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PubMed1993

Evidence that the SRY protein is encoded by a single exon on the human Y chromosome.

To facilitate studies of the SRY gene, a 4741-bp portion of the sex-determining region of the human Y chromosome was sequenced and characterized. Two RNAs were found to hybridize to this genomic segment, one transcript deriving from SRY and the second cross-hybridizing to a pseudogene located 2.5 kb 5' of the SRY open reading frame (ORF). Analysis of the SRY transcript using 3' and 5' rapid amplification and cloning of ends suggested that the entire SRY protein is encoded by a single exon. A 700-bp CpG island is located immediately 5' of the pseudogene (and 2 kb 5' of the SRY ORF). Within this CpG island lies the sequence CGCCCCGC, a potential binding site for the EGR-1/WT1 family of transcription factors, some of which appear to function in gonadal development.

Adult↗
PubMed1995

Toward a cDNA map of the human genome.

Advances in the Human Genome Project are shaping the strategies for identifying the 50,000-100,000 human genes. High-resolution genetic maps of the human genome combined with sequencing herald an era of rapid regional definition of disease genes. However, only once their chromosome band location is known will the systematic partial sequencing of thousands of random cDNA clones provide the reagents for teh rapid assessment of the genes responsible for the inherited disorders. We now present an approach to the rapid determination of map position and therefore to the creation of a transcribed map of the human genome. Sensitive fluorescence in situ hybridization has been combined with high-resolution chromosome banding and random cDNA sequencing to map 41 cDNAs with an average insert size of <2 kb to single human chromosome bands. The result provide 15 new genes, with database and functional information, as candidates for human disease. These include the large extracellular signal-related kinase (HUMERK), the ERK activator kinase (PRKMK1), a new member of the RAS oncogene family, protein phosphatase 2 regulatory subunit B alpha isoform (PPP2R2A), and a novel human gene with very high homology to a plant membrane transport family. Further, an analysis of expressed genes associated with pseudogenes showed that by using these techniques, it is possible to detect accurately the transcribed locus within a multigene or processed pseudogene family in most cases. These findings suggest that direct cDNA mapping using fluorescence in situ hybridization provides an accurate and rapid approach to the definition of a transcribed map of the human genome. This low-cost, high-resolution (2-5 Mb) mapping greatly enhances the speed with which these genes can be subsequently assigned to contigs. This assignment provides a necessary first step in understanding the relationship of the genes to both acquired and inherited human diseases.

Cells, Cultured↗
PubMed1996

Systematic sequencing of the human HLA-A/HLA-F region: establishment of a cosmid contig and identification of a new gene cluster within 37 kb of sequence.

The class I region of the human histocompatibility complex is characterized by a high density of genes and pseudogenes and a complex structural organization. To elucidate the complete structure of the HLA-A/HLA-F region with a view to defining its contents in genes and pseudogenes, we developed a strategy of systematic sequencing. This report describes the establishment of a cosmid contig spanning most of the region and the analysis of a 37-kb sequence from one of the cosmids. Four new genes, organized with the HCG-V gene in a clustered structure, have been identified. Two of these contain a zinc finger motif characteristic of DNA-binding proteins. The former, a member of the C3HC4 protein family, is highly expressed in prostate and contains a B30-2-like sequence identified in several genes mapped within the class I region. The latter, which is ubiquitously expressed, is the human equivalent of the yeast polymerase IA12.2 subunit and of the murine tctex6 gene. Of the two other genes, one remains an anonymous gene with no particular feature, while the fourth, specifically expressed in testis, is the human equivalent of the murine tctex4 gene. This cluster, located in a region corresponding to a syntenic unit between mouse and human, appears to be highly conserved.

Amino Acid Sequence↗
PubMed1997

Nucleotide sequence analysis of the HLA class I region spanning the 237-kb segment around the HLA-B and -C genes.

To elucidate the detailed gene organization of the human leukocyte antigen (HLA) class I region on chromosome 6, seven contiguous cosmid genomic clones covering the 237-kb segment around the HLA-B and -C loci were subjected to DNA sequencing by the shotgun strategy to give a single contig of 236,822 bp from the MICA gene (58.2 kb centromeric of HLA-B) to 90.8 kb telomeric of HLA-C. This region was confirmed to contain four known genes, MICA, HLA-17, HLA-B, and HLA-C, from centromere to telomere. Further, a new member of the P5 multicopy genes was found to be about 1.3 kb upstream of the HLA-17 gene and designated P5.8. Five novel genes designated NOB1-5 were identified by RT-PCR and Northern blot hybridization. In addition, two pseudogenes, dihydrofolate reductase pseudogene (DHFRP) and ribosomal protein L3 homologous gene (RPL3-Hom), were also found in the vicinity of the HLA-B and -C genes, respectively. The two segments (about 40 kb) downstream of the HLA-B and HLA-C genes showed high sequence homology to each other, suggesting that segmental genome duplication including the major histocompatibility complex (MHC) class I gene must have occurred during the evolution of the MHC.

