Heterogeneity of the 5' terminus of hen ovalbumin messenger ribonucleic acid

Antibodies specific for branched ribonucleic acids

A chemically synthesized branched tetranucleotide, G3'p5'A [2'p5'G]3'p5'C corresponding to the consensus sequence at the branch point in introns undergoing RNA splicing, was used as a hapten to elicit antibranch antibodies. Binding assays with 32P-labeled hapten and unlabeled structurally related haptens indicated that the antibodies are highly specific for the branch structure and have some specificity for the A2'p5'G sequence at the branch point, but have essentially none for a variety of other 2'p5' or 3'p5' dinucleotides or for the linear trinucleotide G3'p5'A3'p5'C. Purification of these antibodies by binding to A2'p5'G covalently linked to Sepharose followed by covalent attachment of the purified antibodies to protein A-Sepharose has provided an adsorbent that immunospecifically retains branched oligonucleotides as well as branched introns released from RNAs during in vitro splicing.

Control of transcription initiation in vitro requires binding of a transcription factor to the distal promoter of the ovalbumin gene

We used a cell-free HeLa cell transcription system to identify and characterize transcription factors and the promoter elements that they recognize in RNA polymerase II-transcribed genes. Deletion of the region (-71 to -83) containing the GTCAAA direct repeat resulted in a marked decrease of specific transcription of the ovalbumin gene; transcription could be competed with DNA fragments containing this sequence. Furthermore, DNase I footprinting identified a protein-binding site including this direct repeat with crude extracts and one of the partially purified protein fractions required for transcription. We propose that a soluble factor activates transcription through binding to the direct repeat of GTCAAA sequence upstream from the ovalbumin gene.

The Drosophila melanogaster actin 5C gene uses two transcription initiation sites and three polyadenylation sites to express multiple mRNA species

At least six mRNAs are made from the Drosophila melanogaster act5C gene. We investigated the structures of these RNAs in detail and determined that they are heterogeneous at both their 5' and 3' ends. At the 5' end there were two nonhomologous leader exons which were alternately spliced to the remainder of the gene. These leader exons mapped to 1.7 and 0.7 kilobases, respectively, upstream of a common splice acceptor site which was eight base pairs 5' to the translation initiator AUG. Exon 1 is 147 bases in length, while exon 2 is 111 bases. A consensus TATA sequence was found roughly 30 base pairs upstream from exon 1, but none was found in the analogous position upstream of exon 2. The transcript length diversity arose principally from the use of three polyadenylation sites. This gave rise to RNA molecules with 3'-untranslated regions of roughly 375, 655, and 945 base pairs. With two start sites and three termination sites, this gene has the potential to produce six different transcripts. All six possible transcripts were present in whole fly mRNA. Transcripts containing the two different leader exons were found in roughly the same relative quantities through development. In contrast, the various 3' ends were differentially represented through development.

Terminal structure of hypovirulence-associated dsRNAs in the chestnut blight fungus Endothia parasitica

The 3'- and 5'-terminal sequences of the five large double-stranded RNA species (L-dsRNA; 4.5-6.0 X 10(6) daltons) of EP713, a hypovirulent strain of Endothia parasitica, were determined by mobility-shift and enzymatic methods. All the L-dsRNAs appeared to have identical terminal sequences. A heteropolymer sequence was found at one 3'-terminus and a poly(A) sequence of variable length at the other. It was possible to label only one 5'-terminus using polynucleotide kinase and [gamma-32P]ATP, and this was shown to be a poly(U) sequence of variable length. We propose that the dsRNAs have the following structure, where X represents a blocking group: (Formula: see text). A recombinant plasmid containing dsRNA-related sequences was constructed. Hybridization analysis using the recombinant probe indicated that the sequence homology among the L-dsRNAs extended beyond these terminal regions and was also shared by small dsRNAs (0.3-0.45 X 10(6) daltons).

