RNA Arbitrarily Primed Polymerase Chain Reaction Research Articles

Use of RNA‐arbitrarily‐primed PCR to detect the induction of gene expression in freshwater bivalves (Unio tumidus) transplanted into the Moselle River

RNA-arbitrarily-primed PCR (RAP-PCR) can be used to detect changes in gene expression in organisms for which only minimal genomic information is available. In this study, RAP-PCR was used to detect modification of mRNA expression in the freshwater bivalve Unio tumidus, a mussel commonly used as a sentinel species in field studies. RNA expression was analyzed in the digestive glands of mussels from a control pond and in mussels transplanted into two sites on the Moselle River. The analysis identified a product in all animals exposed to sediments at the river station located downstream of a heavily populated area. This product was not present in animals exposed at the upstream station or at the control site. The additional PCR product was cloned and sequenced, and specific oligonucleotides for the sequence were designed to amplify cDNAs from control and transplanted mussels. A signal was obtained only with the cDNAs from animals exposed at the downstream station, confirming that the variation detected by RAP-PCR corresponds to an increase of gene expression. Chemical analysis of sediments from the control and river sites indicated that the levels of several potential pollutants were similar at the three locations and below currently accepted pollution thresholds. Our results indicate that RAP-PCR is a sensitive technique that can be applied in field studies to identify modifications in the gene expression of bioindicator species. This approach can complement chemical, biochemical and population studies to assess the impact of human activity on the ecological quality of aquatic systems.

Laser-mediated microdissection as a tool for molecular analysis in arthritis.

Most current approaches to the analysis of gene expression in arthritic tissue samples are based on RNA isolated either from cultured synovial cells or from synovial biopsies. However, this strategy does not distinguish between specific gene expression profiles of cells originating from separate tissue areas. Therefore, we established the combination of laser-mediated microdissection and RNA arbitrarily primed polymerase chain reaction (RAP-PCR) for differential display to analyze profiles of gene expression in histologically defined areas of arthritic tissue. Cryosections derived from synovial tissue were used to obtain cell samples from different tissue areas using a microbeam laser microscope. RNA was isolated and analyzed using nested RAP-PCR to generate a fingerprint of the expressed gene sequences. Differentially expressed bands were isolated, cloned, and sequenced. Differential expression of identified sequences was confirmed by in situ hybridization and immunohistochemistry.

RNA fingerprinting using RAP-PCR identifies an EBAF homologue mRNA differentially expressed in rat oviduct

As a step towards the identification of genes preferentially expressed in the oviduct during early rat embryo development, we isolated a cDNA fragment (Pr14) by using RNA arbitrarily primed PCR (RAP-PCR), being its expression restricted to oviduct and uterus; its mRNA is mainly expressed in oviduct during late luteal phase and early pregnancy. This fragment is 100% identical to a rat DNA sequence (Accession No. NW_047400) downstream the terminal exon of a Ratturs norvegicus gene (Locus Link Accession No. LOC289316) similar to ebaf (endometrial bleeding-associated factor), a novel member of the Transforming Growth Factor superfamily. Northern analyses showed that this sequence hybridizes with 2.9 kb and 4.1 kb mRNAs in early pregnant rat oviducts. However, only the 4.1 kb mRNA was detected in the oviduct of non-pregnant rats, showing an increase from proestrus to diestrus. The expression of this oviduct-uterus specific mRNA suggests that the products of this gene may play a role in the oviductal reproductive process.

Laser-mediated microdissection facilitates analysis of area-specific gene expression in rheumatoid synovium.

