Polymorphisms in the transcribed 3' untranslated region of eukaryotic genes

EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human

A molecular understanding of porcine reproduction is of biological interest and economic importance. Our Midwest Consortium has produced cDNA libraries containing the majority of genes expressed in major female reproductive tissues, and we have deposited into public databases 21,499 expressed sequence tag (EST) gene sequences from the 3' end of clones from these libraries. These sequences represent 10,574 different genes, based on sequence comparison among these data, and comparison with existing porcine ESTs and genes indicate as many as 4652 of these EST clusters are novel. In silico analysis identified sequences that are expressed in specific pig tissues or organs and confirmed the broad expression in pig for many genes ubiquitously expressed in human tissues. Furthermore, we have developed computer software to identify sequence similarity of these pig genes with their human counterparts, and to extract the mapping information of these human homologues from genome databases. We demonstrate the utility of this software for comparative mapping by localizing 61 genes on the porcine physical map for Chromosomes (Chrs) 5, 10, and 14.

A candidate chimeric mammalian mRNA transcript is derived from distinct chromosomes and is associated with nonconsensus splice junction motifs

The process of creating chimeric mRNA transcripts derived from separately transcribed genes via known spliceosome mechanisms is termed trans-splicing, and has been primarily described in lower eukaryotes. Isolation of cDNA clones containing sequences from distinct genes has raised the possibility of trans-splicing across distinct genes in mammalian systems; however, the possibility of cloning artifacts or splicing via nonspliceosome mechanisms has been difficult to rule out. In most cases, the absence of corresponding genomic clones has limited assessment of splice donor and acceptance sites and associated intronic elements that would be expected to participate in spliceosome-based reactions. We have previously reported a cDNA clone encoding the rat Leukocyte Common Antigen-Related (LAR) tyrosine phosphatase receptor that contains an alternative 3' UTR. In the present study Northern, RT-PCR and RNase protection assays verified the existence of developmentally regulated 3' UTR alternative splicing of LAR transcripts in vivo. FISH and radiation hybrid mapping demonstrated that loci encoding LAR and its alternative 3' UTR are present on distinct chromosomes, raising the possibility that alternatively spliced transcripts resulted from trans-splicing. Exon/intron analysis of corresponding genomic clones revealed nonconsensus splice junctions along with elements known to promote both cis- and trans-splicing. Verification in a mammalian in vivo system of chimeric transcripts derived from distinct genes along with identification of atypical nonconsensus-associated genomic elements points to the novel possibilities of atypical spliceosome-based trans-splicing or nonconventional, nonspliceosome-based mechanisms leading to chimeric transcripts.

The untranslated region of (mu)-opioid receptor mRNA contributes to reduced opioid sensitivity in CXBK mice

It is well known that there are individual differences in a sensitivity to analgesics. Several lines of evidence have suggested that the level of opioid-induced analgesia is dependent on the level of expression of the mu-opioid receptor (mu-OR). However, the molecular mechanisms underlying the diversity of the level of the opioid receptor and the opioid sensitivity among individuals remain to be elucidated. In the present study, we analyzed the opioid-receptor genes of CXBK recombinant-inbred mice, which show reduced sensitivity to opioids. Northern blotting, nucleotide sequencing, and in situ hybridization histochemical analyses demonstrated that CXBK mice possessed mu-OR mRNA with a normal coding region but an abnormally long untranslated region (UTR). In addition, the mu-OR mRNA level in CXBK mice was less than in the control mice. Next, we produced littermate mice that had inherited two copies of the wild-type mu-OR gene, had inherited two copies of the CXBK mu-OR gene, and had inherited both copies of the mu-OR genes. In these mice, inheritance of the CXBK mu-OR gene was well correlated with less mu-OR mRNA and reduced opioid effects on nociception and locomotor activity. We conclude that the CXBK mu-OR gene is responsible for the CXBK phenotypes. Because UTR differences are known to affect the level of the corresponding mRNA and protein and because UTRs are more divergent among individuals than coding regions, the present findings suggest that opioid sensitivity may vary, depending on different mu-OR levels attributable to divergent UTR of mu-OR mRNA.

