Showing papers on "Pseudogene published in 1986"
TL;DR: If this cytochrome P-450 enzyme is defective, cortisol cannot be synthesized, resulting in congenital adrenal hyperplasia, and the 21-OHase A gene is, therefore, a pseudogene.
Abstract: We have determined the structure of cDNA and two genomic genes encoding steroid 21-hydroxylase [21-OHase; steroid 21-monooxygenase; steroid, hydrogen-donor:oxygen oxidoreductase (21-hydroxylating); EC 1.14.99.10]. If this cytochrome P-450 enzyme is defective, cortisol cannot be synthesized, resulting in congenital adrenal hyperplasia. The cDNA encoding this enzyme is 2.0 kilobases long, and the encoded protein is predicted to contain 494 amino acid residues with a molecular weight of 55,000. This enzyme is at most 28% homologous to other P-450 enzymes that have been studied. The 21-OHase genomic genes, which are located in the HLA major histocompatibility complex on chromosome 6, each contain 10 exons. This structure is distinct from other characterized P-450 genes, which contain 7 or 9 exons. Studies of individuals with homozygous deletions of the 21-OHase A or B genes suggest that only the B gene encodes an active enzyme. This is confirmed by the finding that the A gene has an 8-base deletion within codons 110-112, resulting in a frameshift that brings a stop codon into the reading frame at codon 130. A second frameshift and a nonsense mutation occur downstream. In contrast, the sequence of the exons of the B gene is identical to the cDNA sequence. The 21-OHase A gene is, therefore, a pseudogene.
530 citations
TL;DR: Two 21-hydroxylase genes have been isolated from a human genomic library using a bovine P-450(C21) cDNA and it is found that the two genes are highly homologous including their introns and flanking sequences, but that three mutations render one of the two P- 450(C 21) genes nonfunctional.
Abstract: Two 21-hydroxylase [P-450(C21)] genes have been isolated from a human genomic library using a bovine P-450(C21) cDNA. The insert DNAs containing the P-450(C21) genes were also hybridized with the sequences of the 5' or 3' end regions of human C4 cDNA, indicating a close linkage of the P-450(C21) gene to the C4 gene. Sequence analysis has revealed that the two P-450(C21) genes are both approximately equal to 3.4 kilobases long and split into 10 exons. Comparing the two sequences, we found that the two genes are highly homologous including their introns and flanking sequences, but that three mutations render one of the two P-450(C21) genes nonfunctional--1 base insertion, an 8-base deletion, and a transition mutation--all of which may cause premature termination of the translation. Tandem arrangement of the highly homologous pseudo- and genuine genes in close proximity could account for the high incidence of P-450(C21) gene deficiency by homologous gene recombination.
523 citations
TL;DR: Nine T cell gamma variable (V) gene segments isolated from human DNA show that major rearrangements can be observed that are attributable to the five active V gamma genes, and human cells with the phenotype of helper T cells can undergo productive V gamma-J gamma joining.
308 citations
TL;DR: The amino acid sequence of human hsp27 shows striking homology with mammalian alpha crystallin, and contains a region towards the carboxy terminus which shares homological with the small hsp of Drosophila and other organisms.
Abstract: The 27 kDa human heat shock protein (hsp27) is encoded by a gene family of 4 members. Two genomic fragments hybridizing to cDNA encoding hsp27 have been isolated, characterized, and sequenced. One clone is a member of a cluster of three genes linked within a 14-18 kb region of the genome and encodes a transcript interrupted by two intervening sequences. A single open reading frame encodes a polypeptide of 22,300 deduced molecular weight. The 5' flanking region contains two transcription start sites and sequences homologous to the Drosophila consensus heat inducible control element. Induction of both potential transcripts follows heat shock in vivo. Accurate heat inducible transcription occurs at both start sites after injection into Xenopus oocytes. The second genomic clone is a processed pseudogene lacking promoter elements and is unlinked with the other members of the hsp27 gene family. The amino acid sequence of human hsp27 shows striking homology with mammalian alpha crystallin, and contains a region towards the carboxy terminus which shares homology with the small hsp of Drosophila and other organisms.
