cDNA Populations Research Articles

Analysis of stem cell factor for mast cell proliferation in the human myometrium.

The proliferation and differentiation of human mast cells (MCs) occur under the influence of the mitogenic agent known as stem cell factor (SCF). This study analyses the distribution of SCF and SCF receptor in human myometrial tissue to further the understanding of the role(s) of MCs in the uterus. Immunohistochemical staining revealed that the majority of uterine MCs are located in close proximity to myometrial smooth muscle cells, and also among fibroblast-like spindle shaped cells. RNA extracts from myometrial tissues were subjected to reverse transcription. The resulting cDNA population was amplified by polymerase chain reaction (PCR) using a pair of 20-mer primers that were specific for SCF cDNA. Electrophoresis of the PCR products showed that the myometrial tissues contained transcripts for SCF. In-situ reverse transcription-PCR also revealed the expression of the transcripts for SCF in myometrial smooth muscle cells. Furthermore, enzyme-linked immunosorbent assays confirmed that the cultured myometrial cells produced SCF. Since immunohistochemical staining indicated there are SCF receptors on the surface of myometrial MCs, the results suggest that MC proliferation and differentiation in the myometrium is regulated by SCF secretion from the uterine smooth muscle cells. The mature MCs might, in turn, secrete mediators that influence tissue remodelling during the human menstrual cycle.

Encystment-specific mRNA is accumulated in the resting cysts of the ciliate Colpoda inflata.

From a random amplified polymorphism cDNA study using vegetative, precystic and mature resting cysts of the ciliate Colpoda inflata, a stage-specific fragment was isolated from the resting cyst cDNA population. This fragment was used as an encystment probe to study the corresponding mRNA expression during this eukaryotic cell differentiation process. This transcript is accumulated in the resting cyst of this ciliate, and it is the first time that accumulation of specific mRNA molecules associated with the ciliate cryptobiosis process is reported. The meaning of this stored mRNA in microbial cryptobiotic stages is discussed.

Increasing the average abundance of low-abundance cDNAs by ordered subdivision of cDNA populations.

It is estimated that 50,000–100,000 genes are expressed across the cell types of higher eukaryotes. As a consequence of differential expression (either regionally, temporally, or environmentally specific), a large proportion of all transcripts (approx 40–45%) represent low-abundance mRNAs, present at 1–20 molecules/cell (). In a given cell type, “low-abundance” mRNAs are likely to represent >95% of the different mRNAs expressed. The lower the abundance of a given transcript, the larger the number of clones in a representative cDNA library which must be screened in order to have a reasonable chance of isolating that message; for example, employing a statistical calculation (), it can be estimated that approx 500,000 clones need be screened to have a 99% probability of finding one representative of a gene expressed at the level of 0.001% (a low-abundance message) of total cellular mRNA. This is of practical significance in all cases, except where high-abundance mRNAs (accumulating to a few percent of total cellular mRNA) are sought. The implications are particularly severe for Human Genome Project expressed sequence tag (EST) studies, which on the basis of automated sequencing, aim to identify all the unknown genes expressed in a particular cell or tissue. Utilizing an unmodified cDNA library, well-resourced laboratories are forced to employ approaches incorporating a 10- to 100-fold redundancy in screening in order to isolate rare mRNAs. However, such approaches are not an option available to the majority of investigators.

Analysis of differential gene regulation in adequate versus inadequate secretory-phase endometrial complementary deoxyribonucleic acid populations from the rhesus monkey.

The ability to create artificial menstrual cycles in the rhesus monkey provides a model for studies on the regulation of genes and gene networks by estradiol or progesterone (P) in the primate endometrium. This model allowed us to create both a normal level of secretory phase P or an inadequate level of secretory phase P, i.e. endometria that cannot support implantation. The objective of our present study focused on PCR analyses of genes for several factors that are believed to be important in the proper maturation of the endometrium. Complementary DNA (cDNA) populations were prepared from endometria harvested on day 13 (peak E level), days 21-23 of an adequate secretory phase (PcDNA) and days 21-23 of an inadequate secretory phase (IcDNA). Although placental protein 14, leukemia inhibitory factor and 17-beta hydroxysteroid dehydrogenase displayed highly upregulated levels in PcDNA (P-activated genes), there was little or no up-regulation in IcDNA. Transforming growth factor-beta 2 and its receptor and insulin growth factor-I and its receptor were up-regulated in PcDNA, whereas little or no expression was observed in IcDNA. Regulators of the cell cycle and transcription, such as retinoblastoma, c-fos, and c-jun genes, were also greatly underexpressed in IcDNA compared with PcDNA. Interestingly, one gene that we studied, keratinocyte growth factor, that was up-regulated by P (peak E levels vs. PcDNA) was more highly expressed in IcDNA. This latter result suggests that low levels of circulating P are sufficient for expression of this gene, whereas high sustained P levels result in an autologous down-regulation. These data show that the regulation of genes that may play pivotal roles in endometrial maturation are differentially expressed in IcDNA vs. PcDNA and may, in part, characterize improper endometrial maturation.

