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At least 613 records · Page 34Linked to original sources
PubMed1991

Characterization of an alpha 1----3-galactosyltransferase homologue on human chromosome 12 that is organized as a processed pseudogene.

UDP-Gal:Gal beta 1----4GlcNAc alpha 1----3-galactosyltransferase is a terminal glycosyltransferase that is widely expressed in a variety of mammalian species, with the notable exception of man, apes, and Old World monkeys. We recently reported the isolation of a bovine cDNA clone that contains the complete coding sequence for this enzyme (Joziasse, D. H., Shaper, J. H., Van den Eijnden, D. H., Van Tunen, A. J., and Shaper, N. L. (1989) J. Biol. Chem. 264, 14290-14297). Using this cDNA as a probe, we have demonstrated that, although transcripts cannot be detected in a variety of established human cell lines by Northern blot analysis, homologous sequences are present in human genomic DNA. To establish that these sequences represent a human homologue of alpha 1----3-galactosyltransferase, we have used the bovine cDNA as a probe to isolate two nonoverlapping clones (HGT-2 and HGT-10) from a human genomic DNA library. Clone HGT-2 contains a 1.5-kilobase uninterrupted linear sequence similar to bovine alpha 1----3-galactosyltransferase that is organized as a processed pseudogene. This sequence, flanked by Alu type repeats, contains a short 5'- and 3'-untranslated region and a complete recognizable coding region that is 81% similar at the nucleotide level to bovine alpha 1----3-galactosyltransferase. This putative coding region contains multiple frameshift mutations and nonsense codons in all three reading frames which precludes the synthesis of a functional enzyme. Nevertheless, after optimal alignment, translation predicts a polypeptide that is 68% similar at the amino acid level to the bovine enzyme. Based on Southern analysis and limited sequence analysis, clone HGT-10 contains coding sequences similar to the NH2-terminal region of bovine alpha 1----3-galactosyltransferase. By analysis of panels of human-rodent somatic cell hybrids we have established that the nonfunctional, processed pseudogene and the human homologue represented by HGT-10 are located on human chromosomes 12 and 9, respectively. Interestingly, a comparison of the predicted amino acid sequence of the carboxyl-terminal two-thirds of human alpha 1----3-galactosyltransferase, with the corresponding region of the human blood group A, UDP-GalNAc:[Fuc alpha 1----2]Gal beta 1----4GlcNAc alpha 1----3-GalNAc-transferase (Yamamoto, F., Marken, J., Tsuji, T., White, T., Clausen, H., and Hakomori, S. (1990a) J. Biol. Chem. 265, 1146-1151), reveals a significant similarity (39%) suggesting that these two enzymes may have arisen from the same ancestral gene as a result of gene duplication and subsequent divergence.

Amino Acid Sequence↗
PubMed1990

[Tissue-specific blocking of the EcoRI site adjacent to the pseudogene for mouse oncoprotein p53].

EcoRI fragments of DNA isolated from the different mouse organs were hybridized to radioactivity labelled probe specific for the gene of oncoprotein p53. The analysis of the blot-hybridization points to the existence of the specific blockage of an EcoRI site flanking a 3.3 kb fragment of DNA including the pseudogene p53, isolated from the skin tissue. The existence of a polymorphous EcoRI site localized distally to the pseudogene p53 has been demonstrated in the DNA of mice of different lines.

Animals↗
PubMed1990

Identification of rabbit genomic Ig-VH pseudogenes that could serve as donor sequences for latent allotype expression.

Synthetic DNA oligomers specific for the VHa allotypes of rabbit Ig genes have been used to identify latent allotypic sequences in homozygous a1 and a2 rabbits. Two Ig VH pseudogenes containing latent a3 regions have been cloned from the genome of a homozygous a2 rabbit. Analysis of the regions associated with allotype expression indicates that these two pseudogenes contain VHa- sequences in framework region 1 (FR1) and VHa3 sequences in FR3. One gene has undergone an unusual rearrangement with a third VH gene, deleting their intervening sequences and recombining in FR3 with sequences 5' to the leader exon. Our results demonstrate the presence of latent VH sequences in the genomic DNA of normal rabbits and suggest that a mechanism such as gene conversion is responsible for expression of genetically-unexpected Ig VH genes.

Amino Acid Sequence↗
PubMed1990

Cloning and sequencing of a processed pseudogene derived from a human class III alcohol dehydrogenase gene.

