Fluorescent differential display: arbitrarily primed RT-PCR fingerprinting on an automated DNA sequencer

Control of expression of a gene encoding an extensin by phytochrome and a blue light receptor in spores of Adiantum capillus-veneris L

In the present study, using a newly developed fluorescent differential display technique, we have carried out large-scale screening for genes whose expression was regulated by phytochrome and antagonistically by a blue light receptor in the spores of the fern Adiantum capillus-veneris L. Spores after imbibition were briefly irradiated with red, red/blue or blue light and collected 8 h after the irradiation. Total RNA was isolated from each sample and used to make cDNA with an oligo-dT primer. The cDNA was then used as a template for PCR with the oligo-dT primer and 80 arbitrary primers. The resulting PCR products were analyzed by an automated fluorescent DNA sequencer. Among 8000 displayed bands, we identified 15 up-regulated and four down-regulated bands by red light, and this red light effect was irreversibly reversed by blue light. We cloned one of the up-regulated cDNA fragments and used it to screen a cDNA library prepared from the spores. The isolated insert is predicted to encode Ser-(Pro)n repeats and showed homology with cell wall-associated extensins. The expression of this cDNA was induced 8 h after a red light treatment and the red light induction was photoreversibly prevented by far-red light and photoirreversibly by blue light. The mRNA of this gene was detectable 4 h after red light irradiation and gradually increased in germinating spores.

Molecular cloning and cell-cycle-dependent expression of a novel NIMA (never-in-mitosis in Aspergillus nidulans)-related protein kinase (TpNrk) in Tetrahymena cells

With the intention of investigating the signal-transduction pathway that mediates the cold-stress response in Tetrahymena, we isolated a gene that encodes a novel protein kinase of 561 amino acids, termed Tetrahymena pyriformis NIMA (never-in-mitosis in Aspergillus nidulans)-related protein kinase (TpNrk), by differential display from Tetrahymena cells exposed to temperature shift-down. TpNrk possesses an N-terminal protein kinase domain that is highly homologous with other NIMA-related protein kinases (Neks) involved in the control of the cell cycle. The TpNrk protein is 42% identical in its catalytic domain with human Nek2, 41% identical with mouse Nek1 and 37% with A. nidulans NIMA. In addition, TpNrk and these NIMA-related kinases have long, basic C-terminal extensions and are therefore similar in overall structure. In order to further explore the function of the TpNrk gene and the association of the cold stress with the cell cycle of Tetrahymena, changes of TpNrk mRNA were determined during the course of the synchronous cell division induced by the intermittent heat treatment. The level of TpNrk transcription increased immediately after the end of the heat treatment, with a peak at 30 min, and declined thereafter reaching the minimum level when nearly 80% of the cells synchronously entered cell division (75 min after the end of heat treatment). The accumulation of TpNrk mRNA starting from 0 min to 30 min after the end of the heat treatment was assumed to be a prerequisite for the start of synchronous cell division. These results suggest that TpNrk may have a role in the cell cycle of Tetrahymena, and that mRNA expression, at least, is under tight cell-cycle control.

Identification and cloning of differentially expressed genes by long-distance differential display

Differential mRNA display (DD-PCR) amplifies short cDNAs (average size 100-350 bp), representing mainly the 3' untranslated regions (3' UTR) of transcripts. Sequencing of these cDNAs is predominantly uninformative for prediction of function and selection of clones for further analysis. Differential display of longer amplicons (0.5-2.0 kb) could enable isolation of cDNAs that encompass both 3' UTR and at least part of the 3' end of the coding region. The coding sequence information could facilitate selection of candidate clones for further analysis without the necessity of screening cDNA libraries. By combining DD-PCR protocols with long-distance PCR and using hot-start PCR with rTth DNA polymerase we have successfully amplified and comparatively displayed cDNAs ranging in size from 150 bp to 2 kb. Long-distance DD-PCR (LDD-PCR) has generated highly reproducible primer-specific patterns of cDNA fragments, as well as reproducible duplicate fingerprints, obtained from different RNA and cDNA samples. Sequencing and expression analyses of LDD-PCR clones have shown that LDD-PCR (a) enables nonredundant clone sampling, (b) generates many clones that encompass part of the coding region, and (c) samples both abundant and rare transcripts, approximately 60% of which are differentially expressed as confirmed by Northern analysis. Coupled with high-throughput cDNA sequencing and multiplex hybridization of cDNA microarrays for confirmation of differential expression, LDD-PCR could prove to be useful for simultaneous scanning of transcripts from multiple cDNA samples and faster selection of differentially expressed transcripts of interest.