Preparation of a differentially expressed, full-length cDNA expression library by RecA-mediated triple-strand formation with subtractively enriched cDNA fragments.

We have developed a fast and general method to obtain an enriched, full-length cDNA expression library with subtractively enriched cDNA fragments. The procedure relies on RecA-mediated triple-helix formation of single-stranded cDNA fragments with a double-stranded cDNA plasmid library. The complexes were then captured from the solutions using the digoxigenin-antidigoxigenin paramagnetic beads followed by recovery of the enriched double-stranded cDNA expression library. We have observed a linear relation between the capture of full-length cDNAs in the library and the fold enrichment in the subtracted cDNA population.

Conservation of the organization of the mitochondrial nad3 and rps12 genes in evolutionarily distant angiosperms.

The organization of the genes nad3 and rps12 has been investigated in the mitochondrial genome of two dicotyledonous plants - Helianthus and Magnolia - and one monocotyledonous plant (Allium). These plants all contain a complete rps12 gene downstream of the nad3 gene. This arrangement is thus highly conserved within angiosperms. The two genes are co-transcribed and the transcript is modified at several positions by RNA editing of the C to U-type, thus confirming that both genes encode functional proteins. Some 26, 35 and 27 editing events have been identified in the PCR-derived nad3-rps12 cDNA population from sunflower, Magnolia and onion, respectively. Editing of the nad3-rps12 transcript is thus more extensive in Magnolia than in the other angiosperms so far investigated and radically changes the genomically encoded polypeptide sequence. A novel species-specific codon modification was observed in Magnolia. Several homologous sites show differences in editing pattern among plant species. A C-to-U alteration is also found in the non-coding region separating the nad3 and rps12 genes in sunflower. The PCR-derived cDNA populations from the nad3-rps12 loci analysed were found to be differently edited. In addition the plant species show marked variations in the completeness of RNA editing, with only the Magnolia nad3 mRNA being edited fully.

Stage-specific gene expression during rat spermatogenesis: application of the mRNA differential display method.

Spermatogenesis is a complex differentiation process which requires the coordinate synthesis of diverse stage-specific proteins. In attempting a large-scale identification and characterization of those proteins, we have made use of the recently described mRNA differential display method (Liang and Pardee, Science 257: 967-971, 1992). This method is based on the reverse transcription of mRNAs obtained from two different cell populations (pachytene spermatocytes and spermatids in the present study) followed by a PCR reaction and comparison of the individual cDNA populations in a polyacrylamide gel system. Up to the present we have been able to identify 268 cDNA bands. Most of them (77%) are common to both cell stages. From the differentially expressed bands (23%) an ample majority was spermatid-specific (74%). According to our present results we conclude that the mRNA differential display is a promising approach for investigations on stage-specific gene expression during a differentiation process like spermatogenesis.

A general strategy for cloning viroids and other small circular RNAs that uses minimal amounts of template and does not require prior knowledge of its sequence

Two PCR-based methods are described for obtaining clones of small circular RNAs of unknown sequence and for which only minute amounts are available. To avoid introducing any assumption about the RNA sequence, synthesis of the cDNAs is initiated with random primers. The cDNA population is then PCR-amplified using a primer whose sequence is present at both sides of the cDNAs, since they have been obtained with random hexamers and then a linker with the sequence of the PCR primer has been ligated to their termini, or because the cDNAs have been synthesized with an oligonucleotide that contains the sequence of the PCR primer at its 5' end and six randomized positions at its 3' end. The procedures need only approximately 50 ng of purified RNA template. The reasons for the emergence of cloning artifacts and precautions to avoid them are discussed.