Blotting, Northern↗
PubMed1998

Structure and organization of the RBMY genes on the human Y chromosome: transposition and amplification of an ancestral autosomal hnRNPG gene.

The RBMY (RNA-binding motif, Y chromosome) gene family encodes a germ-cell-specific nuclear protein implicated in spermatogenesis. It consists of approximately 30 genes and pseudogenes, found on both arms of the Y chromosome. RBMY shares high homology with an autosomal hnRNPG gene that contains an RNA-binding motif and one of the four SRGY repeats found in RBMY. One proposal is that RBMY represents an ancestral hnRNPG gene, transposed to the Y chromosome and then amplified. We characterized seven RBMY genes in interval 6 of the Y chromosome long arm. Four have the normal structure with 12 exons spanning 15 kb, whereas one lacks the first 3 exons, therefore representing a pseudogene. The remaining two genes belong to a different subfamily, resembling the autosomal hnRNPG gene with only one SRGY repeat. We also found that most RBMY genes in interval 6 are arranged in tandem. The structure and organization of the Y-linked RBMY genes support the transposition-amplification hypothesis.

Amino Acid Sequence↗
PubMed2001

WHSC1L1, on human chromosome 8p11.2, closely resembles WHSC1 and maps to a duplicated region shared with 4p16.3.

We have identified and characterized a gene (60% on protein level) and a pseudogene (93% on DNA level) that show high similarity to the Wolf-Hirschhorn syndrome candidate gene-1 (WHSC1). These genes, WHSC1L1 and WHSC1L2P, map to human chromosomes 8p11.2 and 17q21, respectively. WHSC1L1 is ubiquitously expressed and, like WHSC1, generates two major transcripts, a short (s-type) and a long (l-type). The WHSC1L1 l-type transcript encodes a 1437-amino-acid protein containing 2 PWWP (proline-trypto-phan-proline-tryptophan) domains, 5 PHD (plant-home-domain)-type zinc finger motifs, a SAC (SET-associated Cys-rich) domain, and a SET (Suppressor of Variegation, Enhancer of Zeste and Trithorax) domain. The s-type transcript encodes a protein of 645 amino acids containing a PWWP domain only. WHSC1L2P is an unexpressed, intronless pseudogene of a WHSC1L1 s-type transcript. The 8p11.2 region around WHSC1L1 contains a set of genes including TACC1, FGFR1, LETM2, and WHSC1L1, which seems to be derived from a recent duplication involving 4p16.3 where a similar set of genes is located. Rearrangements of 8p are frequently found in human cancer, including breast cancer. These characteristics indicate that WHSC1L1 might have a role in embryonic development and, when disregulated, in cancer development.

Carrier Proteins↗
PubMed2001

Assessment of the total number of human transcription units.

Variation in the estimates of the number of genes encoded by the human genome (28,000-120,000) attests to the difficulty of systematically identifying human genes. Sequencing of human chromosome 22 (Chr22) provided the first comprehensive, unbiased view of an entire human chromosome, and intensive analysis of this sequence identified 545 genes and 134 pseudogenes that had similarity or identity to known proteins and/or ESTs and which were listed in the gene annotation (http://www.sanger.ac.uk/HGP/Chr22). This analysis yielded an estimate of approximately 36,000 functional expressed genes in the human genome (and 9000 pseudogenes). However, a key uncertainty in this estimate was that hundreds of additional genes beyond those annotated in the Chr22 sequence are predicted by the gene prediction program Genscan, an unknown number of which might represent additional expressed genes. To determine what fraction of these "predicted novel genes" (PNGs) represents expressed human genes, we used a sensitive RT-PCR assay to detect predicted transcripts in 17 tissues and one cell line. Our results indicate that at least 5000-9000 additional human genes which lack similarity to known genes or proteins exist in the human genome, increasing baseline gene estimates to approximately 41,000-45,000.

Chromosomes, Human, Pair 22↗
PubMed2002

Genomic organization and mapping of the gene encoding the PP2A B56gamma regulatory subunit.

