Access to a messenger RNA sequence or its protein product is not limited by tissue or species specificity

Application of the polymerase chain reaction to the diagnosis of human genetic disease

In vitro DNA amplification by means of the polymerase chain reaction is currently revolutionizing human molecular genetics. Since its inception in 1985, a wide variety of different methods and their applications in the diagnosis of disease have been described. This review is intended to serve as a brief guide to current and emerging possibilities in this rapidly expanding field.

A past mutation at isoleucine 397 is now a common cause of moderate/mild haemophilia B

Of the factor IX sequence changes that we have identified in 65 consecutive males with haemophilia B, 11 (17%) are the same mutation. This mutation is a T----C transition at base 31311 which substitutes threonine for isoleucine397 (ile397) in the factor IX molecule. The 11 patients are of Western European descent and have the same haplotype: Hinf1 (-), Xmn1 (-), Taq1 (-), BamH1 (+), Malmö allele = thr148. The frequency of this haplotype was estimated and the probability of the same mutation occurring independently 11 times in this haplotype was miniscule. We conclude that these patients have a common ancestor despite the lack of overlapping pedigrees. The clinical symptoms of the disease were consistently moderate/mild in these 11 patients, whereas factor IX coagulation values obtained from the medical records varied more than sixfold between individuals. However, when plasma from five individuals was assayed by the same laboratory concurrently, the values varied less than twofold. Thus, in routine practice, clinical severity may correlate better with the presence of a given mutation than the factor IX coagulant activity. The high frequency of the mutation at ile397 indicates that carrier testing in families of Northern European descent with moderate/mild haemophilia B can be expedited by first determining whether this particular mutation is present. We demonstrate here that the technique of polymerase chain reaction (PCR) amplification of specific alleles (PASA) can be used to rapidly perform carrier testing in families with the ile397 mutation.

Aberrant gene expression and aging: examination of tissue-specific mRNAs in young and old rats

It has been suggested that aberrant gene expression may play a role in aging. To test this possibility, we examined the steady-state mRNA levels for five tissue-specific genes of known function in young (6 month) and old (24 month) rats. Six different tissues from three animals of each age were analyzed using a hybridization assay estimated to be able to detect one mRNA copy per cell. At this level of sensitivity, no aberrant gene expression was seen. The results indicate that these tissue-specific genes retain their fidelity of expression with age.

Endothelin-1 mRNA is widely expressed in porcine and human tissues

Endothelin-1 (ET-1) is a potent vasoconstrictor peptide isolated from porcine endothelial cells. We have previously demonstrated widespread binding sites for ET-1 in blood vessels, heart, kidney, adrenal, lung, and brain in a distribution that paralleled that of endothelial cells. To determine whether these cells are capable of synthesizing ET-1 in close proximity to its binding sites, amplification of cDNA using the polymerase chain reaction and in situ hybridization were used to study the distribution of ET-1 mRNA. We have found widespread transcription of ET-1 mRNA in human and porcine tissues. The identity of the transcripts was confirmed by prediction of restriction fragment lengths or sequencing. In situ hybridization in the kidney showed that the regional expression of these transcripts is localized, probably to small blood vessels, but the failure to visualize ET-1 mRNA in the capillaries may reflect absence of expression or insufficient sensitivity of the technique. These results should permit investigation of the role of ET-1 as a local factor in vascular pathophysiology.

Characterization of polymerase chain reaction amplification of specific alleles

Under certain conditions, polymerase chain reaction (PCR) can be used to differentially amplify one allele over another. To characterize the phenomenon, we have made a series of PCR primers and determined whether differential amplification could be detected after agarose gel electrophoresis. Two allele pairs were examined; one pair represents a transversion and one pair represents a transition. The following conclusions emerge: (i) when the 3' or the 3' penultimate base of the oligonucleotide mismatched an allele, no amplification product could be detected; (ii) when the mismatches were 3 and 4 bases from the 3' end of the primer, differential amplification was still observed, but only at certain concentrations of magnesium chloride; (iii) the mismatched allele can be detected in the presence of a 40-fold excess of the matched allele; (iv) primers as short as 13 nucleotides were effective; and (v) the specificity of the amplification could be overwhelmed by greatly increasing the concentration of target DNA.

