Showing papers on "Exon published in 1988"

Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man.

Abstract: L1 sequences are a human-specific family of long, interspersed, repetitive elements, present as approximately 10(5) copies dispersed throughout the genome. The full-length L1 sequence is 6.1 kilobases, but the majority of L1 elements are truncated at the 5' end, resulting in a fivefold higher copy number of 3' sequences. The nucleotide sequence of L1 elements includes an A-rich 3' end and two long open reading frames (orf-1 and orf-2), the second of which encodes a potential polypeptide having sequence homology with the reverse transcriptases. This structure suggests that L1 elements represent a class of non-viral retrotransposons. A number of L1 complementary DNAs, including a nearly full-length element, have been isolated from an undifferentiated teratocarcinoma cell line. We now report insertions of L1 elements into exon 14 of the factor VIII gene in two of 240 unrelated patients with haemophilia A. Both of these insertions (3.8 and 2.3 kilobases respectively) contain 3' portions of the L1 sequence, including the poly (A) tract, and create target site duplications of at least 12 and 13 nucleotides of the factor VIII gene. In addition, their 3'-trailer sequences following orf-2 are nearly identical to the consensus sequence of L1 cDNAs (ref. 6). These results indicate that certain L1 sequences in man can be dispersed, presumably by an RNA intermediate, and cause disease by insertional mutation.

Transcription of the dystrophin gene in human muscle and non-muscle tissues

Abstract: The gene that is defective in patients with Duchenne and Becker muscular dystrophy consists of about 60 short exons scattered along a gigantic DNA region that spans some 2 megabase pairs1,2. The encoded protein, dystrophin, was recently characterized as a component of muscle intracellular membranes of low abundance3,4. The dystrophin messenger RNA is difficult to study in both normal and pathological tissue specimens because it is large (14 kilobases) and scarce (0.01–0.001% of total muscle mRNA)2. We report here that efficient in vitro co-amplifications of the mRNAs of the dystrophin gene and of a reporter gene, aldolase A, by the poly-merase chain reaction procedure5 enables us to obtain a quantitative estimate of the dystrophin gene transcript. A processed, transcribed segment was thus detected in 13 different human tissues. It ranged from 0.02–0.12% of total mRNA in skeletal muscle to 25,000 times less in lymphoblastoid cells.

Inactivation of the retinoblastoma susceptibility gene in human breast cancers.

Abstract: Mutational inactivation of the retinoblastoma susceptibility (RB) gene, a recessive cancer gene, has been implicated in the genesis of retinoblastoma and certain other human neoplasms. This gene is now shown to be inactivated in two of nine human breast cancer cell lines examined. The RB gene of one cell line had a homozygous internal duplication of a 5-kilobase region containing exons 5 and 6. The RB messenger RNA transcript was correspondingly lengthened, and its translation was probably terminated prematurely due to a shifted reading frame. The other cell line had a homozygous deletion of the RB gene that removed the entire gene beyond exon 2. The RB gene product, pp110RB, was not detectable in either cell line by immuno-precipitation with specific antibodies. These findings are significant in relation to proposed genetic mechanisms of breast cancer formation.

A survey on intron and exon lengths

Abstract: The lengths of introns and exons in various parts of genes of vertebrates, insects, plants and fungi are tabulated. Differences between the various groups of organisms are apparent. The results are discussed and support the idea that, generally speaking, introns were present in primitive genomes, though in some cases they may have been inserted into pre-existing genes.

Splice site selection, rate of splicing, and alternative splicing on nascent transcripts.

Abstract: Based on ultrastructural analysis of actively transcribing genes seen in electron micrographs, we present evidence that pre-mRNA splicing occurs with a reasonable frequency on the nascent transcripts of early Drosophila embryo genes and that splice site selection may generally precede polyadenylation. The details of the process observed are in agreement with results from in vitro splicing systems but differ in the more rapid completion of in vivo splicing. For those introns that are removed cotranscriptionally, a series of events is initiated following 3' splice site synthesis, beginning with ribonucleoprotein (RNP) particle formation at the 3' splice site within 48 sec, intron loop formation within 2 min, and splicing within 3 min. The initiation of the process is correlated with 3' splice site synthesis but is independent of 5' splice site synthesis, the position of the intron within the transcript, and the age or length of the transcript. In some cases, introns are removed from the 5' end of a transcript before introns are synthesized at the 3' end, supporting a possible role for the order of transcription in splice site pairing. In general, our observations are consistent with the 'first-come-first-served' principle of splice site selection, although an observed example of exon skipping indicates that alternative splicing possibilities can be accommodated within this general framework.