Identification and cloning of human G-protein gamma 7, down-regulated in pancreatic cancer

Differentially expressed genes between normal and cancer tissues of the pancreas were investigated using differential display. Consequently, we identified a fragment cDNA that was expressed in the normal tissue but was rarely expressed in the cancer tissue. This cDNA was screened in cDNA library prepared from the normal pancreatic tissue by rapid amplification of cDNA ends (5'RACE). 859 bp of cDNA was cloned and sequenced, and the inferred amino acid sequence was found to encode a G protein gamma subunit with 98% homology to cow G protein gamma 7 and complete homology to human G protein gamma 7. The decreased expression of the G protein gamma 7 was confirmed by Northern blot assay in twelve pancreatic malignancies which included nine duct cell carcinomas, two cystoadenocarcinomas and one blastoma. Reverse transcriptase (RT)-polymerase chain reaction (PCR) assay showed no expression of G protein gamma 7 in five of six pancreatic carcinoma cell lines and two pancreatic cancer tissues. Immunohistochemical analysis also displayed positive staining in the normal tissue but no staining in the cancer tissue. The findings demonstrated that the reduced or suppressed expression of human G-protein gamma 7 may play an important role in pancreatic carcinogenesis.

Identification of cystatin B in human esophageal carcinoma, using differential displays in which the gene expression is related to lymph-node metastasis

Identification of the genes that are specifically expressed in either tumor or normal tissue is important for understanding cancer biology. Using differential displays, we obtained one gene which was specifically expressed in normal tissue but is only rarely expressed in carcinoma tissue of the human esophagus. The sequence of this gene was identical with cystatin B, known to be one of the cysteine-proteinase inhibitors, mainly inhibiting cathepsin L. There is little information on the clinical significance of cystatin B expression in human esophageal carcinoma. We thus studied the mRNA expression of cystatin B in 45 tumor/normal pair specimens of the esophagus, using the semi-quantitative reverse transcriptase polymerase chain reaction technique. The expression of cystatin B in tumor tissue was found to be markedly decreased compared with that of the corresponding normal tissue. The cases with a tumor/normal ratio of less than 0.5 showed high frequency of lymph-node metastasis and more advanced clinical stage as compared with those whose tumor/normal ratio was equal to or more than 0.5. The decreased expression of cystatin B protein in carcinoma tissue was confirmed by immunohistochemical staining. Our study suggests that reduced expression of cystatin B in esophageal-carcinoma tissue is associated with lymph-node metastasis and may therefore prove to be a useful marker for predicting the biologic aggressiveness of human esophageal carcinoma.

Identification of the pro-oncogene stathmin/op18 mRNA in the brain of mitochondrial Mn-superoxide dismutase-deficient mice by a modified differential display PCR

Differential gene expression plays a critical role in many biological processes. To facilitate the screening of the entire mRNA species for cloning differentially expressed genes, we have made an effort to merge two polymerase chain reaction (PCR)-based methods, differential display (DD) and arbitrarily primed RNA fingerprinting (APR-FP), with some modifications. Using this modified method to screen the mRNAs of the brain tissues of manganese superoxide dismutase (MnSOD)-deficient mice, we found several differentially expressed mRNA species. One mRNA species that was further analyzed by Northern hybridization and sequencing, and was confirmed to be induced only in the brain of MnSOD-deficient mice, encoded stathmin/op18. The MnSOD deficiency causes oxidative stress and mitochondrial dysfunction. Thus, the induction of stathmin/op18, a gene linked with microtubule catastrophe (disassembly) and often upregulated in neoplastic tissues and proliferating cells, may provide some understanding of the pathological changes in the brain of MnSOD-deficient mice.

Recovering and reamplifying of the differentially expressed cDNA bands isolated from mRNA differential display. A modified method

Methods for retrieving and reamplifying the differentially expressed cDNA bands have been modified. Direct reamplification of differentially expressed bands after cutting from a polyacrylamide gel (PAG) followed by a simple rinse and crush step has proved to be more convenient and effective than the traditional glycogen-precipitation method. Combination of 30 cycles of differential display (DD) polymerase chain reaction (PCR) and 20 cycles of standard PCR reaction also yielded higher reamplification rates.

