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Biomedical subjects

D Levens

Publications and source records attributed to D Levens.

At least 37 records · Page 2Linked to original sources
PubMed1995

Targeted melting and binding of a DNA regulatory element by a transactivator of c-myc.

A far upstream element (FUSE) of c-myc stimulates promoter activity when bound by a newly identified trans-acting protein, which is expressed in cycling cells. Since FUSE binding protein (FBP) binds only the noncoding strand (NCS) of its regulatory element in a sequence-specific manner, and not double-stranded (ds) DNA, formation of the protein DNA complex in vivo first requires unwinding of the DNA helix. In this report, we show evidence that FBP forces strand separation of short stretches of linear dsDNA. Because FUSE is contained within a region of helical instability that is partially unwound in negatively supercoiled DNA, it is a target for more extensive duplex strand separation by FBP, which first exposes and then selectively binds its NCS cognate sequence. In contrast, other single-stranded DNA binding proteins (SSBs) do not demonstrate this FUSE targeting activity. The novel linkage of regional dsDNA melting with cis-element binding by a transcriptional activator has broad implications in the regulation of eukaryotic gene expression.

Base Sequence↗
PubMed1995

Heterogeneous nuclear ribonucleoprotein K is a DNA-binding transactivator.

We have previously reported that heterogeneous nuclear ribonucleoprotein K (hnRNP K) binds to the pyrimidine-rich strand of the CT element found in the human c-myc gene and activates CT reporter-driven gene expression in vivo. We now characterize the DNA and protein requirements for the interaction of hnRNP K with the CT element. First, hnRNP K is shown to preferentially bind single-stranded DNA over RNA or native double-stranded DNA. Using specific oligoribonucleotide or deoxyribonucleotide probes with specific or nonspecific RNA or DNA competitors, electrophoretic mobility shift assay revealed hnRNP K to be a DNA-binding protein. Specific binding was not simply a reflection of binding to pyrimidine-rich sequences as the number and arrangement of individual CT elements governed interactions with hnRNP K; at least two CT repeats separated by at least three nucleotides are required for binding, indicating the existence of particular stereochemical constraints regulating CT-hnRNP K complex formation. Deletion analysis showed that hnRNP K possesses several nonoverlapping, DNA binding domains, each capable of specific binding with the CT element and preferring DNA over RNA. Each sequence recognition domain is composed of at least one K homology motif, while a larger portion of hnRNP K may be required for stable RNA binding. Additional experiments indicate that the N-terminal 35 residues of hnRNP K are necessary for transactivating the CT element. These results indicate that hnRNP K is a DNA-binding protein and transcriptional activator.

Animals↗
PubMed1994

Purification and characterization of a multicomponent AP-1.junD complex from T cells. Dependence on a separate cellular factor for enhanced DNA binding activity.

TAP-1 (T-cell AP-1) is a previously identified DNA-binding activity that is rapidly induced in activated T cells in the absence of protein synthesis. This activity has been purified over 2,000-fold from the T-cell line MLA144. Purified TAP-1 is a multicomponent complex composed of 38-kDa and 43-kDa junD polypeptides in association with a separate factor(s), distinct from fos, that partly dissociate from the complex during affinity purification but is required for full TAP-1 DNA-binding activity. When reconstituted with TAP-1, this partly dissociated component strongly enhances the DNA-binding activity of the TAP-1 complex. UV-cross-linking analysis identifies the dissociable component of the TAP-1 complex as a separate class of low molecular mass (23-29-kDa) DNA-binding polypeptide(s). 23-29-kDa polypeptides have been partially purified from nuclear extracts derived from MLA144 that enhance TAP-1 DNA-binding activity over 100-fold and increase its contacts with flanking DNA sequence. These results define TAP-1 as a distinct AP-1.junD-containing complex in T cells whose DNA-binding activity is regulated by the interaction of distinct and separate cellular factor(s).

Animals↗
PubMed1994

A sequence-specific, single-strand binding protein activates the far upstream element of c-myc and defines a new DNA-binding motif.