Alternative promoters and exons, somatic mutation and deregulation of the Bcl-2-Ig fusion gene in lymphoma.

Abstract: The most common translocation in human lymphoma, the t(14;18)(q32;q21), generates heterogeneous 4.2-7.2 kb Bcl-2-immunoglobulin (Ig) chimeric mRNAs resulting from alternative Bcl-2 5' exons and varied Ig 3' untranslated regions (UT). The normal human Bcl-2 gene has a three exon structure with an untranslated first exon, a facultative 220 bp intron I, but an enormous 370 kb intron II. S1 protection and primer extension analysis defined initiation sites in exon II associated with classic promoter elements and a decanucleotide (ATG-CAAAGCA) homologous with Ig variable region enhancers. Multiple initiation sites were also found in a GC-rich region with Sp1 binding motifs in exon I. Most t(14;18) breakpoints cluster within the 3' UT of Bcl-2 implicating that event in gene deregulation. The Bcl-2 gene introduced into the Ig constant (C gamma) locus of SU-DHL-6 displayed somatic mutation. While Bcl-2--Ig mRNAs demonstrated an unaltered 2.5 h half-life, the Bcl-2--Ig gene revealed an inappropriately high rate of transcription for a mature B-cell. This indicates the translocated Bcl-2 allele has escaped normal control mechanisms.

The Human FGF-5 Oncogene Encodes a Novel Protein Related to Fibroblast Growth Factors

Abstract: We previously described the isolation of a human oncogene which had acquired transforming potential by a DNA rearrangement accompanying transfection of NIH 3T3 cells with human tumor DNA (X. Zhan, A. Culpepper, M. Reddy, J. Loveless, and M. Goldfarb, Oncogene 1:369-376, 1987). We now term this oncogene the FGF-5 gene, since it specifies the fifth documented protein related to fibroblast growth factors (FGFs. Two regions of the FGF-5 sequence, containing 122 of its 267 amino acid residues, were 40 to 50% homologous to the sequences of acidic and basic FGFs as well as to the sequences of the FGF-related oncoproteins int-2 and hst/KS3. The FGF-5 gene bears the three exon structures typical for members of this family. FGF-5 was found to be expressed in the neonatal brain and in 3 of the 13 human tumor cell lines examined. Several experiments strongly suggested that FGF-5 is a growth factor with properties common to those of acidic and basic FGFs. The rearrangement which activated the FGF-5 gene during DNA transfection had juxtaposed a retrovirus transcriptional enhancer just upstream from the native promoter of the gene.

Structural rearrangement of the retinoblastoma gene in human breast carcinoma.

Abstract: Structural changes of the human retinoblastoma gene have been demonstrated previously in retinoblastoma and some clinically related tumors including osteosarcoma. Structural aberrations of the retinoblastoma locus (RB1) were observed in 25% of breast tumor cell lines studied and 7% of the primary tumors. These changes include homozygous internal deletions and total deletion of RB1; a duplication of an exon was observed in one of the cell lines. In all cases, structural changes either resulted in the absence or truncation of the RB1 transcript. No obvious defect in RB1 was detected by DNA blot analysis in primary tumors or cell lines from Wilms' tumor, cervical carcinoma, or hepatoma. These results further support the concept that the human RB1 gene has pleiotropic effects on specific types of cancer.

A new type of transforming growth factor-beta, TGF-beta 3.

