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The human 3 beta-hydroxysteroid dehydrogenase (3 beta-HSD) gene cluster on chromosome 1p13 contains a presumptive pseudogene; 3 beta-HSD and CYP17 do not segregate with dominantly inherited hirsutism.

Four hirsute females from a family exhibiting idiopathic dominant hirsutism were examined. Basal blood levels of delta 5 and delta 4 steroids were within the normal range, but ACTH stimulation led to increases in 17-hydroxypregnenolone and dehydroepiandrosterone that were significantly above control levels. Using polymorphic genetic markers, the genes for cytochrome P450c1717 encoded by CYP17, and the type I and II forms of 3 beta-hydroxysteroid dehydrogenase (3 beta-HSD) were found not to segregate with hirsutism in this family, though a base substitution was detected in the 3' end of exon 1 of the gene for 3 beta-HSD type I in three of the four patients investigated. Analysis of PCR patients amplification products by denaturing gradient gel electrophoresis (DGGE) and sequencing revealed a novel homologue of exon 3 of 3 beta-HSD. DNA of one of the affected patients was used to create a genomic library in lambda gem 11 and clones containing the novel homologue were obtained and partially sequenced. The equivalent clone was obtained from a genomic library of an unrelated normal individual. The sequences of the clones from patient and control were identical and homologous to exons 2-4 of human 3 beta-HSD types I and II. No difference was found in the PCR primer sites that flanked the exons 3 homologue which led to its detection on DGGE gels. In both clones, stop codons and deletions were identified in the exon 4 homologue, leading to the deduction that the sequence comes from a pseudogene, which we call 3 beta-HSD psi 1. The pseudogene mapped to chromosome 1p13. It was concluded that dominantly inherited idiopathic hirsutism in this rare kindred was not due to deficiencies in 3 beta-HSD types I, II, or psi or of CYP17).

3-Hydroxysteroid Dehydrogenases↗

Structural analysis of the locus containing the human C-reactive protein gene and its related pseudogene.

The gene for human C-reactive protein (CRP) is mapped within a 34-kilobase pair genomic DNA segment identified by chromosome walking through overlapping DNA fragments cloned into a lambda phage library. Within 16 kilobase pairs upstream and downstream of the locus for the authentic CRP gene, only one other sequence homologous to that for CRP could be found. Sequencing analysis indicates this sequence to be a pseudogene with 50-80% region-specific homology. Comparison of the authentic CRP gene cloned from genomic DNA libraries independently prepared from three patients indicates no difference in the 5' and 3' flanking region, promoter region, or coding sequence. Only a polymorphism in the length of the poly(GT) stretch located in the intron is observed. There appears to be only one gene locus and copy per haploid chromosome for the authentic CRP gene and its pseudogene.

Bacteriophage lambda↗

Characterization and evolution of the expressed rat ferritin light subunit gene and its pseudogene family. Conservation of sequences within noncoding regions of ferritin genes.

The iron storage protein ferritin consists of two types of subunits of different molecular weight, heavy (H) and light (L). The rat genome contains approximately 20 copies of the ferritin L-subunit gene, of which we have sequenced seven. One is an expressed ferritin gene containing three introns located between the alpha-helical domains of the L-subunit protein. The remaining six have the characteristics of processed pseudogenes. Sequence divergence suggest that these pseudogenes arose approximately 3-12 X 10(6) years ago, well within the 30 X 10(6) years of divergence of rat and mouse. By using intron probes derived from the expressed ferritin L-gene, a homologous second copy has been identified in some Fischer rats. Comparison of the 5'-untranslated region of the rat L-gene with the published sequences of this region of the human L (Santoro, C., Marone, M., Ferrone, M., Costanzo, F., Colombo, M., Minganti, C., Cortese, R., and Silengo, L. (1986) Nucleic Acids Res. 14, 2863-2876) and H (Costanzo, F., Colombo, M., Staempfli, S., Santoro, C., Marone, M., Frank, R., Delius, H., and Cortese, R. (1986) Nucleic Acids Res. 14, 721-735) genes and of a bullfrog cDNA (Didsbury, J. R., Theil, E. C., Kaufman, R. E., and Dickey, L. F. (1986) J. Biol. Chem. 261, 949-955) show a strongly conserved 28-base pair sequence, suggesting a translational regulatory function. The 5' flanking region of the rat L-gene contains sequences homologous to those in the flanking areas of the human L- and H-genes. The implications of these conserved sequences for control of ferritin expression are discussed.