Current approaches to analyzing gene expression in rheumatoid arthritis (RA) synovium are based on RNA isolated either from cultured synovial cells or from synovial biopsy specimens. This strategy does not, in general, allow distinction of specific gene expression between cells originating from different synovial areas, due to potential mixture of expression profiles. Therefore, we established the combination of laser-mediated microdissection (LMM) and differential display to analyze profiles of gene expression in histologically defined areas of rheumatoid synovium. The present study was undertaken to establish parameters for this technique and assess its usefulness for gene expression analysis. Cryosections derived from RA synovial tissues were used to obtain cell samples from synovial lining versus sublining, using a microbeam laser microscope. RNA was isolated and analyzed by nested RNA arbitrarily primed-polymerase chain reaction (RAP-PCR) for differential display fingerprinting. Differentially expressed bands were cut out, and PCR products were eluted, cloned, and sequenced. Differential expression of identified sequences was confirmed by in situ hybridization and immunohistochemistry analysis. Microdissected sections of RA synovial tissue containing approximately 600 cells yielded enough RNA to produce a reproducible RNA fingerprint pattern. Several genes could be identified as being expressed differentially between the synovial lining and the sublining, and their expression could be confirmed at the messenger RNA and protein levels. The combination of LMM and RAP-PCR presents a valuable tool to obtain novel insights into the area-dependent differential regulation of gene expression in RA synovium. Both known and previously unknown genes were revealed with this technique. This study is the first to demonstrate the potential of this analytic strategy in the investigation of a nonmalignant, multifactorial, inflammatory disease.

Differential expression of genes influenced by changing salinity using RNA arbitrarily primed PCR in the archaeal halophile Haloferax volcanii.

Extreme halophiles belonging to the domain Archaea require a minimum of approximately 10% NaCl for growth. Many of these obligate halophiles will continue to grow even as NaCl concentrations approach saturation. The haloarchaeon Haloferax volcanii is a model organism in which to study the effects of changes in medium salinity on gene expression, as this organism grows over a wide range of NaCl concentrations, between 12% and 23%, with little effect on growth rate. An RNA arbitrarily primed PCR (RAP-PCR) approach has been applied to identify those genes that are differentially expressed in response to changing salinity. Differences in gene expression can be detected using this methodology, as each sample generates its own unique RNA fingerprint for each growth condition examined. RNA was prepared from H. volcanii cultures grown with two different NaCl concentrations in the medium, RAP-PCR was performed, and seven differentially expressed transcripts were identified. These fragments were cloned, sequenced, and subjected to transcript analysis to confirm their regulation. One of the sequences identified in this study displays homology to the eukaryotic Ser/Thr protein kinase Ire1p, a sensor of protein unfolding in yeast and mammalian cells. Evidence for serine phosphorylation in H. volcanii is also presented.

Octylphenol (OP) alters the expression of members of the amyloid protein family in the hypothalamus of the snapping turtle, Chelydra serpentina serpentina.

The gonadal estrogen estradiol-17beta (E(2)) is important for developing and regulating hypothalamic function and many aspects of reproduction in vertebrates. Pollutants such as octylphenol (OP) that mimic the actions of estrogens are therefore candidate endocrine-disrupting chemicals. We used a differential display strategy (RNA-arbitrarily primed polymerase chain reaction) to isolate partial cDNA sequences of neurotransmitter, developmental, and disease-related genes that may be regulated by OP or E(2) in the snapping turtle Chelydra serpentina serpentina hypothalamus. Hatchling and year-old male snapping turtles were exposed to a 10 ng/mL nominal concentration of waterborne OP or E(2) for 17 days. One transcript [421 base pairs (bp)] regulated by OP and E(2) was 93% identical to human APLP-2. APLP-2 and the amyloid precursor protein (APP) regulate neuronal differentiation and are also implicated in the genesis of Alzheimer disease in humans. Northern blot analysis determined that the turtle hypothalamus contains a single APLP-2 transcript of 3.75 kb in length. Exposure to OP upregulated hypothalamic APLP-2 mRNA levels 2-fold (p < 0.05) in month-old and yearling turtles. E(2) did not affect APLP-2 mRNA levels in hatchlings but stimulated a 2-fold increase (p < 0.05) in APLP-2 mRNA levels in yearling males. The protein beta-amyloid, a selectively processed peptide derived from APP, is also involved in neuronal differentiation, and accumulation of this neurotoxic peptide causes neuronal degeneration in the brains of patients with Alzheimer disease. Therefore, we also sought to determine the effects of estrogens on the expression of beta-amyloid. Using homology cloning based on known sequences, we isolated a cDNA fragment (474 bp) from turtle brain with 88% identity to human APP. Northern blot analysis determined that a single 3.5-kb transcript was expressed in the turtle hypothalamus. Waterborne OP also increased the expression of hypothalamic APP after 35 days of exposure. Our results indicate that low levels of OP are bioactive and can alter the expression of APLP-2 and APP. Because members of the APP gene family are involved in neuronal development, we hypothesize that OP exposure may disrupt hypothalamic development in young turtles.

