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PubMed1991

Molecular cloning and characterization of a high affinity dopamine receptor (D1 beta) and its pseudogene.

We have cloned a novel human intronless gene encoding a G-protein-coupled receptor of the dopamine receptor family. Expression of this receptor in Cos-7 cells led to the high affinity binding of a number of dopamine D1 antagonists, with a binding profile similar to that of the previously described dopamine D1 receptor. In contrast, the agonist binding profile of this new receptor did not exactly match any previously defined dopamine D1 receptor and was notable for its unusually high affinity for dopamine. This new receptor caused a 13-fold increase in adenylylcyclase activity in transfected Cos-7 cells, following addition of dopamine. Messenger RNA encoding this new receptor appears to be widely distributed in the human brain, including cortical regions, choroid plexus, hippocampus, and brain stem. This new receptor appears to be identical to the recently described dopamine D5 receptor. A second closely related gene, GL39, was isolated and shown to represent a pseudogene, the first to be described in the G-protein-coupled receptor superfamily. This pseudogene exhibits 94% nucleotide sequence homology to the GL30 sequence and may have arisen from a gene duplication event followed by a mutation approximately 8 million years ago, prior to the emergence of man. This recently evolved pseudogene is transcribed in the human brain with a tissue distribution similar to that for its closely related functional gene.

Amino Acid Sequence↗
PubMed1991

DNA analysis in a MHC heterozygous patient with complete C4 deficiency--homozygosity for C4 gene deletion and C4 pseudogene.

Virtually all cases of inherited C4 deficiency appear to be caused by homozygosity for rare MHC haplotypes carrying combined defects of genes coding for the C4A and C4B isotypes. The present analysis concerned a C4-deficient patient with two different MHC haplotypes, [HLA-A2, B40, SC00, DR6] and [HLA-A30, B18, F1C00, DR3]. Digestion of genomic DNA from the patient with Taq I and probing with a 5' cDNA C4 probe and a CYP21-specific probe gave only a 7.0-kb and a 3.7-kb band, respectively. The analysis of restriction fragment length polymorphism in family members showed that both C4-deficient haplotypes contained a C4 pseudogene at the C4 locus I and a CYP21 gene together with a deletion of the C4B gene and the adjacent CYP21P gene. None of the C4 pseudogenes contained C4A- or C4B-specific nucleotide sequences as judged from hybridization studies of polymerase chain reaction products. The findings illustrate the high degree of polymorphism in C4 genes and that both gene deletions and presence of a C4 pseudogene are common as reasons for C4 null alleles. The rare C4 double null alleles appear to have arisen in different MHC haplotypes independently.

Adolescent↗
PubMedDate not supplied

[The loss of dinucleotides CpG from DNA. IV. Methylation and divergence of genes and pseudogenes of small nuclear RNA].

The frequency of neighboring base pairs in nucleotide sequences of over 80 genes and pseudogenes of low molecular weight RNAs U1-U8, 4.5S and 7S in different eukaryotes was determined. The probable frequency of CpG----TpG + CpA substitutions, caused as a result of the deamination of 5-methylcytosine residues in DNA, was determined. It was found that the genes of small RNAs do not reveal a single level of CpG methylation for all the species studied. In most cases CpG in the genes of U1, 4.5S and 7S RNA are methylated, whereas in the genes of U2-U6-RNA these sites must have never been subjected to methylation. Nearly all the investigated pseudogenes of different small RNAs are strongly methylated due to a considerable lack of CpG. It was established that CpG----TpG + CpA transitions may amount to as much third of all the mutations accumulated in the genes of the same RNAs in different species. Such transitions in pseudogenes may account for 40% of all the nucleotide substitutions. This disproportionately high level of mutations in CpG dinucleotides (3-5-fold higher than in other DNA dupletes) must be the direct result of the methylation of these sites. Consequently, CpG methylation causes a dramatic acceleration of the divergence rate of DNA sequences. It has been concluded that protection of most vital genes against methylation is one of the essential conditions for sustaining the high level of stability of the macromolecular structure and for the reliability of macromolecular functioning in a cell.

Animals↗
PubMed1987

Evolutionary implications of the human aldolase-A, -B, -C, and -pseudogene chromosome locations.

The aldolase genes represent an ancient gene family with tissue-specific isozymic forms expressed only in vertebrates. The chromosomal locations of the aldolase genes provide insight into their tissue-specific and developmentally regulated expression and evolution. DNA probes for the human aldolase-A and -C genes and for an aldolase pseudogene were used to quantify and map the aldolase loci in the haploid human genome. Genomic hybridization of restriction fragments determined that all the aldolase genes exist in single copy in the haploid human genome. Spot-blot analysis of sorted chromosomes mapped human aldolase A to chromosome 16, aldolase C to chromosome 17, the pseudogene to chromosome 10; it previously had mapped the aldolase-B gene to chromosome 9. All loci are unlinked and located on to two pairs of morphologically similar chromosomes, a situation consistent with tetraploidization during isozymic and vertebrate evolution. Sequence comparisons of expressed and flanking regions support this conclusion. These locations on similar chromosome pairs correctly predicted that the aldolase pseudogene arose when sequences from the aldolase-A gene were inserted into the homologous aldolase location on chromosome 10.

