An Estradiol-dependent Protein from Chicken Liver Binds Single-stranded DNA and RNA

The -148 to -124 region of c-jun interacts with a positive regulatory factor in rat liver and enhances transcription

The c-jun gene encodes the protein Jun, a component of the essential transcription factor, AP1. Jun/AP-1 occupies a central position in signal transduction pathways as it is responsible for the induction of a number of genes in response to growth promoters. However, the exact mechanisms leading to an enhanced expression of the c-jun gene itself during proliferation, differentiation, cell growth and development are not fully understood. Cell culture studies have given some insight in the mechanisms involved in the up-regulation of c-jun expression by UV irradiation and phorbol esters. However, it is well known that transformed cells do not accurately reflect the biology of a normal cell. We now report the identification of a positive regulatory factor from normal rat liver that activates transcription from the c-jun promoter by binding to the -148 to -124 region of c-jun. Preincubation of fractionated rat liver nuclear extract with an oligonucleotide encompassing this region of the gene significantly reduced transcription from cloned c-jun promoter. In vitro transfection studies using green fluorescent protein as a reporter gene under the control of the c-jun promoter with (-148 to +53) and without (-123 to +53) this region further confirmed its role in transcription. A DNA-binding protein factor, interacting with this region of c-jun was identified from rat liver by using electrophoretic mobility shift assays. This factor binds to its recognition sequence only in the phosphorylated form and exhibits high affinity and specificity. UV cross-linking studies, South-Western analysis and affinity purification collectively indicated the factor to be approximately 40 kDa and to bind to its recognition sequence as a dimer.

Cloning of a cDNA encoding a sequence-specific single-stranded-DNA-binding protein from Rattus norvegicus

In this paper, we report the isolation of a cDNA clone encoding a sequence-specific single-stranded-DNA-binding protein (SSDP) from rat (Rattus norvegicus). The full-length nucleotide sequence was determined and encodes a 361 amino acid protein with a predicted molecular mass of 37.7 kDa. This clone has approximately 80% homology to a previously isolated partial cDNA clone for SSDP from chicken (Gallus gallus). Northern blot analysis revealed two transcripts of 2.0 and 3.0 kb. The protein appears to be evolutionarily highly conserved with > 97% identity between chicken, rat, mouse and human. Chicken SSDP has been proposed to be involved in the transcriptional regulation of the alpha 2(I) collagen gene.

Single-stranded DNA-protein binding in the procyclic acidic repetitive protein (PARP) promoter of Trypanosoma brucei

We performed gel retardation analyses of DNA-protein interactions using DNA from the procyclic acidic repetitive protein (PARP) promoter of the protozoan parasite Trypanosoma brucei. The PARP genes of Trypanosoma brucei are transcribed in an alpha-amanitin resistant manner, and it has been proposed that RNA polymerase I, rather than RNA polymerase II, transcribes the PARP genes. Double-stranded restriction fragments containing the essential PARP-promoter regions bound only sequence-nonspecific nuclear factors, even though protein factors that bind specifically to double-stranded DNA from the snRNA U2 promoter were present in the extracts. In contrast, single-stranded DNA-binding proteins bound with high affinity, nucleotide-sequence and strand-specificity to the -69/-55 element and the coding and non-coding strands of the -37/-11 element.

DNA recognition and binding by the Euplotes telomere protein

The 51-kDa telomere protein from Euplotes crassus binds to the extreme terminus of macronuclear telomeres, generating a very salt-stable telomeric DNA-protein complex. The protein recognizes both the sequence and the structure of the telomeric DNA. To explore how the telomere protein recognizes and binds telomeric DNA, we have examined the DNA-binding specificity of the purified protein using oligonucleotides that mimic natural and mutant versions of Euplotes telomeres. The protein binds very specifically to the 3' terminus of single-stranded oligonucleotides with the sequence (T4G4) > or = 3 T4G2; even slight modifications to this sequence reduce binding dramatically. The protein does not bind oligonucleotides corresponding to the complementary C4A4 strand of the telomere or to double-stranded C4A4.T4G4-containing sequences. Digestion of the telomere protein with trypsin generates an N-terminal protease-resistant fragment of approximately 35 kDa. This 35-kDa peptide appears to comprise the DNA-binding domain of the telomere protein as it retains most of the DNA-binding characteristics of the native 51-kDa protein. For example, the 35-kDa peptide remains bound to telomeric DNA in 2 M KCl. Additionally, the peptide binds well to single-stranded oligonucleotides that have the same sequence as the T4G4 strand of native telomeres but binds very poorly to mutant telomeric DNA sequences and double-stranded telomeric DNA. Removal of the C-terminal 15 kDa from the telomere protein does diminish the ability of the protein to bind only to the terminus of a telomeric DNA molecule.