Differential display with carboxy-X-rhodamine-labeled primers and the selection of differentially amplified cDNA fragments without cloning

Differential display (DD) has been used extensively to detect differentially expressed genes. However, the low reproducibility of displayed bands makes verification by Northern blot difficult and the technique is labor-intensive. This report describes a fluorescent DD with a ROX (carboxy-X-rhodamine)-labeled anchor primer and a revised RT-PCR, utilizing AMV reverse transcriptase, a more thermostable reverse transcriptase than Mu-MLV, and optimized concentrations of dNTPs and of MgCl2. Our technique yielded clear fingerprints with high reproducibility. Further, we have developed a method of rapid screening to select the cDNA fragments of interest in excised bands from a polyacrylamide gel without cloning. This method consists of electrophoresis with an agarose gel containing a base-specific DNA ligand to separate the equally sized fragments differing in base composition, and side-by-side comparison of the reamplified products from the experimental and control lane. Most of the cDNA fragments selected by this protocol provided readable sequences by direct sequencing and were confirmed to exhibit differential expression by Northern blot analysis or semiquantitative RT-PCR.

Identification of genes involved in human mesothelial cancer progression using a modified differential display technique

A modified differential display method called RNA fingerprinting was used to identify mRNAs that were differentially expressed during human mesothelial cancer progression. We report the isolation of five different clones. Two clones were expressed in the metastatic mesothelioma cell line M1A and the malignant mesothelioma cell line M1, one clone was expressed uniquely in the metastatic cell line M1A and one clone was solely expressed in the normal mesothelial cells. The other clone was downregulated in the metastatic cell line M1A. The different expression patterns were confirmed by Northern blot analysis. Three clones had no homology to known genes, whereas the other two clones had a striking sequence homology to the M130 antigen and rab 12 mRNA, respectively. The clone that contained a high sequence homology to the M130 antigen mRNA was expressed in the mesothelioma cell lines M1 and M1A and not in any further investigated cancer cell line. This sequence tag may be of interest as a specific mesothelioma tumor marker.

Preferential expression of the gene for a putative inositol 1,4,5-trisphosphate receptor homologue in the mushroom bodies of the brain of the worker honeybee Apis mellifera L

A gene expressed preferentially in the mushroom bodies of the brain of the worker honeybee Apis mellifera L. was identified by the differential display method and its cDNA was isolated. The cDNA fragment of 534 bp (clone A1) contained an open reading frame encoding 177 amino acid residues having 78, 72, 70, 59 and 55% sequence identities with the inositol 1,4,5-trisphosphate (IP3) receptors of Drosophila melanogaster, Xenopus laevis and humans (types 1, 2 and 3), respectively, suggesting that it encodes a putative IP3 receptor homologue of the honeybee. In situ hybridization revealed that the gene encoding clone A1 was expressed preferentially in the mushroom bodies and not in the optic lobes, antennal lobes and central bodies; in the mushroom body, it was expressed strongly in the large type Kenyon cells and weakly in the small type Kenyon cells. Reverse transcription polymerase chain reaction analysis showed that the gene was expressed strongly in the head and weakly in the antennae, legs, thorax, and abdomen. These results suggest that the A1 gene product plays a crucial role in neural transmission in the mushroom bodies of the worker bee brain.

Isolation and expression study of a maternally expressed novel Xenopus gene Xem1 encoding a putative evolutionarily conserved membrane protein

A novel Xenopus maternally expressed gene, Xem1, was isolated by differential display PCR and 5'-RACE. Xem1 coded for a putative transmembrane protein of 172 amino acids. Sequence analysis, including the clustering and reconstruction of ESTs (Expressed Sequence Tags), revealed that homologs of Xem1 are widely distributed in eukaryotic phyla, suggesting that Xem1 is a member of evolutionarily conserved proteins. Expression of Xem1 mRNA occurred from the previtellogenic stage and its level increased during oogenesis, maintained throughout oocyte maturation to blastula stage and then decreased in post gastrula stages. In cleavage stage, Xem1 RNA was distributed uniformly, and in adult, occurred predominantly in ovary and testis. We assume that Xenopus Xem1 may have its function in gametogenesis and in early phase of embryogenesis, whose function may be related to transport mechanism of small molecular weight substances like metal ions, from analogy to the function of its homologs in other organisms.