Base Sequence↗
PubMed1994

Nucleotide sequence of a human genomic DNA fragment containing the PCNA pseudogene and its localization on chromosome 4.

A one kb human genomic DNA fragment, containing a processed pseudogene of a proliferating cell nuclear antigen (PCNA/DNA polymerase delta auxiliary protein), was isolated and sequenced. The PCNA pseudogene consisted of the 3' half of exon 4 and the 5' half of exon 5 of the PCNA gene, and shared 84% nucleotide homology with the human PCNA cDNA. The PCNA pseudogene was localized on human chromosome 4, based on data obtained from a panel of human-mouse hybrid cell lines.

Animals↗
PubMed1994

How many 5S rRNA genes and pseudogenes are there in Aspergillus nidulans?

We have estimated the number of 5S rRNA genes in Aspergillus nidulans using two-dimensional agarose gel electrophoresis and hybridization to appropriate probes, representing the 5'-halves, the 3'-halves of the 5S rRNA sequence and a sequence found at the 3'-end of all known A. nidulans pseudogenes (block C). We have found 23 5S rRNA genes, 15 pseudogenes consisting of the 5'-half of the 5S rRNA sequence (of which 3 are flanked by block C) and 12 copies of block C which do not seem to be in the vicinity of 5S rRNA sequences. This number of genes is much lower than our earlier estimates, and makes our previously analyzed sample of 9 sequenced genes and 3 pseudogenes much more representative.

Aspergillus nidulans↗
PubMed1993

Cloning and structural analysis of a human thymidylate synthase pseudogene splitted by several Alu sequences.

An unidentified genomic DNA fragment of 2.4kb that is weakly hybridizable with thymidylate synthase (TS) cDNA was cloned from a human genomic DNA library. Sequencing of the cloned DNA fragment and comparison of the sequence with that of the known human TS cDNA revealed that the DNA fragment contained a human TS processed pseudogene with unusual features. Based on the rate of nucleotide substitutions for neutral mutations in the 3'-untranslated regions between the gene and the pseudogene, it was estimated that the human TS pseudogene was formed about 16 million years ago.

Biological Evolution↗
PubMed1997

Nucleotide sequence of nuclear tRNA(Gly) genes and tRNA(Gly) pseudogenes from yellow lupin (Lupinus luteus): expression of the tRNA(Gly) genes in vitro and in vivo.

A nuclear DNA fragment (7.8 kb) from yellow lupin (L. luteus) was sequenced and shown to contain tRNA(Gly) (GGC) genes and tRNAGly (GGC) pseudogenes organized in three tandemly repeated units: of 2565 bp and 2564 bp, and one, truncated from its 3' end, of 1212 bp. Each unit contains an identical pair of a tRNA(Gly) gene and a pseudogene, both having the same polarity. The nucleotide sequence of the gene appears colinear to L. luteus cytoplasmic tRNA(Gly) (GGC) primary structure. All three genes are efficiently transcribed in HeLa-cell nuclear extract giving two primary transcripts. The main, longer primary transcripts have each an extremely long 3' trailer of about 100 nucleotides, the structure of which is specific only for tRNAGly genes and pseudogenes (80% homology) of the studied tandem (but not for other tRNA(Gly) genes of the yellow lupin genome) as it has been shown by Southern hybridization. This distinctive feature allowed to isolate putative tRNAGly precursor(s) encoded by at least one of the three tRNA(Gly) (GGC) genes from L. luteus seedlings.

Base Sequence↗
PubMed1998

[Interference of human processed pseudogene and corresponding counter-measures in reverse transcriptase-polymerase chain reaction].

OBJECTIVE: This study aimed to set up an effective method to find the interference of processed pseudogene and overcome it in RT-PCR. METHODS: Using RT-PCR methods, the authors amplified the cytokeratin 19 cDNA or DNA sequence in human lung squamous cell carcinoma samples. RESULTS: They could find the influence of pseudogene through performing genomic DNA and nonreversed transcribed RNA controls. By digesting the extracted RNA sample with RNase-free DNase or regulating the annealing temperature based on mismatched primers, they could effectively eliminate the interference. CONCLUSION: The presence of processed pseudogene usually interferes in the experimental protocol in RT-PCR. This problem can be resolved with the method aforementioned.