Differential gene expression in response to copper inAcidithiobacillus ferrooxidans analyzed by RNA arbitrarily primed polymerase chain reaction

Acidithiobacillus ferrooxidans is a chemoautotrophic bacterium that plays an important role in metal bioleaching processes. Despite the high level of tolerance to heavy metals shown by A. ferrooxidans, the genetic basis of copper resistance in this species remains unknown. We investigated the gene expression in response to copper in A. ferrooxidans LR using RNA arbitrarily primed polymerase chain reaction (RAP-PCR). One hundred and four differentially expressed genes were identified using eight arbitrary primers. Differential gene expression was confirmed by DNA slot blot hybridization, and approximately 70% of the RAP-PCR products were positive. The RAP-PCR products that presented the highest levels of induction or repression were cloned, sequenced and the sequences were compared with those in databases using the BLAST search algorithm. Seventeen sequences were obtained. The RAP-PCR product with the highest induction ratio showed similarity with the A. ferrooxidans cytochrome c. A high similarity with the thiamin biosynthesis gene thiC from Caulobacter crescentus was observed for another RAP-PCR product induced by copper. An RAP-PCR product repressed by copper showed significant similarity with the carboxysome operon that includes the ribulose-1,5-bisphosphate carboxylase/oxygenase complex from A. ferrooxidans and another copper-repressed product was significantly similar to the XyIN outer membrane protein from Pseudomonas putida. Finally, RAP-PCR products of unknown similarities were also present.

Identification of differentially expressed genes in rheumatoid arthritis by a combination of complementary DNA array and RNA arbitrarily primed-polymerase chain reaction.

There is increasing evidence that T cell-independent pathways, such as the up-regulation of protooncogenes and the production of growth factors and matrix-degrading enzymes, lead to progressive destruction of affected joints. Therefore, identification of differentially regulated genes restricted to rheumatoid arthritis (RA) synovial fibroblasts is essential. A combination of RNA arbitrarily primed-polymerase chain reaction (RAP-PCR) and complementary DNA (cDNA) array with defined genes was used for a highly sensitive differential screening using small amounts of RNA. RNA was extracted from cultured synovial fibroblasts obtained from 6 patients with RA and 6 patients with osteoarthritis (OA). RAP-PCR was performed using different arbitrary primers for first- and second-strand synthesis. PCRs were hybridized to cDNA array membranes. RA samples were compared with OA samples for differentially expressed genes. In contrast to standard cDNA array, the identification of 12 differentially expressed genes in RA compared with OA (approximately 6%) was possible. Differentially expressed genes of interest were confirmed using semiquantitative RT-PCR and in situ hybridization. Numerous variants of the differential display method and continuous improvements, including RAP-PCR, have proven to be both efficient and reliable for examining differentially regulated genes. Our results show that RAP-PCR combined with cDNA arrays is a suitable method for identifying differentially expressed genes in rheumatoid synovial fibroblasts, using very small amounts of RNA.

Use of RNA arbitrarily primed PCR to identify genomic alterations in the digestive gland of the freshwater bivalve Unio tumidus at a contaminated site.