Screening for imprinted genes by allelic message display: identification of a paternally expressed gene impact on mouse chromosome 18

A systematic screen termed the allelic message display (AMD) was developed for the hunting of imprinted genes. In AMD, differential display PCR is adopted to image allelic expression status of multiple polymorphic transcripts in two parental mouse strains, reciprocal F1 hybrids and pooled backcross progenies. From the displayed patterns, paternally and maternally expressed transcripts can be unequivocally identified. The effectiveness of AMD screening was clearly demonstrated by the identification of a paternally expressed gene Impact on mouse chromosome 18, the predicted product of which belongs to the YCR59c/yigZ hypothetical protein family composed of yeast and bacterial proteins with currently unknown function. In contrast with previous screening methods necessitating positional cloning efforts or generation of parthenogenetic embryos, this approach requires nothing particular but appropriately crossed mice and can be readily applied to any tissues at various developmental stages. Hence, AMD would considerably accelerate the identification of imprinted genes playing pivotal roles in mammalian development and the pathogenesis of various diseases.

Identification of maternal transcripts that progressively disappear during the cleavage period of rabbit embryos

In order to characterize the changes that occur in the population of maternally inherited transcripts before the transition from maternal to zygotic control of embryonic development (MZT) in mammals, we used rabbit embryos where zygotic transcription becomes necessary only after the fourth cleavage division, during the second day that follows fertilization. In the present work we have associated mRNA differential display and an RT-PCR based-method that allows amplification of the whole population of messengers to identify and characterize maternal transcripts which are degraded throughout this early period of development. While there is no major degradation of the polyA RNA population before MZT we identify 4 transcripts which progressively disappear up until the 8-16 cell stage. We also show that the degradation of one of these maternal messengers is controlled by zygotic transcription, which is not the case for the three others. This messenger shows homology with the human FGF9 gene and is potentially a good candidate to address the question of the molecular control of maternal to zygotic transition in early mammalian embryogenesis.

Isolation of mRNAs induced by a hazardous chemical in white-rot fungus, Coriolus versicolor, by differential display

White-rot fungus Coriolus versicolor, a ligninolytic basidiomycete, has been studied because of its ability to degrade hazardous chemicals. In this study, we searched for genes that are induced by a hazardous chemical using the mRNA differential-display technique and C. versicolor IFO30340 that has been exposed to pentachlorophenol (PCP). Five cDNA fragments were cloned and the DNA sequences of two fragments were analyzed in further detail. The clones corresponded to novel genes that have not previously been identified in C. versicolor. One of the cDNAs exhibited strong sequence homology to the gene for an enolase and the other exhibited homology to a heat shock protein. The expression of the two genes was up-regulated in PCP-treated C. versicolor.

Capillary electrophoresis methodology for identification of cancer related gene expression patterns of fluorescent differential display polymerase chain reaction

The mRNA differential display technique is a method for molecular survey and analysis of differential gene expression in eukaryotic cells and tissues. We have previously described the use of ABI Prism fluorescent technology to specifically amplify expressed sequence tags (ESTs) from several different biological paradigms. High throughput, fluorescent differential display performed on an automated sequencer (ABI 377) has proven to have significant cost cutting and time saving attributes compared to that of the radioactive differential display. Additionally, fluorescent tagged mRNA specific reverse transcription and PCR decreases the number of the inherent artifacts associated with radioactive differential display. We report here the application of a capillary electrophoresis system (ABI 310) to the identification of fluorescent differential display generated EST patterns. RNA samples from human and animal breast cancer paradigms were exposed to this technique and analyzed by the ABI 310 and the ABI 377. GeneScan and Genotyper software applications were used for rapid and semi-automated characterization of fluorescently labeled ESTs. Automated sample loading and uniform sample electrophoresis are among the main advantages of this system which significantly increase the precision and reproducibility of fluorescent differential display.