Abstract: A new type of TGF-beta, TGF-beta 3, has been identified by cDNA characterization. The amino acid sequence of mature TGF-beta 3 and its precursor has been derived from porcine and human cDNA sequences. The human TGF-beta 3 gene is spread over seven exons as in the case of the TGF-beta 1 gene. Comparison with TGF-beta 1 and -beta 2 indicates a strong conservation of the mature sequences, but a relaxed homology in the precursor segments. TGF-beta 3 mRNA is mainly expressed in cell lines from mesenchymal origin, suggesting a biological role different from the other TGFs-beta.

Human Ig superfamily CTLA-4 gene: chromosomal localization and identity of protein sequence between murine and human CTLA-4 cytoplasmic domains.

Abstract: The mouse CTLA-4 gene has been shown to code for an activated lymphocyte-associated sequence belonging to the Ig gene superfamily. We now report on the molecular cloning and study of the human corresponding gene isolated from a genomic library and designated Hu-CTLA-4. The Hu-CTLA-4 gene exists as a single copy per human haploid genome and maps to band q33 of chromosome 2. It comprises 3 exons notwithstanding the leader sequence. The first exon encodes a V-like domain of 116 amino acids, the second one a hydrophobic putative transmembrane region of 37 amino acids and the third one a 34 amino acid putative cytoplasmic domain. Whereas the overall homology between the human and murine CTLA-4 proteins is 76%, there is, remarkably, a complete identity of their cytoplasmic domains. This complete interspecies conservation comes in support of an important role for this domain in CTLA-4 function.

Isolation and characterization of the human Gs alpha gene.

Abstract: The gene for Gs alpha (the alpha subunit of the guanine nucleotide-binding protein Gs) was isolated from human genomic libraries using rat Gs alpha cDNA as a probe. Comparison of the nucleotide sequence of the human gene with that of the rat cDNA revealed that the human Gs alpha gene spans approximately equal to 20 kilobases and is composed of 13 exons and 12 introns. Genomic Southern blot analysis suggests that the human haploid genome contains a single Gs alpha gene. Previous reports indicated the presence of multiple species of Gs alpha cDNA. The structure of the human Gs alpha gene suggests that four types of Gs alpha mRNAs may be generated from a single Gs alpha gene by alternate use of exon 3 and/or of two 3' splice sites of intron 3, where an unusual splice junction sequence (TG) instead of the consensus (AG) is used. S1 nuclease mapping analysis of human Gs alpha mRNA identified multiple transcriptional initiation sites. The promoter region of the human Gs alpha gene has extremely high G + C content (85%). It contains 4 "GC" boxes, but no typical "TATA" or "CAAT" box sequence. In the 5' flanking region, there are several blocks of sequences that are similar to the sequences of the 5' flanking region of the human c-Ki-ras2 gene.

Genomic structure of the murine IL-6 gene. High degree conservation of potential regulatory sequences between mouse and human.

Abstract: The genomic clone of mouse IL-6 was isolated and compared with the human IL-6 gene. The comparison revealed that the mouse IL-6 consists of five exons and four introns and that the overall organization is similar to that of the human IL-6 gene although the third intron is about 2 kb longer. The sequence similarity in the coding region is about 60%, whereas the 3'-untranslated region and the first 300-bp sequence of the 5'-flanking region are highly conserved (greater than 80%). Several sequence blocks with high homology are also found in the introns. Furthermore, sequences similar to transcriptional enhancer elements such as the c-fos serum responsive element and the consensus sequences for cAMP induction, activator protein 1 binding, and the glucocorticoid receptor binding are identified within the highly conserved 5'-flanking regions of the genes from the two species. These sequences may play an important role in transcriptional activation of the IL-6 gene.

Identification of germline and somatic mutations affecting the retinoblastoma gene.

