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PubMed2005

A novel 13-bp deletion in exon 1 of CYP21 gene causing severe congenital adrenal hyperplasia.

Congenital adrenal hyperplasia (CAH) is a common autosomal recessive disorder mainly caused by defects in the steroid 21-hydroxylase gene (CYP21). In most cases, this defect is the result of gene conversion events between the functional CYP21 gene and the adjacent inactive pseudogene (CYP21P). Previous screening for mutations of 21-hydroxylase gene in 51 unrelated Tunisian CAH patients revealed 4 novel mutations that have not been reported to occur in the CYP21P pseudogene. The present paper describes the fifth new small 13-bp deletion in exon 1 found after sequencing the CYP21 gene of a Tunisian patient suffering from the salt-wasting form of CAH. The patient is a girl born to consanguineous parents; she is homozygous for a novel deletion. The 13-bp deletion causes a stop codon at amino acid 47, which is likely to result in an enzyme with no activity. Both parents are heterozygous for the small deletion as confirmed by nested PCR method. This novel mutation has not been reported to occur in the CYP21P pseudogene, indicating a casual mutagenic event rather than a conversion one.

Adrenal Hyperplasia, Congenital↗
PubMed2005

Characterization of new members of the human type II keratin gene family and a general evaluation of the keratin gene domain on chromosome 12q13.13.

The recent completion of a reference sequence of the human genome now allows a complete characterization of the type II keratin gene domain on chromosome 12q13.13. This, domain, approximately 780 kb in size, is present on nine bacterial artificial chromosome clones sequenced by the Human Genome Sequencing Project. The type II keratin domain contains 27 keratin genes and eight pseudogenes. Twenty-three of these genes and four pseudogenes have been previously reported. This study describes, in addition to the genomic sequencing of the K2p gene and the bioinformatic identification of four keratin pseudogenes, the characterization of cDNA corresponding to three previously undescribed keratin genes K1b, K6l, and Kb20, as well as cDNA sequences for the previously described keratin genes hHb2, hHb4, and K3. Northern analysis of the new keratins K1b, K6l, K5b, and Kb20 using mRNA of major organs as well as of specific epithelial subtypes shows singular expression of these keratins in skin, hair follicles and, for K5b and Kb20, in tongue, respectively. In addition, the obvious discrepancies between the current reference sequence of the human genome and the previously described gene/cDNA sequences for K6c, K6d, K6e, K6f, K6h are investigated, leading to the conclusion that K6c, K6d as well as K6e, K6f are probably polymorphic variants of K6a and K6h, respectively. All 26 human type II keratins found on this domain as well as K18, dtype 1 Keratin, are identified at the genomic and transcriptional level. This appears to be the total complement of functional type II keratins in humans.

Chromosomes, Human, Pair 12↗
PubMed1988

The sheep metallothionein gene family. Structure, sequence and evolutionary relationship of five linked genes.

Southern blot analysis of the sheep genome revealed a metallothionein gene family with at least nine members. Two overlapping cosmid clones spanning approximately 67 kb and containing five metallothionein genes have been isolated. DNA sequence analysis reveals that one of these is a metallothionein II variant, three are metallothionein I variants and one is a truncated metallothionein pseudogene containing only the first exon. The predicted amino acid sequence was compared with previously reported amino acid composition data of sheep metallothioneins [Whanger, P. D., Oh, S.-H. & Deagen, J. T. (1981) J. Nutr. 111, 1207-1215], and this suggests that we have isolated the genes encoding the major protein isoforms found in the sheep liver. The promoter regions of these genes contain many conserved elements, among them metal-regulatory elements and putative glucocorticoid-responsive elements. However, there are a number of differences between these genes in the arrangement of these elements. Sequence comparisons indicate that the multiple metallothionein I genes and the pseudogene appear to have resulted from sequential duplication events, and a larger cluster of metallothionein I genes may have been disrupted leading to the formation of the pseudogene.

Amino Acid Sequence↗
PubMed1992

Mutations of the tyrosinase gene in oculocutaneous albinism.