Identification of differentially expressed mRNAs during rat C6 glial cell differentiation by mRNA fingerprinting using arbitrarily primed PCR (RAP)

Differentiation of glial cells is controlled by a complex program of differential expressions of many genes. To identify differentially expressed genes that are involved in rat C6 glial cell differentiation induced by dibutyryl cyclic AMP and theophylline, mRNA fingerprinting using arbitrarily primed PCR (RAP) was used. Four cDNA fragments, that were differentially expressed during differentiation, were isolated. Sequence analysis revealed that one of them, abundantly expressed during differentiation, was homologous to a hamster calcium-dependent serine protease. Another one was highly similar to rabbit dystrobrevin and the other two clones were identical to rat triose phosphate isomerase and calnexin. The results obtained suggest that the expressions of particular genes were changed and that RAP is a useful method to identify genes which are differentially expressed during glial cell differentiation.

A novel gene suppressed in the ventricle of carnitine-deficient juvenile visceral steatosis mice

In order to clarify the pathogenesis and pathophysiology of cardiac hypertrophy in carnitine-deficient juvenile visceral steatosis (JVS) mice, we performed mRNA differential display analysis with total RNA extracted from the ventricles of control and JVS mice at 14 days of age. We identified four up-regulated genes, two known and two unknown, and a novel down-regulated gene. Northern blot analysis with a novel cDNA probe derived from the down-regulated gene fragment 8A2 revealed three mRNA species of 1.1-, 1.3-, and 2.6-kb. The 1.1- and 1.3-kb mRNA species were found only in the heart, and the 2.6-kb species was found in the heart, kidney and brain, but not in skeletal muscle or liver. The 1.1- and 1.3-kb species were down-regulated in the ventricles of JVS mice, but not in the auricles, and increased to the control level with carnitine treatment. We isolated cDNA clones from ventricle RNA, termed CDV-1 (carnitine deficiency-associated gene expressed in ventricle) and from brain RNA, termed CDV-1R (CDV-1-related gene) by 5'- and 3'-RACE analyses. The entire nucleotide sequence except the 5'-terminal 64 bp of CDV-1 cDNA was completely identical to the 992 bp sequence from the 3'-end of CDV-1R cDNA. The CDV-1 cDNA contained an open reading frame predicting a peptide of 107 amino acids, which composed the C-terminal portion of CDV-1R peptide consisting of 414 amino acids.

Representational difference analysis of cDNA of genes expressed in embryonic kidney

Representational difference analysis of cDNA (cDNA-RDA) is a PCR-based differential cloning method. It involves hybridization of two populations of cDNA with selective amplification of differentially expressed genes. To isolate the differentially expressed genes during renal development, mRNAs from embryonic kidneys at day 13 (E13) and postnatal kidneys from three-week-old (P3) mice were extracted, and double stranded cDNAs prepared. Double stranded cDNAs were digested with DpnII, adaptor-ligated, and amplified by PCR, using adaptor primer to generate "representative amplicons." These reflect the "representation" of most of the cDNA population. The term "amplicons" denotes amplified PCR product. Among the two populations of cDNA, E13 kidney cDNA was used as a "tester," containing target genes, and P3 kidney cDNA as a "driver," driving the process of subtraction, following which, they were subjected to cDNA-RDA under low stringency conditions. During the first round of cDNA-RDA embryonic globin genes were isolated. To competitively eliminate these genes, plasmid DNAs of globin genes were supplemented into driver, and subjected to the second round of cDNA-RDA. This resulted in the isolation of four cDNA clones: H19 gene, mesoderm-specific cDNA, COL2A1 gene, and a novel cDNA. By Northern blot analyses, the H19 gene and mesoderm-specific cDNA exhibited a high degree of developmental regulation, that is, they were abundantly expressed in E13 kidney, and their expression was barely detectable in P3 kidney. The differential developmental regulation of mesoderm-specific cDNA was confirmed by tissue in situ hybridization experiments. The COL2A1 and novel cDNA were rare transcripts in the embryonic Kidney. However, Southern blot analyses of representations indicated their up-regulated expressions in E13 kidneys. The novel gene was differentially expressed in 13-day embryonic lung, and Northern blot analysis revealed an approximately 10 Kb transcript. These results indicate that cDNA-RDA is a sensitive technique to identify rare transcripts with differential expression, and since there is a minimal chance to isolate false positive clones, cDNA-RDA may serve as a powerful tool for delineating up- or down-regulation of the genes involved in various pathological or physiological states of the kidney.