Analysis of cytokine mRNA and DNA: detection and quantitation by competitive polymerase chain reaction

The expression of two cytokines, granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin 3 (IL-3), has been investigated in MLA-144 cells before and after induction with phorbol 12-myristate 13-acetate. We describe an adaptation of the polymerase chain reaction (PCR) for highly accurate quantitation of mRNA or DNA from a small number of cells. Aliquots of the PCR mixture containing cDNA copies of the RNA to be assayed were added to serial dilutions of a competitor DNA fragment that differed from the cDNA of interest by having either a small intron or a mutated internal restriction enzyme site. Therefore, the same primers were used to coamplify the unknown and the competitor. The ratio of products remains constant through the amplification and can be readily quantitated. In unstimulated cells, no GM-CSF or IL-3 mRNA could be detected. However, with appropriate induction, mRNA for both cytokines was detected and quantitated in as few as 200 cells. Competitive PCR was also used to accurately quantitate the copy number of the human GM-CSF gene in normal human cells, in a clonal population of cells from a patient with 5q- syndrome, and in a human-hamster cell line known to have only one copy of the human GM-CSF gene.

Amplified RNA synthesized from limited quantities of heterogeneous cDNA

The heterogeneity of neural gene expression and the spatially limited expression of many low-abundance messenger RNAs in the brain has made cloning and analysis of such messages difficult. To generate amounts of nucleic acids sufficient for use in standard cloning strategies, we have devised a method for producing amplified heterogeneous populations of RNA from limited quantities of cDNA. Whole cerebellar RNA was primed with a synthetic oligonucleotide containing the T7 RNA polymerase promoter sequence 5' to a polythymidylate region. After second-strand cDNA synthesis, T7 RNA polymerase was used to generate amplified antisense RNA (aRNA). Up to 80-fold molar amplification has been achieved from nanogram quantities of cDNA. The amplified material is similar in size distribution to the parent cDNA and shows sequence heterogeneity as assessed by Southern and Northern blot analysis. Specific messages for moderate-abundance mRNAs for actin and guanine nucleotide-binding protein (G-protein) alpha subunits have been detected in the amplified material. By using in situ transcription to generate cDNA, sequences for cyclophilin have been detected in aRNA derived from single cerebellar tissue sections. cDNA derived from a single cerebellar Purkinje cell also has been amplified and yields material that hybridizes to cognate whole RNA and mRNA but not to Escherichia coli RNA.

Mutations and a polymorphism in the factor VIII gene discovered by denaturing gradient gel electrophoresis

Hemophilia A results from mutations in the gene coding for coagulation factor VIII. We used denaturing gradient gel electrophoresis to screen for mutations in the region of the factor VIII gene coding for the first acidic domain. Amplification primers were designed employing the MELTMAP computer program to optimize the ability to detect mutations. Screening of amplified DNA from 228 unselected hemophilia A patients revealed two mutations and one polymorphism. Rescreening the same population by making heteroduplexes between amplified patient and control samples prior to electrophoresis revealed one additional mutation. The mutations include two missense and one 4-base-pair deletion, and each mutation was found in patients with severe hemophilia. The polymorphism, located adjacent to the adenine branch site in intron 7, is useful for genetic prediction in some cases where the Bcl I and Xba I polymorphisms are uninformative. These results suggest that DNA amplification and denaturing gradient gel electrophoresis should be an excellent strategy for identifying mutations and polymorphisms in defined regions of the factor VIII gene and other large genes.

Active beta-globin gene transcription occurs in methylated, DNase I-resistant chromatin of nonerythroid chicken cells

We report active, inappropriate transcription of the chicken beta A-globin gene in normal fibroblasts, cultured MSB cells, and brain. We were unable to detect ovalbumin gene transcription in these same tissues. Most of the globin gene transcripts were found to be truncated near the beginning of the gene, suggesting the existence of a premature termination process that is preferentially active under conditions of inappropriate transcription. The inappropriately transcribed beta A-globin gene chromatin remained DNase I resistant and highly methylated. Thus, the DNase I-sensitive conformation of erythrocyte beta A chromatin was correlated not with beta A transcription per se but with beta A expression. Although both transcribed and nontranscribed genes within the globin domain exhibited the same DNase I sensitivity in erythrocyte nuclei, a housekeeping gene active in erythrocytes exhibited a different level of DNase I sensitivity. However, this gene exhibited the same level of DNase I sensitivity in both erythrocytes and a cultured cell line. These observations are consistent with the proposal (G. Blobel, Proc. Natl. Acad. Sci. USA 82:8527-8529, 1985) that the DNase I sensitivity of a gene may reflect properties of chromatin related to cotranscriptional and posttranscriptional aspects of mRNA production rather than to transcription per se.