Carcinoma, Squamous Cell↗
PubMed1984

The glyceraldehyde 3 phosphate dehydrogenase gene family: structure of a human cDNA and of an X chromosome linked pseudogene; amazing complexity of the gene family in mouse.

In an experiment designed to find sequences common to a skeletal muscle cDNA library and an X chromosome specific library, we have isolated cDNA clones corresponding to glyceraldehyde 3 phosphate dehydrogenase (GAPD), (whose gene is assigned to chromosome 12), and a DNA fragment from the X chromosome short arm which contains an intron-less GAPD pseudogene. A 1210-bp cDNA sequence has been established which covers all of the protein-coding region, most of the 5' non-coding region and part of the 3' non-coding region. It corresponds to the major (and possibly unique) GAPD mRNA present in skeletal muscle. Unexpectedly, the amino acid sequence derived from the cDNA clones differs at 10% of the residues from that established for the human protein purified from skeletal muscle. The X-linked pseudogene has been localised in the p22-p11 region of the human X chromosome. It has the structure of a complete retrotranscript of a processed mRNA, including the poly(A) tail and is 96% homologous to the cDNA sequence. The pseudogene is flanked by a 15-bp direct repeat, and an Alu-like sequence is found in the 3'-flanking region. About 25 GAPD sequences are found in the human genome, 12 of which have high homology to the cDNA probe. A similar complexity is found in hamster. In contrast, the mouse genome contains an amazing number of GAPD related fragments (at least 200). The hybridization pattern suggests that this multiplicity has been generated by two different mechanisms: first the generation of approximately 40 different sequences, which were subsequently amplified (probably by tandem duplication).

Animals↗
PubMed1985

Functional and pseudogenes are similarly organized and may equally contribute to the extensive antibody diversity of the IgVHII family.

Eleven germ-line immunoglobulin VH genes have been isolated from a BALB/c genomic library, using a cDNA probe specific for the GAT/NPa variable region. Restriction fragments of all genes were sequenced: two over 800 bp, covering signals of the 5'- and 3'-non-coding regions, three encompassing the complete coding region and part of the 5', the remaining sequences covering most of the V coding region. All sequences pertained to the VHII family, and were compared with the other 13 homologous genes already published. Characteristic features defining the family are clearly visible all along the sequences analyzed, including the 5'-non-coding region, the leader fragment and the intron organization. About half of the compared genes have pseudogene characteristics, defined either by a stop codon in the coding region or the lack of an initiator codon in the leader segment. Analysis of the replacement mutations, as compared with silent ones, indicate that they are highly clustered in complementarity determining regions, for both the functional and the pseudogenes, suggesting that all genes have been submitted to similar selective pressure, and that the pseudogene repertoire may be actively used, by recombination and/or conversion process. Signals that regulate transcription are highly conserved through the family barriers. The VHII group is the largest Ig V genes family, with extreme sequence divergences reaching 22% nucleotide differences. As no two genes were found identical out of the 24 members compared, and as two genes were found to differ by as little as three nucleotides, it seems that the previous estimate of 60 members might be much too low.

Animals↗
PubMed1987

Non-methylated CpG-rich islands at the human alpha-globin locus: implications for evolution of the alpha-globin pseudogene.

We have analysed CpG frequency and CpG methylation across part of the human alpha-globin locus. Clusters of CpG at the alpha 1 and alpha 2 genes resemble the 'HpaII tiny fragment (HTF) islands' that are characteristic of mammalian 'housekeeping' genes: CpG frequency is not suppressed; testable CpGs are not methylated in DNA from erythroid or nonerythroid tissues, although flanking CpGs are methylated; CpG clusters are approximately 1.5 kb long and extend both upstream and downstream of the alpha-globin transcription start site. These features are not found at genes of the beta-globin locus. The alpha-globin pseudogene (psi alpha 1) is highly homologous to the alpha 2 and alpha 1 genes, but it lacks an HTF island. Sequence comparison shows that a high proportion of CpGs in the alpha 2 gene are substituted by TpG or CpA in the pseudogene. This strongly suggests that an ancestral HTF island at the pseudogene became methylated in the germline, and was lost due to the mutability of 5-methylcytosine.

Base Sequence↗
PubMed1983

Analysis of the base substitutions found in the Xenopus laevis 5 S RNA pseudogene.

A 5 S RNA pseudogene is associated with the major oocyte 5 S RNA gene of Xenopus laevis. X. borealis has several oocyte specific 5 S RNA genes. Gene 1 is the dominant 5 S RNA gene. Gene 3 has sometimes been referred to as a pseudogene. We show that the base substitutions in the X. laevis 5 S pseudogene are non-random with respect to double and single-stranded regions of the 5 S RNA using the chi 2 test of homogeneity with Yates correction for continuity. In addition, conserved positions of eukaryotic 5 S RNAs are predominantly maintained. X. borealis gene 3 is random in mutations.