Since our first report showing that the phenotype of tyrosinase-negative or type IA oculocutaneous albinism (OCA) is a consequence of a mutation in the tyrosinase gene (Tomita et al., Biochem. Biophys. Res. Commun., 164:990-996, 1989), a number of mutations were found in the tyrosinase gene of OCA patients. However, to establish the molecular basis of OCA in each patient, we must carry out several important experiments as summarized here. First, we should confirm that the cloned or amplified genomic DNA segments are not derived from the pseudogene or related gene. It should be noted that the putative tyrosinase pseudogene contains the sequence almost identical to exons 4 and 5, including their exon/intron boundaries of the authentic tyrosinase gene. Thus, the mutations, detected in exon 4 or 5 amplified from genomic DNA, must be carefully analyzed to exclude a possibility that the mutation is located in the pseudogene. Second, it is of significance to confirm the promoter activity of the patients' tyrosinase gene. Accordingly, we established the cell-free transcription system derived from melanoma cells where the cloned tyrosinase gene is faithfully transcribed. Finally, transient expression assay of mutant tyrosinase is invaluable to conclude that OCA phenotypes are associated with the mutant tyrosinase alleles. I also discuss the implications of a cluster of mutation sites in exon 1 coding for the amino-terminus of tyrosinase.

Albinism, Oculocutaneous↗
PubMed2005

Progress in rickettsial genome analysis from pioneering of Rickettsia prowazekii to the recent Rickettsia typhi.

Three rickettsial genomes have been sequenced and annotated. Rickettsia prowazekii and R. typhi have similar gene order and content. The few differences between R. prowazekii and R. typhi include a 12-kb insertion in R. prowazekii, a large inversion close to the origin of replication in R. typhi, and loss of the complete cytochrome c oxidase system by R. typhi. R. prowazekii, R. typhi, and R. conorii have 13, 24, and 560 unique genes, respectively, and share 775 genes, most likely their essential genes. The small genomes contain many pseudogenes and much noncoding DNA, reflecting the process of genome decay. R. typhi contains the largest number of pseudogenes (41), and R. conorii the fewest, in accordance with its larger number of genes and smaller proportion of noncoding DNA. Conversely, typhus rickettsiae contain fewer repetitive sequences. These genomes portray the key themes of rickettsial intracellular survival: lack of enzymes for sugar metabolism, lipid biosynthesis, nucleotide synthesis, and amino acid metabolism, suggesting that rickettsiae depend on the host for nutrition and building blocks; enzymes for the complete TCA cycle and several copies of ATP/ADP translocase genes, suggesting independent synthesis of ATP and acquisition of host ATP; and type IV secretion system. All rickettsiae share two outer membrane proteins (OmpB and Sca 4) and LPS biosynthesis machinery. RickA, unique to spotted fever rickettsiae, plays a role in induction of actin polymerization in R. conorii, but not in R. prowazekii or R. typhi. The genome of R. typhi contains four potentially membranolytic genes (tlyA, tlyC, pldA, and pat-1) and five autotransporter genes, sca 1, sca 2, sca 3, ompA, and ompB. The presence of six 50-amino acid repeat units in Sca 2 suggests function as an adhesin. The high laboratory passage of the sequenced strains raises the issue of the occurrence of laboratory mutations in genes not required for growth in cell culture or eggs. Resequencing revealed that eight annotated pseudogenes of E strain are actually intact genes. Comparative genomics of virulent and avirulent strains of rickettsial species may reveal their virulence factors.

Genome, Bacterial↗
PubMed2004

Not all amino acid substitutions of the common cluster E6 mutation in CYP21 cause congenital adrenal hyperplasia.