Two versions of the gene encoding the 41-kilodalton subunit of the telomere binding protein of Oxytricha nova

Macronuclear chromosomes of the ciliated protozoan Oxytricha nova terminate with a single-stranded (T4G4)2 overhang. The (T4G4)2 telomeric overhang is tenaciously bound by a protein heterodimer. We have cloned and sequenced the gene encoding the 41-kDa subunit of this telomere binding protein. The predicted amino acid sequence comprises two distinct regions, a carboxyl-terminal two-thirds that is 23% lysine and bears similarity to histone H1 and an amino-terminal one-third containing a hydrophobic stretch of about 15 amino acids. Two macronuclear versions of the gene differ in nucleotide sequence at several positions, but the derived polypeptides differ only at a single position, Ser-110 or Ala-110. Both versions harbor a small intron. The existence of this intron demonstrates that, despite the elimination of 95% of the micronuclear genome from the developing macronucleus, at least some noncoding DNA is retained during macronuclear development of hypotrichous ciliates.

Active beta-globin gene transcription occurs in methylated, DNase I-resistant chromatin of nonerythroid chicken cells

We report active, inappropriate transcription of the chicken beta A-globin gene in normal fibroblasts, cultured MSB cells, and brain. We were unable to detect ovalbumin gene transcription in these same tissues. Most of the globin gene transcripts were found to be truncated near the beginning of the gene, suggesting the existence of a premature termination process that is preferentially active under conditions of inappropriate transcription. The inappropriately transcribed beta A-globin gene chromatin remained DNase I resistant and highly methylated. Thus, the DNase I-sensitive conformation of erythrocyte beta A chromatin was correlated not with beta A transcription per se but with beta A expression. Although both transcribed and nontranscribed genes within the globin domain exhibited the same DNase I sensitivity in erythrocyte nuclei, a housekeeping gene active in erythrocytes exhibited a different level of DNase I sensitivity. However, this gene exhibited the same level of DNase I sensitivity in both erythrocytes and a cultured cell line. These observations are consistent with the proposal (G. Blobel, Proc. Natl. Acad. Sci. USA 82:8527-8529, 1985) that the DNase I sensitivity of a gene may reflect properties of chromatin related to cotranscriptional and posttranscriptional aspects of mRNA production rather than to transcription per se.

A method of sequencing without subcloning and its application to the identification of a novel ORF with a sequence suggestive of a transcriptional regulator in the water mold Achlya ambisexualis

Genomic amplification with transcript sequencing (GAWTS) is a method of direct sequencing that involves amplification with PCR using primers containing phage promoters, transcription of the amplified product, and sequencing with reverse transcriptase. GAWTS requires the generation of PCR primers that are specific for the sequences on both sides of a region. Here we describe promoter ligation and transcript sequencing (PLATS), a direct method for rapidly obtaining novel sequences that utilizes generic primers and only requires knowledge of the sequence on one side of a region. PLATS involves restriction digestion of the amplified vector insert, ligation with a phage promoter, and then GAWTS using phage promoter sequences as the PCR primers. The method is rapid and economical because it uses a limited set of oligonucleotides, and it is potentially amenable to automation because it does not require in vivo manipulations. PLATS facilitates the determination of a genomic sequence responsible for cross-hybridization in a Southern blot. Using PLATS, sequence has been obtained from a 1.1-kb segment in Achlya ambisexualis, which cross-hybridizes to the DNA-binding region of the chicken and Xenopus estrogen receptors. To our knowledge, this represents the first sequence reported from the Oomycetes, a large and widely distributed group of fungi. The sequence reveals a large, transcribed open reading frame that is markedly deficient in the dinucleotide TpA. A putative zinc finger containing three cysteines and one histidine (C-X2-C-X12-H-X3-C) and an acidic segment hint that this clone may be a member of a novel class of transcriptional regulators.