Amino Acid Sequence↗

A unique element resembling a processed pseudogene.

We describe a unique DNA element with structural features of a processed pseudogene but with important differences. It is located within an 8.4-kilobase pair region of chicken DNA containing five histone genes, but it is not related to these genes. The presence of terminal repeats, an open reading frame (and stop codon), polyadenylation/processing signal, and a poly(A) rich region about 20 bases 3' to this, together with a lack of 5' promoter motifs all suggest a processed pseudogene. However, no parent gene can be detected in the genome by Southern blotting experiments and, in addition, codon boundary values and mid-base correlations are not consistent with a protein coding region of a eukaryotic gene. The element was detected in DNA from different chickens and in peafowl, but not in quail, pheasant, or turkey.

Amino Acid Sequence↗

Physical mapping of the serotonin 5-HT(7) receptor gene (HTR7) to chromosome 10 and pseudogene (HTR7P) to chromosome 12, and testing of linkage disequilibrium between HTR7 and autistic disorder.

The gene encoding the serotonin 5-HT(7) receptor (HTR7) has been considered as a candidate locus in several neuropsychiatric disorders, based on pharmacological evidence and ligand-binding studies. After determining over 3 kb of previously unpublished sequence from introns 1 and 2 of HTR7, a single base (C/T) polymorphism in the second intron of HTR7 was found. Allele-specific PCR was used to genotype the HTR7 marker in 53 trios consisting of subjects with autistic disorder and both parents. Using the transmission disequilibrium test (TDT), no evidence of preferential transmission of either allele was found (TDT chi(2) = 0.252, p = 0.602). Sequence data obtained from both intron 1 and intron 2 of HTR7, and from the 5-HT(7) pseudogene (HTR7P), was used to confirm localization of HTR7 to 10q23 and HTR7P to 12p13 using radiation hybrid analyses.

Autistic Disorder↗

Detection of a putative HLA-A*31012 processed (intronless) pseudogene in a laryngeal squamous cell carcinoma.

HLA class I and beta-2-microglobulin (beta2m) expression in a moderately differentiated laryngeal squamous cell carcinoma appeared to be downregulated when analyzed by immunohistochemical procedures using the monomorphic anti-HLA class I monoclonal antibody (mAb; W6/32), locus-specific (HCA2 and HC10) and allele-specific (LT129.11 and KRE501) mAbs and anti-beta2m mAbs. To reveal the molecular basis of downregulated HLA class I expression, HLA-A typing was performed on DNA derived from peripheral blood lymphocytes (PBL) and the tumor. Sequencing-based typing (SBT) revealed HLA-A*02011, 31012. In addition to HLA-A*02011, 31012 alleles, the tumor contained an HLA-A*31012 allele, which lacked all introns when sequenced from the initiation codon through exon eight. The 3' UTR region was intact up to at least 200 bp downstream. The mutant HLA-A*31012 is restricted to laryngeal tumor tissue since it was not amplified in flanking tumor-free laryngeal tissue. The mutant HLA-A*31012 shares structural characteristics with processed pseudogenes, i.e., absence of introns and an intact 3' UTR. This indicates that the mutant HLA-A*31012 allele resulted from a retroposition (reverse transcription and integration) from the processed transcript of the wild-type HLA-A*31012 allele within a clonal tumor cell. Genes Chromosomes Cancer 27:26-34, 2000.

3' Untranslated Regions↗

Signal joint of immunoglobulin V lambda 1-J lambda and novel joints of chimeric V pseudogenes on extrachromosomal circular DNA from chicken bursa.