More than 90% of all cases of congenital adrenal hyperplasia result from steroid 21-hydroxylase (CYP21) gene mutations. Around 95% of these are either gene deletions or any of nine sequence aberrations that have been transferred from the nearby pseudogene through apparent gene conversions. One such recurrent pseudogene-derived mutation is Cluster E6, a combination of three amino acid substitutions in exon 6: I236N, V237E, and M239K. Cluster E6 is associated with the most severe, salt-wasting form of congenital adrenal hyperplasia. We studied the functional consequences of each missense mutation individually as well as the combined effect of the three mutations comprising Cluster E6. V237E abolished enzyme function and is thus a null mutation, whereas very low but measurable activity remained for I236N. M239K, on the other hand, had no effect on enzyme activity and consequently does not contribute to the disease. Although no allele has been reported yet to contain only one or two missense mutations of Cluster E6, it is a well-known feature of CYP21 that it can harbor many different combinations of pseudogene-derived mutations. The exclusion of M239K as a disease-causing mutation is thus relevant when designing protocols for genetic diagnostics.

Adrenal Hyperplasia, Congenital↗
PubMed1989

Gene conversions and rearrangements cause discordance between inheritance of forms of 21-hydroxylase deficiency and HLA types.

Congenital adrenal hyperplasia (CAH) can be caused by a variety of defects in the functional gene encoding 21-hydroxylase (P450c21), which lies in the midst of the human leukocyte antigen (HLA) locus on chromosome 6. As a result, Mendelian genetics permit clinically distinct forms of CAH to be traced genetically by HLA and complement typing of family members. The recent cloning of probes for P450c21 now permits tracing of the affected gene directly. A consanguineous family had three members affected with three clinically distinct forms of CAH. Two of these individuals had identical extended haplotypes, including nine HLA and complement loci. Despite this extensive identity, the patterns of genomic DNA fragments digested with endonuclease EcoRI and detected by a P450c21 cDNA probe differed greatly in these two individuals. Thus, the DNA diagnosis of allelic variation was much more sensitive than the HLA diagnosis. Genomic DNA digested with endonuclease TaqI and probed with P450c21 cDNA revealed the 3.2-kilobase (kb) band, which is generally associated with the nonfunctional P450c21 A pseudogene, in all family members, and also revealed the 3.7-kb band associated with the functional P450c21 B gene in all family members except the severely affected index case. Probing of the same blots with a genomic probe also permitted examination of the adjacent downstream TaqI fragments, showing retention of both the 2.4-kb (A pseudogene) and 2.5-kb (B gene) fragments. Similarly, BglII-digested genomic DNA from all individuals contained both the 12-kb (A pseudogene) and 11-kb (B gene) bands. These data indicate that the basis of 21-hydroxylase deficiency in the index case was due to a homozygous gene conversion event and not to gene deletion. These results show that the DNA in and around the 21-hydroxylase gene is genetically very active, so that the usual generalization concerning linkage and inheritance may yield incorrect conclusions and diagnoses.

Adolescent↗
PubMed1999

Allele-specific amplification for the diagnosis of autosomal recessive spinal muscular atrophy.

The SMN1 gene is homozygously deleted for at least exon 7, interrupted or converted to a non-functional telomeric copy in most cases of proximal spinal muscular atrophies. The presence of a pseudogene hampers direct detection of the exon 7 deletion. We describe a method for the detection of the of exon 7 deletion, based on the amplification refractory mutation system (ARMS), in a multiplex PCR with fluorescent-labelled primers. The gene and pseudogene amplification products differ in the dye bound and in their size, which allows distinction of both products on electrophoresis. The pseudogene is used as an internal control, and this method gives a clear and specific pattern for the patients. Amplification is achieved with 30 cycles, and specificity is retained up to 40 cycles.

Alleles↗
PubMed2005

Study on the expression and mutation of human telomeric repeat binding factor (hTRF1) in 10 malignant hematopoietic cell lines.