Protein phosphatase 2A (PP2A) is a major serine/threonine phosphatase that regulates a wide variety of cellular processes. The enzymatic activity and intracellular localization of PP2A are determined by three distinct families of cellular regulatory subunits (B, B'', and B''). The B' subunit, also known as B56, is the most diverse, consisting of five isoforms (alpha, beta, gamma, delta, and epsilon). The gene encoding B56gamma has been designated as PPP2R5C and encodes three differentially spliced variants: B56gamma1, -gamma2, and -gamma3. However, conflicting chromosomal loci have been reported in human genomic databases. The original cytogenetic mapping placed the gene on chromosome 3p21.3, whereas subsequent studies using radiation hybrid analysis localized PPP2R5C to chromosome 14q. In this study, by radiation hybrid mapping, FISH analysis, BAC clone sequencing, and RT-PCR analysis, we show that the functional gene PPP2R5C exists at 14q32.2 and gives rise to three splicing variants, B56gamma1, -gamma2, and -gamma3, whereas a nonfunctional B56gamma1 pseudogene, PPP2R5CP, is present at 3p21.3. We also report the genomic organization of both the functional gene and the pseudogene.

Base Sequence↗
PubMed2000

Use of TaqI digestion may lead to incorrect molecular diagnosis of congenital adrenal hyperplasia due to 21-hydroxylase deficiency.

Congenital adrenal hyperplasia (CAH) is a common autosomal recessive disorder mainly caused by defects in the steroid 21-hydroxylase (CYP21) gene. For reliable and accurate mutation detection in the CYP21 gene it is important to separate the CYP21 gene from the highly homologous CYP21P pseudogene. For this, several different strategies have been developed. In the analysis of the common eight nucleotide deletion at codon 110-112, a strategy using the TaqI restriction enzyme was first applied. In one family, the results showed discordance between parents and offspring. The use of microsatellite markers flanking the genuine CYP21 gene did not lead to a correct assignment. The problem was finally resolved by using differential PCR amplification for generating a CYP21-specific template. It was concluded that incomplete TaqI digestion, although not visible on an agarose gel, allowed the amplification of the CYP21P pseudogene, thus leading to a false positive diagnosis. Therefore, we recommend the use of direct gene-specific primers for the essential step in the molecular diagnosis of congenital adrenal hyperplasia due to steroid 21-hydroxylase deficiency.

Adrenal Hyperplasia, Congenital↗
PubMed1994

Phylogenetic analysis of green plant rbcL sequences.

DNA and derived amino acid sequences of the rbcL gene from selected photosynthetic bacteria, green algae, bryophytes, "fern allies," ferns, and seed plants were used to construct phylogenetic trees using parsimony algorithms. Internal support of clades was determined by the bootstrap and decay indices. External support was judged by comparison of trees with previous morphological and molecular cladograms. Some clades on all the trees are supported both internally and externally, but all of the trees are characterized by unsupported relationships of the bryophytes and fern allies. Trees produced by analyses of all three DNA positions have the highest levels of internal support, but many clades are still not supported externally or internally. Analyses using only the first and second positions of the DNA sequences and derived amino acid sequences produced trees with odd groupings and low levels of internal support for most of the clades. These results indicate that rbcL sequences may be too divergent to test phylogenetic relationships among major groups of green plants. Additional problems with constructing phylogenetic trees from rbcL sequences may be caused by RNA editing, pseudogenes, unequal rates of evolution, and inadequate taxon sampling. Whether RNA editing is a problem can be determined by sequencing amplified RNAs from selected taxa. If pseudogenes are suspected, purified chloroplast DNA should be used for amplification. It may be beneficial to include more taxa in subsequent analyses, but there are indications that historical extinctions will prevent adequate sampling of some groups, such as the bryophytes and fern allies.

Amino Acid Sequence↗
PubMed1987

Rat metallothionein multigene family.

Southern blot analysis of rat genomic DNA reveals the presence of numerous sequences homologous to the rat MT-1 gene. We have isolated and characterized by sequence analysis the rat MT-1 gene and three related processed pseudogenes. We discuss mechanisms by which these pseudogenes were formed. The rat MT-1 and MT-2 structural genes are shown to be separated by 4 kb of intergenic DNA. By sequence analysis of the MT-2 structural gene, we compare features of the MT gene sequences which regulate promoter activity, and which specify transcription termination and polyadenylation. From an examination of homologous sequences in the MT promoters, we suggest that there may be both regulatory features in common with the MT gene isotypes, and regulatory mechanisms which may allow for differential expression of these genes. We discuss possible applications of recombinant DNA technology to investigating both the expression of MT genes and the functioning of MT proteins, in a tissue specific manner and during development.

Amino Acid Sequence↗
PubMed1995

Organization and evolution of the cytochrome P450 CYP2A-2B-2F subfamily gene cluster on human chromosome 19.

