Heterogeneous initiation regions for transcription of the chicken ovomucoid gene

A non-statistical approach to protein mutational variability

The non-statistical, non-Markovian model of protein mutational variability is described. There are presented the essential features of the algorithm of genetic semihomology and some examples of its application. The results of genetic semihomology approach are compared with the results obtained by using statistical algorithms and matrices which are assumed in widely used programs such as ClustalW, FASTA, MultAlin and BLAST. The aim of the new algorithm elaboration is to improve the accuracy of the results of protein sequence comparison, avoid the wrong assumptions and misinterpretation of the results, and increase the amount of information available from such study.

Differential regulation of gamma-crystallin genes during mouse lens development

Using gene-specific probes derived from four mouse gamma-crystallin cDNAs, we have examined the regulation of different members of the mouse gamma-crystallin gene family during lens development. Our analysis revealed that, while the different gamma-crystallin genes appear to be coordinately activated during embryogenesis, the steady-state levels of their corresponding transcripts are differentially regulated, resulting in variations in the relative abundance of individual species at different stages of development. This complex pattern of gene regulation presumably accounts for one of the mechanisms determining the spatial distribution of different gamma-crystallins within the lens.

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.

RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon

Rats and mice have two, equally expressed, nonallelic genes encoding preproinsulin (genes I and II). Cytological hybridization with metaphase chromosomes indicated that both genes reside on rat chromosome I but are approximately 100,000 kilobases apart. In mice the two genes reside on two different chromosomes. DNA sequence comparisons of the gene-flanking regions in rats and mice indicated that the preproinsulin gene I has lost one of the two introns present in gene II, is flanked by a long (41-base) direct repeat, and has a remnant of a polydeoxyadenylate acid tract preceding the downstream direct repeat. These structural features indicated that gene I was generated by an RNA-mediated duplication-transposition event involving a transcript of gene II which was initiated upstream from the normal capping site. Sequence divergence analysis indicated that the pair of the original gene and its retroposed, but functional, counterpart (which appeared about 35 million years ago) is maintained by strong negative selection operating primarily on the segments encoding the chains of the mature hormone, whereas the segments encoding the parts of the polypeptide that are eliminated during processing and also the introns and the flanking regions are evolving neutrally.

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.

Sequence divergence and selection of cap sites in the rat gamma-crystallin gene family

The transcription initiation sites of the six rat gamma-crystallin genes were mapped by combining the results of primer extension and S1 nuclease mapping experiments. To obtain more accurate results from the S1 nuclease mapping experiments, intron-deleted clones were constructed by a novel and efficient modification of existing methods involving the use of primer extension products to seal the exons. Four of the six gamma-crystallin genes have multiple transcription start sites. The major and most of the minor transcripts start with an adenosine. Analysis of the 5' flanking sequences of the gamma-crystallin genes shows that the sequence determining the position of the cap site is merely -CA- and that its optimal distance from the first T of the TATA box is 32 base pairs. Our data further suggest that an A to G transition in the first two base pairs of the Goldberg/Hogness box of one the genes does not affect the position of its major cap site. This, together with the fact that most minor transcription start sites are located upstream from the major cap sites, suggests that in the long TATA boxes of the rat gamma-crystallin genes the major RNA polymerase 'trap site' is not directly at the beginning of the TATA sequence.

alpha-Fetoprotein synthesis in transformed fetal rat liver cells

We have reported that transformed fetal liver cells produced a variant alpha-fetoprotein of 65K that differed from the mature alpha-fetoprotein of 69K and 73K in the polypeptide backbone. In the present study, we demonstrated that the biosynthetic pathway of the variant alpha-fetoprotein differed from that of the mature alpha-fetoprotein. The 65K variant was synthesized first as a preprotein of 49.5K which was processed to a polypeptide of 59K in the presence of microsomal membranes. The latter was the precursor of the variant alpha-fetoprotein found in cells and medium of transformed fetal liver cells. The 65K alpha-fetoprotein was encoded by a mRNA of 16S while mature AFP was encoded by a mRNA of 20S.