The technique of RNA arbitrarily primed polymerase chain reaction (RAP-PCR) was developed to detect DNA damage and variations in gene expression in response to exposure to toxic compounds. This approach was tested on the freshwater bivalve Unio tumidus to explore the ability of RAP-PCR to detect effects induced by river sediment contaminated with polycyclic aromatic hydrocarbons (PAHs), polychlorobiphenyls (PCBs), and metals. In a first step the primer concentration was optimized to obtain reproducible amplifications of both high- and low-molecular-weight products. Optimized conditions allowed us to detect variations corresponding to the loss of PCR products in some animals exposed at the contaminated site compared with the control. Our results for the RAP-PCR approach performed on separate animals in field studies showed that interindividual variations could correspond to DNA damage and/or variations in gene expression.

Identification of transcripts expressed under functional differentiation in primary culture of cerebral cortical neurons.

In this study, we utilized primary cultures of cerebral cortical neurons and RNA arbitrarily primed polymerase chain reaction (RAP-PCR) to identify differentially expressed transcripts in neurons of different culture ages. Eleven cDNA fragments with high sequence similarity to known genes and Expressed Sequence Tags (ESTs) were cloned. From the National Center for Biotechnology Information (NCBI) sequence database, two clones were shown to be identical to known sequences, Mus musculus HP1-BP74 protein mRNA and Mus musculus KRAB-containing zinc finger protein, both were up-regulated. These genes have never before been shown to be involved in neuronal functional maturation. Among the remaining clones, clone 8-14 (239 bp) was very similar to Rattus norvegicus rS-Rex-b mRNA, which was further confirmed by sequencing its shortest isoform (1.5 kb) obtained by computer cloning. This study has identified eleven potential genes and transcripts, which might be involved in the development and differentiation of GABAergic neurons in culture.

Downregulation of integrin-linked kinase mRNA expression by nitric oxide in rat glomerular mesangial cells

Inflammatory glomerular diseases are accompanied by changes in the expression patterns of growth factors, mediators and matrix-associated proteins in mesangial cells and by the production of nitric oxide via the cytokine-inducible form of the nitric oxide synthase. Nitric oxide has been shown to act potently on gene transcription. To identify genes that are differentially expressed by endogenously produced nitric oxide, we forced rat mesangial cells to produce high amounts of nitric oxide by exposure to inflammatory cytokines and compared the mRNA expression patterns of cytokine-stimulated mesangial cells with cells that were additionally treated with the nitric oxide synthase inhibitor L-NMMA to block endogenous NO synthesis. We used a modification of a low stringency RT-PCR approach designated as RNA arbitrarily-primed polymerase chain reaction (RAP-PCR). In this way, we identified among others the integrin-linked kinase (ILK) as an NO-regulated gene. The NO-mediated changes in the mRNA and protein expression patterns of ILK were compared to that of “secreted protein acidic and rich in cystein” (SPARC), a gene that was identified as NO-regulated in the same set of experiments (Walpen et al., J. Am. Soc. Nephrol., 11, 468–476). ILK and SPARC mRNA levels by were downregulated by cytokines via endogenously produced nitric oxide in a comparable manner as verified by Northern blot analysis. In contrast, cytokine- induced NO production or administration of exogenous NO-donors strongly reduced SPARC protein levels without altering ILK protein content in mesangial cells over a period up to 72 hours. Blocking de novo protein synthesis showed a short half-life of SPARC (< 2 hours) whereas ILK-protein was stable over a period of 7 hours, indicating that NO-mediated reduction of ILK mRNA levels does not influence protein content of ILK in mesangial cells under the time limitations given under cell culture conditions. However, a role for cytokines/NO in ILK-long-term regulation in chronic inflammatory diseases that may influence phenotypic responses such as apoptosis or cell proliferation remains to be elucidated.