We isolated extrachromosomal circular DNA from the bursa of 18-day chick embryos and cloned their BamHI fragments into a phage vector. We found examples of the signal joint fused by V lambda 1-J lambda rearrangement and the sequences homologous to V lambda 1 segments that showed: (1) clustered V pseudogene (psi V) germ-line segments containing new psi V26, (2) a head-to-tail duplication of psi V13-psi V12 region and (3) chimeric structures composed of 5'-V lambda 1 and 3'-psi V segments. Both intrachromosomal tandem duplications and extrachromosomal circles may be generated by unscheduled DNA synthesis and recombination. The chimeric structure of V lambda 1 joined with upstream psi V segments suggests the involvement of V gene replacement for somatic diversification of the immunoglobulin genes in addition to a mechanism of segmental gene conversion.

Animals↗

Polymorphism of the functional immunoglobulin variable region genes in the chicken by exchange of sequence with donor pseudogenes.

We have isolated a number of new allelic variants of the unique functional genes encoding chicken immunoglobulin heavy and light chain variable regions (VH1 and VL1, respectively). The distribution and nature of nucleotide variation among these and previously identified VH1 and VL1 alleles demonstrates that random point mutations are likely not the predominant cause of allelic variation at these loci. Comparison of the variant nucleotides with sequences from the pseudo-VH and pseudo-VL gene families, which lie 5' to VH1 and VL1, respectively, suggests that the great majority of allelic variants can be accounted for by segmental transfer of sequence from donor pseudogenes into the germ-line VH1 and VL1 genes. These results demonstrate that the chicken VH1 and VL1 genes are susceptible to sequence replacement at the germ-line level as well as somatically during antibody diversification. The limited repertoire of B cell specificities produced by gene rearrangement in the chicken has led to speculation that these specificities may play a critical role in the progression of chicken B cell development. The results presented here do not support this hypothesis since many of the allelic variant nucleotides described here encode non-conservative amino acid substitutions within the antigen-binding sites of the Ig molecule.

Alleles↗

High microvariation sequence polymorphism at short tandem repeat loci: human beta-actin related pseudogene as an example.

The human beta-actin related pseudogene (HUMACTBP2) seems to be one of the most informative microsatellite markers known because of the high number of length and sequence variants. A total of 50 alleles found in white Caucasians from the Pomerania-Kujawy region of Poland were analyzed by automated sequencing. In addition to STR length polymorphism, seven different types of sequence variation were observed. Alleles ranging in size between 233 and 273 bp showed regular sequence structure with tetranucleotide repeats AAAG. In the alleles ranging in size from 275 to 323 bp, hexamer units AAAAAG or AGAAAG occurred in the repeat region in addition to AAAG repeats. Two alleles (317 and 321 bp) contained two hexamers in the repeat region. There was considerable polymorphism of the hexamer position leading to allelic variants of the same size but different sequence structures. A large amount of variation in both 5' and 3' flanking regions was also observed. Allelic designation based on the number of all types of units within the repeat region (including the hexamer unit) is proposed. An allelic ladder composed of 21 sequenced alleles was constructed to add precision and accuracy to the identification of alleles at ACTBP2 locus.

Actins↗

mRNA retroposition in human cells: processed pseudogene formation.

Using a sensitive assay for detection of reverse transcription events, we demonstrate that human HeLa cells can 'retropose', i.e. reverse transcribe and integrate, the mRNA of a naive reporter gene, at a low but detectable frequency. Furthermore, we show that the retroposed copies have all the hallmarks of the processed pseudogenes naturally found in the mammalian genome: they lack intron and 5' promoter sequence, they have acquired a 3' poly(A) tail, and they are flanked by short repeats (< 15 bp) of target DNA sequence. These results demonstrate that human cells possess an endogenous reverse transcription activity, which is not restricted to transcripts of transposable elements, and which is likely to be involved in the formation, still ongoing, of a large fraction of the eukaryotic genome.

Base Sequence↗

17 beta Hydroxysteroid dehydrogenase 1 "pseudogene" is differentially transcribed: still a candidate for the breast-ovarian cancer susceptibility gene (BRCA1).