Alpha-amanitin insensitive transcription of the human epsilon-globin gene

In vitro transcription was used to show that RNA polymerase III is responsible for the initiation of transcription at a position 200 bp upstream from the epsilon-globin major cap site. High levels of -200 transcription interferes with the RNA polymerase II major cap site transcription. Using DNA mediated transient expression, the ratio of -200 to +1 transcription can be modulated by either the direction of replication or the presence of an enhancing element in the vector. We suggest that this heterogeneous usage of cap sites is not related to epsilon-globin gene transcription in vivo, but is instead the result of a combination of factors inherent to transient expression experiments.

Nucleotide sequence of a cDNA clone for human aldolase: a messenger RNA in the liver

Nearly complete cDNA clones for human aldolase A mRNA were isolated from human liver cDNA library and the nucleotide sequence determined. Using the cDNA clone as a probe the length of human aldolase A mRNAs, isolated from the skeletal muscle, liver and placenta tissues, was measured by RNA blotting and estimated to be 1,600 nucleotides for skeletal muscle mRNA and 1,700 nucleotides for both the liver and placenta mRNAs, indicating that different species of mRNA coding for human aldolase A were expressed in the different tissues.

RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon

Rats and mice have two, equally expressed, nonallelic genes encoding preproinsulin (genes I and II). Cytological hybridization with metaphase chromosomes indicated that both genes reside on rat chromosome I but are approximately 100,000 kilobases apart. In mice the two genes reside on two different chromosomes. DNA sequence comparisons of the gene-flanking regions in rats and mice indicated that the preproinsulin gene I has lost one of the two introns present in gene II, is flanked by a long (41-base) direct repeat, and has a remnant of a polydeoxyadenylate acid tract preceding the downstream direct repeat. These structural features indicated that gene I was generated by an RNA-mediated duplication-transposition event involving a transcript of gene II which was initiated upstream from the normal capping site. Sequence divergence analysis indicated that the pair of the original gene and its retroposed, but functional, counterpart (which appeared about 35 million years ago) is maintained by strong negative selection operating primarily on the segments encoding the chains of the mature hormone, whereas the segments encoding the parts of the polypeptide that are eliminated during processing and also the introns and the flanking regions are evolving neutrally.

Human aldolase isozyme gene: the structure of multispecies aldolase B mRNAs

A complete nucleotide sequence of human aldolase B mRNA was determined with a recombinant cDNA (pHABL120-3). The cDNA insert was composed of 1,652 bases excluding poly(A) tail and the sequence was consistent with the previous results reported by others. However, S1 nuclease mapping and subsequent genomic analysis allowed us to know that the clone possesses two more sites corresponding to 5'-termini in the 5'-noncoding region and another site of polyadenylation in the 3'-noncoding region. In fact, the major aldolase B mRNA species occupying 90% of the total mRNAs initiated at the predominant position corresponding to the position around -82 of the 5'-noncoding sequence in pHABL120-3 and terminated at the distal polyadenylation site. Second species accounting for 9% of the mRNAs initiated at the same site and terminated at the proximal polyadenylation site. The remainings have a longer 5'-noncoding sequence which starts from further upstream region of the major one and pHABL120-3 corresponds to one of these largest clones.

Expression of tissue-specific Ren-1 and Ren-2 genes of mice: comparative analysis of 5'-proximal flanking regions