299 citations
TL;DR: Comparison of the nucleotide sequences of VH segments within each family showed that profiles of accumulation of mutations in framework (FR) and complementarity-determining (CDR) regions were different, and the possibility that conserved pseudogenes serve as a reservoir of Vh segments is discussed.
199 citations
TL;DR: Comparison of the upstream regions of the SAA genes with those of the rat fibrinogen genes, whose expression is also induced by inflammation, reveals sequences common to all six genes which are very improbable on a random basis.
173 citations
TL;DR: A map of the cluster indicates which of the cloned hCG beta genes reflect somatic genotypes rather than recombinant artifacts and will thus permit investigation of factors regulating expression during gestation.
118 citations
TL;DR: Two linked members of the wheat (Triticum aestivum) gliadin multigene family are cloned and sequenced, showing the presence of a highly conserved region that could be involved in tissue specific and developmental regulation.
113 citations
TL;DR: It is concluded that only one gene is responsible for the synthesis of the majority of apoferritin H mRNA in various tissues examined, and that probably all the other DNA segments hybridizing with apferritin cDNA are pseudogenes.
Abstract: Ferritin is composed of two subunits, H and L. cDNA's coding for these proteins from human liver (1,2,3), lymphocytes (4) and from the monocyte-like cell line U937 (5) have been cloned and sequenced. Southern blot analysis on total human DNA reveals that there are many DNA segments hybridizing to the apoferritin H and L cDNA probes (1,2,4,6). In view of the tissue heterogeneity of ferritin molecules (7,8), it appeared possible that apoferritin molecules could be coded by a family of genes differentially expressed in various tissues (1,2). In this paper we describe the cloning and sequencing of the gene coding for human apoferritin H. This gene has three introns; the exon sequence is identical to that of cDNA's isolated from human liver, lymphocytes, HeLa cells and endothelial cells. In addition we show that at least 15 intronless pseudogenes exist, with features suggesting that they were originated by reverse transcription and insertion. On the basis of these results we conclude that only one gene is responsible for the synthesis of the majority of apoferritin H mRNA in various tissues examined, and that probably all the other DNA segments hybridizing with apoferritin cDNA are pseudogenes.
112 citations
TL;DR: The number of small gene conversions that the laboratory has been able to detect leads it to suggest that gene conversions are the consequence of a general mechanism whereby DNA strand invasions enable chromosomes to find their homologues during meiosis.
Abstract: Gene conversion is the non-reciprocal transfer of DNA sequences from one gene to a related gene elsewhere in the genome. Molecular evidence for its occurrence in higher eukaryotes was first described by our laboratory in 1980 in the two linked human foetal $\gamma$ -globin genes. Over a kilobase of DNA was converted in this initial example. Other investigators have since described more examples of gene conversion including some in which the sequence that was transferred is much shorter. We have now accumulated evidence for a series of such small gene conversions in the human foetal globin gene pair. The number of small gene conversions that we have been able to detect leads us to suggest that gene conversions are the consequence of a general mechanism whereby DNA strand invasions enable chromosomes to find their homologues during meiosis.
105 citations
TL;DR: Data is reported suggesting that a single gene is mainly expressed in several tissues examined, and its sequence shows three introns that are identical to that of cDNA clone isolated from human liver.
Abstract: A recently reported cDNA clone coding for human promyelocytic L apoferritin, shows some differences with a liver L apoferritin cDNA. We have investigated if these differences are due to the expression of different genes or to an alternative transcription of an unique gene. In this paper we report data suggesting that a single gene is mainly expressed in several tissues examined. This gene has been cloned and characterized. Its sequence shows three introns: the exon sequence is identical to that of cDNA clone isolated from human liver. A minimum of five related pseudogenes have been also analysed. One of them is a processed pseudogene interrupted by an intron-like fragment.
TL;DR: The gene coding for the α-subunit of the mitochondrial ATPase was localized in the mitochondrial genome of Oenothera and created a pseudogene, where a reading frame continuous with upstream sequences has abolished normal levels of transcription.