OBJECTIVE: Detecting the expression and mutation of human telomeric repeat binding factor (hTRF1) in 10 malignant hematopoietic cell line cells on the base of determining its genomic structure and its four pseudogenes to clarify if hTRF1 mutation is one of the factors of the activation of telomerase. METHODS: hTRF1cDNA sequences were obtained from GenBank, its genome structure and pseudogenes were forecasted by BLAST and other biology information programs and then testified by sequencing. Real-time RT-PCR was used to detect the expression of hTRF1mRNA in 10 cell line cells, including myelogenous leukemia cell lines K562, HL-60, U-937, NB4, THP-1, HEL and Dami; lymphoblastic leukemia cell lines 6T-CEM, Jurkat and Raji. Telomerase activities of cells were detected by using telomeric repeat amplification (TRAP)-ELISA protocol. PCR and sequencing were used to detect mutation of each exon of hTRF1 in 10 cell line cells. RESULTS: hTRF1 gene, mapped to 8q13, was divided into 10 exons and spans 38.6 kb. Four processed pseudogenes of hTRF1 located on chromosome 13, 18, 21 and X respectively, was named as PsihTRF1-13, PsihTRF1-18, PsihTRF1-21 and PsihTRF1-X respectively. All cell line cells showed positive telomerase activity. The expression of hTRF1 was significantly lower in malignant hematopoietic cell lines cells (0.0338, 0.0108-0.0749) than in normal mononuclear cells (0.0493, 0.0369-0.128) (P=0.004). But no significant mutation was found in all exons of hTRF1 in 10 cell line cells. Four variants were found in part of intron 1, 2 and 8 of hTRF1. Their infection on gene function is unknown and needs further studies. CONCLUSION: hTRF1 mutation is probably not one of the main factors for telomerase activation in malignant hematopoietic disease.

Base Sequence↗
PubMed1999

Expression of 17beta-hydroxysteroid dehydrogenase types 1, 2, 3 and 4 in the human temporal lobe.

Sex steroid hormones exert important biological effects on the brain. Moreover, an extensive sex steroid metabolism occurs in the brain. In sex steroid metabolism 17beta-hydroxysteroid dehydrogenases (17beta-HSDs) play essential roles in catalyzing the final steps in androgen and estrogen biosynthesis. Recently four types of human 17beta-HSDs and a pseudogene of the type 1 isoform were identified. To date, 17beta-HSD has not been extensively studied in the human brain. Therefore, we investigated the mRNA expression of the four isozymes of 17beta-HSD as well as the pseudogene of the type 1 isoform in the human temporal lobe to determine the predominant isoforms and, moreover, to elucidate the existence of possible sex and age differences. We studied biopsy materials from the temporal lobe of 34 women, 32 men and 10 children. Quantification of different mRNAs was achieved by competitive reverse transcription-PCR. 17beta-HSD 1, 17beta-HSD 3 and 17beta-HSD 4 were expressed in the human temporal lobe of children and adults, whereas 17beta-HSD 2 and the pseudogene of 17beta-HSD 1 were not expressed. In adults, 17beta-HSD 3 and 17beta-HSD 4 mRNA concentrations were significantly higher in the subcortical white matter (17beta-HSD 3: 14 591+/-3457 arbitrary units (aU), mean+/-s.e.m.; 17beta-HSD 4: 1201+/-212 aU) than in the cortex (17beta-HSD 3: 5428+/-1057 aU, P<0. 0002; 17beta-HSD 4: 675+/-74 aU, P<0.004). 17beta-HSD 1 concentrations did not differ significantly between the white matter (3860+/-1628 aU) and the cortex (2525+/-398 aU) of adults. In conclusion, the present study demonstrates the expression of 17beta-HSD 1, 3 and 4 mRNAs in the human temporal lobe. Together with CYP19AROM and 5alpha-reductase, known to be expressed in the human brain, the expression of 17beta-HSD 1, 3 and 4 mRNAs indicates the major importance of local steroid biosynthesis in the brain.

17-Hydroxysteroid Dehydrogenases↗
PubMed2001

Gene duplications at the chemokine locus on mouse chromosome 4: multiple strain-specific haplotypes and the deletion of secondary lymphoid-organ chemokine and EBI-1 ligand chemokine genes in the plt mutation.