Differential display of genome subsets containing specific interspersed repeats

A genomic differential display method was developed that analyzes many restriction fragment length polymorphisms simultaneously. Interspersed repeat sequences were used to reduce DNA sample complexity and to target genomic subsets of interest. This work focused on trinucleotide repeats because of their importance in human inherited diseases. Immobilized repeat-containing oligonucleotides were used to capture genomic DNA fragments containing sequences complementary to the oligonucleotide. Captured fragments were amplified by PCR and fluorescently labeled using primers complementary to the repeat sequence and/or to the known sequences ligated to the ends of the restriction fragments. The labeled PCR fragments were displayed by size on a high-resolution automated fluorescent DNA sequencing instrument. Although there was a conservation in the overall pattern of displayed genome subsets, many clear and reproducible differences were detected when genomes from different individuals were compared. Fewer differences were detected within, than between, monozygotic twin pair genomes. In control experiments, the method distinguished between Huntington disease alleles with normal and expanded CAG repeat lengths.

Fluorescent differential display analysis of gene expression in differentiating neuroblastoma cells

Identification of differentially-expressed genes provides an important step toward the elucidation of molecular mechanisms underlying a variety of biological processes. A novel PCR-based approach to detect and clone such transcripts is the so-called differential display (DD). We established an improved DD protocol that can be performed on an automated fluorescent DNA sequencer to ensure high throughput as well as operational safety. Using this fluorescent DD (FDD) technique, we analyzed the gene expression profile in the retinoic acid-induced differentiation of a human neuroblastoma cell line SH-SY5Y. Screening with 102 primer combinations at eight different time points revealed 66 cDNA bands with variously different behaviors out of approximately 6000 bands displayed. Subsequent analyses with 15 cloned species confirmed the differential expression of corresponding transcripts in all the cases, thereby demonstrating the high reliability of FDD analysis. These clones were composed of seven novel and eight known genes, the latter of which included those that had never been described in the context of neuronal differentiation. These results indicate that FDD is an effective approach to obtain not only novel genes but also clues to possible novel functions of known genes involved in various biological phenomena.

Early molecular specification in the hippocampal rudiment: isolation of genes expressed in a region-specific manner in the embryonic telencephalon

During development, the structure of the telencephalon is dramatically transformed by region-specific proliferation and differentiation of neuroepithelial cells. To understand mechanisms of morphogenesis in the telencephalon, a search was made for genes expressed in a region-specific manner in the dorsal telencephalon of embryonic rats. Dorso-lateral and dorso-medial portions of the telencephalon were taken from rat fetuses on embryonic day (E) 13. Genes expressed in each portion were compared by a modified differential display method. Among more than 4000 cDNA fragments, four fragments termed M1, M1', M2 and M3 were found only after amplification of cDNAs derived from the dorso-medial portion of the telencephalon. Nucleotide sequence and Northern blot analyses showed that M1 and M1' were identical and that M2 and M3 were related genes. In situ hybridization revealed that M1 was expressed in a restricted portion of the hippocampal rudiment with a sharp boundary. M2 and M3 were expressed in the hippocampal rudiment with a more diffuse boundary than that of M1. Expression of M2 and M3 was also found in the most anterior part of the medial diencephalon with a caudal extension along the dorsal midline. These results suggest that at least two types of molecular specification occur in the dorso-medial telencephalon, contributing to the construction of the hippocampal elements during early stages of development.

Messenger RNA fingerprinting analysis using arbitrarily primed PCR (RAP) of genes expressed during rat C6 glioma cell differentiation

To identify differentially expressed genes involved in rat C6 glioma cell differentiation induced by cyclic AMP, we adopted mRNA fingerprinting using arbitrarily primed polymerase chain reaction (PCR) (RAP). Four complementary DNA (cDNA) fragments differentially expressed during differentiation were isolated, and they appeared to contain coding regions of corresponding mRNAs. RAP can be used to efficiently identify cDNA fragments by comparing nucleotide and deduced amino acid sequences with those in databases, and is thus a useful method to search for and identify important genes involved in complex cellular processes such as glioma cell differentiation.