Abstract: The gene coding for the α-subunit of the mitochondrial ATPase was localized in the mitochondrial genome of Oenothera. Several pseudogenes are encoded besides the single intact reading frame. A rearrangement in the initiation codon of the open reading frame has created a pseudogene, where a reading frame continuous with upstream sequences has abolished normal levels of transcription. A second reorganisation 264 bp downstream has created a third locus containing the 5′ portion of the first pseudogene. This latter sequence is located on one of the small circular mitochondrial molecules.
TL;DR: Most of the observed L1 repeats are at a dead end with respect to either the expression of the L1 protein or the potential to elaborate further copies of themselves, but the turnover of L1 pseudogenes is sufficient to constitute a vast flux of sequences into and then out of the flanking regions of all cellular genes.
Abstract: L1 is a family of long interspersed repetitive sequences in mammals that includes the BamHI family in rodents and the KpnI family in primates. Previous studies have shown that L1 repeats contain a long open reading frame and that the family evolves in concert. Working with 32 rodent elements for which DNA sequence is available, we used the distribution of replacement and synonymous changes to determine which L1 lineages had been expressing their reading frame. The evidence obtained is consistent with there having been a small number of L1 genes that have been expressing a functional protein. Much of the concerted evolution in L1 is accounted for by the tendency of these functioning L1 genes to continually create nonfunctional pseudogenes by reinsertion into the genome of sequences derived from their transcripts. The gain of new pseudogenes is balanced by the loss of old pseudogenes with a half-life of 2 Myr. Therefore, most of the observed L1 repeats are at a dead end with respect to either the expression of the L1 protein or the potential to elaborate further copies of themselves. However, the turnover of L1 pseudogenes is sufficient to constitute a vast flux of sequences into and then out of the flanking regions of all cellular genes. If the presence of flanking L1 pseudogenes affects the expression of other genes in even a subtle fashion, this process should represent a major source of genetic variation. A second level of concerted evolution occurs within the functional L1 sequences in a pattern that did not meet our expectations for selfish DNA. Also, in spite of the marked suppression of replacement relative to synonymous changes in functioning L1 genes, they evolve at an overall rate accelerated to the level of their own pseudogenes.
TL;DR: It is predicted that the p21 protein encoded by the Harvey virus differs from the cellular c-rasH-1-encoded p21 at only two amino acids; those at positions 12 and 59; Alterations at each of these positions may play a role in activating the viral p21protein.
Abstract: We present the nucleotide sequence of the coding region of the rat c-rasH-1 gene and a partial sequence analysis of the rat c-rasH-2 gene. By comparing these sequences with the Harvey murine sarcoma virus ras gene, we predict that the p21 protein encoded by the Harvey virus differs from the cellular c-rasH-1-encoded p21 at only two amino acids; those at positions 12 and 59. Alterations at each of these positions may play a role in activating the viral p21 protein. The c-rasH-2 gene is likely to be a nonfunctional pseudogene because it lacks introns, cannot be activated to transform NIH 3T3 cells, and differs in sequence from both c-rasH-1 and v-rasH at several base pair positions.
TL;DR: The isolation of several members of a human heat shock protein 70 (hsp 70) multigene family which contains at least 10 different genes and/or pseudogenes exhibiting sequence homology to the hsp70 gene of Drosophila melanogaster is reported.
TL;DR: The rabbit gene cluster is unique in the absence of duplicated alpha-globin genes that are undergoing concerted evolution, and a partial sequence reveals frameshift mutations that probably make psi zeta a pseudogene.
TL;DR: It is demonstrated that the human lambda gene family is more complex than previously recognized, with at least two genes potentially functional, with open reading frames.
Abstract: Three new human lambda L chain-like Ig genes are identified by restriction enzyme and nucleotide sequence analysis. Two genes, 14.1 and 16.1, have intact J and C regions, and are potentially functional, with open reading frames. A third gene, 18.1, is a pseudogene. The evolutionary lineage of these genes compared to the known functional locus lambda C1-lambda C6 can be surmised from Southern blot and nucleotide homologies. This study demonstrates that the human lambda gene family is more complex than previously recognized.
