Showing papers on "Exon published in 1981"

Vitellogenesis and the Vitellogenin Gene Family

Abstract: Vitellogenin is synthesized under estrogen control in the liver, extensively modified, transported to the ovary, and there processed to the yolk proteins lipovitellin and phosvitin. In the frog Xenopus laevis there are at least four distinct but related vitellogenin genes. The two genes A1 and A2 have a 95 percent sequence homology in their messenger RNA coding regions, and contain 33 introns that interrupt the coding region (exons) at homologous positions. Sequences and lengths of analogous introns differ, and many introns contain repetitive DNA elements. The introns in these two genes that have apparently arisen by duplication have diverged extensively by events that include deletions, insertions, and probably duplications. Rapid evolutionary change involving rearrangements and the presence of repeated DNA suggests that the bulk of the sequences within introns may not have any specific function.

Primary structure and evolution of rat growth hormone gene.

Abstract: The rat growth hormone gene was isolated on a cloned 11.4-kilobase EcoRI-generated DNA fragment from a bacteriophage "library" of chromosomal DNA. The structural gene sequence, approximately 2.1 kilobases long, was identified by hybridization to the corresponding cloned rat growth hormone cDNA and shown to contain four intervening sequences. The complete primary structure of the gene and the 5' and 3'-flanking regions was determined. The mosaic structure of exons and introns can be related to the different biological activities of growth hormone and to the evolution from ancestral sequences of a gene that was the precursor to the growth hormone and the related prolactin and placental lactogen (chorionic somatomammotropin) genes. The largest intron was found to contain a dispersed repetitive DNA sequence flanked by perfect 18-base pair direct repeats. The mobility of sequences of this kind could play a role in the observed variation of intron sizes and in rearrangements of mammalian genes.

Sequence of U1 RNA from Drosophila melanogaster: implications for U1 secondary structure and possible involvement in splicing

Abstract: U1 RNA from cultured Drosophila melanogaster cells (Kc) was identified by its ability to be recognized, as an RNP, by anti-(U1)RNP antibodies from human lupus patients. Its sequence was deduced largely from direct analysis of the RNA molecule and then confirmed by DNA sequence determinations on a genomic clone isolated by hybridization to Drosophila U1 RNA. The Drosophila U1 RNA sequence exhibits 72% agreement with human U1 RNA. Nucleotides 3-11, which are complementary to the entire consensus sequence for donor (5') splice junctions in hnRNA, and to part of the acceptor (3') consensus, are exactly conserved. However, nucleotides 14-21, postulated to interact only with acceptor junctions, differ. Comparison of the Drosophila U1 sequence with vertebrate U1 sequences allows a particular secondary structure model to be preferred over others. These results are consistent with the hypothesis that U1 snRNPs are involved in splicing, but suggest specific modifications of the model detailing molecular interactions between U1 RNA and hnRNA during the splicing reaction.

Controls of RNA splicing and termination in the major late adenovirus transcription unit.

Abstract: The major late adenovirus promoter is active early after infection, selectively producing messenger RNAs coding for polypeptides with molecular weights of 55,000, 52,000 and 14,000. This selective expression suggests that a differential splicing pattern occurs at the transition from early to late viral gene expression. Activation of the late promoter and splicing of the 55, 52K mRNAs does not require newly synthesized virus polypeptides.

Expression of IgD may use both DNA rearrangement and RNA splicing mechanisms

Abstract: From a library of mouse sperm DNA, we have isolated two overlapping clones which contain the Cδ gene. One of these clones also contains the Cμ gene. The Cδ gene is separated from the Cμ membrane exons by approximately 2 kilobases (kb) of DAN. The Cδ gene was identified by (a) hybridization to poly(A)+RNA prepared from the IgD-producing rat plasma cell tumor IR731, and (b) homology of a translated nucleotide sequence to the amino acid sequence of the human δ chain. The Cδ gene spans 8 kb of DNA in the germ line. Plasmid subclones of the Cδ gene were used as probes in Southern and RNA blot experiments. RNA blot analysis of cytoplasmic poly(A)+RNA from IR731 and a μ+δ+ B-cell hybridoma revealed 1.6- and 2.7-kb δ mRNA species with different 3′ ends, which presumably encode the secreted and membrane-bound forms, respectively, of the δ chain. Southern blot analysis of DNA from two μ+δ+ lymphomas revealed that the Cδ gene is in the germ-line configuration in each case. Restriction map analysis of Cμ and Cδ genomic clones isolated from a library of normal μ+δ+ B-cell DNA also gave no evidence for DNA rearrangement in the region between the Cμ and Cδ genes. Taken together, these data suggest that IgD expression in μ+δ+ B cells does not involve a VH-to-Cδ DNA switch rearrangement. We propose that simultaneous expression of Cδ and Cδ with a single VH gene is mediated by two alternative routes of RNA processing of a primary nuclear transcript which contains the VH, Cμ, and Cδ genes. In contrast, analogous experiments with myeloma IR731 DNA revealed that the Cμ gene has been deleted from the myeloma DNA and that the Cδ gene has undergone DNA rearrangement, presumably including a switch recombination of the VH gene from the Cμ to the Cδ gene. These results indicate that two alternative mechanisms may be used in the expression of IgD molecules—RNA splicing in B cells and DNA rearrangement in plasma cells.