Comparison of differentially expressed genes in the salivary glands of male ticks, Amblyomma americanum and Dermacentor andersoni

Genes expressed differentially in the salivary glands of unfed and fed male ticks, Amblyomma americanum (L.), were identified, cloned and sequenced, and some were compared with those expressed in the salivary glands of Dermacentor andersoni. Total protein and RNA increased sixfold in the salivary glands of fed male A. americanum, while in fed male D. andersoni salivary glands, RNA increased approximately 3.5 times. Feeding D. andersoni in the presence of females increased total RNA by 25% over those fed in the absence of females. Complementary DNAs were synthesized from RNA obtained from unfed and fed ticks and amplified using RNA arbitrarily primed polymerase chain reaction (RAP-PCR) with three different primers in separate reactions. Differential display showed clear banding differences between the fed and the unfed ticks in A. americanum and D. andersoni. Sixty-one cDNA fragments that appeared to be from differentially expressed genes in A. americanum were isolated, cloned and sequenced. Hybridization reactions with labeled cDNA probes confirmed the differential expression of many of the genes in unfed and fed ticks' salivary glands; however, many of the bands contained more than one fragment and some of the fragments isolated from apparently differential bands were not specific. Sequences for 28 of the cDNA fragments (150–600 nucleotides in length) demonstrated similarity to genes in the databases, but nine of these were similar to sequences of unknown function. Some of the gene fragments identified may be important to tick feeding or tick salivary gland physiology, including a histamine-binding protein, an organic ion transporter, an apoptosis inhibitor, a cathepsin-B-like cysteine protease, proteins involved in gene regulation and several proteins involved in protein synthesis. Cross-hybridization of identified cDNAs from A. americanum with cDNA probes synthesized from D. andersoni total RNA did not show significant similarity between the two species.

Analysis of developmentally regulated genes of the parasite Haemonchus contortus

Differential regulation of gene expression in the development of Haemonchus contortus was analysed using RNA arbitrarily-primed PCR. A study of third-stage larval and adult H. contortus revealed large differences between the two stages; 32 and 30% unique third-stage larval and adult RNA arbitrarily-primed PCR products, respectively. This finding is consistent with a high degree of differential gene expression between these developmental stages. A number of adult products were sequenced, revealing 11 molecules to be similar to deposits within sequence databases. Four other molecules that did not have significant similarity to sequences in the databases may represent developmentally regulated genes specific to H. contortus. Northern analysis of the putative adult-expressed molecules with homologues in the databases confirmed that four were expressed only in adults, while four were expressed in both stages, but had different sized transcripts. This may reflect differential splicing, or expression of closely related but different molecules at different life cycle stages. Two molecules were present in mRNA populations from both stages, suggesting these were false stage-associated molecules. No transcript was detected for one molecule by Northern analysis, probably due to low level of expression. In situ hybridisation analysis was used to localise expression of transcripts in the adult parasite, in particular, to gain some insight into the nature of those molecules with no known predicted function.

Modulation of bovine articular chondrocyte gene expression in vitro by oxygen tension

Objective Adult articular cartilage is a physiologically hypoxic tissue with a proposed gradient of oxygen tension ranging from <10% oxygen at the cartilage surface to <1% in the deepest layers. This gradient may be disturbed during diseases of the joint, for example in rheumatoid arthritis when synovial fluid pO2falls. We investigated whether changes in oxygen tension modulate gene expression in articular chondrocytes.Design Bovine articular chondrocytes were cultured in alginate beads in medium maintained at <0.1, 5, 10 or 20% oxygen. A modified RNA arbitrarily primed polymerase chain reaction (RAP-PCR) technique was used to identify several genes whose mRNA abundance in articular chondrocytes was dependent upon oxygen tension. Northern hybridization slot blots were used to quantify changes in mRNA level relative to a housekeeping gene, β-actin.Results Genes found by RAP-PCR to undergo up-regulation in hypoxia included TIMP-1 and integrin-linked kinase. Collagen V mRNA levels were down-regulated in hypoxic chondrocytes. This led us to examine mRNA levels for various cytokines, matrix structural molecules and β1 integrin. Interleukin 1β, transforming growth factor β and connective tissue growth factor were all up-regulated by low oxygen tensions, as was β1 integrin. Collagen II (COL2A1) was down-regulated by hypoxia but aggrecan mRNA levels remained unchanged. The mRNA levels for GAPDH, the archetypal hypoxia responsive gene, were not modulated in articular chondrocytes by changes in oxygen tension.ConclusionsOxygen tension modulates the abundance of mRNAs encoding structural molecules, several cytokines, β1 integrin and integrin-linked kinase in articular chondrocytes. This may be important during disease progression. Chondrocytes are unusual in their response to hypoxia, presumably because they exist physiologically in a low oxygen environment.