The far upstream element (FUSE) of the human c-myc proto-oncogene stimulates expression in undifferentiated cells. A FUSE-binding protein (FBP) is present in undifferentiated but not differentiated cells. Peptide sequences from the purified protein allowed cloning of cDNAs encoding FBP. Expression of FBP mRNA declined upon differentiation, suggesting transcriptional regulation of FBP. Features in the FBP cDNA suggest that FBP is also regulated by RNA processing, translation, and post-translational mechanisms. Both cellular and recombinant FBP form sequence-specific complexes with a single strand of FUSE. Transfection of FBP into human leukemia cells stimulated c-myc-promoter-driven expression from a reporter plasmid in a FUSE-dependent manner. Deletion and insertion mutagenesis of FBP defined a novel single-strand DNA-binding domain. Analysis of the primary and predicted secondary structure of the amino acid sequence reveals four copies of a reiterated unit comprised of a 30-residue direct repeat and an amphipathic alpha-helix separated by an 18- to 21-residue spacer. The third and fourth copies of this repeat-helix unit constitute the minimum single-stranded DNA-binding domain. To determine whether the FUSE site, in vivo, possesses single-strand conformation, and therefore could be bound by FBP, cells were treated with potassium permanganate (KMnO4) to modify unpaired bases. Modification of genomic DNA in vivo revealed hyperreactivity associated with single-stranded DNA in the FUSE sequence and protection on the strand that binds FBP in vitro. The role of single-stranded DNA and single-strand binding proteins in c-myc regulation is discussed.

Amino Acid Sequence↗
PubMed1993

An early response of an AP1-junD complex during T-cell activation.

Activated T-cell extracts contain an activity (T-AP1) composed of at least two dissociable protein components which bind to the AP1 consensus sequence in the enhancer of the gibbon ape leukemia virus (GALV)-LTR (GALV-TRE). This activity is inducible by 12-O-tetradecanoyl-phorbol-14-acetate (TPA) even in the presence of protein synthesis inhibitors. Although one component of this complex (CORE) is related immunologically and biochemically to junD, it nevertheless displays significant biochemical properties which distinguish CORE from recombinant junD. The second component of the complex, flowthrough, interacts more efficiently with CORE than with recombinant junD. GALV-TRE enhancer activity is increased within 2 h in vivo with T cells treated with TPA in the presence of protein synthesis inhibitors; this increase in enhancer activity is paralleled by the increased GALV-TRE-mediated transcriptional activity present in extracts of these cells. Purified T-cell junD activates GALV-TRE-driven RNA synthesis in vitro. The rapidity and the protein synthesis-independent nature of TPA-induced T-AP1 activation suggests that this complex is involved in the earliest stages of T-cell activation.

Animals↗
PubMed1993

Specific binding of heterogeneous ribonucleoprotein particle protein K to the human c-myc promoter, in vitro.

A homopurine/homopyrimidine-like sequence is found 100-150 base pairs upstream of the human c-myc promoter P1. This element, termed the CT-element, has been shown to augment expression from P1, and it serves as a positive transcriptional element when coupled to a heterologous promoter in vivo and in vitro. Synthetic oligonucleotides comprising this element were used to form DNA-protein complexes in electrophoretic mobility shift assays. By using conventional and affinity methods, 61- and 34-kDa proteins were shown to be associated with these complexes. Amino acid sequence analysis and immunological methods have identified these proteins as heterogeneous ribonucleoprotein particle (hnRNP) proteins K and A1. Surprisingly, hnRNP protein K binds to the pyrimidine-rich strand of the CT-element in a sequence-specific manner as well as to the double-stranded molecule. Cotransfection of vectors encoding hnRNP protein K in the sense or anti-sense orientations with reporter plasmids driven by wild-type or mutant CT-elements demonstrates that hnRNP protein K augments gene expression in a cis-element-dependent manner. Taken together, these results suggest that hnRNP protein K may play a role in the transcriptional regulation of the human c-myc gene.

Amino Acid Sequence↗
PubMed1990

A far upstream element stimulates c-myc expression in undifferentiated leukemia cells.

A sensitive exonuclease assay revealed multiple sites for interaction, in vitro, of sequence specific factors with c-myc upstream elements. At one site, more than 1500 base pairs upstream of the c-myc promoter P1, binding activity was lost as dimethyl sulfoxide (Me2SO) induced shut-off of c-myc expression in HL-60 and U-937 leukemia cells. The disappearance of other specific binding activities was not noted. In addition, the binding activity was noted to be cell-line specific. The sequence binding the Me2SO-regulated factor was precisely located allowing confirmation of the temporal pattern of regulation by electrophoretic mobility shift analysis. Because the binding activity was most abundant before the decrease of c-myc expression during differentiation, it was inferred that the far upstream element (FUSE) served a positive role, potentiating c-myc expression. A 4-base pair deletion which eliminated binding to FUSE also reduced expression of a transfected, chimeric c-myc-CAT gene in untreated, but not in Me2SO-treated U-937 cells. FUSE and its binding protein may contribute to cell line- and differentiation-specific modes of c-myc regulation.