Cytochrome P450 genes from the CYP2A, CYP2B, and CYP2F subfamilies form a tight cluster which we have localized on the detailed physical map of human chromosome 19. The corresponding three gene subfamilies are also clustered in the mouse genome, on the region of chromosome 7 known to be syntenic to human chromosome 19. One hundred eight cosmid clones from the human P450 region were assembled into a single contig of 350 kb, restriction mapped, and probed with cDNAs from the three gene subfamilies. A total of 11 genes were identified in humans, including five from the 2A subfamily, three from the 2B subfamily, and three from the 2F subfamily; at least six of the 11 are pseudogenes. The organization of the genes, with members of the three subfamilies intermixed, indicates that the evolution of this gene cluster has been complex. The modern gene arrangement in humans is probably the result of a series of tandem duplications, plus at least one inverted duplication. The identification of all genes and pseudogenes in this cluster also makes it possible to determine the origins of some previously known variant P450 transcripts.

Animals↗
PubMed1990

Hypervariability of intronic simple (gt)n(ga)m repeats in HLA-DRB genes.

We have investigated the extent of DNA variability in intronic simple (gt)n(ga)m repeat sequences and correlated this to sequence polymorphisms in the flanking exon 2 of HLA-DRB genes. The polymerase chain reaction (PCR) was used to amplify a DNA fragment containing exon 2 and the repeat region of intron 2. The PCR products were separated on sequencing gels in order to demonstrate length hypervariability of the (gt)n(ga)m repeats. In a parallel experiment, the PCR products were cloned and sequenced (each exon 2 plus adjacent simple repeats) to characterize the simple repeats in relation to the HLA-DRB sequences. In a panel of 25 DRB1, DRB4, and DRB5 alleles new sequences were not detected. Restriction fragment length polymorphism (RFLP) subtyping of serologically defined haplotypes corresponds to translated DNA sequences in 85% of the cases, the exceptions involving unusual DR/DQ combinations. Many identical DRB1 alleles can be distinguished on the basis of their adjacent simple repeats. We found group-specific organization of the repeats: the DRw52 supergroup repeats differ from those of DRB1*0101, DRB4*0101, and DRB5*0101 alleles and from those of pseudogenes. Finally, we amplified baboon DNA and found a DRB allele with extensive similarity to DRB1 sequences of the DRw52 supergroup. The simple repeat of the baboon gene, however, resembles that of human pseudogenes. In addition to further subtyping, the parallel study of polymorphic protein and hypervariable DNA alleles may allow conclusions to be drawn on the relationships between the DRB genes and perhaps also on the theory of trans-species evolution.

Amino Acid Sequence↗
PubMed1993

Mhc-DRB genes of platyrrhine primates.

The two infraorders of anthropoid primates, Platyrrhini (New World monkeys) and Catarrhini (Old World monkeys and the hominoids) are estimated to have diverged from a common ancestor 37 million years ago. The major histocompatibility complex class II DRB gene and haplotype polymorphism of the Catarrhini has been characterized in several recent studies. The present study was undertaken to obtain information on the DRB polymorphism of the Platyrrhini. Fifty-five complete exon 2 DRB sequences were obtained from six species of Platyrrhini representing both the Callitrichidae and the Cebidae families. Combined with the results of a parallel contig mapping study, our data indicate that at least three loci (DRB1*03, DRB3, and DRB5) are shared by the Catarrhini and the Platyrrhini. However, the three loci are occupied by functional genes in the former infraorder and mostly by pseudogenes in the latter. Instead of the pseudogenes, the Platyrrhini have evolved a new set of apparently functional genes-DRB11 and DRB*W12 through DRB*W19, which have thus far not been found in the Catarrhini. The DRB*W13, *W14, *W15, *W17, *W18, and *W19 genes seem to be restricted to the Cebidae family, whereas the DRB*W16 locus has so far been documented in the Callitrichidae family only. The DRB alleles of the cotton-top tamarin, and perhaps also those of the common marmoset (both members of the family Callitrichidae), are characterized by low nucleotide diversity, possibly indicating that they diverged from a common ancestral gene relatively recently.

Amino Acid Sequence↗
PubMed1992

Differential expression of four genes encoding molluscan insulin-related peptides in the central nervous system of the pond snail Lymnaea stagnalis.

