Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction

Molecular genetic approaches to understanding brain development and behaviour

An understanding of brain development and brain function at the level of the genome is developing rapidly, because of the availability of new technologies in molecular and cellular biology. This understanding can be further enhanced by an interactive exchange between the disciplines of behavioural neuroscience and molecular genetics. New genes are being cloned almost daily, but their function remains an enigma. The purpose of this review is to illustrate how reporter genes can be used to map the brain's genetic activity in developmental time and anatomical space. The production of mutants in the homozygous condition may further lead to a morphological or behavioural phenotype. A knowledge of behavioural neuroscience can provide a prescreen of the reporter distribution and thereby make predictions concerning the type of behavioural analysis required. This approach allows selective cloning and sequencing of those genes which have either a morphological or behavioural phenotype but are transcribed at low levels. It is known that genomic imprinting influences brain development, and also that human genetic mutations and deletions influence imprinting in mental retardation as well as certain behavioural disorders. Precisely how such imprinted genes influence brain development and behaviour is being pursued by the use of chimeras. The distribution of maternal or paternal disomy cells in the brain and the way they influence behaviour may reveal the phenotype and how this is brought about.

RNA fingerprinting using arbitrarily primed PCR identifies differentially regulated RNAs in mink lung (Mv1Lu) cells growth arrested by transforming growth factor beta 1

RNA fingerprinting using arbitrarily primed PCR (RAP) samples an RNA population and allows the detection of differentially expressed genes between two or more populations. This method was applied to mink lung epithelial cells, which respond to treatment with transforming growth factor beta (TGF-beta) by undergoing cell cycle arrest at or near the G1/S-phase boundary. The steady-state abundances of approximately 200 RNAs were surveyed, a few of which displayed differential regulation in response to TGF-beta 1. Three products were isolated, cloned, and sequenced. One differentially regulated RNA corresponded to cyclin A, a gene known to be required for the progression of mammalian fibroblasts through S phase. Northern blot analysis confirmed that the cyclin A mRNA steady-state abundance decreased dramatically in response to a 24-hr TGF-beta 1 treatment and also in response to cell cycle arrest caused by contact inhibition. A second RAP product corresponded to a previously unknown 7.5-kb mRNA, the level of which decreased dramatically in response to TGF-beta 1 treatment. Unlike the cyclin A mRNA, the abundance of this transcript did not decrease in response to growth arrest induced by contact inhibition. A third RAP product corresponded to the mRNA for osteonectin, an extracellular matrix protein. The abundance of this mRNA increased at least 2-fold during TGF-beta 1 treatment. This observation is consistent with other reports of increases in extracellular matrix proteins during TGF-beta treatment. RAP should be able to identify many of the genes that change in steady-state expression during the cell cycle.

Identification of differentially expressed mRNA species by an improved display technique (DDRT-PCR)

We have significantly improved a method originally developed by Liang and Pardee [Science 257 (1992) 967-971] to display a broad spectrum of expressed genes and to detect differences in expression between different cell types. We have analysed various aspects of the technique and have modified it for both, the application to fast and efficient identification of genes and the use with automatic analysis systems. Based on the mathematical background we have devised the appropriate number of optimal PCR primers. We have also introduced nondenaturating gels for separating double stranded fragments as single bands. By applying the method to regenerating mouse liver, we have identified, out of a total of 38,000 bands, about 70 fragments where the expression of the corresponding genes seems to be differentially regulated at different time points. Application of the method to an automatic DNA sequencer was successfully done. Thus, we have confirmed the usefulness and increased the power of the RNA display technique, which we named differential display reverse transcription PCR (DDRT-PCR), and have extended the range of its application.