The murine paucity of lymph node T cell (plt) mutation leads to abnormalities in leukocyte migration and immune response. The causative defect is thought to be a loss of secondary lymphoid-organ chemokine (SLC) expression in lymphoid tissues. We now find that the plt defect is due to the loss of both SLC and EBI-1 ligand chemokine (ELC) expression in secondary lymphoid organs. In an examination of the plt locus, we find that commonly used inbred mouse strains demonstrate at least three different haplotypes. Polymorphism at this locus is due to duplications of at least four genes, three of them encoding chemokines. At least two cutaneous T cell-attracting chemokine (CTACK), three SLC, and four ELC genes or pseudogenes are present in some haplotypes. All haplotypes share a duplication that includes two SLC genes, which demonstrate different expression patterns, a single functional ELC gene, and an ELC pseudogene. The plt mutation represents a deletion that includes the SLC gene expressed in secondary lymphoid organs and the single functional ELC gene, leaving only an SLC gene that is expressed in lymphatic endothelium and an ELC pseudogene. This lack of CCR7 ligands in the secondary lymphoid organs of plt mice provides a basis for their severe abnormalities in leukocyte migration and immune response.

Animals↗
PubMed1992

Characterization of the human gene encoding cytokeratin 17 and its expression pattern.

Among the members of the cytokeratin (CK) subfamily of intermediate filament (IF) proteins, CK 17 is remarkable as it is normally expressed in the basal cells of complex epithelia but not in stratified or simple epithelia. Because of its unusual expression pattern in normal and diseased states and because of the potential importance of CK 17 in tumor diagnosis, we have characterized the gene(s) and its cDNA-derived amino acid sequence. A cDNA clone encoding CK 17 was isolated from a HeLa cDNA library and used for the determination of the amino acid sequence, for studies of expression and for the screening of human genomic libraries. A number of lambda phage clones were isolated that covered three distinct, non-contiguous gene regions. Only one of these loci contains the functional CK 17 gene which is located only approximately 5 kbp 5'-upstream of the CK 16 gene, whereas the other two contain unprocessed CK 17 pseudogenes. Each of these genes is part of a larger CK type I gene locus the arrangement of which suggests that these genes and pseudogenes have arisen during evolution by duplication events comprising whole multigene loci. The functional CK 17 gene differs from the pseudogenes by the extent of methylation of certain DNA sequences in the 5'-upstream region. The 5 kbp CK 17 gene with 8 exons and 7 introns encodes a polypeptide of 432 amino acids with a calculated molecular weight of 48,000. Using S1-nuclease protection assays and RNAs from several cell lines we identified a single transcriptional start point 26 nucleotides down-stream from a TATA box element. Northern blot hybridization experiments showed a restricted pattern of CK 17 gene expression, supporting the notion that CK 17 synthesis is essentially regulated at the transcriptional level. From these findings and from immunohistological observations, CK 17 synthesis seems to be a marker of basal cell differentiation in complex epithelia and therefore indicative of a certain type of epithelial "stem cells".

Amino Acid Sequence↗
PubMed2003

[In silico data mining of the human programmed cell death 5 (PDCD5) sequences].

OBJECTIVE: To lay foundation for the functional studies of programmed cell death 5 (PDCD5) and develop new technical pathway for bioinformatics analysis of human functional genes. METHODS: Using PDCD5 as the target molecule, intensive bioinformatics analysis of the nucleic acid and protein sequences were conducted. Data mining and comprehensive analysis by sequence against database similarity searching, ortholog structure comparison, expression profile analysis and gene "neighbor" listing were performed. RESULTS: Two human putative pseudogenes on chromosomes 12 and 5, and one mouse putative pseudogene on chromosome 1 were identified. The methanobacterium thermoautotrophicum ortholog was classified as the same fold as ubiquitin and ribosomal protein S13. The C. elegans ortholog, ubiquitin and IAP (inhibitor of apoptosis proteins) belonged to the same expression profile cluster. This cluster was related to biosynthesis and protein synthesis. PDCD5 orthologs in various genomes were adjacent to various ribosomal proteins on the chromosome. CONCLUSION: The human genome contains at least two processed pseudogenes of PDCD5. Besides the relationship with cell apoptosis, PDCD5 is predicted to have functional relationship with ubiquitin and participate in the translation regulation.

Amino Acid Sequence↗
PubMed2005

[NEMO Delta 4-10 deletion of NEMO gene in Chinese incontinentia pigmenti cases].