Base Sequence↗
PubMed1990

Phosphorylation-dependent binding of a 138-kDa myc intron factor to a regulatory element in the first intron of the c-myc gene.

A 138-kDa nuclear protein was identified from HeLa cell extracts as a factor which binds to a previously described 20-base pair cis element located in the intron I of the c-myc gene. This myc intron factor (MIF) binds to the wild type c-myc sequence but does not bind under similar conditions to c-myc from Burkitt's lymphoma which contain point mutations in this binding region. We have demonstrated that the 138-kDa MIF is a phosphoprotein and that treatment of the purified MIF with potato acid phosphatase abolished binding to its 20-base pair c-myc recognition sequence; binding activity was protected by inclusion of phosphatase inhibitors. These results suggest that phosphorylation is required for the specific DNA-MIF interaction in vitro and that the phosphorylation state of MIF may be an important factor in controlling c-myc expression in vivo.

Acid Phosphatase↗
PubMed1989

fos/jun and octamer-binding protein interact with a common site in a negative element of the human c-myc gene.

A negative element has previously been localized to a 57-base pair segment approximately 300 base pairs upstream of the human c-myc promoter P1. Within this element, a 26-base pair region was protected in vitro from DNase I digestion with a HeLa cell nuclear factor(s). Two specific DNA-protein complexes were identified in gel retardation assays using HeLa cell nuclear extracts and an oligonucleotide probe spanning the footprinted region. Exonuclease and chemical footprint analyses suggested that the binding sites for both complexes are almost entirely overlapping. One of the complexes was eliminated by oligonucleotide competitors possessing known AP-1 binding sites. This same complex reacted strongly with anti-fos immunoglobulin suggesting a role for c-fos in governing c-myc expression. Precipitation of fos protein bound to c-myc DNA that was immobilized on beads confirmed the involvement of c-fos in a specific complex with the c-myc upstream sequence. In contrast, the other complex seen by the c-myc probe could not be competitively inhibited by AP-1 binding sites and was not affected by anti-fos antibody. Instead, this complex was efficiently eliminated by unlabeled oligonucleotides containing the octamer DNA motif found in immunoglobulin gene promoters. Purified octamer-binding proteins formed stable complexes with the 26-base pair c-myc sequences. These results demonstrate that degeneracy in the consensus recognition sequences of these distinct factors allows each of them to bind the c-myc negative element. The interaction of known transcriptional activators with a negative element suggests that the same factors can mediate both transcriptional activation and repression.

Base Sequence↗
PubMed1989

Distinct factors bind the AP-1 consensus sites in gibbon ape leukemia virus and simian virus 40 enhancers.

We have demonstrated that the gibbon ape leukemia virus (GALV) enhancer AP-1 element and the simian virus 40 AP-1 enhancer element bind different factors in HeLa nuclear extracts. A 39-kilodalton HeLa nuclear protein and the c-fos protein bind to the GALV element. Antibodies to c-fos abolish binding to the GALV AP-1 site. In contrast, anti-c-fos immunoglobulin fails to inhibit formation of the simian virus 40-specific complex from extracts of HeLa cells. Thus, AP-1-binding complexes are subject to compositional variation at different binding sites.

Animals↗
PubMed1989

Multiple components are required for sequence recognition of the AP1 site in the gibbon ape leukemia virus enhancer.

At least two subunits contributed to the formation in vitro of a specific complex binding to the AP1 consensus sequence (TGAGTCA) in the gibbon ape leukemia virus (GALV) enhancer in MLA144 cells. This complex can be dissociated on a monomeric GALV oligonucleotide affinity column. One protein, termed the core protein, was retained on the oligonucleotide affinity column. The second protein flowed through the oligonucleotide affinity column and, when alone, did not bind to DNA; however, when present with the core protein, it bound strongly and very specifically to the GALV sequence. MLA144 cells contained only trace amounts of c-fos and c-jun by immunoblot analysis, suggesting that the proteins specifically binding to the GALV AP1 site were distinct from c-fos and c-jun. In addition to the major complex that recognized the GALV element, MLA144 cells contained a minor complex that is chromatographically different from and antigenically related to c-fos. The factor in the flowthrough complemented a human T-cell nuclear extract (Jurkat cell line), which, when alone, had no assayable complex that specifically bound to the GALV enhancer; this complementation gave rise to a specific complex similar to that seen in MLA144 cells. Together, these results suggest that the GALV enhancer can interact with multicomponent protein complexes in a cell-line-specific manner.