Sequence of κ-opioid receptor cDNA in the R1.1 thymoma cell line

To our knowledge, this is the first demonstration of κ-opioid receptor mRNA in cells of the immune system. While the presence of opioid receptors on cells of the immune system has been controversial, cell-binding analysis has indicated that the κ-opioid receptor is expressed by the immature T cell line R1.1 We have developed a reverse transcriptase-polymerase chain reaction protocol to amplify the mRNA extracted from R1.1 cells with primers derived from the cDNA sequence of the mouse κ-opioid receptor. Nucleotide sequences of the amplified products were examined and two populations of cDNA were detected which differ in the 5′ region upstream of the ATG start codon. Comparison of these sequences to the previously published κ-opioid receptor cDNA sequence suggests the presence of an intron-exon junction in the 5′ non-coding region.

Differential gene expression during early murine yolk sac development.

The visceral yolk sac (VYS), composed of extraembryonic mesoderm and visceral endoderm, is the initial site of blood cell development and serves important nutritive and absorptive functions. In the mouse, the visceral endoderm becomes a morphologically distinct tissue at the time of implantation (E4.5), while the extraembryonic mesoderm arises during gastrulation (E6.5-8.5). To isolate genes differentially expressed in the developing yolk sac, polymerase chain reaction (PCR) methods were used to construct cDNA from late primitive streak to neural plate stage (E7.5) murine VYS mesoderm and VYS endoderm tissues. Differential screening led to the identification of six VYS mesoderm-enriched clones: ribosomal protein L13a, the heat shock proteins hsc 70 and hsp 86, guanine-nucleotide binding protein-related gene, cellular nucleic acid binding protein, and alpha-enolase. One VYS endoderm-specific cDNA was identified as apolipoprotein C2. In situ hybridization studies confirmed the differential expression of these genes in E7.5 yolk sac tissues. These results indicate that representative cDNA populations can be obtained from small numbers of cells and that PCR methodologies permit the study of gene expression during early mammalian postimplantation development. While all of the mesoderm-enriched genes were ubiquitously expressed in the embryo proper, apolipoprotein C2 expression was confined to the visceral endoderm. These results are consistent with the hypothesis that at E7.5, the yolk sac endoderm provides differentiated liver-like functions, while the newly developing extraembryonic mesoderm is still a largely undifferentiated tissue.

PCR-generated cDNA libraries from reduced numbers of mouse oocytes.

We describe a rapid and reproducible method for cloning cDNA amplified from 10 mouse oocytes. The procedure consists in priming cDNA synthesis from a crude cellular extract using an oligo d(T) containing primer and submitting the size-limited cDNA first strand to poly(dG) tailing. The whole cDNA population is then polymerase chain reaction (PCR) amplified using two primers complementary to oligo d(A) and oligo d(G) ends of the cDNA. In this procedure no purification steps are required. We obtained about 5 x 10(6) clones from 10 oocytes. Screening of the library showed that the relative abundance of the transcripts was preserved during amplification and cloning and that the procedure allows cloning of low-abundance sequences at least as rare as 0.008% of the mRNA. The repeatable generation of representative cDNA libraries from reduced numbers of oocytes or embryos should open new opportunities for obtaining genetic information from mammalian preimplantation embryos.

Analysis of G protein α subunit mRNA abundance in preimplantation mouse embryos using a rapid, quantitative RT‐PCR approach

We have developed a novel reverse transcription-polymerase chain reaction (RT-PCR)-based approach for systematically quantifying in a single experiment the abundances of many different mRNAs in preimplantation mouse embryos. With this approach, the entire mRNA population from a small number of embryos is amplified while preserving the relative abundance of each mRNA in the cDNA population. The cDNA is analyzed by quantitative hybridization to radiolabeled probes. The approach is very sensitive and provides reliable, quantitative data regarding changes in mRNA abundance. A major advantage of this method is that estimates of mRNA copy number can be obtained and compared between different mRNAs. With this approach, we analyzed the patterns of expression of nine G protein alpha subunit mRNAs (G alpha s, G alpha i, G alpha q, G alpha o, and G alpha 11-15) in oocytes, eggs, and preimplantation embryos from fertilization to the blastocyst stage. Six alpha subunit mRNAs were expressed at significant levels, all of which underwent significant temporal alterations in expression. The mRNAs encoding some alpha subunit types were expressed predominantly in the egg and 1-cell embryo, underwent sharp reductions during the 2-cell stage, and were re-expressed between the 8-cell and blastocyst stages. One alpha subunit mRNA increased in abundance at the early blastocyst stage. The possible significance of these alterations in G protein mRNA abundance to embryonic development is discussed.