OBJECTIVE: Incontinentia pigmenti (IP) is a rare X-linked dominant disorder that affects ectodermal tissues. In IP, mutations in NEMO lead to the complete loss of NF-kB activation creating a susceptibility to cellular apoptosis in response to TNF-alpha. Recently, a second nonfunctional copy of the gene, Delta NEMO was identified, opposite in direction to NEMO. Almost 90% of IP whose gene mutation type had been recognized have a recurrent genomic deletion of exons 4-10 of the NEMO (IKK gamma) gene, called NEMO Delta 4-10, which is necessary to activate the NF-kB pathway. Therefore, PCR-based detection of the NEMO deletion is a diagnostic measurement for IP. This study sought to analyze the NEMO Delta 4-10 deletion in NEMO gene of Chinese IP cases. METHODS: Seven IP cases and part of their families totally 15 persons were enrolled in this study. The 7 IP cases were aged 41 days to 8 years. Among them 1 was male and 6 were female. Four cases had family history of IP, the other 3 were sporadic cases. Fifty healthy children without any congenital diseases were taken as normal control group. According to the gene characteristics of IP, by PCR measurement NEMO Delta 4-10 deletion in NEMO gene was tested with specific primers In2/JF3R, and NEMO Delta 4-10 deletion in pseudogene Delta NEMO was checked out by primers Rev-2/JF3R. RESULTS: Five out of the 7 tested cases (case 1, 2, 3, 4, and 6) showed NEMO Delta 4-10 deletion in NEMO gene. The mothers of case 1 and case 6, 1a and 6a, also suffered from this disease, and their results were just the same as their daughters. For pseudogene Delta NEMO only case 2 and case 4 were proved having NEMO Delta 4-10 deletion, while other cases and families had negative results. For normal control group, NEMO Delta 4-10 deletion was not found either in NEMO gene or in their pseudogene Delta NEMO. CONCLUSION: Incontinentia pigmenti in most cases were caused by NEMO Delta 4-10 deletion in NEMO gene.

Child↗
PubMed1989

Characterization of the 3' region of the human DNA topoisomerase I gene.

Previous studies suggest that topoisomerase I (Topo I) plays a critical role in cell growth. However, the structure of the Topo I gene has not yet been determined. Two complementary DNA (cDNA) clones for the human Topo I 4.1-kilobase mRNA were isolated independently from HeLa and KB cell cDNA libraries. These clones were identical and they contained 679 base pairs of coding and 1138 base pairs of noncoding sequences. The clones had a two-base difference in the 3' noncoding region compared to the Topo I cDNA from human placenta. The structure of the 3' end of the human Topo I gene from six human tumor cell lines was examined. The Topo I cDNA recognized 16.5, 24.2, and 16.0 kilobases of genomic DNA restricted with EcoRI, HindIII and PstI, respectively. The individual genomic fragments were ordered by double digestion and hybridization with cDNA subclones. digestion and hybridization with cDNA subclones. The results indicate that the human Topo I gene contains several intervening sequences. The gene arrangement was similar in all six cell lines and no polymorphism was observed. However, each digestion contained genomic fragments that hybridized with all the subclones, suggesting that at least one Topo I pseudogene, or another Topo I gene with a different structure, was present in every cell line. As predicted, double digestions generated at 161 base pair fragment that indicates the presence of an intronless pseudogene. In contrast to the DNA topoisomerase I gene, the presumptive pseudogene(s) appears to be hypomethylated. In addition to the 4.1-kilobase Topo I mRNA, a larger 6-kilobase RNA was identified in human KB and HeLa cells which could be a processed Topo I mRNA intermediate.

Base Sequence↗
PubMed1986

Isolation and nucleotide sequence of the rabbit globin gene cluster psi zeta-alpha 1-psi alpha. Absence of a pair of alpha-globin genes evolving in concert.

