized to map possible transcriptional promoters and initiation sites. In vitro transcripts extending into c-myc sequences were initiated at two sites within the downstream long terminal repeat (LTR) closest to c-myc coding sequences. Both initiation sites have been precisely mapped by S1 nuclease and DNA sequencing methods. One site (I1) lies at the U3-R junction of the LTR, and the other site (I2) lies approximately 160 nucleotides upstream. Transcriptional control signals, including TATA- and CAAT-like sequences are present at appropriate distances upstream from the initiation sites. Both initiation sites are utilized to a similar extent. The upstream chicken syncytial virus LTR was also shown to be transcriptionally active in vitro. Two strong transcriptional initiation sites were also found in the LTR of spleen necrosis virus, a related member of the reticuloendotheliosis virus family; therefore, it seems likely that the existence of two transcriptional initiation sites is a common feature of the reticuloendotheliosis virus LTR, in contrast to other previously studied retroviral LTRs that exhibit one such site. The possible implications of these findings are discussed.
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PMID:In vitro transcription analysis of the viral promoter involved in c-myc activation in chicken B lymphomas: detection and mapping of two RNA initiation sites within the reticuloendotheliosis virus long terminal repeat. 298 11

DNA sequence-specific binding proteins eluted from chicken erythrocyte and thymus nuclei, and fractionated as described by Emerson and Felsenfeld (19), have been investigated by filter binding and footprint analyses. The erythrocyte nuclear protein fraction specifically binds to at least two sites within the 5' flanking chromatin hypersensitive site of the chicken beta A-globin gene, and to a site 5' to the human beta-globin gene. The major chicken beta A globin gene binding site [G)18CGGGTGG) and the human beta-globin gene binding site [TA)6(T)8C(T)4) occur at or near sequences which are hypersensitive to S1 nuclease cleavage in supercoiled plasmids. Downstream, the second chicken beta A-globin gene binding site includes the beta-globin gene CACCC consensus sequence. Filter binding studies also show other sequence specific binding activities to human N-ras and human (but not chicken) c-myc gene sequences.
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PMID:Multiple sequence-specific DNA binding activities are eluted from chicken nuclei at low ionic strengths. 298 85

Five novel murine plasma cell (PC) tumors with chromosome translocations 350-500 bp 5' of the first c-myc exon are described. The t(12;15)s of TEPC 1194, ABPC 33 and TEPC 1165 position the intact c-myc locus 5' of the Cu, C gamma 2a and C alpha IgCH genes respectively. In ABPC 17, the IgH enhancer element and adjacent switch (Su) sequences were found 5' of the first c-myc exon while this enhancer is associated with the reciprocal products of the TEPC 1194, ABPC 33 and TEPC 1033 translocations. Quantitative S1 nuclease analyses demonstrate that the ratios of transcription from the two c-myc promoters (P1 and P2) are increased 4-to 7-fold in these five tumors. With the exception of TEPC 1165, (which contains a small deletion in exon 1), such increases in P1:P2 ratios appear to be manifested by a reduction in P2 usage in comparison to other tumors without such promoter shifts. A survey of 27 additional PC and non-PC B lymphoid tumors and cell lines revealed that myc promoter shifts of this magnitude are unique to PC tumors with 5'-proximal translocations. We propose that (i) these clustered breakpoints identify a normal c-myc regulatory element located at least 350 bp 5' of c-myc exon 1; (ii) the loss or disruption of this cis-acting upstream element and the linkage of c-myc to the IgCH locus would result in abnormal expression of this oncogene in these as well as most other PC tumors.
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PMID:Chromosome translocations clustered 5' of the murine c-myc gene qualitatively affect promoter usage: implications for the site of normal c-myc regulation. 299 31

Chromosomal rearrangements involving the c-myc oncogene are a prevalent feature of plasmacytomas that arise after inoculating BALB/c mice with pristane and Abelson murine leukaemia virus (A-MuLV). With this observation in mind, we decided to determine if any genetic alterations of the c-myc locus could be observed in cells of a different type, when transformed in vitro by A-MuLV. Here we have analysed three independent A-MuLV-transformed NIH 3T3 lines (ANN-I, 54c12 and N25), and found that the c-myc locus is amplified 8-19-fold in each transformant. Quantitative S1 nuclease mapping performed on ANN-I and 54c12 RNAs demonstrated that: (1) c-myc messenger RNAs accumulated to double the levels found in NIH 3T3 cells; and (2) a shift in the use of the two normal c-myc transcription initiation sites (P1 and P2) occurred in favour of the 3' site, P2. Analysis of c-myc chromatin by DNase I treatment of 54c12 nuclei revealed that most, if not all, of the c-myc gene copies were transcriptionally competent. We present alternative ideas to explain why amplification of the c-myc gene occurs repeatedly in A-MuLV-transformed fibroblasts. Finally, we discuss our results in relation to the hypothesis linking the phenomenon of tumour progression with the amplification of oncogenes.
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PMID:Amplification and altered expression of the c-myc oncogene in A-MuLV-transformed fibroblasts. 299 29