In situ isolation of mRNA from individual plant cells: creation of cell-specific cDNA libraries.

A method for isolating and cloning mRNA populations from individual cells in living, intact plant tissues is described. The contents of individual cells were aspirated into micropipette tips filled with RNA extraction buffer. The mRNA from these cells was purified by binding to oligo(dT)-linked magnetic beads and amplified on the beads using reverse transcription and PCR. The cell-specific nature of the isolated mRNA was verified by creating cDNA libraries from individual tomato leaf epidermal and guard cell mRNA preparations. In testing the reproducibility of the method, we discovered an inherent limitation of PCR amplification from small amounts of any complex template. This phenomenon, which we have termed the "Monte Carlo" effect, is created by small and random differences in amplification efficiency between individual templates in an amplifying cDNA population. The Monte Carlo effect is dependent upon template concentration: the lower the abundance of any template, the less likely its true abundance will be reflected in the amplified library. Quantitative assessment of the Monte Carlo effect revealed that only rare mRNAs (< or = 0.04% of polyadenylylated mRNA) exhibited significant variation in amplification at the single-cell level. The cDNA cloning approach we describe should be useful for a broad range of cell-specific biological applications.

A modified procedure for PCR-based differential display and demonstration of use in plants for isolation of genes related to fruit ripening

We have modified and optimized PCR-based differential display for efficient identification and isolation of genes whose expression patterns are correlated with changes in growth, development, physiology, and/or environmental response. This protocol is general in nature and can be applied for analysis of virtually any plant tissues from which several μg of total RNA can be extracted. We report here the use of tomato fruit ripening as a model system in which to test and optimize differential display in plants. Specifically, mRNA from ripe, early breaker, mature green, and ethylene-treated mature green tomato fruit were examined to identify and distinguish non-ethylene-inducible from ethylene-inducible genes related to ripening. DNA-free total RNA was utilized as template for synthesis of first-strand complementary DNA using each of 12 possible 5′-T11 XY-3′ anchor primers (X=A, C, or G; Y=A, C, G, or T). PCR amplification products of the resulting cDNA populations were generated via use of random primers in combination with the corresponding anchor primer employed for cDNA synthesis. We demonstrate that degenerative anchor primers are useful for making representative cDNA populations, but are not effective for representative display-PCR. cDNA, resulting from degenerative anchor primer synthesis, yielded substantially fewer ripening-related display-PCR products when amplified with the same degenerative anchor primer employed in cDNA synthesis, versus the corresponding set of specific anchor primers. Amplification products specific to ripe fruit cDNA were isolated directly from display gels, reamplified, cloned, and confirmed for ripening-related gene expression via RNA gel-blot analysis.

PCR-generated cDNA library of transition-stage maize embryos: cloning and expression of calmodulin genes during early embryogenesis

One hundred maize zygotic embryos microdissected at the transition stage were used to construct a cDNA library after non-selective PCR (NS-PCR) amplification of whole cDNA populations. The library contains 2.3 x 10(5) recombinants and two different calmodulin cDNAs were cloned using a heterologous probe from petunia. Calmodulin expression was confirmed throughout maize embryogenesis at the mRNA, amplified cDNA and protein levels. Sequence analysis suggests a maize origin for both clones and negligible nucleotide changes linked to PCR. This library is the first described for early plant embryos and represents a breakthrough to isolate genes involved in embryo differentiation.

Direct selection of cDNAs using whole chromosomes.

We have developed a method for direct selection of cDNAs using whole chromosomes as target DNA. Double-strand cDNAs were synthesized from human fetal brain polyadenylated mRNAs. Flow-sorted chromosomes 17 and 19 were amplified by degenerate oligonucleotide primed polymerase chain reaction (DOP-PCR) and used to capture ds cDNAs by an improved magnetic bead capture protocol. To demonstrate the capabilities of this method, the selected cDNAs were used as probes in FISH experiments. The selected cDNA populations specifically painted chromosomes 17 or 19 on metaphase spreads. These results demonstrate that it is possible to do chromosome painting using cDNA probes and that this method is a means to rapidly select expressed sequences encoded by any portion of the genome.