BRCA1, the susceptibility gene for hereditary breast-ovarian cancer, is located on chromosome 17q12-21 but has not yet been identified. Two tandem oestradiol 17 beta hydroxysteroid dehydrogenase genes (17HSD) are assigned to this region. The active 17HSDII gene encodes the normal enzyme which regulates local synthesis of oestrogens, whereas 17HSDI is considered to be a pseudogene. We used reverse transcription coupled to polymerase chain reaction (RT-PCR) and found that the 17HSDI gene was also transcribed in half of the human cell lines and most of the biopsies studied, suggesting that 17HSDI could modulate normal 17HSDII activity in oestrogen target cells. We hypothesize that altered 17HSDI gene expression could lead to both hereditary and/or sporadic breast cancer by increasing local oestrogen concentration and that it is still a potential candidate for BRCA1.

17-Hydroxysteroid Dehydrogenases↗

Identification of an EWS-pseudogene using translocation detection by RT-PCR in Ewing's sarcoma.

The presence of a t(11;22)(q24;q12) translocation is one of the characteristic features of the Ewing family of tumors. The detection of the fusion gene product by RT-PCR using primers at both sides of the breakpoints has been advocated as a diagnostic tool. By applying this technique appropriate internal controls are required. We found that the use of normal non-rearranged EWS mRNA as an internal control for RNA quality may lead to conflicting data. We obtained PCR products of the expected size for the normal EWS mRNA in both RNA and DNA samples, suggesting, the existence of one or more EWS pseudogenes. A 109 bp sequence at the 5' end of this PCR-product contained a correctly spliced exon junction and was 97% homologous to the EWS cDNA sequence. Similarly two such junctions were found in a 346 bp sequence of the 3' end, which was 89% homologous. Hence EWS should not be used as an internal control for the RNA quality in a RT-PCR based test for the presence of the translocation.

Base Sequence↗

Molecular cloning of human mitochondrial glycerophosphate dehydrogenase gene: genomic structure, chromosomal localization, and existence of a pseudogene.

cDNA of mitochondrial glycerophosphate dehydrogenase (mGPDH), a defect of which is a possible cause of non-insulin dependent diabetes mellitus, was cloned from a human insulinoma cDNA library. The deduced amino acid sequence showed 91% and 92% homology with those of rat and mouse mGPDH, respectively. The mGPDH gene was mapped to chromosome 2q23 by FISH analysis. Genomic clones for mGPDH were then isolated using mouse mGPDH cDNA and PCR products of human mGPDH cDNA as probes. Genomic structure was studied by sequencing the exon-intron boundaries and by PCR amplification of intronic regions using genomic clones as templates. The human mGPDH gene was shown to be composed of 15 coding exons, containing a (CA)n repeat region inside the gene, which was not polymorphic in the Japanese population. Genomic cloning also identified a pseudogene located on chromosome 19q13.4. These results provide information useful for analyzing the mGPDH gene in patients with non-insulin dependent diabetes mellitus.

Amino Acid Sequence↗

Cloning of P2Y6 cDNAs and identification of a pseudogene: comparison of P2Y receptor subtype expression in bone and brain tissues.

Cellular responses to ATP/UTP and analogs are mediated by G-protein coupled P2Y receptors and have been proposed to play a role in the regulation of bone metabolism. Using a degenerate PCR approach on MG-63 cell cDNA we found PCR fragments coding for human P2Y1 and a new receptor, P2Y6. cDNA cloning of the P2Y6 receptor identified three cDNA isoforms. Two contained the same contiguous ORFs but differed in their 5' UTRs and may therefore originate by alternative splicing whereas the third represents a pseudogene. Analysis of P2Y receptor subtype expression in human bone and the osteoblastic cell lines OHS-4 and MG-63 by RT-PCR showed that all known human P2Y receptor subtypes (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y7) were expressed. In contrast, analysis of brain-derived cell lines suggests that a selective expression of P2Y receptor subtypes occurs in brain tissue.

Alternative Splicing↗

Isolation of a cyp2b10-like cDNA and of a clone derived from a cyp2b10-like pseudogene.