Control of transcription initiation in vitro requires binding of a transcription factor to the distal promoter of the ovalbumin gene

We used a cell-free HeLa cell transcription system to identify and characterize transcription factors and the promoter elements that they recognize in RNA polymerase II-transcribed genes. Deletion of the region (-71 to -83) containing the GTCAAA direct repeat resulted in a marked decrease of specific transcription of the ovalbumin gene; transcription could be competed with DNA fragments containing this sequence. Furthermore, DNase I footprinting identified a protein-binding site including this direct repeat with crude extracts and one of the partially purified protein fractions required for transcription. We propose that a soluble factor activates transcription through binding to the direct repeat of GTCAAA sequence upstream from the ovalbumin gene.

The Drosophila melanogaster actin 5C gene uses two transcription initiation sites and three polyadenylation sites to express multiple mRNA species

At least six mRNAs are made from the Drosophila melanogaster act5C gene. We investigated the structures of these RNAs in detail and determined that they are heterogeneous at both their 5' and 3' ends. At the 5' end there were two nonhomologous leader exons which were alternately spliced to the remainder of the gene. These leader exons mapped to 1.7 and 0.7 kilobases, respectively, upstream of a common splice acceptor site which was eight base pairs 5' to the translation initiator AUG. Exon 1 is 147 bases in length, while exon 2 is 111 bases. A consensus TATA sequence was found roughly 30 base pairs upstream from exon 1, but none was found in the analogous position upstream of exon 2. The transcript length diversity arose principally from the use of three polyadenylation sites. This gave rise to RNA molecules with 3'-untranslated regions of roughly 375, 655, and 945 base pairs. With two start sites and three termination sites, this gene has the potential to produce six different transcripts. All six possible transcripts were present in whole fly mRNA. Transcripts containing the two different leader exons were found in roughly the same relative quantities through development. In contrast, the various 3' ends were differentially represented through development.

Cellular heterogeneity in the expression of the delta-crystallin gene in non-lens tissue

RNA transcripts of the delta-crystallin genes, which code for the major chicken lens protein, have been detected at low levels in many non-lens tissues. Here it is demonstrated by in situ hybridisation that these transcripts are concentrated at a high level in small, infrequent clusters of cells in many non-lens tissues. While the nuclei of these cells are very heavily labelled, there is only light labelling of the cytoplasm. The unlabelled cells surrounding the labelled clusters are of similar morphology and staining properties as the labelled cells, and all have the characteristic morphology of cells of the embryonic tissue used. With the exception of neural retina, it is not yet known whether the labelled clusters are found in specific locations in the tissues, or whether they arise at random.

An unusually long poly(purine)-poly(pyrimidine) sequence is located upstream from the human thyroglobulin gene

A region of human genomic DNA encompassing the 5' end of the thyroglobulin gene has been sequenced and the position of the transcriptional start site has been determined. The 5' non-translated portion of the mRNA displays a quasi-palindromic sequence which could allow this region to adopt a hairpin structure. The first exon of the gene encodes a 19 amino-acids signal peptide and the 3 first amino acids of the mature protein. Apart from the canonical TATA-Box and from a CAAT-Box homology, the promoter region contains a 209 bp-long poly(purine)-poly (pyrimidine) sequence located between positions-512 and -304 relative to the transcription start. When contained in a supercoiled plasmid, this sequence exhibits sensitivity to S1 nuclease at two distinct positions. A precise mapping of the borders of the sensitive regions was achieved by extending primers from both ends of the sequence after digestion by the enzyme. The resulting data can be explained by a model involving the formation of a triple helix structure.