Rapidly evolving mouse alpha-globin-related pseudo gene and its evolutionary history.

Abstract: The nucleotide sequences of a mouse pseudo alpha-globin gene and two adult alpha-globin genes from mouse and rabbit were compared. A close examination of sequence differences among the three genes revealed that the mouse pseudo alpha-globin gene was derived from one of the mouse alpha-globin genes about 24 million years ago by gene duplication and lost its original function, presumably due to loss of both the intervening sequences or frameshift mutations that prevented production of a functional globin polypeptide, and eventually became an inactive gene about 17 million years ago. After this event, this gene evolved at a very high rate, approximately 1.9 times the rate of synonymous codon change in productive genes. This suggests the presence of functional constraints against synonymous codon changes in normally functioning genes and also suggests that the "nucleotide arrangements" serve almost no important functions beside protein coding ability in the greater part of this gene, except for a very limited number of nucleotides. A continuous stretch of the pseudo alpha-globin gene consisting of a third exon and a 5' half of the 3' noncoding region shows marked sequence homology to the alpha-globin gene, suggesting transfer from one of the globin or globin-like genes by recombination very recently.

Fine structure and evolution of the rat serum albumin gene.

Abstract: The exons, their boundaries, and approximately half of the intronic deoxyribonucleic acid of the rat serum albumin gene were sequenced. In addition to the 14 exons identified earlier by R-loop analysis, a small exon was detected between the "leader" exon (Z) and exon B. The leader exon encoded the 5'-untranslated portion of albumin messenger ribonucleic acid and the "pre-pro" oligopeptide present on the nascent protein. The sites of initiation and termination of transcription were tentatively identified by comparison of the 5' and 3' gene-flanking sequences with those of other eucaryotic genes. All 28 intron/exon junctions conformed to the "GT-AG rule" (Breathnach et al., Proc. Natl. Acad. Sci. 75:4853-4857, 1978). The three homologous domains of albumin were encoded by three subgenes that consisted of four exons each and evolved by intragenic duplication of a common ancestor. The second and forth exons of each subgene appeared to be the result of an even earlier duplication event. We propose a model for the evolution of this gene that accounts for the observed patterns of exon size and homology.

Structure of the pro alpha 2 (I) collagen gene.

Abstract: Fifty-four kilobase pairs (kbp) of cloned chicken DNA containing the entire 38-kbp pro alpha 2 (I) collagen gene have been isolated and characterized. DNA sequence analysis of a select 4 kbp of the gene has precisely described 14 exons which comprise one-third of the sequences encoding the triple-helical domain of the collagen protein. These exons range in size from 45 to 108 base pairs (bp), are all multiples of the 9 bp that code for the repeating triplet, Gly-X-Y, and have an average size of 70 bp. About 50 introns interrupt this gene. Nevertheless, introns do not separate the coding sequences for the ends of the central triple-helical structural domain and the ends of the propeptide domains.

Intragenic amplification and divergence in the mouse alpha-fetoprotein gene.

Abstract: The DNA sequences of the 14 exon junctions in the murine α-fetoprotein gene were determined using cloned genomic DNA. When these exons were examined with respect to the polypeptide segments they encoded, a direct correspondence between a threefold repeat of four exons and three protein domains was observed. Nucleotide sequence comparisons among the four exons of each domain were used to deduce the likely structure of the primordial domain, and the order and mechanism of its triplication to form the tripartite ancestral gene from which both α-fetoprotein and serum albumin arose. Sequence homologies among the four exons that constitute a single domain also suggest that they were derived, at least in part, from a common sequence which underwent successive amplification and divergence.

Mouse IgA heavy chain gene sequence: implications for evolution of immunoglobulin hinge axons

Abstract: The complete nucleotide sequence of the gene and mRNA coding for the constant (C) region of the secreted form of the BALB/c mouse IgA immunoglobulin alpha heavy (H) chain has been determined. As in other immunoglobulins, the three C region domains of the alpha protein, C alpha 1, C alpha 2, and C alpha 3 are coded in separate exons. However, the hinge region of C alpha is not coded on a separate exon as it is in other hinge-containing immunoglobulins. Instead, the alpha hinge is coded as a 5' extension of the C alpha 2 exon, and we suggest that it may have evolved by duplication leading to incorporation of an acceptor RNA splice site into the coding portion of the C alpha 2 exon. Extensions of this concept could provide an explanation for duplications in the human alpha 1 chain.