Covalent attachment of ribonucleic acids to proteins

As a prerequisite for the synthesis of affinity labels, we describe methods to couple histones to ribonucleic acids. For the synthesis of these covalent hybrid molecules, we used a population of histones H1, H2A, H2B, H3, and H4 from calf thymus and polyadenylic acid with an average chain length of up to 260-280 bases, representing the size of poly(A)-tails from mature mRNAs. Three methods were investigated. (a) Poly(A) containing an 8-N3-A residue was cross-linked to histones by ultraviolet irradiation. (b) The 3'-end of the polynucleotide was connected to a mononucleotide containing an aliphatic amino group, and the resulting poly(A)-derivative was coupled to histones via derivation with a bromoacetyl group. (c) The 3'-end of the polynucleotide was oxidized with sodium periodate and bound covalently to an amino group of the polypeptide. To demonstrate the RNA content of the hybrid molecule, the poly(A) was removed with RNase T2.

Specific sequences and a hairpin structure in the template strand are required for N4 virion RNA polymerase promoter recognition

Coliphage N4 virion-encapsidated, DNA-dependent RNA polymerase (vRNAP) is inactive on double-stranded N4 DNA; however, denatured promoter-containing templates are accurately transcribed. We report that all determinants of vRNAP promoter recognition exist in the template strand, indicating that this enzyme is a site-specific, single-stranded DNA-binding protein. We show that conserved sequences and the integrity of inverted repeats present at the promoters are essential for activity, suggesting the necessity for specific secondary structure. Evidence for such a structure is presented. We propose a model for in vivo utilization of vRNAP promoters in which template negative supercoiling yields single-strandedness at the promoter to reveal the determinants of vRNAP binding. This structure is stabilized by the binding of E. coli single-stranded DNA-binding protein to yield an "activated promoter."

Multiple sequence-specific single-strand-binding proteins for the promoter region of the rat albumin gene

Previous work from our laboratory described a protein that binds to single-stranded DNA in the early promoter of simian virus 40 in a sequence specific fashion. We have now used the gel retardation assay to search for similar sequence-specific single-strand-binding proteins for the promoter region of the rat albumin gene in nuclear extracts of rat hepatoma cells. Several proteins of this kind were detected, three of which are described in the present paper. Two of them bind specifically to the noncoding strand and the third one binds to the coding strand. The most abundant of these proteins binds to a pyrimidine stretch inside the coding region of the gene and appears to be homologous to the previously observed SV40-binding protein. Possible functions for sequence-specific single-strand-binding proteins in transcription are discussed.

Sequence-specific single-strand-binding protein for the simian virus 40 early promoter stimulates transcription in vitro

We have detected, in nuclear extracts of non-infected cultured monkey cells, a protein (protein H16) that binds a specific single-stranded DNA sequence in the early promoter of simian virus 40 (SV40). This protein does not bind double-stranded DNA, nor RNA. In the present paper, the DNA-binding properties of protein H16 and its effects on transcription by RNA polymerase II in vitro have been investigated. The protein binds only to the late strand of the early promoter, within the region of the 21 base-pair repeats, and shows no affinity for any other SV40 sequence. The high percentage of cytosine residues in the late strand in this region appears to be important for recognition by the protein. Protein H16 does not bind the control region of SV40 in negatively supercoiled DNA circles. When bound to the late strand, the protein is displaced from its binding site by reassociation of the early strand with the late strand. Its binding to DNA is not sensitive to methylation of the dinucleotide CG in its binding site. The protein has been purified to near homogeneity by preparative gel retardation, and has an apparent molecular weight of 70,000. Purified protein H16 stimulates transcription by purified RNA polymerase II in vitro. The possible role of sequence-specific single-strand-binding proteins in transcription is discussed.