Animals↗
PubMed1988

A point mutation in the c-myc locus of a Burkitt lymphoma abolishes binding of a nuclear protein.

A 20-base pair region in the first intron of the human c-myc gene was identified as the binding site of a nuclear protein. This binding site is mutated in five out of seven Burkitt lymphomas sequenced to date. To investigate the protein-recognition region in greater detail, the abnormal c-myc allele from a Burkitt lymphoma line (PA682) that carries a t(8;22) chromosomal translocation was used. A point mutation in the binding region of the PA682 c-myc DNA abolished binding of this nuclear protein. This protein may be an important factor for control of c-myc expression, and mutations in its recognition sequence may be associated with c-myc activation in many cases of Burkitt lymphoma.

Base Sequence↗
PubMed1987

Regulatory elements that modulate expression of human c-myc.

Regulation of transcription from the proto-oncogene c-myc apparently plays an important part in cellular proliferation and the genesis of diverse tumors. Here, we report that the abundance of transcripts from the two principal promoters for human c-myc (P1 and P2) is governed by a composite of positive and negative regulators, located within a 2.3-kb domain upstream of the gene. In actively proliferating cells, the action of the positive elements is apparently dominant over that of the single negative regulator that we have identified. Nuclear proteins bind specifically to nucleotide sequences within the negative regulator and at least one of the positive regulators. The cooperative and counteracting actions of the regulatory elements described here presumably contribute to the plasticity of transcription from c-myc and may be affected by the tumorigenic damage that sometimes afflicts c-myc.

Animals↗
PubMed1987

B-cell nuclear proteins binding in vitro to the human immunoglobulin kappa enhancer: localization by exonuclease protection.

Proteins capable of interacting with the enhancer of the immunoglobulin kappa gene in vitro have been detected in extracts of nuclei from human B cells and from human, mouse, and rabbit spleens. The experiments, based on an exonuclease protection technique, demonstrate nuclear protein factors binding to a 30- to 35-base-pair domain containing both the simian virus 40 enhancer core element (TTTCCA) and the octamer CAGGTGGC that was previously identified as the consensus sequence for protein-binding sites in the murine immunoglobulin heavy-chain enhancer. This 30- to 35-base-pair domain in the human kappa enhancer is homologous to a site of protein binding detected in the murine kappa enhancer by other investigators using a gel retardation assay. Our results complement in vivo dimethyl sulfate footprinting studies of the human immunoglobulin kappa enhancer which demonstrated B cell-specific changes in guanine reactivity immediately 5' to the consensus octamer. Together, these findings suggest that DNA-binding proteins in B-cell nuclei interact with the 5' portion of the human kappa-gene enhancer. Such proteins could play a role in the B cell-specific transcription of the human immunoglobulin kappa gene.

B-Lymphocytes↗
PubMed1987

Binding of a cellular protein to the gibbon ape leukemia virus enhancer.

The gibbon ape leukemia virus (GALV) contains enhancer activity within its long terminal repeat. In the GALV Seato strain this activity resides in a 48-base-pair (bp) repeated element. We demonstrate the existence of a cellular protein which binds in this region of the Seato strain. A sensitive method for enriching protein-DNA complexes from crude extracts coupled with exonuclease and DNase footprint analysis revealed the specific binding of this protein to a 21-bp region within each repeated element. A 22-bp oligonucleotide fragment defined solely by the 21-bp footprint binds a protein in vitro and displays enhancer activity in vivo, suggesting that this protein is a major determinant of GALV enhancer activity. The protein is present in three cell lines which are positive for enhancer activity and is not detected in Jurkat cells, which are negative for enhancer activity. Only GALV long-terminal-repeat variants which support high levels of enhancer activity in vivo compete with this protein for specific binding in vitro, suggesting a potential role for the protein in determining enhancer activity. This protein binding is not inhibited by competition with heterologous retroviral enhancers, demonstrating that it is not a ubiquitous retroviral enhancer binding protein.

Animals↗