All inbred strains of mice carry the Ren-1 structural gene, which encodes the renin-1 isozyme, the classical renin activity found in kidneys. In addition, some strains carry a second renin structural gene, Ren-2, which encodes the predominantly expressed submaxillary gland renin isozyme, renin-2. Ren-1 and Ren-2 exhibit markedly different patterns of tissue-specific expression. In an effort to understand the molecular basis for this differential expression, detailed analysis of the genomic sequences corresponding to the Ren-1 and Ren-2 genes, and the transcripts originating from these loci, was undertaken. Sequence analysis of regions proximal to the structural genes indicated the presence of eucaryotic consensus sequences for transcription. These sequence motifs were strongly conserved between Ren-1 and Ren-2. Approximately 150 bases upstream from the major transcription initiation site, significant differences between these genes were apparent, including the presence of a repetitive DNA element in the Ren-2 copy as well as other breaks in homology and sequence curiosities. Strong homology between Ren-1 and Ren-2 resumed at a point ca. 200 bases further upstream on Ren-1. S1 analysis of submaxillary gland and kidney RNA populations indicated that the majority of transcripts initiate at homologous positions on Ren-1 and Ren-2. On a per cell basis, the accumulation of Ren-1 transcripts in the kidney and Ren-2 transcripts in the submaxillary gland are probably equivalent. These results suggest that it is tissue-specific utilization of the homologous start sites that is critical to their differential patterns of expression. Models which can account for this observation are presented. Interestingly, we found a minor fraction of transcripts initiating 5' to the major transcription start site. These transcripts encoded an open reading frame which may add an additional 23 amino acids to the N-terminus of the renin precursor.

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.

alpha-Amanitin-insensitive transcription of mouse beta major-globin 5'-flanking and structural gene sequences correlates with mRNA expression

A small proportion of the RNAs of mouse reticulocytes consists of beta major-globin mRNA sequences linked to sequences transcribed from the 5'-flanking region of the beta major-globin gene. These upstream RNAs are polyadenylylated and contain 700-800 nucleotides, and their 5' regions are heterogeneous. RNAs with similar or identical 5' regions are transcribed in cell-free extracts from a circular mouse beta major-globin gene template. Synthesis of most of the upstream RNAs in vitro is not inhibited by low levels (1 microgram/ml) of alpha-amanitin, indicating that they are transcribed by an enzyme(s) different from RNA polymerase II. During culture of mouse erythroleukemia cells with dimethyl sulfoxide, globin mRNA and upstream RNAs accumulate with similar kinetics. In contrast, upstream RNAs are not detected in hemin-treated cells.

Expression of tissue-specific Ren-1 and Ren-2 genes of mice: comparative analysis of 5'-proximal flanking regions

All inbred strains of mice carry the Ren-1 structural gene, which encodes the renin-1 isozyme, the classical renin activity found in kidneys. In addition, some strains carry a second renin structural gene, Ren-2, which encodes the predominantly expressed submaxillary gland renin isozyme, renin-2. Ren-1 and Ren-2 exhibit markedly different patterns of tissue-specific expression. In an effort to understand the molecular basis for this differential expression, detailed analysis of the genomic sequences corresponding to the Ren-1 and Ren-2 genes, and the transcripts originating from these loci, was undertaken. Sequence analysis of regions proximal to the structural genes indicated the presence of eucaryotic consensus sequences for transcription. These sequence motifs were strongly conserved between Ren-1 and Ren-2. Approximately 150 bases upstream from the major transcription initiation site, significant differences between these genes were apparent, including the presence of a repetitive DNA element in the Ren-2 copy as well as other breaks in homology and sequence curiosities. Strong homology between Ren-1 and Ren-2 resumed at a point ca. 200 bases further upstream on Ren-1. S1 analysis of submaxillary gland and kidney RNA populations indicated that the majority of transcripts initiate at homologous positions on Ren-1 and Ren-2. On a per cell basis, the accumulation of Ren-1 transcripts in the kidney and Ren-2 transcripts in the submaxillary gland are probably equivalent. These results suggest that it is tissue-specific utilization of the homologous start sites that is critical to their differential patterns of expression. Models which can account for this observation are presented. Interestingly, we found a minor fraction of transcripts initiating 5' to the major transcription start site. These transcripts encoded an open reading frame which may add an additional 23 amino acids to the N-terminus of the renin precursor.