Detection of human autoantibodies specific for 5'-m7GMP and m7G(5')ppp(5')N

An enzyme-linked immunosorbent assay was utilized for the detection of spontaneously occurring antibodies with apparent specificities for m7G, 5'-m7GMP, and m7G(5')ppp(5')C. From the sera of 50 patients containing anti-nuclear antibodies, 48 (96%) possessed antibodies which bound to one or more immobilized nucleoside-BSA antigens (A-, G-, C-, U-, and T-BSA). Additionally, 8 (16%) of these sera contained immunoglobulins that reacted with m7G-BSA antigen. In these latter sera, soluble competitors such as m7G, 5'm7GMP, and m7G(5')ppp(5')C (but not 5'-AMP, -GMP, -CMP, -UMP, and -TMP or m1G and m22G) effectively inhibited antibody-binding to immobilized m7G-BSA. These results indicate the existence of spontaneously occurring anti-m7G antibodies in autoimmune diseases which are distinct from anti-G antibody populations.

Human Cu/Zn superoxide dismutase gene: molecular characterization of its two mRNA species

Two cytoplasmic superoxide dismutase (SOD-1) mRNAs of about 0.7 and 0.9 kilobases (Kb.) were previously found in a variety of human cells. The two SOD-1 mRNAs are transcribed from the same gene and the major 0.7 Kb. species is approximately four times more abundant than the minor 0.9 Kb. mRNA. These two mRNAs differ in the length of their 3'-untranslated region and both have multiple 5'-ends. The longer transcript contains 222 additional nucleotides beyond the 3'-polyadenylated terminus of the short mRNA. S1 nuclease mapping and sequence analysis showed that these extra 222 nucleotides are specified by sequences contiguous to those shared by the two SOD-1 mRNAs. The 5'-termini of the two SOD-1 mRNAs were identified and mapped by both primer extension and S1 mapping. The majority of SOD-1 mRNA molecules (90-95%) have a 5'-start site located 23 base pairs (b.p.) downstream of the hexanucleotide -TATAAA-. The rest of the SOD-1 mRNA molecules have 5'-termini 30, 50 and 65 b.p. upstream from the major start region.

Isolation and characterization of the rat tyrosine aminotransferase gene

Tyrosine aminotransferase (TAT; L-tyrosine:2-oxoglutarate aminotransferase, EC 2.6.1.5) from rat liver is subject to glucocorticoid, cAMP, and developmental control. To study the underlying regulatory mechanisms, the TAT structural gene was isolated from a lambda bacteriophage rat DNA library. Heteroduplex analysis revealed that the 2.4-kilobase-long TAT mRNA is encoded by a gene that extends over 11 kilobases and is interrupted by 11 introns. To characterize the presumptive control region, the DNA sequence around the 5' end of the gene was determined and the start site of transcription was identified by nuclease S1 protection experiments. A short sequence homology in an equivalent position relative to the cap site was detected between TAT and tryptophan oxygenase, another glucocorticoid-controlled gene from rat liver. This sequence is related to the sequence 5' T-G-T-T-C-T 3' found in regions of the long terminal repeat of mouse mammary tumor virus, which has been shown to interact with the glucocorticoid receptor [Scheidereit, C., Geisse, J., Westphal, H. M. & Beato, M. (1983) Nature (London) 304, 749-752].

Seminal vesicle secretion IV gene: allelic difference due to a series of 20-base-pair direct tandem repeats within an intron

The rat seminal vesicle secretion IV (SVS IV) gene was isolated from a lambda Charon 4A library. The SVS IV gene transcription unit was found to be on one 3.3-kilobase (kb) EcoRI fragment. Restriction mapping and DNA sequence analysis demonstrated that the entire length of the SVS IV transcription unit is 1,930 base pairs (bp) and contains two introns. The 3.3-kb EcoRI fragment contains 144 bp of 5'-flanking region. At -113 bp from the presumed transcription initiation site an interesting structure with perfect dyad symmetry is noted. In another lambda clone, a 3.5-kb EcoRI fragment was isolated that contains the SVS IV gene and was shown to be identical to the 3.3-kb EcoRI fragment except for 180 bp of DNA in the second intron. The extra DNA consists of several (8-10) 20-bp tandem repeats flanked on each side by seven or eight copies of this same 20-bp repeat. Fisher X Sprague-Dawley hybrid rats, which contain both the EcoRI 3.5-kb form and the 3.3-kb form of the SVS IV gene, were crossed with each other. Analysis of the F1 generation demonstrated that the presence or absence of the 180-bp intronic insertion in the SVS IV gene defines an allelic difference. This report also presents the DNA sequence of the transcription unit and flanking regions of the SVS IV gene.