TL;DR: The detailed structural and developmental characterization of four chorion genes and a truncated pseudogene located within a 9.5 X 10(3) base chromosomal segment in Bombyx mori revealed numerous, very short sequence elements that are shared.
TL;DR: In this paper, the authors presented the sequence of the MT-1 structural gene and compared its features with other metallothionein genes, and concluded that the absence of detectable transcripts from this pseudogene is due to either a reduced level of transcription or the formation of unstable transcripts as a consequence of the lack of a consensus sequence normally found 3' of transcription termination.
Abstract: As shown by Southern blot analysis, the metallothionein-1 (MT-1) genes in rats comprise a multigene family. We present the sequence of the MT-1 structural gene and compare its features with other metallothionein genes. Three MT-1 pseudogenes which we sequenced apparently arose by reverse transcription of processed mRNA transcripts. Two of these, MT-1 psi a and MT-1 psi c, are retrogenes which derive from the MT-1 mRNA, having diverged from the MT-1 gene 6.9 and 2.6 million years ago, respectively. The third, MT-1 psi b, differs from the MT-1 cDNA by only three nucleotide alterations. Surprisingly, MT-1 psi b also preserves sequence homology for 142 base pairs 5' to the transcription initiation site of the parent gene; it contains a promoter sequence sufficient for specifying metal ion induction. We identified, by S1 nuclease mapping, an RNA polymerase II initiation site 432 base pairs 5' of the MT-1 transcription initiation site of the MT-1 structural gene which could explain the formation of the mRNA precursor to this pseudogene. We were unable to detect MT-1 psi b transcripts, either in liver tissue or after transfection. We conclude that the absence of detectable transcripts from this pseudogene is due to either a reduced level of transcription or the formation of unstable transcripts as a consequence of the lack of a consensus sequence normally found 3' of transcription termination in the MT-1 structural gene.
TL;DR: The complete nucleotide sequence of a gene located immediately downstream from the adult α1-globin gene of the orang-utan, along with its flanking DNA is reported, and it is shown that it contains the essential sequence elements required for an expressive gene.
Abstract: The α-like and β-like globin genes have provided a paradigm for the study of molecular evolution and regulation of multigene families in eukaryotes. The human α-globin gene cluster, which is on chromosome 16 (ref. 1), consists of six genes arranged in the order2–5 5′-ζ(embryonic)-ψζ-ψα2-ψα1-α2(adult)-α1(adult)-3′. DNA sequencing data have demonstrated that ζ (ref. 6) and α2 (or α1, refs 7–9) are the embryonic and adult genes, respectively, while ψζ (ref. 6), ψα2 (ref. 5) ψα1 (ref. 10) are all inactive pseudogenes. Restriction mapping analysis has shown that the structure of this locus in several anthropoid primates is nearly identical to that of the human11,12. Recently, we have isolated the adult α-globin gene region from orang-utan, olive baboon and rhesus macaque by molecular cloning. We report here the complete nucleotide sequence of a gene located immediately downstream from the adult α1-globin gene of the orang-utan, along with its flanking DNA. We designate this gene as θ1, and show that it contains the essential sequence elements required for an expressive gene. The putative polypeptide is 141 amino acids long, identical to that of the α- or ζ-globin, but its predicted amino-acid sequence is nearly as different from the orang-utan α-globin (55 differences) as the human ζ-globin is from the human α-globin (59 differences), suggesting an ancient history for the θ1 -globin gene. Results of blot hybridization experiments using the cloned orang-utan θ1 gene sequence as probe demonstrate a similar α2-α1-θ1 linkage map existing in the human genome. Furthermore, multiple copies of sequences homologous to the θ1 gene are detected in both human and orang-utan. These results cast a new light on the primate α-globin gene family, and have intriguing implications for the existence of previously unreported, functional globin-like gene(s) in the primate genomes.