A yeast prion provides a mechanism for genetic variation and phenotypic diversity

A major enigma in evolutionary biology is that new forms or functions often require the concerted effects of several independent genetic changes. It is unclear how such changes might accumulate when they are likely to be deleterious individually and be lost by selective pressure. The Saccharomyces cerevisiae prion [PSI+] is an epigenetic modifier of the fidelity of translation termination, but its impact on yeast biology has been unclear. Here we show that [PSI+] provides the means to uncover hidden genetic variation and produce new heritable phenotypes. Moreover, in each of the seven genetic backgrounds tested, the constellation of phenotypes produced was unique. We propose that the epigenetic and metastable nature of [PSI+] inheritance allows yeast cells to exploit pre-existing genetic variation to thrive in fluctuating environments. Further, the capacity of [PSI+] to convert previously neutral genetic variation to a non-neutral state may facilitate the evolution of new traits.

Single pass sequencing and physical and genetic mapping of human brain cDNAs

We have performed single pass sequencing of 1,024 human brain cDNAs, over 900 of which seem to represent new human genes. Library prescreening with total brain cDNA significantly reduced repeated sequencing of highly represented cDNAs. A subset of sequenced cDNAs were physically mapped to their chromosomal locations using gene-specific STS primers derived from 3' untranslated regions. We have also determined that human brain cDNAs represent a rich source of gene-associated polymorphic markers. Microsatellite-containing cDNAs can be physically mapped and converted to highly informative genetic markers, thus facilitating integration of the human physical, expression and genetic maps.

Polymorphisms in the 3' untranslated region of the I kappa B/MAD-3 (NFKBI) gene located on chromosome 14

The NF-kappa B transcription factor regulates the expression of a number of genes, including immune function and growth control loci, and several viruses. For example, the long terminal repeat of the human immunodeficiency virus contains NF-kappa B binding sites. NF-kappa B activity in the nucleus is regulated by a cellular inhibitory protein I kappa B. To analyze the potential role of these genes in genetic disease we have mapped the NF-kappa B (NFKB2) and I kappa B/MAD-3 (NFKBI) loci in a panel of somatic cell hybrids to chromosomes 4 and 14, respectively. Amplification of the 3' untranslated region of NFKBI allows the detection of three independent polymorphisms within 410 bp. In combination these polymorphisms were informative in 27 of 36 CEPH families and allowed the gene to be placed onto the linkage map of chromosome 14, between the D14S32 and D14S42 markers.

Identification of type I collagen gene polymorphisms: tolerance of sequence variation at an alpha 2(I) helix Y position

This study has examined the frequency and distribution of polymorphisms in the type I collagen coding sequences. RNA from a group of human skin fibroblast cell lines was analyzed by the chemical cleavage mismatch detection method using hydroxylamine, a reagent specific for C-base mismatches, and overlapping cDNA probes covering the entire prepro alpha 1(I) and prepro alpha 2(I) coding regions. Mismatches were detected at only two nucleotide positions, one in each of the type I collagen sequences, suggesting that polymorphisms are relatively rare within these cDNAs. cDNA sequence analysis demonstrated that the prepro alpha 1(I) mismatch, detected in only one cell line, was due to a sequence polymorphism involving the wobble position of the codon for arginine residue 59 within the amino-propeptide globular subdomain of the pro alpha 1(I) chain and not resulting in a change in the polypeptide primary structure. In contrast, the prepro alpha 2(I) mismatch, detected in 6 of the 16 cell lines, was shown to arise from a sequence polymorphism affecting the identity of Y-position residue 459 of the alpha 2(I) triple helical domain, resulting in an alanine/proline dimorphism at this position. This study is the first to identify a type I collagen coding sequence polymorphism resulting in an alteration at the level of the amino acid sequence. The data suggest that at least some alpha 1(I) and alpha 2(I) helix Y positions may be tolerant of sequence variation, particularly if the replacing amino acid is proline, a residue involved in stabilizing the collagen triple helix.

Sequence variations in the first exon of alpha-galactosidase A

The alpha-galactosidase A gene (GALA), which is deficient in males with Anderson-Fabry disease, is shown to be remarkably polymorphic in the 5' untranslated region. GALA contains seven exons. The first exon contains 60 bp of 5' untranslated sequence before the methionine initiation codon. Single strand conformation polymorphism (SSCP) screening has shown three polymorphic variants from the published sequence within the 60 base pairs. The sequence changes involved are C to T at -10, G to A at -12 (which removes an MspI site), and G to A at -30 (which removes a SacII site). The combined frequency of these is 10%. A further insertion-deletion polymorphism is detected by SSCP of a 400 bp fragment including exon 3. Both polymorphisms can be easily detected using small polyacrylamide gels and ethidium bromide staining. Nine of 20 women were informative for one of these polymorphisms and this simple SSCP analysis should be of great assistance in family studies of Anderson-Fabry disease. Such a high level of polymorphism has not been previously reported in the 5' untranslated region of a human gene and is unusual in any such short stretch of DNA.