Definition of the ovalbumin gene promoter by transfer of an ovalglobin fusion gene into cultured cells

In order to study the initiation of transcription from the ovalbumin gene promoter, we constructed a hybrid gene (ovalglobin) in which 753 bps of ovalbumin gene 5'-flanking sequence were joined to the chicken adult beta-globin gene. When transfected into HeLa S3 cells, ovalglobin gene transcription initiated at the ovalbumin gene cap site, as measured by S1 nuclease and primer extension analysis. Deletion of 5'-flanking sequences to position -95 had little effect on transcription; deletion to -77 reduced transcription to about 20% of the wild type level and deletion to -48 reduced the level to about 2%. A deletion to -24, removing the sequence TATATAT, abolished transcription entirely. Hormonal regulation of the ovalglobin gene was observed when primary oviduct cells were used as recipients for DNA transfection. Under these conditions, addition of progesterone increased the level of ovalglobin transcripts to more than 10 times the uninduced level.

A 5'-flanking sequence essential for progesterone regulation of an ovalbumin fusion gene

Ovalbumin gene transcripts are not detectable in unstimulated chick oviducts but comprise about half of oviduct cell transcripts after steroid hormone induction. This seems to result mostly from an increased level of transcription. When steroid hormones enter the cytoplasm of target cells they bind to specific receptors and the steroid-receptor complex accumulates in the nucleus. Presumably this complex then binds in a sequence- or conformation-specific way near the regulated gene and enhances transcription. Several recent studies have shown that steroid hormone receptors bind preferentially to the 5'-flanking region of steroid-responsive genes in vitro. Transcription of cloned genes for alpha 2u globulin, growth hormone, mouse mammary tumour virus and lysozyme can be induced in vivo by steroid hormones after transfer to cells containing steroid hormone receptors. In some of these studies, 5'-flanking regions were shown to be important for steroid regulation. We have now constructed a hybrid gene containing the ovalbumin gene promoter fused to the chicken adult beta-globin gene and transferred it into primary cultures of chicken oviduct cells. We show that progesterone-mediated induction of transcription in untransformed oviduct cells depends on an ovalbumin gene flanking sequence between positions -95 and -222.

Characterization of a genomic clone for rat seminal vesicle secretory protein IV

The entire coding region for rat seminal vesicle secretory protein IV was obtained on a 3.5 kb Eco RI fragment isolated from a genomic library in lambda Charon 4A. The coding sequence for SVS IV message is interrupted twice by introns. The first lies just downstream from the juncture of the 21 amino acid secretory signal peptide with the start of the mature protein, and the second lies in the 3'-nontranslated region. The major transcriptional start site was mapped by primer extention and is 22 nucleotides upstream from the translational initiation codon. S1 protection experiments indicated additional minor transcriptional starts about 27 and 50 nucleotides further upstream from the major cap site. The entire transcriptional unit comprises about 1740 nucleotides. The SVS IV gene does not belong to an obvious gene family, and it is conserved in mice and guinea pigs.

The nucleotide sequence of the chicken apo very low density lipoprotein II gene

The nucleotide sequence of the chicken apo Very Low Density Lipoprotein II (apoVLDL II) gene and the regions immediately flanking the gene was determined. Nuclease S1 mapping showed that transcription is initiated at two sites, about 11 bp apart, of which the one lying downstream is used preferentially. Comparison of the 2918-base pair gene sequence with the earlier determined cDNA sequence [Wieringa et al. (1981) Nucleic Acids Research 9, 489-501] enabled us to identify the four exons which are 38 (or 49), 100, 160 and 358 bp long. One of the intron-exon junctions has an unusual sequence. In the 5' flanking region several palindromic sequences are observed. Sequences near the 5' and 3' ends show homologies with the ovalbumin gene.