Human fibroblast interferon gene lacks introns

Abstract: A recombinant λ bacteriophage isolated from a human genome library contains the gene for fibroblast interferon (IFN-β1). The DNA sequence of this gene is identical to the sequence of its mRNA and is devoid of introns.

One gene, but two messenger RNAs encode liver L and red cell L' pyruvate kinase subunits

Abstract: Pyruvate kinase subunits of red cells and liver differ in their molecular weights. Peptide mapping of the rat enzymes has shown that this difference is due to a single exon peptide present in the red cell enzyme1‐3. There is strong genetic evidence in man that both enzymes are encoded by the same structural gene (refs 4–8 and G. E. J. Staal et al., personal communication). Here we describe in vitro protein synthesis experiments using RNA extracted from rat red cells and liver which demonstrate that the difference is reflected in tissue-specific mRNAs. Thus the difference is not due to post-translational processing and presumably involves either gene rearrangement or differential processing of a common nuclear RNA precursor.

Structure of the promoter for chicken alpha 2 type I collagen gene

Abstract: The chicken alpha 2 type I collagen gene is 38 kilobases long and its coding information is subdivided into more than 50 exons. In the current study, we used primer extension and S1 nuclease mapping to determine the sequence of the 5' end of alpha 2 collagen mRNA and to locate the start site for transcription of the alpha 2 collagen gene. The DNA sequence around the start site for transcription shows a typical Goldberg-Hogness sequence, 5' T-A-T-A-A-A-T 3', between -33 and -26 and a 5' G-C-C-C-A-T-T 3' sequence ("CAT" box) between -84 and -78. Three AUGs are found in the initial portion of the mRNA, the first from +54 to +56, the second from +117 to +119, and the third from +134 to +136. The first two AUGs are followed by short coding sequences that could specify a hexapeptide a tetrapeptide, respectively. Only the third AUG is followed by an open reading frame coding for a sequence that presents considerable homology with the previously determined amino acid sequence of prepro alpha 1 collagen. In the promoter region sequence there are several extensive dyads of symmetry. Three of these inverted repeats which precede the start site for transcription overlap each other and may have a role in the developmental regulation of this gene.

A gene chimaera of SV40 and mouse β-globin is transcribed and properly spliced

Abstract: A gene chimaera of the first exon from simian virus 40 (SV40) sequences coding for T antigen placed upstream from the third exon from mouse beta-globin, and separated by the resultant new chimaeric intron, was cloned into a bacterial plasmid. When transfected into monkey cells, the gene chimaera was transcribed, polyadenylated and spliced using the donor splice site from SV40 and the acceptor splice site from mouse beta-globin. This result suggests that a donor site from one gene can be spliced to an acceptor site from another gene.

O 2 binding properties of the product of the central exon of β -globin gene

Abstract: The hypothesis that the exons of eukaryotic structural genes code for functional domains and that the partitioned arrangement of coding information may thus serve to mediate the rapid evolution of new and unique proteins from pre-existing exons1–3 is also supported by our recent studies which demonstrate that the product of the central exon of the human β-globin gene is a complete functional domain capable of binding haem tightly and specifically4,5. Moreover, an analysis of the structure/function changes induced by mutations in different parts of the haemoglobin molecule suggests that each of the three exon-encoded segments is primarily associated with different functions of haemoglobin (for example, haem-binding, haem–haem interaction)6. We have now extended our studies to determine whether the central fragment is sufficient for maintenance of a stable complex of ferrous haem with molecular oxygen and, if not, what are the minimal requirements for the expression of this activity. The results of our reconstitution experiments indicate that the isolated central exon peptide is unable to maintain a ferrous haem–dioxygen complex unless the side exon products and the complementary haem-containing subunit are present. A conformational change which accompanies the noncovalent association of fragments may account for the restoration of reversible oxygen binding.

Regulatory interactions between mitochondrial genes: interactions between two mosaic genes

Abstract: We have studied the mitochondrial DNA and the phenotypes of strains of Saccharomyces cerevisiae with specific intervening sequences in two mosaic genes: cob (the gene for apocytochrome b) and oxi3 (the gene for subunit I of cytochrome oxidase). The results suggest the following. (i) The presence of an intervening sequence downstream encompassing the intron box7 is sufficient for the regulation of oxi3 by cob (BOX phenotype); two sequences (containing intron loci box3 and box10) upstream in cob and two in oxi3 are dispensable. (ii) Strains without the two sequences upstream still contain the downstream sequence and the competence to specify a functional trans-acting element. Mutational lesions in this segment are phenotypically indistinguishable from box7 mutants, including the accumulation of polypeptides with homologous amino acid sequences. (iii) A catabolite-sensitive BOX phenotype, characteristic of mutants in the first exon, requires the simultaneous presence of an adjacent intervening sequence. A model is presented in which a hypothetical product specified by an intron (locus box7) of the cob gene controls the expression of a second mosaic gene (oxi3).