We have investigated the nature of regulatory sequences within the vicinity of the murine c-myc locus by analyzing the expression of myc-chloramphenicol acetyl transferase (CAT) vectors transfected into a human lymphoblastoid cell line (BJAB) and a monkey fibroblast line (COS). CAT enzymatic assays and S1 nuclease protection experiments reveal that a negative element resides 428-1188 bp 5' of the first c-myc promoter, P1. This 760-bp segment of 5'-flanking c-myc DNA dramatically inhibits CAT gene expression in the pSV2CAT vector when placed in either orientation approximately 1.7 kb 3' (and approximately 3.2 kb 5' on the circular plasmid) from the SV40 promoter region. By employing this strategy, we were unable to identify an analogous DNA segment that is closer to or within the first c-myc exon. We propose that this 5' c-myc region be termed a 'dehancer' since this negative element has the opposite properties of a transcriptional enhancer.
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PMID:A negative transcriptional control element located upstream of the murine c-myc gene. 301 22

The Burkitt lymphoma cell line KK124, which contains a reciprocal t(8;22) translocation, was shown to have rearranged in a region 3' to the c-myc proto-oncogene on chromosome 8 and 5' to the lambda constant region on chromosome 22. The breakpoint was cloned and sequenced, revealing that c-myc and a portion of its 3' region abutted a complete lambda variable gene that had undergone V-J recombination. Since this cell line expresses kappa light chain, this lambda rearrangement violates the previously proposed hierarchy of immunoglobulin gene rearrangement. A novel duplication of normal chromosome 8 sequences was also found at the breakpoint. The first exon of c-myc and its flanking sequence from the translocated allele was sequenced and compared with a normal counterpart. Extensive mutation was found within the first exon in contrast to its 3' and 5' flanking regions. S1 nuclease analysis revealed that it was the translocated c-myc being expressed and that there was a promoter shift from P2 to P1. The detailed structural analysis of this cell line provides clues concerning mechanisms of chromosomal translocation and c-myc deregulation in Burkitt lymphomas.
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PMID:Burkitt lymphoma cell line carrying a variant translocation creates new DNA at the breakpoint and violates the hierarchy of immunoglobulin gene rearrangement. 301 8

A high frequency (greater than or equal to 65%) of thymomas induced by mink cell focus-forming virus 69L1 in AKR/J mice contain proviral integrations which are clustered 0.7-kilobase upstream of the c-myc oncogene predominantly in the opposite transcriptional orientation. Blot hybridization experiments showed that on the average there was only a twofold elevation of steady-state c-myc RNA in the thymomas as compared with levels in normal AKR/J thymocytes. Such an increase would not appear to be sufficient as a mechanism of oncogene activation in this system. In contrast, S1 nuclease analysis of transcripts initiated from the two known c-myc promoters indicated a strong shift in promoter usage in virtually all thymomas tested. In normal thymus the ratio of transcripts initiated from the proximal promoter P1 to the distal promoter P2 was 0.2 to 0.3. In contrast, most of the thymomas tested (18 of 23) showed an average P1/P2 ratio of 1.2 regardless of whether or not proviral integrations could be detected within a 21-kilobase EcoRI fragment containing the three c-myc exons. We conclude that alterations in P1/P2 ratios are good indicators of c-myc deregulation in thymic lymphomas.
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PMID:Deregulation of the c-myc oncogene in virus-induced thymic lymphomas of AKR/J mice. 302 31

We have employed analytical S1 nuclease analysis to identify sites with altered DNA secondary structure in the human c-myc gene. We have mapped several sites of that kind in vitro at one-base resolution but have focused our attention on one particularly stable conformational isomer which occurs approximately 270 base pairs upstream from the preferred transcription origin. We have analyzed the kinetics of that conformational equilibrium as a function of supercoil density and enzyme concentration and find that DNA structure in this region is adequately modeled as a two-state equilibrium between an undistorted (S1 nuclease insensitive) and a distorted (S1-sensitive) state. We find that at fixed supercoil density, S1 nuclease cleavage at this DNA segment can be altered in vitro by a DNA sequence change as far away as 1500 bases. We also find that the S1 nuclease cleavage at this site can be dramatically enhanced by the binding of small RNA molecules. On the basis of an analysis of S1 cutting kinetics and an analysis of DNA sequence at the S1 cleavage site, we conclude that RNA may bind directly to DNA, thereby shifting the underlying conformational equilibrium. Together, these data suggest that as a class, short RNA molecules could serve as site-specific regulatory elements in the myc gene and elsewhere.
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PMID:DNA structure equilibria in the human c-myc gene. 303 Apr 7


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