Heterogeneous initiation regions for transcription of the chicken ovomucoid gene

We have identified the 5' termini of ovomucoid RNA transcripts isolated from estrogen stimulated chick oviduct by S1-nuclease mapping. Most of the ovomucoid RNA molecules (88-89%) are initiated at a predominant region which is positioned at about 30 basepairs downstream from a "TATATAT" sequence. However, there is at least one additional initiation region which accounts for 9% of the ovomucoid RNA transcripts. It is located at approximately 80 basepairs further upstream (5') from the major initiation region. DNA sequence data reveal that an AT-rich sequence resembling the "TATA" box is also present 30 nucleotides before this minor region. Our finding provides additional insight into the molecular mechanism involved in the transcription initiation of eucaryotic genes, and indicates that in vivo synthesis of mRNA may not require an absolute site for initiation of transcription.

Epsilon globin gene transcripts originating upstream of the mRNA cap site in K562 cells and normal human embryos

RNA transcribed from the human epsilon globin gene was studied in K562 cells and human embryos of 5-10 weeks gestation. Using both primer extension and S1 analysis RNA molecules were found which extend 53 +/- 1 bp, 55 +/- 1 bp and 270 +/- 1 bp upstream from the first coding base and are colinear with the gene. The first pair of molecules represent transcripts initiating at the canonical cap site but the other species represents a transcript over 200 nucleotides longer which initiates upstream of the CAAT and ATAA boxes.

Functional significance and evolutionary development of the 5'-terminal regions of immunoglobulin variable-region genes

The 5'-terminal sequence of the kappa light-chain gene expressed in MPC11 plasmacytoma cells was definitively determined by analysis of both the kappa mRNA and the gene from which it is transcribed. The distance between the cap site and the translation initiation codon is only 3 nucleotides, and in a minor variant only 2 nucleotides, considerably less than that found in other species of nucleus-derived mRNA. S1 nuclease protection experiments with MPC11 nuclear RNA indicate that the cap sites are coincident with the transcriptional start sites, suggesting that the 5'-terminal heterogeneity is caused by imprecision in transcriptional initiation. A comparison of the 5'-terminal structure of the MPC11 V kappa gene with that of several other V genes indicates that the length of the first exon, which is composed of the 5' untranslated region which is composed of the 5' untranslated region and a sequence encoding most of the signal peptide, is highly conserved. Within this set of examples, the 5' untranslated region varies from 3 to 33 nucleotides, and the signal-peptide-coding block from 46 to 76 nucleotides. This analysis has also provided insight into the genetic origins for two anomalous properties of the MPC11 light chain.

Complete sequence of an immunoglobulin mRNA using specific priming and the dideoxynucleotide method of RNA sequencing

The complete sequence of the mouse immunoglobulin kappa light chain MOPC 21 messenger RNA has been determined using a chain termination method and chemically synthesised deoxyoligonucleotides to initiate the synthesis of a DNA molecule complementary to the mRNA template. Five such oligonucleotide primers have been used for the sequence analysis of this messenger RNA. The approach is excellent for comparative studies of mouse k-chain mRNAs because they can be made on impure mRNA preparations. The MOPC 21 light chain mRNA is 943 nucleotides in length excluding the poly(A) region. An unexpected finding was that there are only three bases in the 5' non-coding region and its significance in terms of ribosome binding is discussed; 87 code for the precursor or leader sequence of the protein, 642 for the mature protein and 211 for the 3' non-coding region. The codons for the precursor region allows the previously undetermined amino acid sequence to be predicted. In common with other precursor regions a high proportion of the predicted amino acids are hydrophobic.