Animals↗
PubMed1986

A U3 RNA pseudogene in mouse: sequence and organization in genomic DNA.

A mouse U3 RNA pseudogene has been identified; it corresponds to a U3B full length coding sequence with a 3'-oligo(A) tail, precisely flanked at both ends by a pair of 15 bp direct repeats. These structural features suggest that it has arisen through an RNA-mediated mechanism involving an insertion at staggered nicks in the genome. Sequence data indicate that this mouse specimen has been generated by a different event as compared to the recently described rat pseudogenes. It represents the first reported case, for a pseudogene of this class, to be present at more than one copy per genome.

Animals↗
PubMed1985

Isolation and characterization of a cDNA and a pseudogene for mouse lactate dehydrogenase-A isozyme.

A mouse lactate dehydrogenase-A cDNA was isolated and it was shown to contain the 393bp of the protein-coding sequence and 488bp of the 3' untranslated region. The amino acid sequence deduced from its open reading frame provided independent evidence for the sequence of residues 201-331 of mouse LDH-A subunit (muscle). This cDNA clone was used as a probe to isolate a mouse genomic clone containing a truncated, processed LDH-A pseudogene. This pseudogene showed 81.6% homology at 713 positions compared with the LDH-A cDNA sequence. The divergence of this pseudogene was estimated to have occurred 39 million years ago.

Animals↗
PubMed1986

Complete nucleotide sequences of the nuclear pseudogenes for cytochrome oxidase subunit I and the large mitochondrial ribosomal RNA in the sea urchin Strongylocentrotus purpuratus.

Nucleotide sequencing of the sea urchin nuclear genomic homologues of two mitochondrial genes, cytochrome oxidase subunit I (COI) and 16 S ribosomal RNA, shows clearly that they are both pseudogenes. The COI homologue has accumulated numerous single-base changes causing non-conservative amino acid substitutions, as well as many small insertions and deletions, most of which result in frameshifts. There is no continuous open reading frame and eight unmutated TGA codons persist. A genomic repetitive element is found between the break points of two rearrangements that have occurred in the region. By solution hybridization in RNA excess, we were unable to detect transcripts colinear with the complete nuclear COI sequence, using Strongylocentrotus purpuratus gastrula RNA, at a detection limit of 10(-6) of total RNA. Transcripts restricted to the 3' end of the COI pseudogene may be present, however, but at an extremely low level. Comparison of the 16 S/COI junctions in nuclear and mitochondrial DNA suggests a possible complementary DNA-mediated conversion of the 16 S pseudogene subsequent to its original transposition into nuclear DNA. We have estimated 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. With both methods, an age of more than 30 million years is suggested.

Amino Acid Sequence↗
PubMed1984

Pseudogene IFN-alpha L: removal of the stop codon in the signal sequence permits expression of active human interferon.

Biologically active interferon (10(6)-10(7) units/liter) was produced in Escherichia coli from modified human alpha interferon (IFN-alpha) pseudogene L. IFN-alpha pseudogene L has a stop codon in the signal peptide coding region. The region that contains the stop codon was replaced with the corresponding region of another human IFN-alpha gene, WA, that does not have a stop codon and was previously engineered for expression by fusion to the M13mp11 lac promoter. The interferon L fusion product was induced with IPTG after infecting E. coli JM103 with the M13 bacteriophage that contained the modified human IFN-alpha pseudogene L. Hence, the IFN-alpha L mature interferon coding sequence, which is not identical to any other alpha-interferon gene, has been conserved for active interferon coding information.

Amino Acid Sequence↗
PubMed1985

Novel structure of a human U6 snRNA pseudogene.

A genomic DNA library containing human placental DNA cloned into phage lambda Charon 4A was screened for snRNA U6 genes. In vitro 32P-labeled U6 snRNA isolated from HeLa cells was used as a hybridization probe. A positive clone containing a 4.6-kb EcoRI fragment of human chromosomal DNA was recloned into the EcoRI site of pBR325 and mapped by restriction endonuclease digestion. Restriction fragments containing U6 RNA sequences were identified by hybridization with isolated U6[32P]RNA. The sequence analysis revealed a novel structure of a U6 RNA pseudogene, bearing two 17-nucleotide(nt)-long direct repeats of genuine U6 RNA sequences arranged in a head-to-tail fashion within the 5' part of the molecule. Hypothetical models as to how this type of snRNA U6 pseudogene might have been generated during evolution of the human genome are presented. When compared to mammalian U6 RNA sequences the pseudogene accounts for a 77% overall sequence homology and contains the authentic 5'- and 3'-ends of the U6 RNA.

Bacteriophage lambda↗