Current information on the molecular structure of human alcohol dehydrogenase (ADH) genes is fragmentary. To characterize all ADH genes, we have isolated 63 ADH clones from human genomic libraries made from one individual. Fifty-nine clones have been classified into five previously known loci: ADH1 (18 clones), ADH2 (20 clones), and ADH3 class I (16 clones), ADH4 class II (4 clones), and ADH5 class III (1 clone). Sequencing of one of the remaining four unclassified clones, SY lambda ADHE38, about 1.1 kb in length, shows no introns and three frameshift mutations in the coding region, with a total of 10 internal termination codons. When its deduced amino acid sequence was compared with those of the class I, class II, and class III ADHs, the proportions of identical amino acids were 56.7%, 55.5%, and 88.7%, respectively, suggesting that the processed pseudogene was derived from an ADH5 gene. The duplication event seems to have occurred about 3.5 million years ago, and the pseudogene has undergone a rapid change since then.

Alcohol Dehydrogenase↗
PubMed1989

The human debrisoquine 4-hydroxylase (CYP2D) locus: sequence and identification of the polymorphic CYP2D6 gene, a related gene, and a pseudogene.

The debrisoquine-4-hydroxylase polymorphism is a genetic variation in oxidative drug metabolism characterized by two phenotypes, the extensive metabolizer (EM) and poor metabolizer (PM). Of the Caucasian populations of Europe and North America, 5%-10% are of the PM phenotype and are unable to metabolize debrisoquine and numerous other drugs. The defect is caused by several mutant alleles of the CYP2D6 gene, two of which are detected in about 70% of PMs. We have constructed a genomic library from lymphocyte DNA of an EM positively identified by pedigree analysis to be homozygous for the normal CYP2D6 allele. The normal CYP2D6 gene was isolated; was completely sequenced, including 1,531 and 3,522 bp of 5' and 3' flanking DNA, respectively; and was found to contain nine exons within 4,378 bp. Two other genes, designated CYP2D7 and CYP2D8P, were also cloned and sequenced. CYP2D8P contains several gene-disrupting insertions, deletions, and termination codons within its exons, indicating that this is a pseudogene. CYP2D7, which is just downstream of CYP2D8P, is apparently normal, except for the presence, in the first exon, of an insertion that disrupts the reading frame. A hypothesis is presented that the presence of a pseudogene within the CYP2D subfamily transfers detrimental mutations via gene conversions into the CYP2D6 gene, thus accounting for the high frequency of mutations observed in the CYP2D6 gene in humans.

Amino Acid Sequence↗
PubMed1988

Assignment of the functional gene for human adrenodoxin to chromosome 11q13----qter and of adrenodoxin pseudogenes to chromosome 20cen----q13.1.

Adrenodoxin is a small iron/sulfur protein serving as an electron-transport intermediate for all mitochondrial forms of cytochrome P450. Southern blots of normal genomic DNA cleaved with six restriction endonucleases probed with full-length human adrenodoxin cDNA revealed complex patterns indicating the presence of multiple adrenodoxin genes. Southern blots of DNA from a panel of mouse/human somatic cell hybrids identified cross-hybridizing adrenodoxin DNA in two loci, chromosome 11q13----qter and chromosome 20cen----q13.1. Examination of adrenodoxin clones from a genomic DNA library in phage lambda revealed some clones bearing gene fragments interrupted by introns and other clones bearing processed pseudogenes. By probing the mouse/human hybrids with unique intronic DNA and by correlating restriction maps of the phage clones with that of uncloned genomic DNA, we show that the authentic transcribed adrenodoxin gene lies on chromosome 11, while pseudogenes lie on chromosome 20.

Adrenodoxin↗
PubMed1993

Mutational analysis of a patient with mucopolysaccharidosis type VII, and identification of pseudogenes.

PCR of cDNA produced from patient fibroblasts allowed us to determine the paternal mutation in the first patient reported with beta-glucuronidase-deficiency mucopolysaccharidosis type VII (MPS VII). The G-->T transversion 1,881 bp downstream of the ATG translation initiation codon destroys an MboII restriction site and converts Trp627 to Cys (W627C). Digestion of genomic DNA PCR fragments with MboII indicated that the patient and the father were heterozygous for this missense mutation in exon 12. Failure to find cDNAs from patient RNA which did not contain this mutation suggested that the maternal mutation leads to greatly reduced synthesis or reduced stability of mRNA from the mutant allele. In order to identify the maternal mutation, it was necessary to analyze genomic sequences. This approach was complicated by the finding of multiple unprocessed pseudogenes and/or closely related genes. Using PCR with a panel of human/rodent hybrid cell lines, we found that these pseudogenes were present over chromosomes 5-7, 20, and 22 and the Y chromosome. Conditions were defined which allowed us to amplify and characterize genomic sequences for the true beta-glucuronidase gene despite this background of related sequences. The patient proved to be heterozygous for a second mutation, in which a C-->T transition introduces a termination codon (R356STOP) in exon 7. The mother was also heterozygous for this mutation. Expression of a cDNA containing the maternal mutation produced no enzyme activity, as expected. Expression of the paternal mutation in COS-7 cells produced a surprisingly high (65% of control) level of activity. However, activity was 13% of control in transiently transfected murine MPS VII cells. The level of activity of this mutant allele appears to correlate with the level of overexpression, suggesting that high concentrations of mutant monomers can drive the folding and tetramerization of mutant enzyme to produce an active and stable enzyme.