The two candidate testis-determining Y genes (Zfy-1 and Zfy-2) are differentially expressed in fetal and adult mouse tissues

The candidate testis-determining Y genes of the mouse Zfy-1 and Zfy-2, encode proteins containing an acidic amino terminus and a carboxyl terminus composed of 13 zinc fingers. The zinc finger domain is conserved among human and mouse zinc finger X and Y genes. We report a 6-amino-acid deletion in the Zfy-2 zinc finger domain of laboratory mice possessing musculus Y chromosomes. The effect of this deletion on the function of Zfy-2 is not known. The reverse transcriptase-polymerase chain reaction (RT-PCR) and Northern blot techniques were used to study expression of Zfy in adults and fetuses. In adults, the data suggest that Zfy-1 and Zfy-2 transcription is linked to spermatogenesis, that transcription increases with the initiation of meiosis, and that high levels of these mRNAs are found in postmeiotic round spermatid cells. The data also suggest that differential expression of these two genes is present with expression of Zfy-2 being slightly greater than Zfy-1. In fetuses, Zfy transcripts were detected in several tissues, including the testes. In contrast to the situation in adults, the data suggest that expression of Zfy-1 is greater than that of Zfy-2. The data suggesting that Zfy-1 expression is present in fetal testes support the hypothesis that this gene plays a role in testis differentiation. However, because the Zfy genes are apparently also expressed during spermatogenesis and in fetal organs other than testes, they may serve additional functions besides their postulated role in testis determination.

Direct sequencing of the activation peptide and the catalytic domain of the factor IX gene in six species

By means of RNA amplification with transcript sequencing (RAWTS) under low stringency conditions, sequence was obtained directly without cloning for the activation peptide and the catalytic domain of factor IX from six species--sheep, pig, rabbit, guinea pig, rat, and mouse. The data presented demonstrate that, by the appropriate design of oligonucleotides and by performance of a nested PCR under appropriate conditions, it is possible to obtain sequence on a battery of species with a minimum of oligonucleotide primers. A total of 5.2 kb of cross-species sequence was generated with RAWTS. The results indicate that (1) 69% of the amino acids in the catalytic domain, but only 23% of the amino acids in the activation peptide, are identical in humans and the six species; (2) the catalytic domain evolves at a slower rate, but the extent and pattern of conservation of amino acids in the activation peptide suggest that the peptide functions as more than a cleavage spacer that separates the heavy and light chains in the catalytically inactive zymogen; (3) 37% of the amino acids in the activation peptide and 34% of the amino acids in the catalytic domain are factor IX-specific; i.e., they are either identical or changed in a highly conservative fashion in factor IX, but not in other related coagulation proteases; (4) these conserved factor IX-specific amino acids fall into three clusters, which are candidates for involvement in the protein interactions specific to factor IX; (5) there is a human-specific deletion after lysine 142 and a rodent-specific insertion after alanine 161; (6) in guinea pig, the insertion is associated with a seven-amino-acid repeat that corresponds to a perfect repeat of a 21-bp sequence; (7) humans have lost a potential N-glycosylation site that is conserved in the other species; (8) in each species, a few nonconservative changes occur in amino acids that are otherwise completely conserved, suggesting that compensatory mutations may have occurred; and (9) when compared to that of mouse, the amino acid identity with guinea pig factor IX is no greater than that found for the non-rodent species, a result compatible with the postulated increased rate of evolution in rodents.

A novel method for detecting point mutations or polymorphisms and its application to population screening for carriers of phenylketonuria

We describe a method termed PCR (polymerase chain reaction) amplification of specific alleles (PASA), a generally applicable technique for detection of point mutations or polymorphisms. The ease and technical simplicity of PASA will make genetic analyses more accessible to the general medical community. In addition, PASA shows promise for population screening because the technique is rapid, highly reproducible, inexpensive, nonisotopic, and amenable to automation. PASA is a modification of PCR that depends on the synthesis of a PCR oligonucleotide primer that precisely matches with one of the alleles but mismatches with the other. When the mismatch occurs near the 3' end of the PCR primer, amplification is inefficient. Therefore, preferential amplification of the perfectly matched allele is obtained. We demonstrate the applicability of PASA by performing carrier detection in the family of a patient with phenylketonuria (PKU) and by screening a population of unrelated subjects for the presence of the two mutations most commonly associated with PKU. Multiple persons were screened simultaneously for the mutant alleles because a mutation could be detected in the presence of at least a 40-fold excess of the normal allele. The two PKU mutations could be detected concurrently by using a mixture of only three PCR primers, an indication that simultaneous screening of multiple mutations can be done even if three or more mutations are closely clustered. In addition to the detection of mutations, PASA can be used to detect polymorphic alleles rapidly and to distinguish pseudogenes or repetitive sequences that differ by as little as one base.