Abstract: Retinoblastoma (RB) is a malignant tumor of developing retina that arises when abnormalities resulting in loss of function affect both alleles of the gene at the retinoblastoma locus (RB1) on chromosome 13q. The majority of RB tumors do not show gross alterations in a 4.7-kb fragment (4.7R), which is a candidate RB1 gene. To search for more subtle mutations, the ribonuclease protection method was used to analyze 4.7R messenger RNA from RB tumors. Five of 11 RB tumors, which exhibit normal 4.7R DNA and normal-sized RNA transcripts, showed abnormal ribonuclease cleavage patterns. Three of the five mutations affected the same region of the messenger RNA, consistent with an effect on splicing involving an as yet unidentified 59 exon. The high frequency of mutations in 4.7R supports the identification of 4.7R as the RB1 gene. However, the unusual nature of some of the abnormalities of 4.7 R alleles indicates that the accepted sequence of genetic events involved in the genesis of RB may require reevaluation.

Delta, a Drosophila neurogenic gene, is transcriptionally complex and encodes a protein related to blood coagulation factors and epidermal growth factor of vertebrates.

Abstract: Delta (D1) is required for normal segregation of the embryonic ectoderm into neural and epidermal cell lineages in Drosophila melanogaster. Loss-of-function mutations in D1 and other zygotic neurogenic loci lead to expansion of the neuroblast population at the expense of the dermoblast population within the ectoderm. Characterization of the transcriptional organization and maternal/embryonic expression within the chromosomal interval corresponding to D1 reveals that the locus encodes multiple transcripts: a minimum of two maternal transcripts, approximately 4.5 and 3.6 kb in length, and four zygotic transcripts, approximately 5.4 (two distinct species), 3.5, and 2.8 kb in length. These transcripts differ on the bases of differential splicing and differential polyadenylation site choice. The DNA sequence of a cDNA clone representing the predominant transcripts of the locus indicates that D1 encodes a transmembrane protein homologous to blood coagulation factors and epidermal growth factor. The relationship between coding sequences and transcript-specific exons within the locus suggests that D1 encodes multiple translational products.

Primary structure of the human follistatin precursor and its genomic organization

Abstract: Follistatin is a single-chain gonadal protein that specifically inhibits follicle-stimulating hormone release. By use of the recently characterized porcine follistatin cDNA as a probe to screen a human testis cDNA library and a genomic library, the structure of the complete human follistatin precursor as well as its genomic organization have been determined. Three of eight cDNA clones that were sequenced predicted a precursor with 344 amino acids, whereas the remaining five cDNA clones encoded a 317 amino acid precursor, resulting from alternative splicing of the precursor mRNA. Mature follistatins contain four contiguous domains that are encoded by precisely separated exons; three of the domains are highly similar to each other, as well as to human epidermal growth factor and human pancreatic secretory trypsin inhibitor. The genomic organization of the human follistatin is similar to that of the human epidermal growth factor gene and thus supports the notion of exon shuffling during evolution.

Human gene encoding the 78,000-dalton glucose-regulated protein and its pseudogene: structure, conservation, and regulation.

Abstract: The isolation and characterization of a human functional GRP78 gene and a processed pseudogene are described. We present the complete primary structure of the human GRP78 gene, which spans over 5 kb and consists of eight exons. Sequence comparisons reveal that the GRP78 gene shares unusual homology among the human, rat, and hamster in the protein-coding and 3′ untranslated regions. In addition, short domains highly conserved with HSP70 isolated from human, Drosophila, Xenopus, yeast, and E. coli DNA are identified within the hydrophobic regions of GRP78. The intronless pseudogene resembles that of a processed gene. It is flanked by a short direct repeat and is embedded within an AT-rich genomic region. The highly active promoter from the functional human GRP78 gene contains a TATA box, five CCAAT sequences, and two potential binding sites for the transcriptional factor Spl. It consists of a distal domain that enhances basal level expression and a proximal domain essential for responses to calcium...

The structure and expression of a novel gene activated in early mouse embryogenesis.