RNA arbitrarily primed PCR survey of genes regulated by ToxR in the deep-sea bacterium Photobacterium profundum strain SS9.

We are currently investigating the role of ToxR-mediated gene regulation in Photobacterium profundum strain SS9. SS9 is a moderately piezophilic ("pressure loving") psychrotolerant marine bacterium belonging to the family Vibrionaceae. In Vibrio cholerae, ToxR is a transmembrane DNA binding protein involved in mediating virulence gene expression in response to various environmental signals. A homolog to V. cholerae ToxR that is necessary for pressure-responsive gene expression of two outer membrane protein-encoding genes was previously found in SS9. To search for additional genes regulated by ToxR in SS9, we have used RNA arbitrarily primed PCR (RAP-PCR) with wild-type and toxR mutant strains of SS9. Seven ToxR-activated transcripts and one ToxR-repressed transcript were identified in this analysis. The cDNAs corresponding to these partial transcripts were cloned and sequenced, and ToxR regulation of their genes was verified. The products of these genes are all predicted to fall into one or both of two functional categories, those whose products alter membrane structure and/or those that are part of a starvation response. The transcript levels of all eight newly identified genes were also characterized as a function of hydrostatic pressure. Various patterns of pressure regulation were observed, indicating that ToxR activation or repression cannot be used to predict the influence of pressure on gene expression in SS9. These results provide further information on the nature of the ToxR regulon in SS9 and indicate that RAP-PCR is a useful approach for the discovery of new genes under the control of global regulatory transcription factors.

RNA fingerprinting of specific plant cell types: Adaptation to plants and optimization of RNA arbitrarily primed PCR (RAP-PCR)

Differential gene expression contributes to cell differentiation and underlies plant responses to hormonal and environmental factors. Most methods available to identify differentially expressed genes in plants are biased towards moderately or strongly expressed genes. RNA arbitrarily primed polymerase chain reaction (RAP-PCR) produces populations of amplicons from reverse transcribed RNA in a process similar to differential display, but with a higher degree of reproducibility and sensitivity, thus enabling the identification of low abundance mRNA. A detailed RAP-PCR protocol allowing the rapid identification of differentially expressed genes in scarce plant cells, such as stomatal guard cells, is presented here. In addition, a fast and reliable method for the semi-quantitative confirmation of gene expression patterns is described.

Isolation and characterisation of sex-specific transcripts from Oesophagostomum dentatum by RNA arbitrarily-primed PCR

In light of the lack of molecular data on the sexual differentiation, maturation and interaction of parasitic nematodes of livestock, the present study investigated sex-specific gene expression in the nodule worm, Oesophagostomum dentatum (Strongylida). Using the technique of RNA arbitrarily-primed polymerase chain reaction (RAP-PCR), 31 expressed sequence tags (ESTs) differentially-displayed between the sexes were cloned. Northern blot analysis proved ten ESTs to be expressed exclusively in males (adults and fourth-stage larvae), while two were expressed solely in female stages. None of the ESTs were expressed in infective third-stage larvae. Sequence analysis and subsequent database searches revealed two male-specific ESTs to have significant similarity to Caenorhabditis elegans (predicted) proteins, a protein containing an EGF-like cysteine motif and a serine/threonine phosphatase. Another two male-specific ESTs had similarity to non-nematode sequences. The two female-specific ESTs had similarity to vitellogenin-5 and endonuclease III (predicted) from C. elegans. The remaining ESTs had no similarity to any nucleic acid or protein sequences contained in the databases. The isolation and characterisation of sex-specific ESTs from O. dentatum provides a unique opportunity for studying the reproductive biology of parasitic nematodes at the molecular level, with a view toward novel approaches for parasite control.