Animals↗
PubMed1993

Abundant adrenal-specific transcription of the human P450c21A "pseudogene".

Human adrenal steroid 21-hydroxylase (P450c21) is encoded by the CYP21A1 (21B) gene located in the class III region of the HLA locus. A tandemly duplicated gene designated CYP21A1P (21A), which lies 30 kilobases upstream, contains several point mutations and an 8-base pair deletion so that it cannot encode P450c21 protein; as a result, it is generally considered to be a pseudogene. We previously showed that two additional genes, XA and XB, lie on the opposite strand of DNA overlapping the 3'-ends of the 21A and 21B genes. We have now identified a third pair of duplicated overlapping genes in this locus, termed YA and YB, whose transcriptional orientation is the same as 21A and 21B and opposite to XA and XB. YA transcripts use the 21A promoter, have 5'-ends that are similar to 21B mRNA, and have approximately 10-20% of the abundance of 21B transcripts, but have unique 3'-ends. The YA gene encodes a 7.5-kilobase RNA that overlaps XA completely and a 3.0-kilobase RNA that excludes most of XA. The YB gene appears to be similar in size and organization to YA. The YA and YB genes extend beyond the limit of the duplication in this locus; hence, their cDNAs are distinguishable by differences in their 3'-sequences. YA and YB transcripts are expressed only in the fetal and adult adrenal glands, but their cDNAs do not contain a long open reading frame. Although the function of these genes is not yet clear, the complex genetic organization of three overlapping genes (21/X/Y) appears to be unique among higher eukaryotes. As YA transcription is initiated by the 21A 5'-flanking DNA and includes 21A sequences, the designation of 21A as a "pseudogene" merits reconsideration.

Adrenal Glands↗
PubMed1985

Sequence structures of a mouse major urinary protein gene and pseudogene compared.

Laboratory mouse strains carry approximately 35 major urinary protein (MUP) genes per haploid genome, tightly clustered together on chromosome 4. Most belong to two main groups (Groups 1 and 2). The available evidence strongly suggests that the Group 1 genes are active while the Group 2 genes are pseudogenes. Here we present the complete sequence of a Group 1 gene and a Group 2 gene and 700 bp of flanking sequence. The sequence of the Group 1 gene is consistent with its being active. The Group 2 gene contains two stop codons and a frame-shift mutation in the reading frame defined by the Group 1 gene, and would code for a signal peptide 25 rather than 19 amino acids long. The Group 2 gene differs from the Group 1 gene in other ways: a deletion upstream of the TATA box and another in intron 3, a base change in the TATA box itself, a 2 bp duplication at the splice acceptor boundary of intron 6, an altered poly(A) addition signal and a 1-base deletion 5' to the initiation codon. Some of these differences may explain the 10- to 20-fold higher level of Group 1 mRNA in mouse liver, and the fact that Group 1 and Group 2 transcripts are mainly spliced differently. The presence of the stop codon means that the Group 2 gene is a pseudogene in the context of the Group 1 gene. However, there is some evidence that the mature hexapeptide that it would code for may have biological activity. The 12 acceptor splice sites of the two genes all contain the identical sequence ACAG at the exon boundary.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1980

The structure of a human alpha-globin pseudogene and its relationship to alpha-globin gene duplication.

The complete nucleotide sequence of a human alpha-globin pseudogene (psi alpha 1) is presented. Comparison of this sequence with a normal human alpha-globin gene (alpha 2) reveals that psi alpha 1 contains both an initiator codon mutation and frameshift deletions which would prevent the production of an alpha-globin polypeptide. psi alpha 1 contains two intervening sequences with sizes and locations characteristic of mammalian alpha-globin genes. However, the alteration or absence of putative splicing sequences suggests that a primary transcript of psi alpha 1 would not be processed to produce a mature mRNA. The relationship of pse alpha 1 to the adjacent duplicated alpha-globin genes alpha 1 and alpha 2 has been investigated at the nucleotide sequence level. psi alpha 1, alpha 2 and alpha 1 each possess the sequence GCCTGTGTGTGCCTG directly following their respective poly(A) addition sites. Sequence analysis of alpha 2 and alpha 1 3' flanking regions further reveals that the alpha-globin gene duplication units are exactly bordered by this homologous sequence. We discuss the possible evolutionary origin of psi alpha 1 and other globin pseudogenes in the context of globin gene duplication.