TL;DR: The discovery of another pseudogene, psi alpha 2, between the previously recognized pseudogenes zeta 1 and psi alpha 1, and its discovery by sequence analysis suggests that divergent copies of a large number of genes may comprise a substantial fraction of the slowly renaturing DNA of mammalian genomes.
Abstract: The sequence of the DNA between two pseudogenes in the human alpha-like globin gene cluster has been determined. Comparison of this sequence with sequences from other alpha-like globin gene clusters revealed another pseudogene, psi alpha 2, between the previously recognized pseudogenes zeta 1 and psi alpha 1. Therefore, the human alpha-like globin gene family is organized 5'-zeta 2-zeta 1-psi alpha 2-psi alpha 1-alpha 2-alpha 1-3'. The new pseudogene psi alpha 2 is very close to zeta 1, beginning only 65 base pairs 3' to the polyadenylation site of zeta 1. The first exon and the first intron of psi alpha 2 are interrupted by large inserts which are flanked by short (6 to 8 base pairs) direct repeats. The pseudogene psi alpha 2 lacks a promoter for transcription by RNA polymerase II, the first exon is highly divergent, one splice site is mutated, and five different frameshift mutations have occurred in the coding regions. Thus psi alpha 2 cannot encode a globin polypeptide. This pseudogene was not recognized in previous hybridization analyses of the human alpha-like globin gene cluster, and our discovery of it by sequence analysis suggests that divergent copies of a large number of genes may comprise a substantial fraction of the slowly renaturing DNA of mammalian genomes.
TL;DR: The phylogenetic distribution of the processed pseudogenes analysed to date suggests that these genetic elements are present only in mammals, and certain features of retroviruses themselves make them plausible candidates for mediating processed gene formation.
TL;DR: One of these genes was subcloned in plasmid pUC8 and the recombinant plasmids obtained was shown to direct the synthesis of a low but detectable IFN-α activity in Escherichia coli JM103.
Abstract: Nine distinct genomic clones containing human alpha 1-interferon (IFN-alpha 1) related sequences were isolated from a porcine genomic library constructed in phage lambda Restriction mapping and Southern blot analysis revealed that these clones contained a total of 10 potential porcine IFN-alpha genes or pseudogenes belonging to a multigene family of at least 12 members One of these genes was subcloned in plasmid pUC8 and the recombinant plasmid obtained was shown to direct the synthesis of a low but detectable IFN-alpha activity in Escherichia coli JM103 The sequence of this porcine IFN-alpha gene (Po IFN-alpha 1) was determined As expected, it contained no introns and encoded a 189-amino-acid-long preprotein with a putative signal peptide of 23 residues The homology to human (Hu)IFN-alpha 1 was 785% at the nucleotide level and 64% at the amino acid level
TL;DR: Five germline V beta gene segments that are homologous to the V region of the YT35 cDNA encoding the beta chain of the T cell antigen receptor from the tumor MOLT-3 are isolated and sequenced.
Abstract: We have isolated and sequenced five germline V beta gene segments that are homologous to the V region of the YT35 cDNA encoding the beta chain of the T cell antigen receptor from the tumor MOLT-3. One of these gene segments is identical to the YT35 V segment, and therefore is the corresponding germline V beta gene segment encoding the YT35 cDNA. The other four V beta members exhibit 77-98% homology to the YT35 V gene segment. Two of these V beta gene segments are pseudogenes. Analyses of the coding region sequences reveal that, although the V beta segments are very diverse, they are mutating at a rate comparable to that observed in most eukaryotic genes. Analyses of the genomic clones show that the spacing distance between germline V beta gene segments ranges from 3 kb to greater than 30 kb, and the entire V beta 8 subfamily appears to be linked by a total of no more than 110 kb of DNA.
TL;DR: This report describes the isolation and characterization of genomic and cDNA clones which define a subfamily of type I keratins in Xenopus laevis whose expression is restricted to embryonic and larval stages and indicates that all members of the subfamily have been isolated.
