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At least 271 records · Page 15Linked to original sources
PubMed1996

MHC class I-processed pseudogenes in New World primates provide evidence for rapid turnover of MHC class I genes.

The MHC class I genes of the New World primate, the cotton-top tamarin (Saguinus oedipus), are an exception to the high polymorphism and variability displayed by this multigene family. We report the isolation of the first two processed pseudogenes from the MHC region in primates. These two MHC class I-processed pseudogenes (MHC-PS1 and -PS2) were found in several species of New World primates, suggesting a possible explanation for the cotton-top tamarin's limited MHC class I diversity. The pattern of synonymous and nonsynonymous substitutions in PS1 suggests that the gene that gave rise to this processed pseudogene was once subject to selection for variability in the peptide binding region and might, therefore, have been functional. Additionally, PSI is not closely related to the expressed cotton-top tamarin's MHC class I genes, but does show some similarity to So-N1, a tamarin pseudogene from which no transcript has been found. Thus, PS1 may represent a remnant of a once active MHC class I gene that is no longer functional in the cotton-top tamarin. The MHC class I loci in primates, therefore, appear to be evolving by a continual process of duplication and inactivation. This process seems to be exaggerated in New World primates and may in part be responsible for the cotton-top tamarin's limited MHC class I diversity.

Animals↗
PubMed1982

A pseudogene for human U4 RNA with a remarkable structure.

The human DNA library of Lawn et al. (1978) was screened for sequences complementary to the small nuclear (sn) RNA U4. Several positive clones were identified by screening 100 000 recombinants, indicating that U4 sequences like other snRNA sequences are dispersed in the human genome. One recombinant was characterized in detail by subcloning a Bg/II fragment 1.9 kilobases (kb) long in the pBR322 plasmid. The subcloned fragment was partially sequenced and the results revealed a pseudogene for U4 RNA. The pseudogene was found to have a remarkable structure; it contains a sequence that, except in two positions, matches the first 68 nucleotides of the human U4 RNA sequence and the pseudogene is, moreover, flanked by perfect direct repeats 20 bp long. The results support the model of van Arsdell et al. (1981) suggesting that certain snRNA pseudogenes arise by reverse transcription of the RNA followed by integration of the cDNA copy at a new chromosomal locus.

Base Composition↗
PubMed1986

Tubulin pseudogenes as markers for hominoid divergence.

Processed pseudogenes arise via unimolecular events that result in the integration of nonfunctional (and therefore non-selected) regions of DNA into the germ line. The sequence of such pseudogenes can be used as a novel form of evolutionary clock: the older a particular pseudogene, the more mutations it has acquired relative to the selectively constrained functional gene from which it was originally derived. We have used specific beta-tubulin gene probes to assay for the presence of fully sequenced processed pseudogenes in genomic DNA from various hominoid species. The data suggest that orangutan is more closely related to human, chimpanzee and gorilla than is generally believed.

Animals↗
PubMed1977

A pseudogene structure in 5S DNA of Xenopus laevis.

The 5S DNA of Xenopus laevis, coding for oocyte-type 5S RNA, consists of many copies of a tandemly repeated unit of about 700 base pairs. Each unit contains a "pseudogene" in addition to the gene. The pseudogene has been partly sequenced and appears to be an almost perfect repeat of 101 residues of the gene. The order of components in the repeat unit is (5') long spacer--gene--linker--pseudogene (3') in the "+" strand (or H strand) of the DNA. The possible function of the pseudogene is discussed.

Animals↗
PubMed1981

A transcriptionally active pseudogene in xenopus laevis oocyte 5S DNA.

DNA that encodes the Xenopus laevis 5S pseudogene is transcribed following microinjection into oocyte nuclei. Transcription in injected oocytes is accurate, is mediated by RNA polymerase III and is initiated at the first nucleotide of the pseudogene. The level of pseudogene transcription can be as high as 85% of that of the normal 5S gene. The results suggest that the observed absence of pseudogene transcripts of defined length in vivo probably is due to inefficient termination of transcription.

Animals↗
PubMed1981

A pseudogene homologous to mouse transplantation antigens: transplantation antigens are encoded by eight exons that correlate with protein domains.