Retrotransposons transcribed preferentially in proximal tubules of salt-hypertensive rats

The kidney is considered to play an important etiologic role in salt-sensitive hypertension. The aim of the present study was to isolate genes whose expression differs between the kidneys of salt-hypertensive and control rats using an mRNA differential display method. Dahl salt-sensitive (DS) and control salt-resistant rats (DR) were fed a 0.3% or 8% NaCl diet. Renal RNA was amplified by RNA arbitrarily primed polymerase chain reaction (RAP-PCR) and compared among DR 0.3%, DR 8%, DS 0.3%, and DS 8%. Gene expression and localization were examined by Northern blotting, RNase protection assay, and in situ hybridization. Full-length nucleotide sequence was determined by screening a DS rat kidney cDNA library. We identified one differentially displayed clone, and its expression was greater in DS than DR, which was not affected by salt loading. The sequence was 90% homologous to the 3'-noncoding region of the nicotinic acetylcholine receptor alpha7 subunit gene. Its expression was kidney-specific, and was localized in the proximal tubules. The transcript level was markedly increased precedent to the development of hypertension. Its expression was also high in other salt-sensitive rats, and low in normotensive Sprague-Dawley and Wistar rats. The full-length cDNA contained elements homologous to the retroviral pol gene, a primer binding site sequence for reverse transcriptase, and long-terminal repeats. These results demonstrated that the newly identified transcripts (REPT1) belong to a novel retrotransposon family, which showed unique strain-, age-, tissue-, and cell type-specific expression pattern.

Differential display, subtractive hybridization, and application of methodology to search for point mutations to identify genetic defects responsible for progression in MCF10AT model of human breast disease.

We describe initial studies utilizing three methods to detect differences in gene expression: (i) differential display with polyT-anchored primers; (ii) differential display with RNA arbitrarily primed polymerase chain reaction (RAP-PCR), and (iii) cDNA subtractive hybridization. Subtractive hybridization, which detects qualitative differences in gene expression, revealed no differences between a human cell line (MCF10A), originated by spontaneous immortalization of breast epithelial cells, and MCF10CA1 cells, a recently derived fully malignant, metastatic variant. The standard method of differential display with polyT anchored primers detected in excess of 100 differentially displayed bands but differential expression could seldom be verified by Northern blotting. However, RAP-PCR products frequently represent the coding region and fewer bands are detected. One gene of interest is a zinc finger protein which may be expressed more in the preneoplastic lesion-forming cells than in nonlesion-forming cells. Because most bands are not consistently differentially displayed among the variants of the MCF10 model, we suspect that point mutations rather than differential quantitative gene expression is responsible for some stage of progression. We propose that differential display of RAP-PCR products on nondenaturing gels might also detect point mutation differences.

21] Reduced complexity probes for DNA arrays

Publisher Summary There have been many advances in methods to manufacture and probe arrays of DNAs. Membranes with hundreds or thousands of polymerase chain reaction (PCR) products from cDNA clones are commercially available. Any cDNA clones on the array that are from the most abundant few thousand of mRNAs in a cell can easily be detected using a radiolabeled probe containing the full complexity of the mRNA population in the cell. The only limitation is background hybridization to all clones. This chapter explains a strategy based on cDNA fingerprints generated by RNA arbitrarily primed PCR (RAP-PCR). This method generates different subsets of the mRNA population, depending on the primers used. Some of the mRNAs that are difficult to detect using total cDNA probes are sufficiently represented in these reduced complexity probes to be easily detected on arrays of colonies. This method has the further advantage that it generates a labeled probe using hundreds-fold less RNA than is currently used by any other array probing methods. The chapter discusses the use of statistically primed PCR (SP-PCR) to generate probes.