Quantitative measurement of mRNAs by polymerase chain reaction

Although polymerase chain reaction (PCR) has been used to detect the presence of specific mRNA species, there are no reports indicating that PCR can be used as a reliable, reproducible assay to quantify the relative level of an mRNA. In this study we examined the enzymatic steps (reverse transcription and PCR) required to analyze RNA by PCR and determined the conditions under which the product obtained reproducibly reflects the relative amounts of amplified species in the starting material. Aliquots of total RNA from rat ovaries and GH3 pituitary cells were used to prepare cDNAs for PCR amplification of beta-actin and prolactin (PRL) sequences, respectively. Assay of equivalent dilutions of ovarian cDNAs made from 10, 2, and 0.4 micrograms of RNA demonstrated that the amount of PCR product obtained was proportional to both the amount of cDNA amplified and the amount of RNA transcribed, with a relatively small variability for both reactions. cDNAs were also made against RNA prepared from GH3 cells cultured in the presence or absence of Ca2+, which induces PRL gene expression. Measurement of PRL mRNA by PCR gave results comparable to those obtained by Northern blot (4.7-fold induction vs. 5.9-fold), and again was highly reproducible. Additionally, PCR analysis of cDNA against GH3 nuclear RNA allowed us to detect an apparent splice variant of the PRL nuclear RNA that is also Ca2+ regulated. These results indicate the sensitivity and reliability of PCR as a quantitative assay for specific mRNAs, and demonstrate the possibilities for obtaining data not readily available by other means.

Polymerase chain reaction

The PCR, like recombinant DNA technology, has had an enormous impact in both basic and diagnostic aspects of molecular biology because it can produce large amounts of a specific DNA fragment from small amounts of a complex template. Recombinant DNA techniques create molecular clones by conferring on a specific sequence the ability to replicate by inserting it into a vector and introducing the vector into a host cell. PCR represents a form of "in vitro cloning" that can generate, as well as modify, DNA fragments of defined length and sequence in a simple automated reaction. In addition to its many applications in basic molecular biological research, PCR promises to play a critical role in the identification of medically important sequences as well as an important diagnostic one in their detection.

Isolation and expression of the eclosion hormone gene from the tobacco hornworm, Manduca sexta

Eclosion hormone (EH) is a 62-amino acid neuropeptide that initiates the ecdysis behavior of insects. The EH-encoding gene of the tobacco hornworm, Manduca sexta, was isolated by using a designed 72-mer oligonucleotide probe. Sequence analysis of this gene and its corresponding cDNA showed that the EH gene is 7.8 kilobases and consists of three exons. Exon I is totally nontranslated; exon II contains a 26-amino acid signal peptide and amino acids 1-4 of the EH peptide, and exon III encodes the remainder of the peptide. The EH gene is present in a single copy per haploid genome and transcribes an 0.8-kb mRNA that is expressed in larval, diapausing pupal, and developing adult brains but not in the ventral nerve cord or in nonneural tissues. In situ hybridization showed that the EH gene is expressed in two pairs of ventromedial neurosecretory cells in brains of both larvae and developing adults.

Targeting of nonexpressed genes in embryonic stem cells via homologous recombination

Gene targeting via homologous recombination-mediated disruption in murine embryonic stem (ES) cells has been described for a number of different genes expressed in these cells; it has not been reported for any nonexpressed genes. Pluripotent stem cell lines were isolated with homologously recombined insertions at three different loci: c-fos, which is expressed at a low level in ES cells, and two genes, adipsin and adipocyte P2 (aP2), which are transcribed specifically in adipose cells and are not expressed at detectable levels in ES cells. The frequencies at which homologous recombination events occurred did not correlate with levels of expression of the targeted genes, but did occur at rates comparable to those previously reported for genes that are actively expressed in ES cells. Injection of successfully targeted cells into mouse blastocysts resulted in the formation of chimeric mice. These studies demonstrate the feasibility of altering genes in ES cells that are expressed in a tissue-specific manner in the mouse, in order to study their function at later developmental stages.

Direct carrier testing in 14 families with haemophilia B

Direct carrier testing was done in 54 at-risk female relatives of haemophilic patients by initially analysing 2.46 kb of the factor IX gene in 1 haemophiliac per family by genomic amplification with transcript sequencing. A presumptive mutation was found in all 14 haemophiliacs examined. Analyses were then done either by sequencing the appropriate region in at-risk female relatives or by detection of an altered restriction site. A simulation indicated that the mutation will be associated with an altered restriction site in about half the families. The technique has clinical application.