Molecular cloning of a gene encoding translation initiation factor (TIF) from Candida albicans

The differential display technique was applied to compare mRNAs from two clinical isolates of Candida albicans with different virulence; high (potent strain, 16240) and low (weak strain, 18084) extracellular phospholipase activities. Complementary DNA fragments corresponding to several apparently differentially expressed mRNAs were recovered and sequenced. A complementary DNA fragment seen distinctly in the potent phospholipase producing strain was highly homologous to the yeast translation initiation factor (TIF). The selected DNA fragment was then used as a probe to isolate its corresponding complementary DNA clone from a library of C. albicans genomic DNA. The sequence of isolated gene revealed an open reading frame of 1194 nucleotides with the potential to encode a protein of 397 amino acids with a predicted molecular weight of 43 kDa. Over its entire length, the amino acid sequence showed strong homology (78-89%) to Saccharomyces cerevisiae TIF and (63-80%) to mouse eIF-4A proteins. Therefore, our C. albicans gene was identified to be TIF (Ca TIF). Northern blot analysis in the two strains of C. albicans revealed that Ca TIF expression is 1.5-fold higher in the potent phospholipase producing strain. The restriction endonuclease digestion of genomic DNA from this potent strain revealed at least two hybridized bands in Southern blot analysis, suggesting two or more closely related sequences in the C. albicans genome.

Analysis of differential gene expression by display of 3' end restriction fragments of cDNAs

We have developed an approach to study changes in gene expression by selective PCR amplification and display of 3' end restriction fragments of double-stranded cDNAs. This method produces highly consistent and reproducible patterns, can detect almost all mRNAs in a sample, and can resolve hidden differences such as bands that differ in their sequence but comigrate on a gel. Bands corresponding to known cDNAs move to predictable positions on the gel, making this a powerful approach to correlate gel patterns with cDNA data bases. Applying this method, we have examined differences in gene expression patterns during T-cell activation. Of a total of 700 bands that were evaluated in this study, as many as 3-4% represented mRNAs that are upregulated, while approximately 2% were down-regulated within 4 hr of activation of Jurkat T cells. These and other results suggest that this approach is suitable for the systematic, expeditious, and nearly exhaustive elucidation of subtle changes in the patterns of gene expression in cells with altered physiologic states.

Cataloging altered gene expression in young and senescent cells using enhanced differential display

Recently, a novel PCR-based technique, differential display (DD), has facilitated the study of differentially expressed genes at the mRNA level. We report here an improved version of DD, which we call Enhanced Differential Display (EDD). We have modified the technique to enhance reproducibility and to facilitate sequencing and cloning. Using EDD, we have generated and verified a catalog of genes that are differentially expressed between young and senescent human diploid fibroblasts (HDF). From 168 genetags that were identified initially, 84 could be sequenced directly from PCR amplified bands. These sequences represent 27 known genes and 37 novel genes. By Northern blot analysis we have confirmed the differential expression of a total of 23 genes (12 known, 11 novel), while 19 (seven known, 12 novel) did not show differential expression. Several of the known genes were previously observed by others to be differentially expressed between young and senescent fibroblasts, thereby validating the technique.

Differential display analysis of gene expression in developing embryos of Xenopus laevis

Differential display (DD), an arbitrarily primed RT-PCR fingerprinting technique, is a novel approach for the search of differentially expressed transcripts. Using our improved DD protocol, reproducible cDNA fingerprints were successfully obtained from RNAs of Xenopus laevis embryos at six representative stages. Parallel comparison among the fingerprints revealed a number of bands with differential expression patterns. Analysis with clones of three randomly chosen bands confirmed that their expression patterns were faithfully reflected on fingerprints, thereby proving the reliability and validity of the approach. Nucleotide sequencing of these clones revealed that one is identical with a known transcript (cardiac actin), the second is a novel developmentally regulated gene showing no significant homology with those reported previously, and the last is a close but unique relative of XK endo B gene showing somewhat different spatial expression pattern. These results indicated that the DD analysis provides a rapid and reliable way for the identification of novel differentially expressed genes as well as a unique 'scope' for the survey of the changes in overall gene expression profiles occurring in the early embryonic development of Xenopus as well as of other organisms.

Recent advances in differential display

Differential display and RNA arbitrary primed polmerase chain reaction are methods recently designed to identify and isolate differentially expressed genes. Methodological modifications have since been introduced to streamline the techniques. The major effort has centered on how to eliminate false positives as approached from a variety of angles, ranging from RNA sample preparation, northern blot confirmation, primer length variation, to better experimental design.