Identification and sequence analysis of the 5' end of the major chicken vitellogenin gene

We have precisely determined the positions of the first three exons for the major chicken vitellogenin gene (VTG II) by a combination of S1 nuclease protection, primer extension and DNA sequencing experiments. In addition, we have determined the nucleotide sequences of the 5' flanking nuclease hypersensitive sites that we have previously shown are induced during the estrogen mediated activation of the VTG II gene in liver (1). One of these sites is found to be nearly identical to the enhancer core sequence of SV40. A computer assisted analysis of the DNA sequences upstream from the VTG II gene has revealed four short (7 to 9 base pair) sequence elements that are present in similar positions flanking the other major estrogen inducible gene for liver, very low density apolipoprotein II (apoVLDL II). For VTG II, these sequences are located between two of the induced nuclease hypersensitive sites that are liver specific. Sequences homologous to one element, located approximately 100 base pairs upstream from the mRNA cap sites of the VTG II and apoVLDL II genes, are also observed for three estrogen inducible genes that are expressed in the oviduct, although for each of these genes the sequence falls further upstream, between -220 and -200. We suggest that these conserved sequences may be important in mediating the tissue specific responses of these genes to estrogen.

Human beta-globin promoter and coding sequences transcribed by RNA polymerase III

We have investigated low abundance RNAs transcribed in vitro and in vivo from the human beta-globin gene. These RNAs contain globin mRNA sequences covalently linked to sequences transcribed from the 5' flanking region between -235 and the mRNA cap site (+1). Their synthesis in vitro is sensitive to high (100 micrograms/ml) levels of alpha-amanitin but not to low (2 micrograms/ml) levels, and one region of the DNA template bordering their 5' termini is similar to a small segment of Alu repetitive DNA and to the RNA polymerase III promoter consensus sequence. Therefore, these RNAs are transcribed by RNA polymerase III but extend into the mRNA-coding region that is usually transcribed by polymerase II. The polymerase III transcripts are polyadenylated and are probably spliced. Their presence in bone marrow cells and peripheral blood reticulocytes implies that they play some role in the erythroid cell.

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.

The messenger RNA for alcohol dehydrogenase in Drosophila melanogaster differs in its 5' end in different developmental stages

Alcohol dehydrogenase (EC 1.1.1.1) of Drosophila melanogaster is coded by a single structural gene, active in both larvae and adults. The major larval and adult transcripts of Adh differ in their 5'-untranslated regions. The major larval mRNA is about 1100 bases long, some 50 bases shorter than the major adult transcript. The 5' end of the larval mRNA is colinear with the genomic sequence immediately adjacent to the coding region, starting 70 base pairs (bp) upstream of the initiation codon. By contrast, the adult mRNA shares only 36 of its 123 5'-untranslated bases with the larval mRNA; the remaining 87 are encoded by a sequence 654 bp upstream. Both initiation sites are preceded by a TATA box some 24 bp upstream. The developmental specificity of Adh expression is seen, therefore, to have a counterpart in the specificity of transcription initiation at the two separate promoter regions.

An assessment of the evidence for the role of ribonucleoprotein particles in the maturation of eukaryote mRNA

This article has sought to draw together, on the one hand, what is known of mRNA processing and its control and, on the other hand, what is known of the structure and validity of hnRNP and snRNP particles. At the same time, it has attempted to synthesize these two themes into a critical assessment of the evidence which suggests that the particles are intimately involved in processing. It cannot be said that the case is proven. The evidence is compelling but circumstantial. The last few years have seen the development of the first in vitro splicing systems (Weingartner and Keller, 1981; Goldenberg and Raskus, 1981; Kole and Weissman, 1982), the isolation of monoclonal antibodies to defined snRNP (Lerner et al., 1981a; Billings et al., 1982) and hnRNP proteins (Hugle et al., 1982), and the ability to use artificial lipid vesicles to transfer antisera (Lenk et al., 1982) and radioactive snRNA (Gross and Cetron, 1982) into cells. It is to be hoped that further refinements of these and other techniques will allow us to solve this, one of the major outstanding problems of molecular biology.