By screening Balb/c male mouse liver cDNA library with a rat CYP2B1 cDNA probe, we have isolated a 1795 bp cyp2b10-like clone, referred to as P16. Its sequence exhibited 34 base differences (98% similarity) with the cyp2b10 published sequence, together with a 97% identity at the amino acid sequence level. By RT-PCR and PCR analyses with Balb/c female and male liver RNA and genomic DNA, using a region showing 8 base differences between the P16 and the cyp2b10 sequences, we have confirmed the identity of our cloned cDNA, and failed in finding a PCR product exhibiting a sequence 100% identical with that of cyp2b10. Our results therefore suggest that the P16 sequence is the authentic cyp2b10 sequence. We have also isolated a partial clone, P21, which 1609 bp sequence overlapped with that of P16, except for a T-->G transversion, giving rise to a premature TGA stop codon, indicating that it was derived from a pseudogene.

Amino Acid Sequence↗

Structure of the human ubiquitin fusion gene Uba80 (RPS27a) and one of its pseudogenes.

Ubiquitin is a highly conserved 76 amino acid protein that is generated in the cell by proteolysis of larger proteins containing either polyubiquitin chains or ubiquitin fused to carboxyl extension proteins (CEPs). In humans, the two human ubiquitin-CEP genes are Uba80 and Uba52, which code for ubiquitin fused to ribosomal protein S27a and L40, respectively. Working from a recently generated physical map of human chromosome 2p16, we determined the genetic and physical location and the genomic structure of the Uba80 gene in its entirety. A comparison of Uba80 to Uba52 revealed that the two genes share a conserved 5'-end structure, but that the structure of the ubiquitin coding regions was not conserved. Analysis of 400 bp of the promoter of Uba80 revealed strong similarity not only to the Uba52 promoter, but also to the other known human ribosomal gene promoters that have been identified to date. Homology searches also detected the presence of a pseudogene for Uba80, and the structure of this sequence feature is also reported.

Amino Acid Sequence↗

Structure and localization of the human SULT1B1 gene: neighborhood to SULT1E1 and a SULT1D pseudogene.

The soluble sulfotransferases are involved in the elimination of xenobiotics, the activation of procarcinogens, and the regulation of hormones. They comprise a gene superfamily (SULT). The structure and chromosomal location of nine human SULT genes are known. We have characterized a further gene, SULT1B1. Its structure is similar to that of other SULT1 genes. However, the total length of its eight exons and the introns (33.6 kb) is larger than that of other human SULT1 genes (4 to 21 kb). The SULT1B1 gene sequence is part of a sequence entry in the unfinished High-Throughput Genomic Sequences (HTGS) division of GenBank. However, the order and orientation of the SULT1B1 exons are not correct in this entry. SULT1B1 is located on chromosome 4q13.1, nearly 100 kb downstream of SULT1E1 on the same strand. The intervening sequence contains a SULT-like structure showing substantial homology to the mouse SULT1D1 cDNA recently described. However, in humans this structure represents a pseudogene (SULT1D1P) because of mutated splice donors/acceptors and in-frame stop codons in the sequence corresponding to exon II. This SULT gene cluster is located on the minus strand of chromosome 4 with SULT1B1 being closest to the centromer.

5' Flanking Region↗

Ribosomal protein S19 gene mutations in patients with diamond-blackfan anemia and identification of ribosomal protein S19 pseudogenes.

Diamond-Blackfan anemia (DBA) is a rare congenital pure red cell hypoplasia characterized by a selective defect of erythropoiesis with a normochromic macrocytic anemia and reticulocytopenia often accompanied by various congenital anomalies. The critical region responsible for the pathogenesis of DBA has been mapped in some patients to chromosome 19q13.2 (P Gustavsson, E Garelli, N Draptchinskaia, et al. Am. J. Hum. Genet. 63:1388-1395, 1998) and the gene encoding ribosomal protein S19 (RPS19) is believed to be the candidate gene. Here we present molecular analysis of the RPS19 gene in DBA patients from the Czech National DBA Registry. We found that the RPS19 gene was mutated in 25% (5/20) of DBA patients (insertion, deletion, and point mutations, but no nonsense or splice site mutations). Point mutations were localized to hot spots defined by Willig (TN Willig, N Draptchinskaia, I Dianzani, et al. Blood 94:4294-4306, 1999). Moreover, we describe two processed RPS19 pseudogenes, which were not expressed. Possible models of the DBA pathogenesis in the view of RPS19 mutations are discussed.

Adolescent↗