Animals↗
PubMed1983

Evolutionary history of a multigene family: an expressed human beta-tubulin gene and three processed pseudogenes.

A 3' untranslated region subclone from a human beta-tubulin cDNA clone has been used to dissect the human beta-tubulin multigene family. Four different beta-tubulin sequences were obtained. One consists of an expressed gene that yields two mRNA species of 1.8 kb and 2.6 kb as a consequence of alternative polyadenylation sites. The three remaining beta-tubulin sequences are all intronless pseudogenes, each containing a 3' poly(A) tract downstream from the poly(A) signal, and each flanked by a different short direct repeat. Two of these sequences were derived by integration into the host germ line of cDNA copies of the 1.8 kb mRNA; the third was derived from the 2.6 kb mRNA. Comparison of the functional and nonfunctional sequences suggests that the integration events took place 4, 10, and 13 million years ago. We anticipate that, in multigene families where germ-line expression occurs, a significant portion of sequences will be accounted for by pseudogenes generated via an RNA intermediate.

Amino Acid Sequence↗
PubMed1983

Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites.

We find that both human and rat U3 snRNA can function as self-priming templates for AMV reverse transcriptase in vitro. The 74 base cDNA is primed by the 3' end of intact U3 snRNA, and spans the characteristically truncated 69 or 70 base U3 sequence found in four different human U3 pseudogenes. The ability of human and rat U3 snRNA to self-prime is consistent with a U3 secondary structure model derived by a comparison between rat U3 snRNA and the homologous D2 snRNA from Dictyostelium discoideum. We propose that U3 pseudogenes are generated in vivo by integration of a self-primed cDNA copy of U3 snRNA at new chromosomal sites. We also consider the possibility that the same cDNA mediates gene conversion at the 5' end of bona fide U3 genes where, over the entire region spanned by the U3 cDNA, the two rat U3 sequence variants U3A and U3B are identical.

Animals↗
PubMed1984

A single locus in the mouse encodes both myosin light chains 1 and 3, a second locus corresponds to a related pseudogene.

Two loci have been characterized in the mouse Mus musculus, which are homologous to the mRNAs encoding myosin light chains MLC1F and MLC3F, two proteins with a common -COOH terminal sequence. One of these loci is an intronless pseudogene, absent from the mouse species Mus spretus; alterations in its nucleotide sequence preclude it from generating a functional MLC1F or MLC3F. The other contains the genetic information for the two proteins. The part common to both proteins is encoded by five exons, which cover about 6.5 kb. Genetic information specific for the N-terminal sequences is encoded in four exons, at 3.5 and 14.3 kb for MLC1F, and 3.8 and 4.5 kb for MLC3F, upstream of the first common exon. Each 5' terminus has a TATA-like consensus sequence about 30 bases upstream of the cap site. The pseudogene is not genetically linked to the functional MLC1F/MLC3F locus in the genome of Mus musculus.

Amino Acid Sequence↗
PubMed1987

Rat ribosomal protein L35a multigene family: molecular structure and characterization of three L35a-related pseudogenes.

The rat ribosomal protein L35a gene comprises a multigene family which contains 15-20 members as shown by the Southern blot analysis using L35a cDNA as a probe. We isolated 15 independent clones which contained distinct genes from a rat genomic library. Analysis of the restriction sites showed that all of them lacked the intervening sequences. Thermal stability of the hybrid molecules between these genes and the cDNA indicated that the similarity of the genes to the cDNA sequence varied. The nucleotide sequences of three genes gRL35a-A, gRL35a-B and gRL35a-G were determined. They shared some characteristics; namely: they lacked the intervening sequences, they contained (A)-rich tracts, and they were flanked by direct repeats. Two genes, gRL35a-A and gRL35a-B, contained a sequence completely identical to that of the cDNA. The nucleotide sequence of the 5' flanking region of gRL35a-B showed a significant homology with that of the same region of mouse ribosomal protein L32-related unmutated processed genes. Although this region of gRL35a-B contained the sequences homologous to the TATA box and the CCAAT box, gRL35a-B was not transcribed in an in vitro assay system. Thus, the L35a gene family comprises mostly processed pseudogenes. Further, Southern blot analysis in various animals indicated that the multigene construction of this ribosomal protein gene was a feature of mammalian genes. The origin and the evolutionary aspect of processed pseudogenes are discussed.