A cloned 13.3-kilobase (kb) region of rabbit genomic DNA contains a cluster of alpha-like globin genes arranged 5'-psi zeta-(3.6 kb)-alpha 1-(2.2 kb)-psi alpha-3'. Genomic blot hybridization data show that this is the major alpha-like globin gene cluster in rabbits, although a second alpha-globin gene (alpha 2) is also detected. Repetitive sequences from the C family of short repeats flank the psi zeta gene, and a new repetitive element, the F repeat is located 3' to psi alpha. The sequence was determined for a 4024-base pair (bp) segment that extends from 149 bp 5' to the cap site of alpha 1 to 207 bp 3' to psi alpha. Gene alpha 1 is functional and encodes one of the major allelic variants of rabbit alpha-globin. This gene has very short introns (77 bp in intron 1 and 83 bp in intron 2) and an unusual ATA box in the 5' flanking region (CTTAAA), which does function to promote transcription by RNA polymerase II in a cell-free system. Short (4 or 9 bp) G + C-rich repeats are interspersed throughout the flanking regions and the introns. Gene psi alpha cannot encode a globin polypeptide, and it is probably inactive. This is shown by the absence of a normal globin gene promoter, the replacement of the 5' untranslated sequence by tandem repeats of the sequence GCCCGCCGC, frameshift deletions in exon 2, and the modification of the polyadenylation signal to AGTAAA. The intergenic region between alpha 1 and psi alpha is very G + C rich (65.7% G + C) and contains many short, tandem repeats. Gene psi zeta hybridizes specifically to a human zeta-globin gene probe, but a partial sequence reveals frameshift mutations that probably make psi zeta a pseudogene. Mammalian alpha-globin gene clusters vary in the presence or absence of pseudogenes, and if present, the position of the pseudogene differs in various gene clusters. Among the mammalian alpha-like gene clusters so far analyzed, the rabbit gene cluster is unique in the absence of duplicated alpha-globin genes that are undergoing concerted evolution.

Animals↗
PubMed1986

A human gene family with sequence homology to Drosophila melanogaster Hsp70 heat shock genes.

A growing literature describes the structure and regulation of prokaryotic and eukaryotic heat shock genes. We here report 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. Eight nonoverlapping recombinant lambda phages from a lambda-Charon4A human genomic library were studied by restriction mapping. One lambda clone was sequenced and characterized as a hsp70 pseudogene inserted into a rearranged human HindIII 1.9-kilobase repeated DNA sequence. This pseudogene is probably located on the X chromosome. Its predicted amino acid sequence shows extensive homology to those of Drosophila hsp70, trout hsp70, Xenopus hsp70, yeast hsp70, and some homology to the heat-inducible dnaK gene product of Escherichia coli. Amino acid homology is clustered, suggesting evolutionary conservation of domains critical to the function of this protein in both prokaryotic and eukaryotic cells.

Amino Acid Sequence↗
PubMed1996

Gene conversion contributes to Ig light chain diversity in cattle.

In humans and mice, extensive gene rearrangement is the major mechanism of diversification of the primary Ig repertoire. This study shows that cattle depart from this pattern because rearrangement in the light chain locus is sharply limited. Furthermore, in cattle, gene conversion contributes to the diversification of the primary light chain repertoire. Sequencing of germ-line and expressed Vlambda genes revealed three important features. First, the germ line contained a number of Vlambda pseudogenes. In fact, 14 (70%) of the 20 germ-line genes identified and sequenced were pseudogenes, because they had one or more of the following defects: lack of recombination signal sequences at the 3' end, stop codons within the reading frame or truncations, and/or insertions or deletions that resulted in loss of reading frame. Second, Vlambda cDNA from ileal Peyer's patch B cells demonstrated that the light chain repertoire arises from only a small number of V(J) rearrangements. Even though two J genes were identified in the germ line, all of the expressed Vlambda genes examined contained the same J segment, indicating that only a single J gene participates in rearrangement at the lambda locus. Third, a significant number of departures from the germ-line sequences of rearranged Vlambda can be traced to donor sequences of one or more Vlambda pseudogenes. We conclude that a limited number of rearrangements and gene conversion play a role in contributing to the diversification of the primary lambda repertoire. Furthermore, while clear indications of a role for somatic mutation in lambda diversification was seen, V gene rearrangement was not a major factor.

Amino Acid Sequence↗