We have isolated about 30 to 40 different BALB/c mouse sperm DNA genomic clones that hybridize to cDNA clones encoding proteins homologous to transplantation antigens. One of these clones (27.1) was selected for sequence because it was polymorphic in Southern blot analysis of the DNAs from BALB/c and CBA mice. A fragment of 5.7 kilobases of this clone was completely sequenced and found to contain a pseudogene whose sequence is highly homologous to the sequences of known transplantation antigens. Pseudogene 27.1 is split into eight exons that correlate with the structurally defined protein domains of transplantation antigens. Using Southern blot hybridization on the DNAs of different inbred mouse strains, we mapped the pseudogene to the Qa-2,3 region, a part of the Tla complex on chromosome 17 that is adjacent to the major histocompatibility complex. The Qa2,3 region encodes lymphoid differentiation antigens homologous to the transplantation antigens in size, in peptide map profiles and in their association with beta2-microglobulin. These mapping studies suggest that gene 27.1 may be a pseudogene for eigher a Qa antigen or an as yet undefined transplantation antigen. Accordingly, we may have isolate genes encoding lymphoid differentiation antigens of the Tla complex as well as those encoding transplantation antigens among the 30 to 40 different genomic clones isolated from our sperm library.

Base Sequence↗
PubMed1982

beta-thalassemia-? Selected pseudogenes.

The synthesis of delta-globin is directed by a gene whose inherent characteristics permit only limited expression, a gene resembling in some respects that of beta +-thalassemia. The existence of delta O-thalassemia and the presence of delta-globin genes in this condition recall the molecular findings in most types of beta O-thalassemia. The delta-globin and beta +-thalassemia genes may be evolving pseudogenes. Those for delta O and beta O-thalassemia are, in functional sense, already pseudogenes in that they closely resemble functional genes but lack a discernible protein product. In time they should accumulate sufficient changes in their nucleotide sequences which will make them more analagous to what we now recognize as pseudogenes. the selective pressure of Falciparum malaria infection may help maintain the beta-thalassemia "pseudogene" in many populations.

Adult↗
PubMed1987

Reverse-transcribed pseudogenes of U1 small nuclear RNA presumably amplified in the rat genome together with the flanking region.

We have examined 25 independent rat genomic clones each of which contains a U1 RNA gene or a pseudogene. We have found five clones whose restriction maps are identical with or overlapping one another. These clones contain sequences which are co-linear with that of U1 RNA except for one or two nucleotides (nt). They also contain 21-23-nt poly(A) stretches immediately after U1 RNA homology. In addition, the U1 RNA-poly(A) regions are surrounded by the same direct repeat sequences. Therefore, they seem to be pseudogenes which have been generated by the reverse transcription of poly(A)-tailed U1 RNA followed by the insertion of the transcript into the genome. Furthermore, conservation of the sequences extends over at least 18 kb of the flanking sequences. This suggests a family of conserved reverse-transcribed pseudogenes, which implies amplification of an original pseudogene. It is also suggested that the target sequence without insertion of a U1 RNA sequence has been amplified. The mechanisms for the amplification and sequence conservation are discussed.

Animals↗
PubMed1981

Pseudogenes as a paradigm of neutral evolution.

On the neutral mutation hypothesis, the rate of nucleotide substitution is expected to be higher for functionally less important genes or parts of genes than for functionally more important genes, as the latter would be subject to stronger purifying (negative) selectio. On the other hand, selectionists believe that most nucleotide substitutions are caused by positive darwinian selection, in which case the rate of nucleotide substitution in functionally unimportant genes or parts of genes is expected to be relatively lower because the mutations in these regions of DNA would not produce any significant selective advantages. Kimura and Jukes have argued that the higher substitution rate observed at the third positions of codons than at the first two positions supports the neutral mutation hypothesis, as most third-position substitutions are synonymous and do not change the amino acids encoded, although others have discussed the possibility that third-position substitutions are subject to positive darwinian selection. Recently, Kimura noted that the mouse globin pseudogene, psi alpha 3, evolved faster than the normal mouse alpha 1 gene, although he did not compute the substitution rate. Here, we present a method of computing the rate of nucleotide substitution for pseudogenes, and report that the three recently discovered pseudogenes show an extremely high rate of nucleotide substitution. As these pseudogenes apparently have no function, this finding strongly supports the neutral mutation hypothesis.

Animals↗
PubMed1981

Mouse alpha-globin genes and alpha-globin-like pseudogenes are not syntenic.

A genetic polymorphism for a Bgl I endonuclease site near the alpha-globin-like pseudogene alpha-4 of C57BL/6 and C3H/HeN mice was used to show that alpha-4 was not affected by three independent mutations in which the adult globin genes alpha-1 and alpha-2 were deleted. These results indicated that alpha-4 might not be located adjacent to the adult alpha-globin genes on chromosome 11. Restriction endonuclease analysis of DNA of a primary clone of a Chinese hamster--mouse somatic cell hybrid that had lost mouse chromosomes 11 and 18 showed that this clone lacked the adult murine globin genes alpha-1 and alpha-2 but it did contain the alpha-globin-like pseudogenes alpha-3 and alpha-4. These results indicated that the adult alpha-globin genes and alpha-globin-like pseudogenes are not located on the same chromosome. Similar analyses of several other Chinese hamster--mouse somatic cell hybrids that had segregated other mouse chromosomes indicated that the alpha-globin-like pseudogenes alpha-3 and alpha-4 are located on mouse chromosomes 15 and 17, respectively. These data explain why alpha-3 and alpha-4 were not affected by the three independently induced deletion-type mutations that cause alpha-thalassemia in the mouse.