Quantitation of mRNA species by RT-PCR on total mRNA population.

PCR is commonly used for mRNA quantitation. Previously described procedures are applied to one or a few specific mRNA sequences. We show here that methods used for amplifying heterogeneous cDNA populations can be applied to the quantitation of many mRNA species. This quantitation is achieved by dot blotting and hybridization with the corresponding probes after amplifying a bulk mRNA population. Only a single, two-round-amplification assay is required for quantitation of a whole set of mRNA species. The proportionality of input molecules to output signal was shown by performing a series of control experiments. We applied this technique to measure the relative variations of the MBP, Po, and MAG mRNA sequences in the normal trembler mouse model. The results were consistent with previously described Northern blot data. This quantitative PCR method provides a rapid and reliable way to quantify relative amounts of mRNA species in small amounts of total RNA by using internal controls.

Subtraction Hybridization Cloning of RNA Amplified from Different Cell Populations Microdissected from Cryostat Tissue Sections

We describe a generally applicable and easily reproducible method for the cloning of differentially expressed RNA, amplified from small numbers of enriched cell populations, obtained by microdissection from single cryostat sections. The procedure involves homopolymeric A tailing of cDNA synthesized from released RNA using an anchored (NN)T12 primer. Subsequent entire cDNA population polymerase chain reaction amplification was carried out using a biotinylated (X)nT16 primer-adaptor in the presence of biotin-dATP. This biotinylated driver cDNA was then twice hybridized in 50-fold excess to heterologous target cDNA made with nonbiotinylated (Y)nT16 primer; common hybrids and excess driver cDNA were magnetically removed following the addition of streptavidin-coated magnetospheres which bound biotinylated strands, leaving enriched target population sequences. These were then directly amplified through the tails using a primer containing only the target-specific (Y)n sequence. Insertion into a λ-phage vector was facilitated by means of an EcoR1 site incorporated in the (Y)n primer. Subsequent packaging and transformation into Escherichia coli NM522 resulted in cDNA libraries containing approximately 5 × 103-104 pfu. Screening of these primary libraries with cDNA derived from the starting populations yielded a large number of differentially hybridizing clones which are currently under analysis.

A new, pathogen-inducible gene of Arabidopsis is expressed in an ecotype-specific manner

In this study we describe a novel gene, which was isolated in an attempt to search for specific plant resistance genes of Arabidopsis against isolates of the phytopathogenic bacterium Xanthomonas campestris pv. campestris. The gene was cloned by differential screening of a genomic library of the Xcc 750-resistant ecotype Col-0, using cDNA populations derived from ecotype Col-0 and the Xcc 750-susceptible ecotype Oy-0. The isolated gene, CXc750, is differentially expressed in ecotypes of Arabidopsis thaliana. In addition, although highly expressed in uninfected plants, gene expression increases in response to pathogen attack. CXc750 potentially codes for a small, basic protein of about 10 kDa. The predicted protein product contains a potential signal leader peptide at the amino-terminal end but no ER retention sequence and no further transmembrane domain. This indicates that the gene product is transported to other compartments or out of the cell. The possible function of CXc750 as a member of the plant defense response system is discussed.

Cloning of two gibberellin-regulated cDNAs from Arabidopsis thaliana by subtractive hybridization: expression of the tonoplast water channel, ?-TIP, is increased by GA3

The Arabidopsis ga1 mutant has very low levels of endogenous, active gibberellins and thus has an extreme dwarf phenotype; application of GA3 induces stem elongation and flower development. To test the hypothesis that GA action in this system involves changes in gene expression, we have cloned mRNAs whose abundance changes following GA application. A subtraction cloning scheme for the isolation of differentially regulated cDNAs was established, involving hybridization of single-stranded cDNA to biotinylated mRNA. cDNA populations enriched up to 150-fold in GA-regulated sequences were produced and cDNA libraries generated. Screening of these libraries has isolated two clones that identify mRNAs of ca. 1100 and 750 bases whose abundance is markedly increased 24 h after GA application. One of these clones encodes the vegetative form of the Arabidopsis tonoplast intrinsic protein (gamma-TIP), a water channel protein, the expression of which has recently been shown to be correlated with regions of cell expansion. The second clone is expressed only in the inflorescence and encodes a proline- and glycine-rich protein that may be a cell wall component.