Animals↗
PubMed1984

A human dihydrofolate reductase intronless pseudogene with an Alu repetitive sequence: multiple DNA insertions at a single chromosomal site.

A dihydrofolate reductase (DHFR) pseudogene, hDHFR-psi 3 has been isolated from a human genomic DNA fragment library. Sequence analysis of this gene revealed a lack of introns and the presence of a tract of nine adenines, 90 bp downstream from the end of the coding sequence. These features suggest that hDHFR-psi 3 was derived from a processed RNA molecule that has been converted into DNA and inserted into a chromosome, analogous to the origin of three intronless human DHFR genes previously described. An interesting feature of hDHFR-psi 3 is the presence of a member of the Alu moderately repetitive DNA sequence family within the DHFR coding region. This Alu element is flanked by a 16 bp directly repeated DNA segment derived from DHFR coding sequences. The Alu element apparently has been inserted into the intronless DHFR pseudogene and thus, there have been two insertions at a single chromosomal locus. The hDHFR-psi 3 contains only the 3' half of the DHFR coding sequence. Immediately upstream from the directly repeated sequence before the Alu element is an adenine-rich tract. The DNA farther upstream is moderately repetitive and is related to neither DHFR nor Alu DNA sequence. Therefore, it seems possible that a third insertion has occurred at the same site further disrupting the hDHFR coding sequences.

Base Sequence↗
PubMed1985

The structure of a cloned mouse gamma-actin processed pseudogene.

The complete nucleotide (nt) sequence of a gamma-actin-like pseudogene (M gamma A-psi 1), isolated from a mouse genomic library in phage lambda, was determined. The pseudogene was shown to be of the processed type by the fact that it lacked introns, ended in a poly(dA) region, and was flanked by direct repeats. There were ten differences in the predicted amino acid (aa) sequence from that of the authentic nonmuscle gamma-actin. An unusual feature of M gamma A-psi 1 was the complete absence of DNA corresponding to the 5' end of the mRNA up to the nt preceding the Ala codon at aa position 7. This suggests that M gamma A-psi 1 originated from a truncated mRNA or from an incomplete reverse transcript.

Actins↗
PubMed1983

A human dihydrofolate reductase pseudogene and its relationship to the multiple forms of specific messenger RNA.

The presence of dihydrofolate reductase (DHFRase)-specific sequences that, in contrast to the normal DHFRase gene, are not amplified in a methotrexate-resistant cell line, has been detected in the DNA from human sperm and from several human cell lines. DNA fragments containing some of these sequences have been isolated from a cosmid library of human sperm DNA. One of these fragments contains a DHFRase pseudogene (psi HD1) that completely lacks introns, has 92% sequence homology to the corresponding region of normal DHFRase complementary DNA, but exhibits several alterations that make it nonfunctional. The sequence analysis of the inserts of four different plasmids containing the reading frame and varying lengths of the 3' non-coding regions of human DHFRase-specific cDNAs has revealed that the 3' non-coding segments all are colinear in their corresponding portions. Furthermore, the data indicate that the cDNA of one of the plasmids is probably derived from the smallest of the three main human DHFRase messenger RNAs, the 0.8 X 10(3) base (0.8 kb) mRNA, the cDNA of two others, from the 1.0 kb mRNA, and the cDNA of the fourth, from a longer mRNA. These results are consistent with the idea that the multiple forms of DHFRase mRNA in human cells derive from the same gene by different transcription or RNA-processing events. Moreover, the sequence comparison between the psi HD1 and the different DHFRase cDNAs clearly indicates that, if an mRNA intermediate has participated in the formation of this pseudogene, a form of mRNA larger than the 1.0 kb mRNA, probably the 3.8 kb mRNA, must have been involved.

Base Sequence↗
PubMed2001

Mitochondrial pseudogenes: evolution's misplaced witnesses.

Nuclear copies of mitochondrial DNA (mtDNA) have contaminated PCR-based mitochondrial studies of over 64 different animal species. Since the last review of these nuclear mitochondrial pseudogenes (Numts) in animals, Numts have been found in 53 of the species studied. The recent evidence suggests that Numts are not equally abundant in all species, for example they are more common in plants than in animals, and also more numerous in humans than in Drosophila. Methods for avoiding Numts have now been tested, and several recent studies demonstrate the potential utility of Numt DNA sequences in evolutionary studies. As relics of ancient mtDNA, these pseudogenes can be used to infer ancestral states or root mitochondrial phylogenies. Where they are numerous and selectively unconstrained, Numts are ideal for the study of spontaneous mutation in nuclear genomes.

Journal Article↗