Decrease in the levels of nuclear RNA precursors for alpha 2 collagen in Rous sarcoma virus transformed fibroblasts.

Abstract: We have examined the levels of type I alpha 2 collagen RNA precursors, containing both intron and exon sequences in nuclear RNA preparations of chick embryo fibroblasts (CEF) and of CEF transformed by the Schmidt-Rupin strain of Rous sarcoma virus (RSV). We have used two different fragments of chick alpha 2 collagen genomic DNA as hybridization probes in S1 mapping experiments. Each of these DNA probes contains an entire intron. Our results indicate that the levels of the primary transcript of alpha 2 collagen RNA are much lower in RSV-CEF than in CEF. They suggest, but do not prove that the effect of the transforming protein p60src on the synthesis of alpha 2 collagen is mediated by a transcriptional control mechanism.

Fine structural analysis of the chicken pro alpha 2 collagen gene

Abstract: Forty-two kilobase pairs of cloned chicken DNA containing 80% of the pro alpha 2 (type I) collagen gene and 8 kilobase pairs of 3' flanking sequences have been isolated. Detailed analysis of these clones indicates that this collagen gene spans approximately 40 kilobase pairs of DNA and contains on the order of 50 introns. The fine structure of 40% of the pro alpha 2 gene, including its 3' end, was determined by Southern blot restriction endonuclease mapping using a 2.6-kilobase pair procollagen cDNA clone pCg45, as a probe, and by DNA sequence determination of more than 2 kilobase pairs of this part of the genome. Exons in the triple-helical coding region are all multiples of the 9 base pairs coding for the Gly-X-Y triplet and vary in size from 45 to 108 base paris. The sequences of all six exons in a 3.8-kilobase pair EcoRI fragment were determined. One of these, a 249-base pair exon, joins the collagen domains; it codes for the last 15 amino acids of the triple-helical coding region, the telopeptide, and the first 53 amino acids of the carboxy-terminal propeptide.

Nucleotide sequence of the nbosomal RNA gene of Physarum polycephalum: intron 2 and its flanking regions of the 26S rRNA gene

Abstract: The 26S ribosomal RNA gene of Physarum polycephalum is interrupted by two introns, and we have previously determined the sequence of one of them (intron 1) (Nomiyama et al. Proc.Natl.Acad.Sci.USA 78, 1376-1380, 1981). In this study we sequenced the second intron (intron 2) of about 0.5 kb length and its flanking regions, and found that one nucleotide at each junction is identical in intron 1 and intron 2, though the junction regions share no other sequence homology. Comparison of the flanking exon sequences to E. coli 23S rRNA sequences shows that conserved sequences are interspersed with tracts having little homology. In particular, the region encompassing the intron 2 interruption site is highly conserved. The E. coli ribosomal protein L1 binding region is also conserved.

Nucleotide sequence of a ribosomal RNA gene intron from slime mold Physarum polycephalum.

Abstract: The Physarum polycephalum 26S ribosomal RNA gene contains two intervening sequences (introns). The DNA sequence of one of these introns was analyzed together with that of its flanking regions (exons). In addition, the nucleotide sequence of the corresponding region of the reverse transcript of 26S rRNA was determined, and from comparisons of both sequences the precise location and size of the intron were determined. Our findings, when compared with those for Tetrahymena and Chlamydomonas rRNA gene introns, led to the conclusion that certain characteristics exist near the ends of these introns. (i) An exon ends in T at the exon/intron junction and an intron ends in G at the intron/exon junction in all cases. (ii) For each intron, direct repeats several nucleotides long are present 5 to approximately 30 nucleotides upstream from both the exon/intron and intron/exon junctions.

The chromosomal arrangement of two linked actin genes in the sea urchin S. purpuratus

Abstract: Four distinct actin genes of the sea urchin Strongylocentrotus purpuratus have been isolated from a recombinant Charon 4 phage library of genomic DNA. The four genes differ considerably from each other in many of their restriction sites. Two of the four genes are closely linked; they are present in the same fragment of cloned DNA. This fragment has been extensively mapped, and some parts of the DNA have been sequenced. The two linked genes are oriented in the same direction, separated by 7.5 kb of DNA. One has an intron following the CAG that codes for the glutamine residue at position 121 in the amino acid sequence of actin. This represents the fifth distinct site at which introns have been found in actin genes, suggesting that the primordial actin gene had at least 6 exons and 5 introns. The actin genes from a distinctive family in which most introns have apparently been precisely excised from the genes.