In the pond snail Lymnaea stagnalis, the growth regulating system consists of (1) about 200 neuroendocrine light green cells, located in four clusters in the cerebral ganglia, and (2) the paired canopy cells, located in the lateral lobes. These cells express genes encoding the molluscan insulin-related peptides (MIPs). Six MIP genes have previously been identified. Four of these (I, II, III and V) are expressed in the light green cells and the canopy cells. The MIP-VI gene is a pseudogene. In the present in situ hybridization study, using oligonucleotide probes specific to the transcripts of MIP-I, -II, -III, -IV and -V, no signal was obtained with the MIP-IV probe, indicating that gene IV is also a pseudogene. With the other four probes, two types of light green cells were distinguished. Type-A cells express all four MIP genes, whereas type-B cells do not (or only faintly) express the MIP-I gene. Gene III is relatively strongly expressed in type-B cells. Genes II and V are moderately expressed in both cell types. Type-A cells are mainly located in the periphery of the clusters, whereas type-B cells are present in the center. The canopy cell resembles type-A light green cells. The expression levels of the MIP-II and MIP-V genes are low in the canopy cell. The expression pattern of the MIP genes correlates with the staining pattern of the anti-MIP-C antibody, which has been raised to a synthetic C-fragment shared by MIP-I, -II and -V. Type-A cells stain more intensely with the antibody than type-B cells.

Animals↗
PubMed1992

Assignment of eight loci to bovine syntenic groups by use of PCR: extension of a comparative gene map.

The polymerase chain reaction (PCR) has been combined with hybrid somatic cell technology to extend the bovine physical map. Eight bovine loci--glycoprotein hormone alpha (CGA), coagulation factor X (F10), chromogranin A (CHGA), low-density lipoprotein receptor (LDLR), human prochymosin pseudogene (CYM), oxytocin (OXT), arginine-vasopressin (ARVP), and cytochrome oxidase c subunit IV pseudogene (COXP)--were assigned to bovine syntenic groups with this approach. CGA was assigned to bovine syntenic group U2, F10 to U27, CHGA to U4 [bovine Chromosome (Chr) 21], LDLR to U22, CYM to U6, OXT and ARVP to U11, and COXP to U3 (bovine Chr 5). Seven of these genes, CGA, F10, CHGA, LDLR, OXT, ARVP, and CYM, further delineate regions of chromosomal conservation on human Chrs 6, 13, 14, 19, 20, 20, and 1, respectively. CHGA, OXT, and ARVP are unmapped in the mouse. Comparative mapping predicts the mouse CHGA will map to Chr 12, and mouse OXT and ARVP will map to mouse Chr 2. Furthermore, human CYM is predicted to be sublocalized to 1p32-q21. The primers developed for these eight loci will be useful for the development of hybrid somatic cell panels in the future as well as establishing a collection of bovine expressed sequence tags.

Animals↗
PubMed1990

The nucleotide sequence of bovine MHC class II DQB and DRB genes.

The nucleotide sequences of most of the exons and parts of the introns of two BoLA-DQB genes and two BoLA-DRB genes have been determined. The structure of these genes is very similar to that of human major histocompatibility complex (MHC) class II genes. The two DQB genes probably represent true alleles. Based on the exons sequenced, both DQB genes and one of the DRB genes seem to be functional. The other DRB gene is a pseudogene; stopcodons are found in the exons encoding the second and transmembrane domain and, furthermore, a 2 base pair (bp) deletion has occurred in the leader exon which places the initiation start codon out of frame. Also in this pseudogene, an almost perfect inverted repeat of 200 bp is found flanking the exon encoding the first domain, which might have been the result of a duplication/inversion event. The sequences presented in this paper do not contain any repetitions. Therefore, DNA fragments containing these sequences can be used as homologous bovine probes in restriction fragment length polymorphism (RFLP) analysis to study disease associations in cattle.

Amino Acid Sequence↗
PubMed1986

Chromatin structure of active and inactive human X-linked phosphoglycerate kinase gene.

We have carried out a comparative analysis of DNase I sensitivity of the active and inactive X-linked phosphoglycerate kinase (Pgk) genes in human lymphoblast and fibroblast cultured cells. Three DNase I-sensitive regions were detected: a 5' hypersensitive site, a sensitive region in the interior of the gene and a 3' slightly sensitive site which we previously reported and have now mapped with some precision. A comparison of these sensitive sites in single and multiple X cell lines indicates that the sensitive sites are unique to the active X chromosome. A similar study of an X-linked Pgk pseudogene shows no difference in DNase I sensitivity between the pseudogenes on the active and inactive X chromosomes. These latter results imply that sex chromatin does not confer a unique level of DNase I resistance to DNA on the inactive X chromosome. The exact role of sex chromatin in differential DNase I sensitivity of genes on the inactive and active X chromosomes is discussed.

Cells, Cultured↗