Use of the single-strand conformation polymorphism technique to detect loss of heterozygosity in neuroblastoma

Human neuroblastomas are characterized by cytogenetic and molecular analysis as frequently containing deletions of distal 1p. Loss of heterozygosity (LOH) studies have localized a region of shared deletion to 1p35-36.1. Using the single-strand conformation polymorphism (SSCP) technique, we developed polymorphic assays for two genes, the amiloride-sensitive Na+/H+ antiporter (APNH) and tumor necrosis factor receptor 2 (TNFR2) genes, which map to this region. We used these SSCPs to detect LOH in a panel of neuroblastomas. Allelic loss was readily detected in 8 of 39 informative tumors. The SSCP-derived LOH results were consistent with LOH results generated from a set of distal 1p probes that identify restriction fragment length polymorphisms (RFLPs). The APNH locus could be excluded from the region of consistent deletion, but the TNFR2 locus could not be excluded. We conclude that the SSCP technique is a precise and efficient method for detecting LOH in human neoplasia.

A polymorphism in the bovine gamma-S-crystallin gene revealed by allele-specific amplification

A polymorphism was detected in the 3' untranslated region of the bovine gamma-S-crystallin gene by direct sequencing of polymerase chain reaction (PCR) products from genomic DNA of an N'Dama bull and a Boran cow. A set of three PCR primers was designed to detect this difference and thus give allele-specific amplification. The two allele-specific primers differ in length by 20 nucleotides so that the allelic products may be distinguished by simple agarose gel electrophoresis following a single PCR reaction. This provides a simple and rapid assay for this polymorphism.

A panel of human chromosome 22-specific sequence tagged sites

A panel of 29 sequence tagged sites (STSs) covering the long arm of chromosome 22 has been assembled. STS primer pairs were synthesized using available chromosome 22 sequence derived from the GenBank and EMBL DNA sequence databases, as well as published cDNA and genomic sequence, or from previously published and communicated primer pairs. Each STS was optimized for the polymerase chain reaction using a chromosome 22-only hybrid and human genomic DNA. Further STS content analysis on a panel of somatic cell hybrids that incorporated two chromosome 22 translocations resulted in the mapping of the X-box binding protein (XBP), D22S156, and transcobalamin II (TCN2) genes to 22q11-q13.1. The panel of STSs was used for the rapid determination of the STS content and thus the chromosomal DNA content of a new irradiation hybrid.

Linkage mapping of the AML1 gene on human chromosome 21 using a DNA polymorphism in the 3' untranslated region

We have detected a polymorphism in the 3' untranslated region of the AML1 gene, which is located at the breakpoint on chromosome 21 in the t(8;21)(q22;q22.3) translocation often associated with patients with acute myeloid leukemia. Informative CEPH families were genotyped for this polymorphism and used to localize the gene on the linkage map of human chromosome 21. The AML1 gene is located between the markers D21S216 and D21S211, in chromosomal band 21q22.3.

Generation of region- and species-specific expressed gene probes from somatic cell hybrids

Human genes expressed in interspecific somatic cell hybrids can be cloned specifically by subtractive cDNA hybridization. This approach is based on the observation that cDNA fragments from noncoding segments of mature human transcripts do not form stable heteroduplexes with their rodent homologues under high-stringency hybridization conditions. Thus, small, oligo-dT primed cDNAs from a rat/human hybrid retaining a fragment of human chromosome 17 were enriched for human sequences by hybridization with RNA from a sister clone containing a smaller human chromosome fragment. The enriched probe was used to screen a human cDNA library, and nine expressed genes from within the non-overlap region were obtained. This method should be useful for cloning active human genes from defined chromosome segments.

Linkage mapping of the carbonyl reductase (CBR) gene on human chromosome 21 using a DNA polymorphism in the 3' untranslated region

A DNA polymorphism has been found in the 3' untranslated region of the carbonyl reductase gene (CBR). Genotypes of the members of the CEPH pedigrees have been obtained and used in linkage analysis to map the CBR gene in the linkage map of human chromosome 21. The gene maps between the interferon-alpha receptor (IFNAR) and the D21S55 loci.