Abstract: This report describes the isolation and characterization of genomic and cDNA clones which define a subfamily of type I keratins in Xenopus laevis whose expression is restricted to embryonic and larval stages. The XK81 subfamily, named after the prototype cDNA clone DG81, contains four members arranged in two pairs of closely homologous loci; they were named 81A1, A2, B1, and B2. Genomic clones were obtained representing all of these regions. The A1 gene has been completely sequenced together with approximately 1 kb of flanking sequences at each end; this gene corresponds to the previously reported cDNA clone 8128 (Jonas, E., T. D. Sargent, and I. B. Dawid, 1985, Proc. Natl. Acad. Sci. USA, 82:5413-5417). The B2 gene is represented by a partial cDNA clone, DG118. Upstream sequences and about half of the coding regions have been sequenced for the B1 and B2 genes, whereas the A2 locus has been identified on the basis of hybridization data and could be a gene or pseudogene. Genomic Southern blotting indicates that all members of the subfamily have been isolated. The keratin proteins encoded by the B1 and B2 genes are 96% homologous in the central rod domain, whereas A/B gene homology in this region is 81%. During development mRNAs derived from A and B genes accumulate coordinately during gastrula and neurula stages; in the tadpole, 81A mRNA decays rapidly, whereas 81B mRNA shows a second abundance peak, persists for most of tadpole life, and decays by metamorphosis. RNAs derived from the XK81 keratin subfamily are undetectable in the adult, where different type I keratin genes are expressed.
TL;DR: The genome of Chinese hamster ovary (CHO) cells contains a complex family of approximately 16 alpha-tubulin genes, many of which may be pseudogenes; one of these genes has been identified only in CHO cells, and members of this class may play a unique role in vivo.
Abstract: The genome of Chinese hamster ovary (CHO) cells contains a complex family of approximately 16 alpha-tubulin genes, many of which may be pseudogenes. We present here the complete cDNA sequences of three expressed alpha-tubulin genes; one of these genes has been identified only in CHO cells. The noncoding regions of these three CHO alpha-tubulin genes differed significantly, but their coding regions were highly conserved. Nevertheless, we observed differences in the predicted amino acid sequences for the three genes. A comparison of the CHO alpha-tubulin sequences with all of the sequences available for mammals allowed assignment of the alpha-tubulin genes to three classes. The proteins encoded by the members of two of these classes showed no class-specific amino acids among the mammalian species examined. The gene belonging to the third class encoded an isoprotein which was clearly distinct, and members of this class may play a unique role in vivo. Sequencing of the three alpha-tubulin genes was also undertaken in CMR795, a colcemid-resistant clonal CHO cell line which has previously been shown to have structural and functional alterations in its tubulin proteins. We found differences in the tubulin nucleotide sequence compared with the parental line; however, no differences in the alpha-tubulin proteins encoded in the two cell lines were observed.
TL;DR: The sequence of a 2.5 kb mRNA in human fibroblasts encoding a 248 amino acid cytoskeletal tropomyosin is determined and the protein product of this mRNA is TM30nm, one of five tropomyOSin-like proteins in human fibre cells.
Abstract: We have determined the sequence of a 2.5 kb mRNA in human fibroblasts encoding a 248 amino acid cytoskeletal tropomyosin. The protein product of this mRNA is TM30nm, one of five tropomyosin-like proteins in human fibroblasts. The structural gene encoding this mRNA can also produce a 1.3 kb mRNA encoding a 285 amino acid skeletal muscle alpha-tropomyosin by tissue-specific alternative mRNA splicing. However, the multiple RNA-copy pseudogenes of this gene family are derived largely if not exclusively from transcripts processed according to the pattern observed in non-muscle cells.
TL;DR: It is shown for the first time that homologous in vitro transcription of mammalian tRNA genes strongly depends on extragenic control regions, and interestingly, as a consequence of different flanking regions, the transcription efficiencies vary by an order of magnitude among the genes for the major and the minor tRNAVal and thus reflect the concentrations of these tRNAs in vivo.
TL;DR: The likely age of the nuclear sequence element from the divergence between nuclear and mitochondrial sequences and from cross-hybridization with the genomes of other sea urchin species is suggested, with an age of more than 30 million years is suggested.