Visualisation and selective elimination of a subpopulation of mitogen-responsive bone marrow stromal cells using bromodeoxyuridine and photo-induced cell killing

Porcine bone marrow stromal cells (PBMSC) are a source of skeletogenic mesenchymal progenitor cells. Unfortunately, the heterogeneous nature of these cells in culture complicates the interpretation of their growth-factor responsiveness. We have therefore pulse-labelled mitogen-stimulated PBMSC with bromodeoxyuridine (BrdU) in order to study individual, growth-factor responsive cells in the presence of large numbers of nonresponsive PBMSC. Transfer of growing cells to low serum medium reduced BrdU labelling from 35% to 4% over a period of 24 hours. Subsequent addition of foetal calf serum (FCS) to serum-arrested cultures increased the number of BrdU positive cells to 54% by 16 hours. Addition of basic fibroblast growth factor (bFGF) to serum-arrested cultures induced DNA synthesis in 28% of cell by 16 hours after stimulation. In order to selectively eliminate mitogen responsive cells from mixed cultures, BrdU-substituted cells were photosensitised with bisbenzimide and exposed to bright light. BrdU-labelled PBMSC died within 20-40 hours of bisbenzimide treatment and subsequent illumination, whereas BrdU-labelled cells survived in the dark despite treatment with bisbenzimide. The photokilling procedure appeared to have no long term effect upon the viability of non-BrdU-labelled cells because if subconfluent cells were brought to serum arrest prior to photokilling, no change in DNA content relative to controls was observed after a subsequent 4 or 7 day incubation in Dulbecco's modified Eagle's medium (DMEM)/10% FCS.(ABSTRACT TRUNCATED AT 250 WORDS)

Distribution and cloning of eukaryotic mRNAs by means of differential display: refinements and optimization

Differential display has been developed as a tool to detect and characterize altered gene expression in eukaryotic cells. The basic principle is to systematically amplify messenger RNAs and then distribute their 3' termini on a denaturing polyacrylamide gel. Here we provide methodological details and examine in depth the specificity, sensitivity and reproducibility of the method. We show that the number of anchored oligo-dT primers can be reduced from twelve to four that are degenerate at the penultimate base from the 3' end. We also demonstrate that using optimized conditions described here, multiple RNA samples from related cells can be displayed simultaneously. Therefore process-specific rather than cell-specific genes could be more accurately identified. These results enable further streamlining of the technique and make it readily applicable to a broad spectrum of biological systems.

Isolating plant genes

The genetic transformation of most agriculturally important plant species is now possible. However, the application of this technology to rational plant-improvement is currently limited by a shortage of cloned genes for important traits. Recent technological advances in plant-gene isolation and identification, such as map-based cloning, insertional mutagenesis and large-scale cDNA sequencing, have accelerated the rate of gene isolation and significantly expanded the opportunities for genetic engineering of crop plants.

Application of poly(A)+RNA patterns method for searching of differentially expressed genes

Poly(A)+RNA composition differences for normal, fetal and cirrhotic human liver before and after retinoic acid-induced differentiation of the F9 embryonal carcinoma cell line were analyzed by a novel poly(A)+RNA patterns method. The method is based on the polyacrylamide gel electrophoretic analysis of short cDNA termination products, synthesized by reverse transcriptase using poly(A)+RNA as a template, a set of short 5'-end labeled primers, three natural and one terminator deoxyribonucleotide. A number of known differentially expressed genes and some unknown ones were then identified by direct sequencing of the differentially represented bands excised from a gel and searching a complementary mRNA target sites in Genbank database.

Analysis of poly(A)+RNA patterns in human tissues

A novel method for analysing and comparing the relative amounts of the most abundant (higher than 0.1% abundance) individual mRNAs present in different poly(A)+RNA preparations has been developed. This method is based on the synthesis of short (10-30 nucleotide) cDNA termination products, by reverse transcription of poly(A)+RNA primed with a 5'-labeled oligonucleotide. A set of 30 different oligonucleotides are used as primers in separate reactions, their length and sequences having been chosen to provide more than a 90% probability of initiating synthesis from any individual RNA present in the poly(A)+RNA. Each primer produces about 10-60 bands per track, following polyacrylamide gel electrophoresis under denaturing conditions. Data presented reveals poly(A)+RNA pattern differences for a number of human tissues and identifies changes in RNA patterns between normal tissues and neoplastic human tumors (myoma of the uterus) from several individuals.