Abstract: We report the cloning and sequence determination of the mouse H19 gene. This gene is under the genetic control of two trans-acting loci in the mouse, termed raf and Rif. These loci determine the adult basal and inducible levels, respectively, of H19 mRNA, as well as the mRNA for alpha-fetoprotein. By elucidating the sequence and structure of the H19 gene we show that it is unrelated to the alpha-fetoprotein gene, and therefore must have acquired its regulation by raf and Rif independently. The sequence also indicates that the H19 gene has a very unusual structure. It is composed of five exons, 1307, 135, 119, 127 and 560 bp in size, along with four very small introns whose combined lengths are 270 bases. The largest open reading frame of the gene, sufficient to encode a protein of approximately 14 kd, is contained entirely within the first large exon, 680 bases downstream of the cap site of the mRNA. Preceding the translation initiation codon are four ATG codons, each of which is followed shortly thereafter by translation terminator codons. The rest of the gene, which encompasses all five exons, is presumed to be untranslated. That the long 5' untranslated region may be used to regulate the translation of the mRNA is suggested from in vitro translation studies. Experiments which utilized tissue culture cell lines of the mesodermal lineage suggest that the gene is activated very early during muscle cell differentiation.

Interferon response element of the human gene 6-16.

Abstract: 1046 base-pairs (bp) of genomic DNA spanning the first exon of the human alpha/beta-interferon (IFN)-inducible gene 6-16 have been analysed for their role in induction. The whole gene or 5'-flanking deletion derivatives of it were assayed for inducibility in populations of stably transfected mouse cells. 5'-Flanking DNA fragments were assayed for their ability to confer inducibility on a reporter gene in stably and transiently transfected mouse and human cells. The data suggest that a 39 bp sequence is sufficient to confer transcriptional inducibility and can account in large part for the response of 6-16. Two copies of this sequence, one of which contains a dinucleotide insert, are located in tandem 88 bp upstream of the 6-16 transcriptional initiation site. For at least one of the repeat units the 5' limit of a subregion required for induction lies in the sequence GGGAAAAT. The motif GGAAA occurs in several well characterized enhancers. Furthermore, one residue 3' of the GGAAA there is a second motif, TGAAACT, which is conserved in the regulatory regions of other IFN-induced genes. In gel retardation assays the oligonucleotide GGGAAAATGAAACT competes with the repeat element for binding to IFN-modulated protein(s) but a mutated oligonucleotide, GGGAAAATGACACT does not. These results identify an alpha/beta IFN response element partially homologous to those described previously for the genes of the MHC complexes.

trans-activation and autoregulation of gene expression by the immediate-early region 2 gene products of human cytomegalovirus.

Abstract: The major immediate-early (IE) gene region mapping at coordinates 0.71 to 0.74 in the genome of human cytomegalovirus (HCMV) gives rise to a series of overlapping spliced IE mRNAs that are all under the transcriptional control of the complex IE68 promoter-enhancer region. We show here that one of the phosphorylated nuclear proteins encoded by this region behaves as a powerful but nonspecific trans-activator of gene expression. In transient chloramphenicol acetyltransferase (CAT) assay experiments with Vero cells all relatively weak heterologous target promoters tested, including those of herpes simplex virus IE175 and delayed-early genes, adenovirus E3, the enhancerless simian virus 40 early gene, and the human beta interferon gene, were stimulated between 30- and 800-fold by cotransfection with the HindIII C fragment of HCMV (Towne) DNA. In contrast, expression of the homologous HCMV IE68-CAT gene but not SV2-CAT was specifically repressed. Inactivation mapping studies of the effector DNA, together with dose-response comparisons with subclones from the region, revealed that an intact 7.1-kilobase sequence encompassing both the IE1 and IE2 coding regions (exons 1 to 5) in the major IE transcription complex was required for both the nonspecific trans-activation and autoregulatory responses. The IE1 coding region alone (exons 1 to 4) was inactive, but both functions were restored by insertion of the IE2 coding region (exon 5) in the correct orientation downstream from the IE1 coding region. Internal deletions or inserted terminator codons in IE1 (exon 4) still gave efficient trans-activation and autoregulation, whereas the insertion of terminator codons in IE2 (exon 5) abolished both activities. Finally, IE2 (exon 5) sequences only (under the direct transcriptional control of the strong simian CMV IE94 promoter) were still able to specifically down regulate IE68-CAT expression but failed to exhibit trans-activation properties. Therefore, the IE2 gene product(s) of HCMV appear likely to be key control proteins involved in gene regulation during HCMV infection.