Animals↗
PubMed1985

Human U1 small nuclear RNA pseudogenes do not map to the site of the U1 genes in 1p36 but are clustered in 1q12-q22.

Human U1 small nuclear RNA is encoded by approximately 30 gene copies. All of the U1 genes share several kilobases of essentially perfect flanking homology both upstream and downstream from the U1 coding region, but remarkably, for many U1 genes excellent flanking homology extends at least 24 kilobases upstream and 20 kilobases downstream. Class I U1 RNA pseudogenes are abundant in the human genome. These pseudogenes contain a complete but imperfect U1 coding region and possess extensive flanking homology to the true U1 genes. We mapped four class I pseudogenes by in situ hybridization to the long arm of chromosome 1, bands q12-q22, a region distinct from the site on the distal short arm of chromosome 1 to which the U1 genes have been previously mapped (Lund et al., Mol. Cell. Biol. 3:2211-2220, 1983; Naylor et al., Somat. Cell Mol. Genet. 10:307-313, 1984). We confirmed our in situ hybridization results by genomic blotting experiments with somatic cell hybrid lines with translocation products of human chromosome 1. These experiments provide further evidence that class I U1 pseudogenes and the true U1 genes are not interspersed. The results, along with those published elsewhere (Bernstein et al., Mol. Cell. Biol. 5:2159-2171, 1985), suggest that gene amplification may be responsible for the sequence homogeneity of the human U1 gene family.

Animals↗
PubMed2006

[Avoiding the interference of ABCD1 pseudogenes in the molecular diagnosis of X-linked adrenoleukodystrophy by double amplification refractory mutation system].

OBJECTIVE: To avoid the interference of ABCD1 pseudogenes, the amplification refractory mutation system (ARMS) was used to analyze the mutation of ABCD1 gene in the molecular diagnosis of X-linked adrenoleukodystrophy (ALD). METHODS: The upstream primers (wild primer and mutation primer) were designed according to the principle of primer-design in ARMS. In addition, a common downstream primer was designed in the same way to discriminate ABCD1 gene from its prologous pseudogenes. The genomic DNA isolated from the peripheral blood leukocytes of the family members and normal controls was amplified by PCR. RESULTS: In double ARMS, a specific product of 107bp could be amplified from genomic DNA of the patient with R617C mutation in ABCD1 gene and his mother, while the same product was not found when the genomic DNA of the patient's father and normal controls was used. Thus, the interference of ABCD1 pseudogenes in molecular diagnosis of ALD was excluded successfully at genomic DNA level. CONCLUSION: Double ARMS is a quick and effective method to eliminate the interference of the pseudogenes in detecting ABCD1 gene mutations.

ATP Binding Cassette Transporter, Subfamily D, Mem↗
PubMed1985

Isolation and characterization of three rat U3 RNA pseudogenes colinear with U3 RNA.

Three different 15-kilobase rat genomic clones that contained sequences colinear with U3 RNA were isolated. These inserts hybridized only to U3 RNA in a mixture of total cellular 4-8 S RNA labeled in vivo which showed that genes or pseudogenes for most other small RNAs were absent in these U3 DNA clones. DNA sequence analysis showed that the three subcloned genes contained full-length U3-coding sequences but each had sequence variations, insertions, and/or deletions when compared to rat U3A or U3B RNA. Two of these pseudogenes contained poly(A) sequences on the 3'-end and were flanked by 6-15-nucleotide long direct repeats. None of the three clones was transcribed when injected into Xenopus oocyte nuclei. One clone was a template for a small RNA slightly larger than U3 RNA, but this transcript was not related to the U3 RNA sequences. The structural features of two of these three U3 DNAs are supportive of the hypothesis that some pseudogenes arose from RNA-mediated DNA synthesis and insertion into the genome at random sites (Van Arsdell, S. W., Denison, R.A., Bernstein, L.B., Weiner, A.M., Manser, T., and Gesteland, R.F. (1981) Cell 26, 11-20). This is the first instance where full-length, colinear, U3 RNA pseudogenes have been isolated and characterized.

Animals↗
PubMed1981

An immunoglobulin VH pseudogene.