Gene expression screening for specific genes associated with mouse mammary tumor development

The preneoplastic hyperplastic alveolar nodule is a frequent and well-characterized precursor to mammary tumors in the mouse. Although the biological characteristics of the preneoplastic state have been understood for many years, the molecular alterations associated with preneoplasia and tumorigenicity are unknown. We applied the technique of differential display of mRNA to two closely matched cell populations of mammary preneoplasias that differed only in their tumorigenic potential. Two mRNAs were isolated that were overexpressed only in tumorigenic preneoplasias and in tumors and not in normal pregnant mammary gland or in nontumorigenic preneoplasias. Partial nucleotide sequencing indicated that one of the mRNAs had not yet been described, whereas the second mRNA was highly homologous to a relatively uncharacteristic gene termed pT-2. These results illustrate the utility of the differential display method for isolating and identifying uniquely expressed genes from tissues maintained in the microenvironment where tumors arise naturally.

Arbitrary primed PCR fingerprinting of RNA applied to mapping differentially expressed genes

Differential gene expression between various tissues and developmental stages or between cells in vitro under different growth conditions can be rapidly and efficiently compared using the RNA arbitrarily primed polymerase chain reaction (RAP) fingerprinting method (Welsh et al., 1992b; Liang and Pardee, 1992). In RAP, a primer of arbitrary sequence primes both first and second strand cDNA synthesis. The mixture of products is then PCR amplified and resolved electrophoretically, yielding highly reproducible fingerprints that are tissue-specific or growth condition-specific. Differences between fingerprints arise from differentially expressed genes, as verified by Northern blot analysis. RAP can be performed on the RNA samples using various DNA primers. Each two day experiment yields a sample of approximately twenty cDNA products per lane making the identification of differentially or developmentally regulated genes no longer rate limiting. Those PCR products representing genes that are regulated can be cloned from the gel and sequenced. Sequences can be compared to the DNA and protein sequence databases to identify homologs, motifs and members of gene families. The clones can be placed on the genetic map as Expression Tagged Sites (ETS, Adams et al., 1991a).

Biomarkers in early breast neoplasia

Early breast neoplasia may be defined in many ways. Any non-invasive or invasive but nonmetastatic breast cancer qualifies as early neoplasia in the sense that they are non-lethal. Before we can prevent lethal breast cancer, we must gain a better understanding of the biological abnormalities underlying its development and progression. Many studies into the mechanisms of breast cancer evolution have evaluated potential precursor lesions (e.g., proliferative disease without atypia [PDWA], atypical ductal hyperplasia [ADH], and ductal carcinoma in situ [DCIS]) for genetic alterations known to occur in fully developed invasive carcinomas. This approach has shed some light on events which may be important in early malignant transformation, including the observations that overexpression of the c-erbB-2 oncogene and mutations of the p53 tumor suppressor gene are present in significant subsets of DCIS, but not PDWA or ADH. This approach is limited by our incomplete knowledge of cancer genetics. However, there is more to learn by evaluating known cancer-associated genes in potential precursor lesions using established techniques such as immunohistochemistry and in situ hybridization. Until recently, technology could not detect unknown genetic abnormalities in microscopic lesions such as PDWA, ADH, or DCIS. Now, PCR-based techniques have the theoretical ability to detect novel tumor promoter and suppressor genes in clinical samples of these very small lesions. For example, suppressor-type genes may be detected using comprehensive mapping probes to identify loss of heterozygosity in PCR-amplified DNA extracted from a few hundred cells microdissected from either fresh or archival tissue.(ABSTRACT TRUNCATED AT 250 WORDS)

Arbitrarily primed PCR fingerprinting of RNA

Fingerprinting of RNA populations was achieved using an arbitrarily selected primer at low stringency for first and second strand cDNA synthesis. PCR amplification was then used to amplify the products. The method required only a few nanograms of total RNA and was unaffected by low levels of genomic double stranded DNA contamination. A reproducible pattern of ten to twenty clearly visible PCR products was obtained from any one tissue. Differences in PCR fingerprints were detected for RNAs from the same tissue isolated from different mouse strains and for RNAs from different tissues from the same mouse. The strain-specific differences revealed are probably due to sequence polymorphisms and should be useful for genetic mapping of genes. The tissue-specific differences revealed may be useful for studying differential gene expression. Examples of tissue-specific differences were cloned. Differential expression was confirmed for these products by Northern analysis and DNA sequencing uncovered two new tissue-specific messages. The method should be applicable to the detection of differences between RNA populations in a wide variety of situations.