In the course of studying the members of the T15 group of VH gene segments, some of which participate in the immune response to phosphorylcholine in the mouse, we identified a VH gene segment that contains three mutations preventing its expression. The mutations are an in-frame stop codon, a 4-base insertion which causes a termination codon to be shifted into the reading frame, and a modification of the recognition elements involved in the joining of VH and D gene segments during variable region formation. This pseudogene, which is 88-96% homologous to the other members of the T15 VH gene group, is probably of relatively recent origin and will presumably be deleted from the VH gene family eventually. We suggest that pseudogenes can only arise in multigene families and that the occurrence of pseudogenes will be a relatively frequent phenomenon in these families. Because the antibody gene families are made up of multiple gene elements, undergo two types of DNA rearrangements during differentiation, and employ several different RNA splicing mechanisms for expression, there are many different ways a particular antibody gene segment may become a pseudogene.

Animals↗
PubMed1996

Characterization of a partial pseudogene homologous to the adrenoleukodystrophy gene and application to mutation detection.

The gene for the most common peroxisomal disorder, X-linked adrenoleukodystrophy (X-ALD, McKusick #300100), encodes a peroxisomal membrane transporter protein (ALDP), and comprises 10 exons spanning approximately 21 kb. So far, however, the mutation analysis at the genomic level was handicapped by the coamplification, in PCR reactions, of sequences related to the distal exons, also detected by Southern blot hybridization on genomic DNA. We isolated one clone from a human genomic phage library, which represents a partial ALD pseudogene, spanning exon 7 to exon 10 and exhibits approximately 93% sequence homology with the ALD gene in this region. Primers designed in the region of maximum mismatch between the pseudogene and the functional gene allowed the amplification of the functional exons without any contaminating sequences of the pseudogene or other related sequences. This information will greatly facilitate the detection of mutations in distal exons of the ALD gene and increase the reliability of the mutation analysis.

ATP Binding Cassette Transporter, Subfamily D, Mem↗
PubMed1996

IDS gene-pseudogene exchange responsible for an intragenic deletion in a Hunter patient.

Hunter disease or mucopolysaccharidosis type II is an X-linked disease caused by the deficiency of the lysosomal enzyme iduronate-2-sulfatase (IDS). The IDS gene (24 kb) contains nine exons and has been completely sequenced. A pseudogene (IDS-2 locus) distal to the functional IDS gene has recently been identified. This work reports the characterization of IDS gene alterations in two severely affected patients. Patient 1 has a partial deletion that removes exons I to VI and extends about 200 kb upstream of the IDS gene. Patient 2 has an internal deletion of exons IV, V, VI, and VII, which results from an IDS gene-pseudogene exchange between highly homologous regions. In the rearranged gene, the junction intron contains pseudogene intron 3- and intron 7-related sequences. An interchromosomal recombination is probably the cause of this rearranged X chromosome.

Gene Rearrangement↗
PubMed2000

Polymorphisms in a pseudogene highly homologous to PMS2.

PMS2 is one of a complex of genes encoding DNA repair proteins that includes MSH2, MLH1, MSH6 and MSH3. Mutation of any of these DNA mismatch repair genes leads to impairment of DNA repair and can lead to tumorigenesis. Germline mutation of PMS2 has been reported as a rare cause of hereditary nonpolyposis colorectal cancer (HNPCC) and Turcot's syndrome. The PMS2 gene is located on chromosome 7p22 and consists of 15 exons. Within exon 11 of PMS2 is a coding repeat of eight adenosines. This study reports on the finding of a nonexpressed pseudogene that is highly homologous to the PMS2 gene in this region. The pseudogene is polymorphic for two alterations in the repeat region: a 3 bp delAAA at a site corresponding to nucleotide 1231 in PMS2; and an AA-->GG change at nucleotide 1238. Due to the high homology in both intronic and exonic sequences, polymorphisms in this pseudogene could be mistaken for mutations in the PMS2 gene and erroneously thought to be a cause of HNPCC and/or Turcot's syndrome.

Adenosine Triphosphatases↗
PubMed1993

Association of a human H1 histone gene with an H2A pseudogene and genes encoding H2B.1 and H3.1 histones.

A cluster of human histone genes was found on three overlapping clones isolated from cosmid and bacteriophage libraries. These three overlapping segments of the human genome comprise genes coding for H3.1, an H2A pseudogene, and an H2B.1 gene downstream of the previously characterized H1.2 gene. The cosmid clone covers 30 kb upstream of the H1.2 gene and overlaps with two phage clones covering the core histone genes and the pseudogene. The same arrangement of an H3 gene, an H2A pseudogene and an H2B gene downstream of an H1 gene has been described within a mouse histone gene cluster [Yang et al.:J Biol Chem 262:17118-17125, 1987; Gruber et al.:Gene 95:303-304, 1990].

Amino Acid Sequence↗